Gene Linkage and Genetic Mapping 4TH PAGES © Jones & Bartlett Learning, LLC

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Gene Linkage and © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC 4NOTGenetic FOR SALE OR DISTRIBUTIONMapping NOT FOR SALE OR DISTRIBUTION CHAPTER ORGANIZATION

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR4.1 SALELinked OR alleles DISTRIBUTION tend to stay 4.4NOT Polymorphic FOR SALE DNA ORsequences DISTRIBUTION are together in meiosis. 112 used in human genetic mapping. 128 The degree of linkage is measured by the Single-nucleotide polymorphisms (SNPs) frequency of recombination. 113 are abundant in the human genome. 129 The frequency of recombination is the same SNPs in restriction sites yield restriction for coupling and repulsion heterozygotes. 114 fragment length polymorphisms (RFLPs). 130 © Jones & Bartlett Learning,The frequency LLC of recombination differs © Jones & BartlettSimple-sequence Learning, repeats LLC (SSRs) often NOT FOR SALE OR DISTRIBUTIONfrom one gene pair to the next. NOT114 FOR SALEdiffer OR in copyDISTRIBUTION number. 131 Recombination does not occur in Gene dosage can differ owing to copy- Drosophila males. 115 number variation (CNV). 133 4.2 Recombination results from Copy-number variation has helped human populations adapt to a high-starch diet. 134 crossing-over between linked© Jones alleles. & Bartlett Learning,116 LLC 4.5 Tetrads contain© Jonesall & Bartlett Learning, LLC four products of meiosis. 135 PhysicalNOT distance FOR is SALE often—but OR not DISTRIBUTION NOT FOR SALE OR DISTRIBUTION always—correlated with map distance. 120 Unordered tetrads have no relation to the One crossover can undo the geometry of meiosis. 136 effects of another. 122 Tetratype tetrads demonstrate that crossing-over takes place at the four- 4.3 Double crossovers are revealed strand stage of meiosis and is reciprocal. 137 © Jones & Bartlettin three-point Learning, crosses. LLC 124 © TetradJones analysis & Bartlett affords a convenient Learning, LLC NOT FOR SALEInterference OR decreasesDISTRIBUTION the chance of NOTtest forFOR linkage. SALE OR DISTRIBUTION137 multiple crossing-over. 127 The geometry of meiosis is revealed in ordered tetrads. 139 Gene conversion suggests a molecular Varieties of maize. mechanism of recombination. 142 [© Katarzyna Citko/ © JonesShutterStock, & Bartlett Inc.] Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION TXX.XX A Head Goes Here 111 4TH PAGES © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. 4.6 Recombination is initiated by a Chapter Summary 145 double-stranded break in DNA. 143 Learning Outcomes 146 © Jones & BartlettRecombination Learning, tends LLC to take place at © IssuesJones & Ideas & Bartlett Learning, LLC 146 NOT FOR SALE ORpreferred DISTRIBUTION positions in the genome. 146 NOTSolutions: FOR Step SALE by Step OR DISTRIBUTION 146 the human connection Concepts in Action: Problems for Solution 148 Starch Contrast 134 GENETICS on the web

tend to remain together in inheritance, a phenom- enetic mapping means determining the rela- enon known as linkage. Nevertheless, the linkage tive positions of genes along a chromosome. is incomplete. Some gametes are produced that have It is one of the main experimental tools in G© Jones & Bartlett Learning, LLC different ©combinations Jones & Bartlett of the white Learning, and miniature LLC genetics. This may seem odd in organisms in which the alleles than those in the parental chromosomes. The DNANOT sequence FOR SALEof the genome OR DISTRIBUTION has been determined. If NOT FOR SALE OR DISTRIBUTION new combinations are produced because homologous every gene in an organism is already sequenced, then chromosomes can exchange segments when they are what is the point of genetic mapping? The answer paired. This process (crossing-over) results in recom- is that a gene’s sequence does not always reveal its bination of alleles between the homologous chro- function, nor does a genomic DNA sequence reveal © Jones & Bartlett Learning, LLC © Jonesmosomes. & Bartlett The probabi Learning,lity of recombinationLLC between which genes interact in a complex biological process. NOT FOR SALE OR DISTRIBUTION NOT FORany two SALE genes OR serves DISTRIBUTION as a measure of genetic distance When a new mutant gene is discovered, the first between the genes and allows the construction of a step in genetic analysis is usually genetic mapping to genetic map, which is a diagram of a chromosome determine its position in the genome. It is at this point showing the relative positions of the genes. The lin- that the genomic sequence, if known, becomes useful, ear order of genes along a genetic map is consistent because in some cases the position of the mutant gene © Jones & Bartlett Learning, LLCwith the conclusion that ©each Jones gene &occupies Bartlett a well- Learning, LLC coincides with a gene whose sequence suggests a role NOT FOR SALE OR DISTRIBUTIONdefined position, or locusNOT, in the FOR chromosome, SALE OR with DISTRIBUTION in the biological process being investigated. For exam- the alleles of a gene in a heterozygote occupying ple, in the case of flower color, a new mutation may corresponding locations in the pair of homologous map to a region containing a gene whose sequence chromosomes. suggests that it encodes an enzyme in anthocyanin In discussing linked genes, it is necessary to distin- synthesis. But the function of a gene is not always © Jones & Bartlett Learning, LLC guish which© Jones alleles are& Bartlettpresent together Learning, in the LLCparen- revealed by its DNA sequence, and so in some cases, NOT FOR SALE OR DISTRIBUTION tal chromosomes.NOT FOR This SALE is done OR by DISTRIBUTION means of a slash further genetic or molecular analysis is necessary to (“/”). The alleles in one chromosome are depicted sort out which one of the genes in a sequenced region to the left of the slash, and those in the homologous corresponds to a mutant gene mapped to that region. chromosome are depicted to the right of the slash. In human genetics, genetic mapping is important For example, in the cross AA BB 3 aa bb, the geno- because it enables genes associated with hereditary © Jones & Bartlett Learning, LLC © Jonestype & of Bartlett the doubly Learning, heterozygous LLC progeny is denoted diseases, such as those that predispose to breast can- A B/a b because the A and B alleles were inherited NOT FOR SALEcer, to ORbe localized DISTRIBUTION and correlated with the genomicNOT FOR SALE OR DISTRIBUTION in one parental chromosome and the alleles a and b sequence in the region. were inherited in the other parental chromosome. In this genotype the A and B alleles are said to be in the 4.1 Linked alleles tend to stay coupling or cis configuration; likewise, the a and together© inJones meiosis. & Bartlett Learning, LLCb alleles are in coupling.© Among Jones the & Bartlettfour possible Learning, LLC NOT FOR SALE OR DISTRIBUTIONtypes of gametes, the A NOTB and FOR a b types SALE are OR called DISTRIBUTION In meiosis, homologous chromosomes form pairs in parental combinations because the alleles are in the prophase I by undergoing synapsis, and the individ- same configuration as in the parental chromosomes, ual members of each pair separate from one another and the A b and a B types are called recombinants at anaphase I. Genes that are close enough together (FIGURE 4.1, part A). in© the Jones same chromosome & Bartlett might Learning, therefore LLC be expected Another© Jones possible & configuration Bartlett Learning, of the A, a andLLC B, b toNOT be transmitted FOR SALE together. OR DISTRIBUTION Thomas Hunt Morgan allele pairsNOT is A FOR b/a B .SALE In this caseOR theDISTRIBUTION A and B alleles examined this issue using two genes present in the are said to be in the repulsion or trans configuration. X chromosome of Drosophila. One was a mutation Now the parental and recombinant gametic types are for white eyes, the other a mutation for miniature reversed (Figure 4.1, part B). The A b and a B types are wings. Morgan found that the white and miniature the parental combinations, and the A B and a b types © Jones & Bartlettalleles present Learning, in each XLLC chromosome of a female do© Jonesare the& Bartlett recombinants. Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION 112 CHAPTER 4 Gene Linkage and Genetic Mapping 4TH PAGES © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. (A)–Parental alleles in coupling (B)–Parental alleles in repulsion The degree of linkage is (A)–or cis configuration (B)–or trans configuration measured by the frequency © Jones & Bartlett Learning, LLC © Jones & BartlettA Learning,B LLC A b of recombination. NOT FOR SALE ORa DISTRIBUTIONb a NOTB FOR SALE OR DISTRIBUTION In his early experiments with Drosophila, Morgan found mutations in each of several Meiosis Meiosis X-linked genes that provided ideal materi- als for studying linkage. One of these genes, © Jones & Bartlett Learning, LLC with alleles w1 and© Jonesw, determines & Bartlett normal Learning, LLC Parental combinations NOT FOR SALEParental OR combinations DISTRIBUTION red eye color versusNOT white FOR eyes; SALEanother suchOR DISTRIBUTION A B A b gene, with the alleles m1 and m, determines a b a B whether the size of the wings is normal or miniature. The initial cross is shown as Recombinants Recombinants Cross 1 in FIGURE 4.2. It was a cross between © JonesA & Bartlettb Learning, LLC A B females© Jones with & white Bartlett eyes andLearning, normal wings LLC NOT FOR SALE OR DISTRIBUTION andNOT males FOR with SALE red eyes OR and miniatureDISTRIBUTION wings: a B a b wmwm++ wmwm++ // ×× ?? FIGURE 4.1 For any pair of alleles, the gametes produced through wmwm++ YY meiosis have the alleles either in a parental configuration or in a recombinant configuration. Which types are parental and which recombinant depends In this way of writing the genotypes, the © Jones &on whether Bartlett the configurationLearning, of LLCthe alleles in the parent is (A) coupling© Jones or & Bartlett Learning, LLC horizontal line replaces the slash. Alleles NOT FOR(B) repulsion. SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

(A) Cross 1 (B) Cross 2 Parents: © Jones & Bartlett Learning, LLCParents: © Jones & Bartlett Learning, LLC White-eyed NOT FORMiniature-wing SALE OR DISTRIBUTIONWhite-eyed and NOT FORWildtype SALE OR DISTRIBUTION females males miniature-wing males females w + && + m (( w m && + + (( Y w m Yןן + w

F©1: Jones & Bartlett Learning, LLC F1: © Jones & Bartlett Learning, LLC NOT FOR SALEw OR + && DISTRIBUTIONw m (( NOT FOR SALEw m OR&& DISTRIBUTIONw m (( Y Mutant alleles + + Yןן Mutant alleles + m in homologous in the same chromosomes chromosomes

F : F : 2 Progeny 1 2 Progeny 2 © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE ORWhite DISTRIBUTION eyes, 226 Parental types:NOT FORRecombinant SALE OR types: DISTRIBUTION 223 normal wings 66.5% have 37.7% have (maternal gamete: w +) parental allele nonparental allele combinations combinations Red eyes, 202 (nonrecombinant). (recombinant). 247 miniature wings (maternal gamete:© Jones + m) & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Red eyes, 114 Recombinant types: Parental types: 395 normal wings 33.5% have 62.3% have (maternal gamete: + +) nonparental allele parental allele combinations combinations White eyes, 102 (recombinant). (nonrecombinant). 382 miniature wings © Jones & Bartlett Learning,644 LLC © Jones & Bartlett1247 Learning, LLC NOT FOR(maternal SALE gamete: OR w mDISTRIBUTION) NOT FOR SALE OR DISTRIBUTION

FIGURE 4.2 An experiment demonstrating that the frequency of recombination between two mutant alleles is independent of whether

they are present in the same chromosome or in homologous chromosomes. (A) Cross 1 produces F1 females with the genotype w 1/1 m,

and the w 2 m recombination frequency is 33.5 percent. (B) Cross 2 produces F1 females with the genotype w m/1 1, and the w 2 m © Jones &recombination Bartlett frequencyLearning, is 37.7 LLC percent. These values are within the© rangeJones of variation & Bartlett expected Learning, to occur by chance. LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION 4.1 Linked Alleles Tend to Stay Together in Meiosis 113 4TH PAGES © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. written above the line are present in one chromo- KEY CONCEPT some, and those written below the line are present in Genes with recombination frequencies smaller than © Jones & theBartlett homologous Learning, chromosome. LLC In the females, both ©X Jones50 percent & Bartlett are presentLearning, in the LLCsame chromosome 1 chromosomes carry w and m . In males, the X chroNOT- FOR(linked). SALE Two OR genes DISTRIBUTION that undergo independent NOT FOR SALE OR DISTRIBUTION1 mosome carries the alleles w and m. (The Y written assortment, indicated by a recombination frequency below the line denotes the Y chromosome in the male.) equal to 50 percent, either are in nonhomologous Figure 4.2 illustrates a simplified symbolism, commonly chromosomes or are located far apart in a single used in Drosophila genetics, in which a wildtype allele chromosome. is denoted by a 1 sign© Jones in the appropriate & Bartlett position. Learning, The LLC © Jones & Bartlett Learning, LLC 1 symbolism is unambiguousNOT FOR because SALE the OR linked DISTRIBUTION genes NOT FOR SALE OR DISTRIBUTION in a chromosome are always written in the same order. The frequency of recombination is Using the 1 notation, the same for coupling and w+ wm+ means repulsion heterozygotes. w+ + © Jones & Bartlett Learning,wm LLC Morgan also© Jones studied & progeny Bartlett from Learning, the coupling LLC con- 1 1 andNOT FOR SALE OR DISTRIBUTION figurationNOT of the FOR w and SALE m alleles, OR DISTRIBUTIONwhich results from the mating designated as Cross 2 in Figure 4.2. In this 1 mw+ m case, the original parents had the genotypes means Y Y wmwm 1111 // ×× ?? wmwm YY © Jones & BartlettThe resulting Learning, F1 female progenyLLC from Cross 1 have the© Jones & Bartlett Learning, LLC NOT FOR SALEgenotype OR w DISTRIBUTION1/1 m (or, equivalently, w m1/w1 m). NOTIn FOR SALE OR DISTRIBUTION this genotype, the w1 and m1 alleles are in repulsion. The resulting F1 female progeny from Cross 2 have the 1 1 When these females were mated with w m/Y males, genotype w m/1 1 (equivalently, w m/w m ). In this the offspring denoted as Progeny 1 in Figure 4.2 were case the wildtype alleles are in the same chromosome. obtained. In each class of progeny, the gamete from When these F1 female progeny were crossed with the female parent is© shownJones in & the Bartlett column atLearning, the left, LLCw m/Y males, they yielded© the Jones types of& progenyBartlett tabu Learning,- LLC and the gamete fromNOT the FOR male SALE parent ORcarries DISTRIBUTION either lated as Progeny 2 in FigureNOT 4.2. FOR SALE OR DISTRIBUTION w m or the Y chromosome. The cross is equivalent Because the alleles in Cross 2 are in the coupling to a testcross, and so the phenotype of each class of configuration, the parental-type gametes carry either progeny reveals the alleles present in the gamete from w m or 1 1, and the recombinant gametes carry the mother. either w 1 or 1 m. The types of gametes are the same ©The Jones results & of Bartlett Cross 1 show Learning, a great departure LLC from as those ©observed Jones in& CrossBartlett 1, but Learning, the parental LLC and theNOT 1 : 1 FOR: 1 : 1 SALEratio of ORthe four DISTRIBUTION male phenotypes that recombinantNOT types FOR are SALE opposite. OR Yet DISTRIBUTION the frequency of is expected with independent assortment. If genes recombination is approximately the same: 37.7 percent in the same chromosome tended to remain together versus 33.5 percent. The difference is within the range in inheritance but were not completely linked, this expected to result from random variation from experi- pattern of deviation might be observed. In this case, ment to experiment. The consistent finding of equal © Jones & Bartlettthe combinations Learning, of phenotypic LLC traits in the parents ©of Jonesrecombination & Bartlett frequencies Learning, in experiments LLC in which the NOT FOR SALEthe original OR DISTRIBUTIONcross (parental phenotypes) were presentNOT FORmutant SALE alleles OR are DISTRIBUTIONin the trans or the cis configuration leads to the following conclusion: in 428/644 (66.5 percent) of the F2 males, and nonparental combinations (recombinant phenotypes) of the traits were present in 216/644 (33.5 percent). The KEY CONCEPT 33.5 percent recombinant X chromosomes is called Recombination between linked genes takes place the frequency of ©recombination Jones & Bartlett, and it Learning,should be LLCwith the same frequency ©whether Jones the & alleles Bartlett of the Learning, LLC contrasted with theNOT 50 percent FOR recombination SALE OR DISTRIBUTIONexpected genes are in the repulsionNOT (trans FOR) configuration SALE orOR DISTRIBUTION with independent assortment. in the coupling (cis) configuration; it is the same no The recombinant X chromosomes w1 m1 and w m matter how the alleles are arranged.

result from crossing-over in meiosis in F1 females. In this example, the frequency of recombination between the© linked Jones w and& Bartlett m genes was Learning, 33.5 percent. LLC With other The frequency© Jones & of Bartlett recombination Learning, LLC pairsNOT of linkedFOR SALEgenes, the OR frequency DISTRIBUTION of recombination differsNOT from FOR one SALE gene OR pair DISTRIBUTION to ranges from near 0 to 50 percent. Even genes in the the next. same chromosome can undergo independent assortment (frequency of recombination equal to 50 percent) The principle that the frequency of recombination if they are sufficiently far apart. This implies the follow- depends on the particular pair of genes may be © Jones & Bartletting principle: Learning, LLC © Jonesillustrated & Bartlett using Learning, the recessive LLC allele y of another NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION 114 CHAPTER 4 Gene Linkage and Genetic Mapping 4TH PAGES © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. X-linked gene in Drosophila, which results in yellow The results of these and other experiments give body color instead of the usual gray color determined support to two general principles of recombination: by the y1 allele. The yellow body (y) and white eye © Jones & Bartlett Learning, LLC © Jones n The & recombination Bartlett Learning, frequency isLLC a characteristic of (w) genes are linked. The frequency of recombina- NOT FOR SALE OR DISTRIBUTION NOT FORa particular SALE pair OR of DISTRIBUTION genes. tion between the genes is as shown in the data in n Recombination frequencies are the same in cis FIGURE 4.3. The layout of the crosses is like that in Figure 4.2. In Cross 1, the female has y and w in (coupling) and trans (repulsion) heterozygotes. the trans configuration (1 w/y 1); in Cross 2, the alleles are in the cis© configuration Jones & Bartlett (y w/1 1Learning,). The LLCRecombination does© not Jones occur & Bartlett Learning, LLC y and w genes exhibitNOT a much FOR lowerSALE frequency OR DISTRIBUTION of in Drosophila males.NOT FOR SALE OR DISTRIBUTION recombination than that observed with w and m in Figure 4.2. To put it another way, the genes y and w Early experiments in Drosophila genetics also indicated are more closely linked than are w and m. In Cross that the organism is unusual in that recombination does not take place in males. The absence of recom- 1, the recombinant progeny are 1 1 and y w, and bination in Drosophila males means that all alleles they ©account Jones for & 130/9027 Bartlett 5 Learning,1.4 percent of LLC the total. © Jones & Bartlett Learning, LLC located in a particular chromosome show complete In Cross 2, the recombinant progeny are 1 w and NOT FOR SALE OR DISTRIBUTION linkage in theNOT male. FOR For SALEexample, OR the DISTRIBUTION genes cn (cin- y 1, and they account for 94/7838 5 1.2 percent of nabar eyes) and bw (brown eyes) are both in chromo- the total. Once again, the parental and recombinant some 2, but they are so far apart that in females, they gametes are reversed in Crosses 1 and 2, because the show 50 percent recombination. Because the genes configuration of alleles in the female parent is trans exhibit 50 percent recombination, the cross © Jones &in BartlettCross 1 but Learning, cis in Cross LLC 2, yet the frequency of © Jones & Bartlett Learning, LLC recombination between the genes is within experi- cncn bwbw cncn bwbw NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION// ×× ?? mental error. 1111 cncn bwbw

Cross 1 Cross 2 Parents: © Jones & Bartlett Learning, LLCParents: © Jones & Bartlett Learning, LLC White-eyed NOT FORYellow-body SALE OR DISTRIBUTIONWhite-eyed and NOT FORWildtype SALE OR DISTRIBUTION females males yellow-body males females + w && y + (( y w && + + (( Y ן Y y w ן w +

F1©: Jones & Bartlett Learning, LLC F1: © Jones & Bartlett Learning, LLC NOT FOR SALE+ wOR&& DISTRIBUTIONy w (( NOT FOR SALEy w OR&& DISTRIBUTIONy w (( Y The cis + + Yןן + The trans y (repulsion) (coupling) heterozygote heterozygote

F : F : 2 Progeny 1 2 Progeny 2 © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE ORWildtype DISTRIBUTION body, 4292 Parental types: NOT FORRecombinant SALE ORtypes: DISTRIBUTION 55 white eyes 98.6% have 1.2% have (maternal gamete: + w) parental allele nonparental allele combinations combinations Yellow body, 4605 (nonrecombinant). (recombinant). 39 red eyes (maternal gamete:© Jones y +) & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Wildtype body, 86 Recombinant types: Parental types: 3946 red eyes 1.4% have 98.8% have (maternal gamete: + +) nonparental allele parental allele combinations combinations Yellow body, 44 (recombinant). (nonrecombinant). 3798 white eyes © Jones & Bartlett Learning,9027 LLC © Jones & Bartlett7838 Learning, LLC NOT FOR(maternal SALE gamete: OR y w )DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

FIGURE 4.3 An experiment demonstrating that the frequency of recombination between two genes depends on the genes. The frequency of recombination between w and y is much less than that between w and m in Figure 4.2. The y2w experiment also confirms the equal frequency of recombination in trans and cis heterozygous genotypes. (A) The trans heterozygous females, 1 w/y 1, yield © Jones &1.4 percent Bartlett recombination. Learning, (B) The LLC cis heterozygous females, y w/11© ,Jones yield 1.2 percent& Bartlett recombination. Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION 4.1 Linked Alleles Tend to Stay Together in Meiosis 115 4TH PAGES © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. yields progeny of genotype cn bw/cn bw and 1 1/cn bw of 3.1 map units therefore equals 3.1 centimorgans and (the nonrecombinant types) as well as cn 1/cn bw and indicates 3.1 percent recombination between the genes. © Jones & 1Bartlett bw/cn bw Learning, (the recombinant LLC types) in the proportions© JonesAn example& Bartlett is shown Learning, in part ALLC of FIGURE 4.5, which NOT FOR SALE1 : 1 : 1 OR : 1. TheDISTRIBUTION outcome of the reciprocal cross is difNOT- FORdeals SALEwith the OR Drosophila DISTRIBUTION mutants w for white eyes and ferent. Because no crossing-over occurs in males, the dm (diminutive) for small body. The female parent in the reciprocal cross testcross is the trans heterozygote, but as we have seen, this configuration is equivalent in frequency of recom- cncn bwbw cncn bwbw ×× bination to the cis heterozygote. Among 1000 progeny // 1111 ?? cncn bwbw© Jones & Bartlett Learning, LLCthere are 31 recombinants.© Using Jones this &estimate, Bartlett we Learning,can LLC express the genetic distance between w and dm in four yields progeny only NOTof the nonrecombinantFOR SALE OR genotypes DISTRIBUTION cn NOT FOR SALE OR DISTRIBUTION completely equivalent ways: bw/cn bw and 11/cn bw in equal proportions. The absence of recombination in Drosophila males is a convenience n As the frequency of recombination—in this often exploited in experimental design; as shown in the case 0.031 case© ofJones cn and &bw Bartlett, all the alleles Learning, present in LLC any chromo- n As the© percent Jones recombination & Bartlett, or Learning,3.1 percent LLC some in a male must be transmitted as a group, without n As the distance in map units—in this example, 3.1 beingNOT recombined FOR SALE with alleles OR DISTRIBUTIONpresent in the homologous NOT FOR SALE OR DISTRIBUTION map units chromosome. The absence of crossing-over in Drosophila n males is atypical; in most other animals and plants, As the distance in centimorgans, or recombination takes place in both sexes, though not nec- 3.1 centimorgans (3.1 cM) essarily with the same frequency. © Jones & Bartlett Learning, LLC © JonesA genetic & Bartlett map based Learning, on these data LLC is shown in Figure 4.5, NOT FOR SALE OR DISTRIBUTION NOT FORpart B. SALE The chromosome OR DISTRIBUTION is represented as a horizontal 4.2 Recombination results from line, and each gene is assigned a position on the line crossing-over between according to its genetic distance from other genes. In this example, there are only two genes, w and dm, and they linked alleles. are separated by a distance of 3.1 centimorgans (3.1 cM), The linkage of the© genes Jones in &a chromosomeBartlett Learning, can be LLCor 3.1 map units. Genetic maps© Jones are usually & Bartlett truncated Learning, to LLC represented in the NOTform of FOR a genetic SALE map ,OR which DISTRIBUTION shows show only the genes of interest.NOT FOR The full SALE genetic OR map DISTRIBUTION the linear order of the genes along the chromosome of the Drosophila X chromosome extends considerably spaced so that the distances between adjacent genes is farther in both directions than indicated in this figure. proportional to the frequency of recombination between Physically, one map unit corresponds to a length of them. A genetic map is also called a linkage map or a the chromosome in which, on the average, one cross- chromosome© Jones &map Bartlett. The concept Learning, of genetic LLC mapping over is formed© Jones in every & Bartlett 50 cells Learning,undergoing meiosis.LLC wasNOT first FOR developed SALE by OR Morgan’s DISTRIBUTION student Alfred H. This principleNOT is FORillustrated SALE in FIGURE OR DISTRIBUTION 4.6. If one meiotic Sturtevant in 1913. The early geneticists understood cell in 50 has a crossover, the frequency of crossing- that recombination between genes takes place by an over equals 1/50, or 2 percent. Yet the frequency of exchange of segments between homologous chromo- recombination between the genes is 1 percent. The cor- somes in the process now called crossing-over. Each respondence of 1 percent recombination with 2 percent © Jones & Bartlettcrossover is Learning, manifested physically LLC as a chiasma, or cross-© Jonescrossing-over & Bartlett is a Learning,little confusing LLC until you consider that NOT FOR SALEshaped ORconfiguration, DISTRIBUTION between homologous chromoNOT- FORa crossover SALE results OR DISTRIBUTIONin two recombinant chromatids and somes; chiasmata are observed in prophase I of meiosis. two nonrecombinant chromatids (Figure 4.6). A cross- Each chiasma results from the breaking and rejoining of over frequency of 2 percent means that of the 200 chro- chromatids during meiosis, with the result that there is mosomes that result from meiosis in 50 cells, exactly an exchange of corresponding segments between them. 2 chromosomes (those involved in the crossover) are The theory of crossing-over© Jones is that & Bartlett each chiasma Learning, results LLCrecombinant for genetic markers© Jones spanning & Bartlett the particu Learning,- LLC in a new associationNOT of genetic FOR markers. SALE ThisOR processDISTRIBUTION is lar chromosome segment. NOTTo put FOR the matter SALE in anotherOR DISTRIBUTION illustrated in FIGURE 4.4. When there is no crossing- way, 2 percent crossing-over corresponds to 1 percent over (part A), the alleles present in each homologous recombination because only half of the chromatids in chromosome remain in the same combination. When a each cell with a crossover are actually recombinant. crossover does take place (part B), the outermost alleles In situations in which there are genetic markers in© two Jones of the chromatids & Bartlett are Learning, interchanged LLC (recombined). along the© chromosome, Jones & Bartlett such as the Learning, A, a and B, LLC b pairs NOTThe unitFOR of SALEdistance OR in aDISTRIBUTION genetic map is called a of allelesNOT in Figure FOR 4.6, SALE recombination OR DISTRIBUTION between the map unit; one map unit is equal to 1 percent recombi- marker genes takes place only when a crossover occurs nation. For example, two genes that recombine with a between the genes. FIGURE 4.7 illustrates a case in frequency of 3.1 percent are said to be located 3.1 map which a crossover takes place between the gene A and units apart. One map unit is also called a centimorgan, the centromere, rather than between the genes A and © Jones & Bartlettabbreviated Learning, cM, in honor LLC of T. H. Morgan. A distance© JonesB. The & Bartlettcrossover Learning,does result in LLC the physical exchange NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION 116 CHAPTER 4 Gene Linkage and Genetic Mapping 4TH PAGES © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. (A) No crossing-over (B) Crossing-over Chiasma a b © Jones & Bartlett Learning, LLC © Jonesa & Bartlettb Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION a b a b Crossing-over between + + + + these chromatids + + + + © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION a b a b Nonrecombinant chromatids a b a +

+ + + b © Jones & Bartlett Learning, LLC © JonesRecombinant & Bartlett Learning, LLC chromatids NOT FOR SALE+ OR DISTRIBUTION+ + NOT+ FOR SALE OR DISTRIBUTION

a a b © Jones & Bartlett Learning, LLC b © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTIONa b NOT FORa SALE+ OR DISTRIBUTION + + + b

+ + + +

Result:© Jones Four & Bartlett Learning,Result: LLC Two recombinant © Jones & Bartlett Learning, LLC nonrecombinant and two nonrecombinant chromatidsNOT FOR SALE OR DISTRIBUTIONchromatids NOT FOR SALE OR DISTRIBUTION

FIGURE 4.4 Diagram illustrating crossing-over between two genes. (A) When there is no crossover between two genes, the alleles are not recombined. (B) When there is a crossover between them, the result is two recombinant and two nonrecombinant products, because the exchange© Jones takes &place Bartlett between onlyLearning, two of the four LLC chromatids. © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION of segments between the innermost chromatids. How- do not result in recombinant chromosomes), there is ever, because it is located outside the region between A an important distinction between the distance between and B, all of the resulting gametes must carry either the two genes as measured by the recombination frequency A B or the a b allele combination. These are nonrecom- and as measured in map units: © Jones &binant Bartlett chromosomes. Learning, The LLCpresence of the crossover is © Jones n The & map Bartlett distance Learning,between two LLC genes equals one- NOT FORundetected SALE OR because DISTRIBUTION it is not in the region between the NOT FORhalf ofSALE the average OR DISTRIBUTION number of crossovers that take genetic markers. place in the region per meiotic cell; it is a measure In some cases, the region between genetic markers of crossing-over. is large enough that two (or even more) crossovers can n The recombination frequency between two genes be formed in a single meiotic cell. One possible con- indicates how much recombination is actually figuration for two crossovers© Jones is shown & Bartlett in FIGURE Learning, 4.8. LLC © Jones & Bartlett Learning, LLC In this example, both crossovers are between the same observed in a particular experiment; it is a measure NOT FOR SALE OR DISTRIBUTIONof recombination. NOT FOR SALE OR DISTRIBUTION pair of chromatids. The result is that there is a physical exchange of a segment of chromosome between the The difference between map distance and recombina- marker genes, but the double crossover remains unde- tion frequency arises because double crossovers that do tected because the markers themselves are not recom- not yield recombinant gametes, like the one depicted bined.© TheJones absence & Bartlett of recombination Learning, results LLC from the in Figure 4.8,© doJones contribute & Bartlett to the map Learning, distance but LLC do fact NOTthat the FOR second SALE crossover OR DISTRIBUTION reverses the effect of not contributeNOT to the FOR recombination SALE OR frequency. DISTRIBUTION The dis- the first, insofar as recombination between A and B is tinction is important only when the region in question concerned. The resulting chromosomes are either A B is large enough for double crossing-over to occur. If the or a b, both of which are nonrecombinant. region between the genes is short enough that no more Because double crossovers in a region between two than one crossover can occur in the region in any one © Jones &genes Bartlett can remain Learning, undetected LLC (this happens when they © Jonesmeiosis, & then Bartlett map units Learning, and recombination LLC frequencies NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION 4.2 Recombination Results from Crossing-Over Between Linked Alleles 117 4TH PAGES © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. (A) Cross (B) Genetic map Parent: © Jones & Bartlett Learning, LLC © Jones & Bartlettwd Learning, LLCm White-eyed Diminutive NOT FOR SALEfemales OR DISTRIBUTIONmales NOT FOR SALE OR DISTRIBUTION 3.1 cM w + && + dm (( Y ן + w

F1: © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC w + w dm OR(( DISTRIBUTION NOT FOR SALE OR DISTRIBUTION ןThe trans NOT FOR&& SALE heterozygote + dm Y

F2: Progeny © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC White eyes, 497 NOT FORnormal SALE size OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION (maternal gamete: w +) Parental types = 969/1000 = 96.9%

Red eyes, 472 diminutive size © Jones & Bartlett Learning,(maternal gamete: LLC + dm) © Jones & Bartlett Learning, LLC

NOT FOR SALE OR DISTRIBUTIONRed eyes, 19 RecombinantNOT types FOR = 31/1000 SALE = 3.1%OR DISTRIBUTION normal size Genetic distance = frequency of recombination, 0.031 (maternal gamete: + +) Genetic distance = percent recombination, 3.1% Genetic distance = map distance in map units, 3.1 map units White eyes, 12 Genetic distance = map distance in centimorgans, 3.1 centimorgans (3.1 cM) diminutive size © Jones & Bartlett1000 Learning, LLC © Jones & Bartlett Learning, LLC (maternal gamete: w dm) NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

FIGURE 4.5 An experiment illustrating how the frequency of recombination is used to construct a genetic map. (A) There is 3.1 percent recombination between the genes w and dm. (B) A genetic map with w and dm positioned 3.1 map units (3.1 centimorgans, cM) apart, corresponding to 3.1 percent recombination. The map distance equals frequency of recombination only when the frequency of recombination© Jones is & sufficiently Bartlett small. Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

are the same (because there are no multiple crossovers frequency between genes y and rb is 7.5 percent, and that can undo each other). This is the basis for defining that between rb and cv is 6.2 percent. The genetic map a map unit as being equal to 1 percent recombination: might be any one of three possibilities, depending on © Jones & Bartlett Learning, LLC © Joneswhich & geneBartlett is in theLearning, middle (y, LLCcv, or rb). Map C, which NOT FOR SALEKEY CONCEPT OR DISTRIBUTION NOT FORhas y SALEin the middle, OR DISTRIBUTION can be excluded because it implies Over an interval so short that multiple crossovers that the recombination frequency between rb and cv are precluded (typically yielding 10 percent should be greater than that between rb and y, and this recombination or less), the map distance equals the contradicts the observed data. In other words, map C recombination frequency because all crossovers can be excluded because it implies that the frequency result in recombinant© Jones gametes. & Bartlett Learning, LLCof recombination between© y andJones cv must & Bartlett be negative. Learning, LLC NOT FOR SALE OR DISTRIBUTIONMaps A and B are both NOTconsistent FOR with SALE the observed OR DISTRIBUTION recombination frequencies. They differ in their predic- Furthermore, when adjacent chromosome regions tions regarding the recombination frequency between separating linked genes are so short that multiple cross- y and cv. Using the principle of additivity of map overs are not formed, the recombination frequencies distances, the predicted y2cv map distance in A is (and© Joneshence the & mapBartlett distances) Learning, between LLCthe genes are 13.7 map© units, Jones whereas & Bartlett the predicted Learning, y2cv map LLC dis- additive.NOT FORThis importantSALE OR feature DISTRIBUTION of recombination, as tance in BNOT is 1.3 FORmap units. SALE In fact, OR the DISTRIBUTION observed recom- well as the logic used in genetic mapping, is illustrated bination frequency between y and cv is 13.3 percent. by the example in FIGURE 4.9. The genes are located Map A is therefore correct. However, there are actually in the X chromosome of Drosophila—y for yellow two genetic maps corresponding to map A. They differ body, rb for ruby eye color, and cv for shortened wing only in whether y is placed at the left or at the right. One © Jones & Bartlettcrossvein. TheLearning, experimentally LLC measured recombination© Jonesmap & is Bartletty2rb2cv, Learning,which is the oneLLC shown in Figure 4.9; NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION 118 CHAPTER 4 Gene Linkage and Genetic Mapping 4TH PAGES © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. (A) A B A B 49 nonrecombinant © Jones & Bartlett Learning, LLC 49 meioses with © Jones & Bartlett Learning, LLC A no crossover NOT FOR SALE OR DISTRIBUTIONB NOT FORA SALE ORB DISTRIBUTION49 nonrecombinant a b a b 49 nonrecombinant

a b a b 49 nonrecombinant © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC (B) NOT FOR SALE OR DISTRIBUTIONA B 1 nonrecombinantNOT FOR SALE OR DISTRIBUTION A B 1 meiosis with a single crossover A Bb A b 1 recombinant a b a B 1 recombinant © Jones & Bartletta Learning,b LLC a © Jonesb &1 Bartlett nonrecombinant Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION 2 (C) Frequency of recombination: r = 1 + 1 = 49 + 49 + 49 + 49 + 1 + 1 + 1 + 1 200

= 1 percent = 1 map unit = 1 cM

© Jones &FIGURE Bartlett 4.6 Diagram Learning, of chromosomal LLC configurations in 50 meiotic cells,© Jones in which 1 & has Bartlett a crossover betweenLearning, two genes. LLC (A) The 49 cells without NOT FORa crossoverSALE resultOR inDISTRIBUTION 98 A B and 98 a b chromosomes; these are all nonrecombinant.NOT FOR (B) SALEThe cell with OR a crossover DISTRIBUTION yields chromosomes that are A B, A b, a B, and a b, of which the middle two types are recombinant chromosomes. (C) The recombination frequency equals 2/200, or 1 percent, also called 1 map unit or 1 cM. Hence, 1 percent recombination means that 1 meiotic cell in 50 has a crossover in the region between the genes.

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC Nonrecombinant for A and B NOTA FORB SALE OR DISTRIBUTIONA B NOT FOR SALE OR DISTRIBUTION A B a b Nonrecombinant for a and b a b A B Nonrecombinant for A and B a b a b © Jones & Bartlett Learning, LLC © JonesNonrecombinant & Bartlett for a Learning, and b LLC NOT FORCrossing-over SALE OR occurs DISTRIBUTION NOTCrossing-over FOR SALE is not OR DISTRIBUTION outside of the region detected because no between the A and recombination between B genes. A and B genes occurred.

© Jones &FIGURE Bartlett 4.7 Crossing-overLearning, outside LLC the region between two genes© isJones not detectable & Bartlett through recombination. Learning, Although LLC a segment of chromosome is exchanged, the genetic markers outside the region of the crossovers stay in the nonrecombinant configurations, in this NOT FORcase SALE A B and OR a b. DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

A Nonrecombinant for A and B A© JonesB & Bartlett Learning, LLC B © Jones & Bartlett Learning, LLC Nonrecombinant for A and B ANOT FORB SALE OR DISTRIBUTIONA B NOT FOR SALE OR DISTRIBUTION a b a b Nonrecombinant for a and b a b a b Nonrecombinant for a and b © Jones &Two Bartlett crossovers Learning, LLC © JonesDouble & crossover Bartlett is not Learning, LLC occur between A detected because it does NOT FORand SALE B, between OR DISTRIBUTIONthe NOTnot FOR result SALE in recombination OR DISTRIBUTION same pair of between A and B genes. chromatids.

FIGURE 4.8 If two crossovers take place between marker genes A and B, and both involve the same pair of chromatids, then neither © Jones &crossover Bartlett is detected Learning, because all LLC of the resulting chromosomes are© nonrecombinant Jones & Bartlett A B or a b. Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION 4.2 Recombination Results from Crossing-Over Between Linked Alleles 119 4TH PAGES © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. yrb (A) 7.5 cM © Jones & Bartlett Learning, LLC rb © Jonescv & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION 6.2 cM If this is the correct genetic map, then the distance y to cv should y rb cv be 7.5 cM + 6.2 cM = 13.7 cM.

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC yrb (B) NOT FOR SALE OR DISTRIBUTION If this is the correctNOT genetic FOR map, SALE OR DISTRIBUTION 7.5 cM then the distance y to cv should cv rb be 7.5 cM – 6.2 cM = 1.3 cM. 6.2 cM

© Jones & Bartletty cv Learning, LLCrb © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOTThis geneticFOR SALEmap is not OR consistent DISTRIBUTION with the data; the map implies that the frequency of recombination rb y cv between y and cv is negative (C) (because 6.2 cM – 7.5 cM = –1.3 cM); 7.5 cM however, a negative frequency of © Jones & Bartlett Learning, LLC 6.2 cM © Jones & Bartlettrecombination Learning, is not LLCpossible. NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

FIGURE 4.9 In Drosophila, the genes y (yellow body) and rb (ruby eyes) have a recombination frequency of 7.5 percent, and rb and cv (shortened wing crossvein) have a recombination frequency of 6.2 percent. There are three possible genetic maps, depending on whether rb is in the middle (part A), cv is in the middle (part B), or y is in the middle (part C). Map (C) can be excluded because it implies that rb and y should be closer than rb and cv, whereas the observed recombination frequency between rb and y is actually greater than that between rb and cv. Maps© (A)Jones and (B) &are Bartlettcompatible withLearning, the data given. LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

the other is cv2rb2y. The two ways of depicting the R1-mb in a cross between a heterozygous genotype and genetic map are completely equivalent because there a homozygous wildtype. is no way of knowing from the recombination data whether© Jones y or &cv Bartlettis closer to Learning, the telomere. LLC (Other data © Jones & Bartlett Learning, LLC indicateNOT thatFOR y is,SALE in fact, OR near DISTRIBUTION the telomere.) NOT FOR SALE OR DISTRIBUTION A genetic map can be expanded by this type of reasoning to include all of the known genes in a

chromosome; these genes constitute a linkage group. Courtesy of M. G. Neuffer, College of Agriculture, Food, and Natural Resources, University of Missouri. The number of linkage groups is the same as the haploid © Jones & Bartlettnumber of Learning, chromosomes LLC of the species. For example,© JonesPhysical & Bartlett distance Learning, is often—but LLC not NOT FOR SALEcultivated OR corn DISTRIBUTION (Zea mays) has ten pairs of chromosomesNOT FORalways—correlated SALE OR DISTRIBUTION with map distance. and ten linkage groups. A partial genetic map of chromosome 10 is shown in FIGURE 4.10, along with the Generally speaking, the greater the physical separa- dramatic phenotypes caused by some of the mutations. tion between genes along a chromosome, the greater The ears of corn shown in parts C and F demonstrate the map distance between them. Physical distance and the result of Mendelian© Jones segregation. & Bartlett The ear Learning, in part C LLCgenetic map distance are© usually Jones correlated, & Bartlett because Learning, LLC shows a 3 : 1 segregationNOT ofFOR yellow SALE : orange OR kernels DISTRIBUTION pro- a greater distance betweenNOT genetic FOR markers SALE affords OR DISTRIBUTIONa duced by the recessive orange pericarp-2 (orp-2) allele in greater chance for a crossover to take place; crossing- a cross between two heterozygous genotypes. over is a physical exchange between the chromatids of paired homologous chromosomes. On the other hand, the general correlation between © Jones & Bartlett Learning, LLC physical ©distance Jones and & geneticBartlett map Learning, distance is LLC by no NOT FOR SALE OR DISTRIBUTION means absolute.NOT FOR We haveSALE already OR DISTRIBUTIONnoted that the frequency of recombination between genes may differ in

Courtesy of M. G. Neuffer, College of Agriculture, Food, and Natural Resources, University of Missouri. males and females. An unequal frequency of recombination means that the sexes can have different map The ear in part F shows a 1 : 1 segregation of distances in their genetic maps, although the physical © Jones & Bartlettmarbled:white Learning, kernels produced LLC by the dominant allele© Joneschromosomes & Bartlett of Learning,the two sexes LLC are the same and the NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION 120 CHAPTER 4 Gene Linkage and Genetic Mapping 4TH PAGES © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. Short arm (10) Long arm (10) Centromere (C) Centromere © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR orp2DISTRIBUTION (B) 61 50.8 php1 zn1 61.5 50.7 glu1 du1 62 li1 62.5

51 og1 © Jones & Bartlett Learning, LLC mgs1 © Jones69.7 & Bartlett Learning, LLC 47.0 les16NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION 46.9 y9 (D) ms10 74

(A) © Jones37 & Bartlettoy1 Learning, LLC © Jonestp2 & Bartlett Learning,81 LLC NOT FOR SALE OR DISTRIBUTION NOT FORg1 SALE OR82 DISTRIBUTION

29.1 cr4

(E)

13 rp1 rps11 100 r1 101.1 © Jones & Bartlett Learning, LLC lc1 © Jones103 & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION mst1 NOT FOR105 SALE OR DISTRIBUTION (F)

Telomere © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

w2 120 gln1 122.1 © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning,o7 LLC125 NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

l13 131

NOT FOR SALE OR DISTRIBUTION TelomereNOT FOR SALE OR DISTRIBUTION

FIGURE 4.10 Genetic map of chromosome 10 of corn, Zea mays. The map distance to each gene is given in standard map units (centimorgans) relative to a position 0 for the telomere of the short arm (lower left). (A) Mutations in the gene oil yellow-1 (oy1) result in a yellow-green plant. The plant in the foreground is heterozygous for the dominant allele Oy1; behind is a normal plant. (B) Mutations in the gene lesion-16© Jones (les16) & result Bartlett in many smallLearning, to medium-sized, LLC irregularly spaced, discolored© spots Jones on the leaf& Bartlettblade and sheath. Learning, The photograph LLC shows the phenotype of a heterozygote for Les16, a dominant allele. (C) The orp2 allele is a recessive expressed as orange pericarp, a maternal tissue NOTthat surrounds FOR the SALE kernels. ORThe ear DISTRIBUTION shows the segregation of orp2 in a cross betweenNOT two heterozygous FOR SALE genotypes, OR yieldingDISTRIBUTION a 3 : 1 ratio of yellow : orange seeds. (D) The gene zn1 is zebra necrotic-1, in which dying tissue appears in longitudinal leaf bands. The leaf on the left is homozygous zn1, that on the right is wildtype. (E) Mutations in the gene teopod-2 (tp2) result in many small, partially podded ears and a simple tassel. An ear from a plant heterozygous for the dominant allele Tp2 is shown. (F) The mutation R1-mb is an allele of the r1 gene, resulting in red or purple color in the aleurone layer of the seed. Note the marbled color in kernels of an ear segregating for R1-mb. [Adapted from an © Jones &illustration Bartlett by E. H.Learning, Coe. Photos courtesy LLC of M. G. Neuffer, College of© Agriculture, Jones Food, & Bartlett and Natural Learning, Resources, University LLC of Missouri.] NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION 4.2 Recombination Results from Crossing-Over Between Linked Alleles 121 4TH PAGES © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. genes must have the same linear order. Distance in map units on genetic map For example, because there is no recom- © Jones & binationBartlett in Learning, male Drosophila LLC, the map dis- © Jones & 54.5Bartlett Learning,3.0 LLC 49.5 NOT FOR SALEtance between OR DISTRIBUTION any pair of genes located in PhysicalNOT map FOR SALE OR DISTRIBUTION the same chromosome, when measured in the male, is 0. (On the other hand, genes Euchromatin Heterochromatin Euchromatin on different chromosomes do undergo independent assortment in males.) Genetic map The general correlation© Jones between & Bartlett phys- Learning, LLC © Jones & Bartlett Learning, LLC ical distance and geneticNOT map FOR distance SALE can OR DISTRIBUTIONnet pr NOTcn FOR SALE ORsp DISTRIBUTION even break down in a single chromosome. For example, crossing-over is much less 0.0 54.5 57.5 107.0 frequent in heterochromatin, which con- Map position sists primarily of gene-poor regions near Very little recombination the© centromeres,Jones & Bartlett than in Learning,euchromatin. LLC © Jones & takesBartlett place Learning,in heterochromatin; LLC Consequently,NOT FOR aSALE given ORlength DISTRIBUTION of hetero- NOT FOR SALEa small distanceOR DISTRIBUTION in the genetic chromatin will appear much shorter in map corresponds to a large the genetic map than an equal length of distance on the chromosome. euchromatin. In heterochromatic regions, therefore, the genetic map gives a dis- FIGURE 4.11 Chromosome 2 in Drosophila as it appears in metaphase of © Jones & Bartletttorted picture Learning, of the physicalLLC map. An mitosis (physical© Jones map, &top) Bartlett and in the geneticLearning, map (bottom). LLC The genes pr and cn NOT FOR SALEexample OR of suchDISTRIBUTION distortion is illustrated in are actuallyNOT in euchromatin FOR SALE but are OR located DISTRIBUTION near the junction with heterochromatin. FIGURE 4.11, which compares the physical The total map length is 54.5 1 49.5 1 3.0 5 107.0 map units. The heterochromatin accounts for 3.0/107.0 5 2.8 percent of the total map length but constitutes map and the genetic map of chromosome approximately 25 percent of the physical length of the metaphase chromosome. 2 in Drosophila. The physical map depicts the appearance of the chromosome in metaphase of mitosis.© JonesTwo genes & nearBartlett the tips Learning, and two LLCcrossover can be canceled ©by Jones another &crossover Bartlett further Learning, LLC near the euchromatin–NOTheterochromatin FOR SALE OR junction DISTRIBUTION are along the way. If two exchangesNOT FOR between SALE the OR same DISTRIBUTION indicated in the genetic map. The map distances across two chromatids take place between the genes A and the euchromatic arms are 54.5 and 49.5 map units, B, then their net effect will be that all chromosomes respectively, for a total euchromatic map distance of are nonrecombinant, either A B or a b. Two of the 104.0 map units. However, the heterochromatin, which products of this meiosis have an interchange of their constitutes© Jones approximately & Bartlett Learning,25 percent LLCof the entire middle segments,© Jones but & the Bartlett chromosomes Learning, are not LLCrecom- chromosome,NOT FOR hasSALE a genetic OR DISTRIBUTION length in map units of binant forNOT the geneticFOR SALE markers OR and DISTRIBUTION so are genetically only 3.0 percent. The distorted length of the hetero- indistinguishable from noncrossover chromosomes. chromatin in the genetic map results from the reduced The possibility of such canceling events means that the frequency of crossing-over in the heterochromatin. In observed recombination value is an underestimate of the spite of the distortion of the genetic map across the true exchange frequency and the map distance between © Jones & Bartlettheterochromatin, Learning, in the LLC regions of euchromatin there© Jonesthe genes.& Bartlett In higher Learning, organisms, LLC double crossing-over is NOT FOR SALEis a good OR correlationDISTRIBUTION between the physical distanceNOT FOReffectively SALE precluded OR DISTRIBUTION in chromosome segments that are between genes and their distance, in map units, in the sufficiently short, usually about 10 map units or less. genetic map. Therefore, multiple crossovers that cancel each other’s effects can be avoided by using recombination data for One crossover can undo the effects closely linked genes to build up genetic linkage maps. The minimum recombination frequency between of another. © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTIONtwo genes is 0. The recombinationNOT FOR frequency SALE also OR has DISTRIBUTION When two genes are located far apart along a chromo- a maximum: some, more than one crossover can be formed between them in a single meiosis, and this complicates the KEY CONCEPT interpretation of recombination data. The probabil- © Jones & Bartlett Learning, LLC No matter© Jones how far &apart Bartlett two genes Learning, may be, the LLC ity of multiple crossovers increases with the distance maximum frequency of recombination between any betweenNOT FORthe genes. SALE Multiple OR DISTRIBUTIONcrossing-over complicates two genesNOT is 50FOR percent. SALE OR DISTRIBUTION genetic mapping because map distance is based on the number of physical exchanges that are formed, and some of the multiple exchanges between two genes do Fifty percent recombination is the same value that not result in recombination of the genes and hence are would be observed if the genes were on nonhomolo- © Jones & Bartlettnot detected. Learning, As we saw LLC in Figure 4.8, the effect of one© Jonesgous & chromosomes Bartlett Learning, and assorted LLC independently. The NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION 122 CHAPTER 4 Gene Linkage and Genetic Mapping 4TH PAGES © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. (A) Two-strand double crossover Chromosomes Recovered a b a b Parental Recombinant © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC b a b a 40 NOT FOR SALE OR DISTRIBUTION+ + NOT FOR SALE OR DISTRIBUTION + + + + + +

(B) Three-strand© Jones double crossover& Bartlett Learning, LLC © Jones & Bartlett Learning, LLC a + NOTa FOR SALEb OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION a b a b 22 + + + b + + + + © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION (C) Three-strand double crossover a b a b a + a b 22 © Jones & Bartlett Learning,+ LLC + © Jones+ & Bartlett+ Learning, LLC NOT FOR SALE OR DISTRIBUTION+ + NOT+ FOR SALEb OR DISTRIBUTION

(D) Four-strand double crossover a + a b © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC b a + a 04 NOT+ FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION + + b + + + b

FIGURENOT 4.12 FOR Diagram SALE showing OR that DISTRIBUTION the result of two crossovers in the interval betweenNOT two FOR genes isSALE indistinguishable OR DISTRIBUTION from independent assortment of the genes, provided that the chromatids participate at random in the crossovers. (A) A two-strand double crossover. (B) and (C) The two types of three-strand double crossovers. (D) A four-strand double crossover.

© Jones &maximum Bartlett frequency Learning, of recombinationLLC is observed © Joneswhich &three Bartlett chromatids Learning, participate. LLC The final possi- NOT FORwhen SALE the OR genes DISTRIBUTION are so far apart in the chromosome NOTbility FOR is thatSALE the ORsecond DISTRIBUTION exchange connects the chro- that at least one crossover is almost always formed matids that did not participate in the first exchange between them. In part B of Figure 4.6, it can be seen (four-strand double crossover, part D), in which case that a single exchange in every meiosis would result all four products are recombinant. in half of the products having parental combinations In most organisms, when double crossovers are and the other half having© Jones recombinant & Bartlett combinations Learning, formed,LLC the chromatids that© Jonestake part & inBartlett the two Learning, LLC of the genes. The NOToccurrence FOR ofSALE two ORexchanges DISTRIBUTION exchange events are selectedNOT at FOR random. SALE In ORthis DISTRIBUTION between two genes has the same effect, as shown case, the expected proportions of the three types of in FIGURE 4.12. Part A shows a two-strand double double exchanges are 1/4 four-strand doubles, 1/2 crossover, in which the same chromatids participate three-strand doubles, and 1/4 two-strand doubles. in both exchanges; no recombination of the marker This means that on the average, (1/4)(0) 1 (1/2)(2) genes© isJones detectable. & Bartlett When the Learning, two exchanges LLC have 1 (1/4)(4) 5© 2 Jones recombinant & Bartlett chromatids Learning, will be found LLC one NOTchromatid FOR inSALE common OR DISTRIBUTION(three-strand double among the NOT4 chromatids FOR SALEproduced OR from DISTRIBUTION meioses with crossover, parts B and C), the result is indistinguish- two exchanges between a pair of genes. This is the able from that of a single exchange; two products same proportion obtained with a single exchange with parental combinations and two with recom- between the genes. Moreover, a maximum of 50 per- binant combinations are produced. Note that there cent recombination is obtained for any number of © Jones &are Bartlett two types Learning, of three-strand LLC doubles, depending on © Jonesexchanges. & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION 4.2 Recombination Results from Crossing-Over Between Linked Alleles 123 4TH PAGES © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. a c b simple method for determining the order of the three c genes, as we will see in the next section. © Jones & Bartlett Learning, LLCa b © Jones & Bartlett Learning, LLC + + NOT FOR SALE OR DISTRIBUTION+ NOT FOR4.3 SALEDouble OR crossoversDISTRIBUTION are revealed + + + in three-point crosses. The data in TABLE 4.1 result from a testcross in corn with three genes in a single chromosome. The © Jonesa c& Bartlettb Learning, LLCanalysis illustrates the approach© Jones to & interpretingBartlett Learning, a LLC NOT FOR SALE OR DISTRIBUTIONthree-point cross. The recessiveNOT FORalleles SALE of the genes OR DISTRIBUTIONin a + b this cross are lz (for lazy or prostrate growth habit), gl (for glossy leaf), and su (for sugary endosperm), and + c + the multiply heterozygous parent in the cross had the genotype © Jones & Bartlett+ Learning,+ + LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALELz Gl Su OR DISTRIBUTION FIGURE 4.13 Diagram showing that two crossovers that occur lz gl su between the same chromatids and span the middle pair of alleles in a triple heterozygote will result in a reciprocal exchange of the middle pair of alleles between the two chromatids. where each symbol with an initial capital letter represents the dominant allele. (The use of this type of sym- © Jones & Bartlett Learning, LLC © Jonesbolism & Bartlettis customary Learning, in corn genetics.) LLC The two classes NOT FOR SALEDouble OR crossing-overDISTRIBUTION is detectable in recombinaNOT- FORof progeny SALE that OR inherit DISTRIBUTION noncrossover (parental-type) tion experiments that employ three-point crosses, gametes are therefore the wildtype plants and those which include three pairs of alleles. If a third pair of with the lazy-glossy-sugary phenotype. The number of alleles, c1 and c, is located between the outermost progeny in these classes is far larger than the number genetic markers (FIGURE 4.13), double exchanges in in any of the crossover classes. Because the frequency the region can be detected© Jones when & Bartlett the crossovers Learning, flank LLCof recombination is never ©greater Jones than & 50 Bartlett percent, Learning,the LLC the c gene. The twoNOT crossovers, FOR SALEwhich in OR this DISTRIBUTIONexample very fact that these progenyNOT are FOR the mostSALE numerous OR DISTRIBUTION take place between the same pair of chromatids, would indicates that the gametes that gave rise to them have result in a reciprocal exchange of the c1 and c alleles the parental allele configurations, in this case Lz Gl Su between the chromatids. A three-point cross is an and lz gl su. Using this principle, we could have inferred efficient way to obtain recombination data; it is also a the genotype of the heterozygous parent even if the © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

TABLE 4.1

© Jones & BartlettInterpreting Learning, a Three-Point LLC Cross © Jones & Bartlett Learning, LLC NOT FOR SALEPhenotype OR of DISTRIBUTIONGenotype of gamete Number of NOT FOR SALE OR DISTRIBUTION testcross progeny from hybrid parent progeny The two most frequent Wildtype Lz Gl Su 286 classes identify the nonrecombinant gametes. Lazy lz Gl Su 33 Glossy © JonesLz gl Su & Bartlett Learning,59 LLC © Jones & Bartlett Learning, LLC Sugary NOT FORLz Gl su SALE OR DISTRIBUTION4 The two rarest classes iden- NOT FOR SALE OR DISTRIBUTION Lazy, glossy lz gl Su 2 tify the double-recombinant gametes. Lazy, sugary lz Gl su 44 Glossy, sugary Lz gl su 40 Lazy,© Jones glossy, sugary & Bartlett lzLearning, gl su LLC272 © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION740 NOT FOR SALE OR DISTRIBUTION

These reciprocal classes result from These reciprocal classes result from single single recombination between one pair of recombination between the other pair of adjacent genes. adjacent genes. © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION 124 CHAPTER 4 Gene Linkage and Genetic Mapping 4TH PAGES © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. genotype had not been stated. This is a point important the parental gamete lz gl su except for the allele Su. enough to state more generally: The middle gene can be identified because the “odd © Jones & Bartlett Learning, LLC © Jonesman out” & Bartlett in the comparisons—in Learning, LLC this case, the alleles NOT FORKEY SALE CONCEPT OR DISTRIBUTION NOTof FOR Su—is SALE always ORthe geneDISTRIBUTION in the middle. The reason is In any genetic cross, no matter how complex, the that only the middle pair of alleles is interchanged by two most frequent types of gametes with respect to double crossing-over. any pair of genes are nonrecombinant; these pro- Taking the correct gene order into account, the vide the linkage phase (cis versus trans) of the alleles genotype of the heterozygous parent in the cross yield- of the genes in the multiply© Jones heterozygous & Bartlett parent. Learning, LLCing the progeny in Table 4.1 should© Jones be written & Bartlett as Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Lz Su Gl In mapping experiments, the gene sequence is lz su gl usually not known. In this example, the order in which the three genes are shown is entirely arbitrary. However, The consequences of single crossing-over in this geno- there© is Jonesan easy &way Bartlett to determine Learning, the correct LLC order type are shown© Jones in FIGURE & Bartlett 4.15. A single Learning, crossover LLC in from NOTthree-point FOR data. SALE The OR gene DISTRIBUTION order can be deduced the lz2su regionNOT (part FOR A) SALE yields theOR reciprocal DISTRIBUTION recom- by identifying the genotypes of the double-crossover binants Lz su gl and lz Su Gl, and a single crossover in gametes produced by the heterozygous parent and the su2gl region (part B) yields the reciprocal recom- comparing these with the nonrecombinant gametes. binants Lz Su gl and lz su Gl. The consequences of Because the probability of two simultaneous exchanges is double crossing-over are illustrated in FIGURE 4.16. © Jones &considerably Bartlett smallerLearning, than that LLC of either single exchange, © JonesThere are& Bartlett four different Learning, types of LLCdouble crossovers: a NOT FORthe SALE double-crossover OR DISTRIBUTION gametes will be the least frequent NOTtwo-strand FOR SALE double OR (part DISTRIBUTION A), two types of three-strand types. It is clear in Table 4.1 that the classes composed doubles (parts B and C), and a four-strand double (part of four plants with the sugary phenotype and two plants D). These types were illustrated earlier in Figure 4.12, with the lazy-glossy phenotype (products of the Lz Gl su where the main point was that with two genetic mark- and lz gl Su gametes, respectively) are the least frequent ers flanking the crossovers, the occurrence of double and therefore constitute© Jones the double-crossover & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC progeny. Now we apply another principle: NOT FOR SALE OR DISTRIBUTION(A) NOT FOR SALE OR DISTRIBUTION Lz Gl Su KEY CONCEPT Lz Gl Su Gl gl Su The effect of double crossing-over is to inter- Lz Su Lz change the members of the middle pair of lz su © Jones & Bartlett Learning, LLC gl © Jones & Bartlett Learning,lz Gl suLLC alleles between the chromosomes. lz gl su NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR lzDISTRIBUTIONgl su

This principle is illustrated in FIGURE 4.14. With (B) three genes there are three possible orders, Lz Su Gl depending on which gene is in the middle. If gl Lz Su Gl © Jones &were Bartlett in the middle Learning, (part A), LLC the double-recom- © Jones Su& Bartlett Learning, LLC Lz Gl Lz su Gl binant gametes would be Lz gl Su and lz Gl su, NOT FOR SALE OR DISTRIBUTION NOTlz FOR SALEgl OR DISTRIBUTION which is inconsistent with the data. Likewise, su lz Su gl if lz were in the middle (part C), the double- lz su gl lz su gl recombinant gametes would be Gl lz Su and gl Lz su, which is also inconsistent with the data. The correct order ©of Jonesthe genes, & Bartlettlz2su2gl ,Learning, (C) LLC © Jones & Bartlett Learning, LLC is given in part B, because in this case, the Gl Lz Su NOT FOR SALE OR DISTRIBUTIONGl Lz Su NOT FOR SALE OR DISTRIBUTION double-recombinant gametes are Lz su Gl and Lz Gl lz Su lz Su gl, which Table 4.1 indicates is actually Gl Su gl su the case. Although one can always infer which lz gl Lz su gene is in the middle by going through all three gl lz su possibilities,© Jones there & Bartlettis a shortcut. Learning, Each double- LLC © Jones & Bartlett Learning,gl lz suLLC recombinantNOT FOR gamete SALE will alwaysOR DISTRIBUTION match one of NOT FOR SALE OR DISTRIBUTION the parental gametes in two of the alleles. In FIGURE 4.14 The order of genes in a three-point testcross may be Table 4.1, for example, the double-recombinant deduced from the principle that double recombination interchanges the gamete Lz Gl su matches the parental gamete middle pair of alleles. For the genes Lu, Gl, and Su, there are three possible orders (parts A, B, and C), each of which predicts a different pair of gametes as Lz Gl Su except for the allele su. Similarly, the the result of double recombination. Only the order in part B is consistent with © Jones &double-recombinant Bartlett Learning, gamete LLC lz gl Su matches the finding© Jones that Lz Gl& su Bartlett and lz gl Su Learning,are the double-recombinant LLC gametes. NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION 4.3 Double Crossovers Are Revealed in Three-Point Crosses 125 4TH PAGES © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. (A) Single crossover in lz–su region crossovers cannot be detected genetically. The Lz Su Gl difference in the present case is that, here, Lz Su Gl the genetic marker su is located in the middle © Jones & Bartlett Learning, LLC ©su Jonesgl & Bartlett Learning, LLC Lz Su Gl Lz NOT FOR SALE OR DISTRIBUTION NOT FOR SALEbetween OR the DISTRIBUTION two crossovers, so some of the lz su gl lz Su Gl double crossovers can be detected genetically. lz On the right in Figure 4.16, the asterisks mark su gl lz su gl the sites of crossing-over between nonsister chromatids. In terms of recombination, the (B) Single crossover© in Jones su–gl region & Bartlett Learning, LLC result is that © Jones & Bartlett Learning, LLC Lz Gl Lz Su NOTGl FOR SALE OR DISTRIBUTIONSu n A two-strand doubleNOT FORcrossover SALE (part ORA) DISTRIBUTION Gl Lz Su gl yields the reciprocal double-recombinant Lz Su su products Lz su Gl and lz Su gl. lz gl lz su Gl n One three-strand double crossover (part B) lz su gl © Jones & Bartlett Learning, LLC lz su gl © yieldsJones the &double-recombinant Bartlett Learning, product LLC Lz su Gl and two single-recombinant NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION FIGURE 4.15 Result of single crossovers in a triple heterozygote, using products, Lz Su gl and lz Su Gl. the Lz2Su2Gl region as an example. (A) A crossover between Lz and Su n The other three-strand double crossover results in two gametes that show recombination between Lz and Su and (part C) yields the double-recombinant two gametes that are nonrecombinant. (B) A crossover between Su and Gl results in two gametes that show recombination between Su and Gl and product lz Su gl and two single-recombinant © Jones & Bartletttwo gametes Learning, that are nonrecombinant. LLC © Jones & Bartlettproducts, Learning, Lz su gl and LLC lz su Gl. NOT FOR SALE OR DISTRIBUTION NOT FOR SALE n The OR four-strand DISTRIBUTION double crossover (part C) (A) Two-strand double crossover yields reciprocal single recombinants Lz Lz Su Gl Su Gl in the lz2su region, namely Lz su gl and * lz Su Gl, and reciprocal single recombi- Su Lz * su Lz Gl Gl nants in the su2gl region, namely Lz Su gl lz gl * su © Jones & Bartlett Learning,lz Su * LLCgl and lz su Gl. © Jones & Bartlett Learning, LLC lz su NOTgl FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION lz su gl Note that the products of recombination in the three-strand double crossovers (parts B and C) (B) Three-strand double crossover are the reciprocals of each other. Because these * two types of double crossovers are equally fre- Lz gl Lz Su Gl Su quent, the reciprocal products of recombination © Jones & Bartlett Learning, LLC * * © Jones & Bartlett Learning, LLC Lz Su Gl Lz su Gl are expected to appear in equal numbers. NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION lz su gl * We can now summarize the data in Table 4.1 lz Su Gl in a more informative way by writing the genes lz su gl lz su gl in the correct order and grouping reciprocal gametic genotypes together. This grouping is (C) Three-strand double crossover shown in TABLE 4.2. Note that each class of © Jones & Bartlett Learning, LLC Lz Su© JonesGl & Bartlettsingle recombinants Learning, consists LLC of two reciprocal Lz Su Gl NOT FOR SALE OR DISTRIBUTION * NOT FOR SALEproducts OR and DISTRIBUTION that these are found in approxi- Lz su gl Lz Su Gl mately equal frequencies (40 versus 33 and lz * su gl lz Su * gl 59 versus 44). This observation illustrates an lz su gl * important principle: lz su Gl © Jones & Bartlett Learning, LLC KEY CONCEPT © Jones & Bartlett Learning, LLC (D) Four-strand double crossover NOT FOR SALE OR DISTRIBUTION The two reciprocal productsNOT FOR resulting SALE from OR any DISTRIBUTION Lz Su * gl Lz Su Gl crossover, or any combination of crossovers, * Lz Su Gl Lz su gl are expected to appear in approximately lz su equal frequencies among the progeny. gl lz * Su Gl © Joneslz &su Bartlettgl Learning, LLC © Jones & Bartlett Learning, LLC lz su * Gl NOT FOR SALE OR DISTRIBUTION NOTIn calculatingFOR SALE the OR frequency DISTRIBUTION of recombination from the data, remember that the FIGURE 4.16 Result of double crossovers in a triple heterozygote, using double-recombinant chromosomes result from the Lz2Su2Gl region as an example. Note that chromosomes showing double recombination derive from the two-strand double crossover (A) or two exchanges, one in each of the chromosome from either type of three-strand double crossover (B and C). The four-strand regions defined by the three genes. Therefore, © Jones & Bartlettdouble crossover Learning, (D) results onlyLLC in single-recombinant chromosomes.© Jones & Bartlettchromosomes Learning, that are recombinantLLC between lz NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION 126 CHAPTER 4 Gene Linkage and Genetic Mapping 4TH PAGES © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. and su are represented by the following chromosome frequency between adjacent genes. You can keep from types: falling into this trap by remembering that the double- recombinant chromosomes have single recombination © Jones & Bartlett Learning,Lz su gl LLC 40 © Jones & Bartlett Learning, LLC in both regions. NOT FOR SALE OR DISTRIBUTIONlz Su Gl 33 NOT FOR SALE OR DISTRIBUTION Lz su Gl 4 lz Su gl 2 Interference decreases the chance 79 of multiple crossing-over. The total implies that© 79/740, Jones or & 10.7 Bartlett percent, Learning, of the LLCThe detection of double crossing-over© Jones &makes Bartlett it pos -Learning, LLC chromosomes recoveredNOT in theFOR progeny SALE are OR recombi DISTRIBUTION- sible to determine whether exchangesNOT FOR in twoSALE different OR DISTRIBUTION nant between the lz and su genes, so the map distance regions of a pair of chromosomes are formed indepen- between these genes is 10.7 map units, or 10.7 centi- dently of each other. Using the information from the morgans. Similarly, the chromosomes that are recom- example with corn, we know from the recombination binant between su and gl are represented by frequencies that the probability of recombination is © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC Lz Su gl 59 0.107 between lz and su and 0.147 between su and gl. If NOT FORlz SALE su Gl OR DISTRIBUTION44 recombinationNOT is independent FOR SALE in the OR two DISTRIBUTION regions (which Lz su Gl 4 means that the formation of one crossover does not lz Su gl 2 alter the probability of the second crossover), the prob- 109 ability of a single recombination in both regions is the product of these separate probabilities, or 0.107 3 0.147 © Jones &In Bartlettthis case theLearning, recombination LLC frequency between su © Jones5 0.0157 & Bartlett(1.57 percent). Learning, This implies LLC that in a sample NOT FORand SALE gl is 109/740,OR DISTRIBUTION or 14.7 percent, so the map distance NOTof FOR 740 gametes, SALE theOR expected DISTRIBUTION number of double recom- between these genes is 14.7 map units, or 14.7 centi- binants would be 740 3 0.0157, or 11.6, whereas the morgans. The genetic map of the chromosome segment number actually observed was only 6 (Table 4.2). Such in which the three genes are located is therefore deficiencies in the observed number of double recombinants are common; they reflect a phenomenon called lz su© Jones & Bartlett Learning,gl chromosomeLLC interference , in© which Jones a crossover & Bartlett in one Learning, LLC 10.7 map units NOT 14.7FOR map SALE units OR DISTRIBUTIONregion of a chromosome reducesNOT theFOR probability SALE ORof a DISTRIBUTION second crossover in a nearby region. Over short genetic The most common error in learning how to interpret distances, chromosome interference is nearly complete. three-point crosses is to forget to include the dou- The coefficient of coincidence is the observed ble recombinants when calculating the recombination number of double-recombinant chromosomes divided © Jones & Bartlett Learning, LLC by the expected© Jones number. & Its Bartlett value provides Learning, a quantita LLC- NOT FOR SALE OR DISTRIBUTION tive measureNOT of the FOR degree SALE of interference, OR DISTRIBUTION which is defined as

i 5 Interference TABLE 4.2 5 1 2 (Coefficient of coincidence) © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC Comparing Reciprocal Products in a From the data in the corn example, the coefficient of NOT FOR SALEThree-Point OR DISTRIBUTION Cross NOTcoincidence FOR SALE is calculated OR DISTRIBUTION as follows: Genotype of gamete Number of Intervals showing n 5 from hybrid parent progeny recombination Observed number of double recombinants 6 n Expected number of double recombinants 5 0.107 Lz Su Gl 286 lz su gl 272 3 0.147 3 740 5 11.6 © Jones & Bartlett Learning, LLCn ©5 Jones5 & Bartlett Learning, LLC Lz su gl 40 Coefficient of coincidence 6/11.6 0.52 NOT FOR SALElz2su OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION lz Su Gl 33 The 0.52 means that the observed number of double Lz Su gl 59 su2gl recombinants was only about half of the number lz su Gl 44 expected if crossing-over in the two regions were Lz su Gl 4 independent. The value of the interference depends on lz2su 1 su2gl lz Su© gl Jones & Bartlett2 Learning, LLC the distance© between Jones the & Bartlettgenetic markers Learning, and on LLC the NOT FOR SALE740 OR DISTRIBUTION species. In someNOT species,FOR SALE the interference OR DISTRIBUTION increases as the distance between the two outside markers becomes smaller, until Total number of recombinants in Total number of recombinants in a point is reached at which double lz2su region: su2gl region: crossing-over is eliminated; that is, 1 1 1 5 1 1 1 5 © Jones & Bartlett40 Learning, 33 4 2 79 LLC 59 44 ©4 Jones 2 109 & Bartlettno Learning, double recombinants LLC are found, NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION 4.3 Double Crossovers Are Revealed in Three-Point Crosses 127 4TH PAGES © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. ) 0.5 r © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC 0.4 No interference NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR(i = 0)DISTRIBUTION

0.3 Interference decreasing with distance (i = 1 – 2r) 0.2 © Jones & BartlettComplete Learning, interference LLC © Jones & Bartlett Learning, LLC (i = 1) Recombination frequency ( 0.1 NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

0 0 20 40 60 80 100 120 140 160 180 200 Distance in map units (cM) © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC FIGURENOT 4.FOR17 A SALEmapping functionOR DISTRIBUTION is the relation between genetic map distance acrossNOT an FOR interval SALE and the observedOR DISTRIBUTION frequency of recombination across the interval. Map distance is defined as one-half the average number of crossovers converted into a percentage. The three mapping functions correspond to different assumptions about interference, i.

© Jones & Bartlettand the coefficient Learning, of coincidence LLC equals 0 (or, to say© Jonesmapping & Bartlett function, Learning, as shown by LLC the three examples in NOT FOR SALEthe same OR thing, DISTRIBUTION the interference equals 1). In DrosophilaNOT FORFigure SALE 4.17. OR DISTRIBUTION this distance is about 10 map units. The effect of interference on the relationship 4.4 Polymorphic DNA sequences between genetic map distance and the frequency of are used in human genetic recombination is illustrated in FIGURE 4.17. Each curve is an example© of Jones a mapping & Bartlettfunction, which Learning, is the LLC mapping. © Jones & Bartlett Learning, LLC mathematical relationNOT between FOR SALEthe genetic OR DISTRIBUTIONdistance Until quite recently, mappingNOT genes FOR in SALE human ORbeings DISTRIBUTION across an interval in map units (centimorgans) and the was very tedious and slow. Numerous practical obstacles observed frequency of recombination across the inter- complicated genetic mapping in human pedigrees: val. In other words, a mapping function tells one how to convert a map distance between genetic markers into 1. Most genes that cause genetic diseases are rare, so a recombination© Jones & frequencyBartlett between Learning, the markers. LLC As we they are© Jonesobserved &in Bartlettonly a small Learning, number of families. LLC haveNOT seen, FOR when SALE the map OR distance DISTRIBUTION between the mark- 2. ManyNOT mutant FOR genes SALE of interest OR inDISTRIBUTION human genetics ers is small, the recombination frequency equals the are recessive, so they are not detected in heterozy- map distance. This principle is reflected in the curves gous genotypes. in Figure 4.17 in the region in which the map distance 3. The number of offspring per human family is is smaller than about 10 cM. At less than this distance, relatively small, so segregation cannot usually be © Jones & Bartlettall of the curves Learning, are nearly LLC straight lines, which means© Jones detected& Bartlett in single Learning, sibships. LLC that map distance and recombination frequency are NOT FOR SALE OR DISTRIBUTION NOT FOR 4. The SALE human OR geneticist DISTRIBUTION cannot perform testcrosses equal; 1 map unit equals 1 percent recombination, and or backcrosses, because human matings are not 10 map units equals 10 percent recombination. For dictated by an experimenter. distances greater than 10 map units, the recombination frequency becomes smaller than the map distance Human genetics has been revolutionized by the use of techniques for manipulating DNA. These tech- according to the pattern© Jones of interference & Bartlett along Learning, the chro- LLC © Jones & Bartlett Learning, LLC mosome. Each pattern of interference yields a different niques have enabled investigators to carry out genetic NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

Q A MOMENT TO THINK Problem: In his pioneering 1913 studies in Drosophila that resulted in the first genetic linkage map, A. H. Sturtevant included three genetic© Jones markers & now Bartlett known to Learning,cover almost the LLC entirety of the euchromatin of the© X Joneschromosome. & BartlettThe marker wLearning, (white eyes) is LLCnear theNOT tip, mFOR (miniature SALE body) OR near theDISTRIBUTION middle, and r (rudimentary wings) near the centromere.NOT FOR In two-point SALE crosses, OR DISTRIBUTIONSturtevant obtained recombination frequencies of 0.32 for the interval w2m, 0.25 for the interval m2r, and 0.45 for the interval w2r. He noted that 0.45 is smaller than the sum of 0.32 1 0.25 5 0.57, which is the value expected if the frequencies of recombination over such large distances were additive. He commented that the discrepancy “is probably due to the occurrence of two breaks in the same chromosome, or double crossing-over.” From Sturtevant’s data, calculate the coincidence and the interference across the region. (The answer can be found at the end of the chapter.) © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION 128 CHAPTER 4 Gene Linkage and Genetic Mapping 4TH PAGES © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. mapping in human pedigrees primarily by using Identifying the particular nucleotide present at each genetic markers present in the DNA itself, rather than of a million SNPs is made possible through the use © Jones through& Bartlett the phenotypesLearning, produced LLC by mutant genes. © Jonesof DNA & Bartlettmicroarrays Learning, composed LLCof about 20 million NOT FORThere SALE are ORmany DISTRIBUTION minor differences in DNA sequence NOTinfinitesimal FOR SALE spots OR on DISTRIBUTION a glass slide about the size of a from one person to the next. On the average, the postage stamp. Each tiny spot contains a unique DNA DNA sequences at corresponding positions in any oligonucleotide sequence present in millions of copies two chromosomes, taken from any two people, differ synthesized by microchemistry when the microarray at approximately one in every thousand base pairs. is manufactured. Each oligonucleotide sequence is A genetic difference ©that Jones is relatively & Bartlett common Learning, in a LLCdesigned to hybridize specifically© Jones with small & Bartlett fragments Learning, LLC population is called a NOTpolymorphism FOR SALE. Most OR polymor DISTRIBUTION- of genomic DNA that includeNOT one FORor the SALEother of OR the DISTRIBUTION phisms in DNA sequence are not associated with any nucleotide pairs present in a SNP. The microarrays inherited disease or disability; many occur in DNA also include numerous controls for each hybridiza- sequences that do not code for proteins. Neverthe- tion. The controls consist of oligonucleotides contain- less, each of the polymorphisms serves as a conve- ing deliberate mismatches that are intended to guard nient© genetic Jones marker, & Bartlett and those Learning, genetically LLC linked to against being© misled Jones by &particular Bartlett nucleotide Learning, sequences LLC genesNOT that FORcause SALEhereditary OR diseases DISTRIBUTION are particularly that are particularlyNOT FOR “sticky” SALE and ORhybridize DISTRIBUTION too readily important. with genomic fragments and other sequences that form structures that hybridize poorly or not at all. Such Single-nucleotide polymorphisms microarrays, sometimes called SNP chips, enable the (SNPs) are abundant in the SNP genotype of an individual to be determined with © Jones &human Bartlett genome. Learning, LLC © Jonesnearly &100 Bartlett percent accuracy. Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FORThe SALEprinciples OR behind DISTRIBUTION oligonucleotide hybridiza- A single-nucleotide polymorphism, or SNP (pro- tion are illustrated in FIGURE 4.18. Here the length nounced “snip”), is present at a particular nucleotide of each oligonucleotide is seven nucleotides, but in site if the DNA molecules in the population often differ practice this is too short. Typical SNP chips consist of in the identity of the nucleotide pair that occupies the oligonucleotides at least 25 nucleotides in length. Part site. For example, some© JonesDNA molecules & Bartlett may Learning,have a ALLC shows the two types of DNA© Jones duplexes & Bartlettthat might Learning, LLC T–A base pair at a particularNOT FOR nucleotide SALE site, OR whereas DISTRIBUTION form a SNP. In this example,NOT some chromosomesFOR SALE carryOR DISTRIBUTION other DNA molecules in the same population may a DNA molecule with a T–A base pair at the position have a C–G base pair at the same site. This difference shown in red, while the DNA molecule in other chro- constitutes a SNP. The SNP defines two “alleles” for mosomes has a C–G base pair at the corresponding which there could be three genotypes among indi- position. Short fragments of genomic DNA are labeled viduals© inJones the population: & Bartlett homozygous Learning, with LLC T–A at the with a fluorescent© Jones tag, & and Bartlett then the Learning, single strands LLC correspondingNOT FOR site SALE in both ORhomologous DISTRIBUTION chromosomes, hybridized withNOT a FORSNP chipSALE containing OR DISTRIBUTION the comple- homozygous with C–G at the corresponding site in both mentary oligonucleotides as well as the numerous homologous chromosomes, or heterozygous with T–A controls. The duplex containing the T–A hybridizes in one chromosome and C–G in the homologous chro- only with the two oligonucleotides on the left, and that mosome. The word allele is in quotation marks above containing the C–G hybridizes only with the two oligo- © Jones &because Bartlett the SNP Learning, need not LLCbe in a coding sequence, or © Jonesnucleotides & Bartlett on the right. Learning, LLC NOT FOReven SALE in a ORgene. DISTRIBUTION In the human genome, any two ran- NOT FORAfter SALE the hybridization OR DISTRIBUTION takes place, the SNP chip domly chosen DNA molecules are likely to differ at one is examined with fluorescence microscopy to detect SNP site about every 1000 bp in noncoding DNA and the spots that fluoresce as a result of the tag on the at about one SNP site every 3000 bp in protein-coding genomic DNA. The possible patterns are shown in DNA. In the definition of a SNP, the DNA molecules part B. Genomic DNA from an individual whose chro- must differ at the nucleotide© Jones site “often.” & Bartlett This provision Learning, mosomesLLC contain two copies© of Jones the T–A & formBartlett of the Learning, LLC excludes rare genetic variationNOT FOR of the SALE sort found OR inDISTRIBUTION less duplex (homozygous TA/TA)NOT causes FOR the twoSALE leftmost OR DISTRIBUTION than 1 percent of the DNA molecules in a population. spots to fluoresce, but the two rightmost spots remain The reason for the exclusion is that genetic variants that unlabeled. Similarly, genomic DNA from a homozy- are too rare are not generally as useful in genetic analy- gous CG/CG individual causes the two rightmost spots sis as the more common variants. SNPs are the most to fluoresce but not the two on the left. Finally, genomic common© Jones form of& geneticBartlett differences Learning, among LLC people. DNA from ©a Jonesheterozygous & Bartlett TA/CG Learning,individual causes LLC AboutNOT 10 million FOR SNPsSALE have OR been DISTRIBUTION identified in which fluorescenceNOT of all FOR four spotsSALE because OR DISTRIBUTION the TA duplex the alternative nucleotides are each relatively common labels the two leftmost spots and the CG duplex labels in the human population, and about half a million of the two rightmost spots. these are typically used in a search for SNPs that might Use of SNP chips or other available technologies be associated with complex diseases such as diabetes or for high-throughput genotyping of millions of SNPs © Jones &high Bartlett blood pressure. Learning, LLC © Jonesin thousands & Bartlett of individuals Learning, allows LLC genetic risk factors NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION 4.4 Polymorphic DNA Sequences Are Used in Human Genetic Mapping 129 4TH PAGES © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. In this example the SNP consists of a TA (A) base pair in some DNA duplexes and a CG base pair in others. © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC Fragments of genomic NOT FOR SALE OR DISTRIBUTIONDNA are labeled with NOT FOR SALE OR DISTRIBUTION a fluorescent molecule.

ACT GCA G Strands from ACC GCA G TGA CGT C each duplex TGG CGT C will hybridize only with their © Jones & Bartlett Learning, LLC complementary © Jones & Bartlett Learning, LLC oligonucleotides. NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

G C T A G C T A A T G C A T G C C G A T C G G C G C C G G C C G © Jones & BartlettEach oligonucleotide Learning, in LLCT A G C © JonesC G& Bartlett Learning,G C LLC a SNP chip is attached C G T A C G T A A A NOT FOR SALEto a glass OR slide. DISTRIBUTIONT CG NOT FORT SALE OR DISTRIBUTIONCG

(B) © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE ORHybridization DISTRIBUTION signal NOT FOR SALE OR DISTRIBUTION from homozygous AT/AT

Hybridization signal from heterozygous AT/CG © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC HybridizationNOT signal FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION from homozygous CG/CG

FIGURE 4.18 (A) Oligonucleotides attached to a glass slide in a SNP chip can be used to identify duplex DNA molecules containing base pairs for a SNP; in this example, a TA base pair versus a CG base pair. (B) The SNP genotype of an individual can be determined by ©hybridization Jones &because Bartlett DNA from Learning, genotypes that LLC are homozygous TA/TA, homozygous© Jones CG/CG, & or Bartlett heterozygous Learning, TA/CG each givesLLC a different pattern of fluorescence. NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

for disease to be identified. A typical study compares lacking the cleavage site will be cleaved into one larger the genotypes of patients with particular diseases with fragment instead of two smaller ones (FIGURE 4.20). healthy people matched with the patients for such fac- More rarely, a mutation in the DNA sequence will cre- © Jones & Bartletttors as sex, Learning, age, and ethnic LLC group. Comparing the SNP© Jonesate a& new Bartlett site rather Learning, than destroy LLC one already present. NOT FOR SALEgenotypes OR amongDISTRIBUTION these groups often reveals whichNOT FORThe main SALE point OR is that DISTRIBUTION any difference in DNA sequence SNPs are in the genome. that alters a cleavage site also changes the length of the DNA fragments produced by cleavage with the SNPs in restriction sites corresponding restriction enzyme. The different DNA yield restriction fragment length fragments can be separated by size by an electric field polymorphisms© Jones(RFLPs). & Bartlett Learning, LLCin a supporting gel and ©detected Jones by & various Bartlett means. Learning, LLC NOT FOR SALE OR DISTRIBUTIONDifferences in DNA fragmentNOT length FOR produced SALE by OR pres DISTRIBUTION- Some polymorphisms in DNA sequence are detected by ence or absence of the cleavage sites in DNA molecules means of a type of enzyme called a restriction endo- are known as restriction fragment length polymor- nuclease, which cleaves double-stranded DNA mol- phisms (RFLPs). ecules wherever a particular, short sequence of bases RFLPs are typically formed in one of two ways. is ©present. Jones For & example,Bartlett the Learning, restriction LLCenzyme EcoRI A mutation© Jones that changes & Bartlett a base sequenceLearning, may LLC result cleavesNOT DNA FOR wherever SALE theOR sequence DISTRIBUTION GAATTC appears in loss orNOT gain ofFOR a cleavage SALE site OR that DISTRIBUTION is recognized by in either strand, as illustrated in FIGURE 4.19. Restric- the restriction endonuclease in use. FIGURE 4.21, part tion enzymes are considered in detail in Chapter 6. A, gives an example. On the left is shown the relevant For present purposes, their significance is related to the region in the homologous DNA molecules in a person fact that a difference in DNA sequence that eliminates who is heterozygous for such a sequence polymor- © Jones & Bartletta cleavage Learning, site can be LLCdetected because the region© Jonesphism. & BartlettThe homologous Learning, chromosomes LLC in the person NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION 130 CHAPTER 4 Gene Linkage and Genetic Mapping 4TH PAGES © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. EcoRI cleavage sites and b types of chromosomes (genotype ab) would yield three bands in a gel. Similarly, © Jones & GABartlettATTC Learning,GA LLCATTC GAATT©C Jones & BartlettDNA from Learning, homozygous LLC aa would yield NOT FOR SALECTTA AGOR DISTRIBUTIONCTTAAG CTT AAGNOT FOR SALEone ORband, DISTRIBUTION and that from homozygous bb would yield two bands. 5’ 3’ 3’ 5’ Simple-sequence repeats Treatment of DNA with EcoRI © Jones & Bartlett Learning, LLC (SSRs) often© differ Jones in & copyBartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION number. NOT FOR SALE OR DISTRIBUTION Yet another type of DNA polymorphism results from differences in the number of Cleavage Cleavage Cleavage copies of a short DNA sequence that may be repeated many times in tandem at a par- DNA fragments© Jones resulting & Bartlett Learning, LLC ©ticular Jones site in& aBartlett chromosome Learning, (Figure 4.21,LLC from EcoNOTRI cleavage FOR SALE OR DISTRIBUTION NOTpart B). FOR In a SALE particular OR chromosome, DISTRIBUTION the tandem repeats may contain any number of copies, typically ranging from ten to a few hundred. When a DNA molecule is cleaved with a restriction endonuclease that cleaves © Jones & Bartlett Learning, LLC © Jones & Bartlettat sites flankingLearning, the tandem LLC repeat, the size NOT FORFIGURE SALE 4. OR19 The DISTRIBUTION restriction enzyme EcoRI cleaves double-strandedNOT DNA FOR SALEof the OR DNA DISTRIBUTION fragment produced is deter- wherever the sequence 59-GAATTC-39 is present. In the example shown here, the mined by the number of repeats present in DNA molecule contains three EcoRI cleavage sites, and it is cleaved at each site, the molecule. Figure 4.21, part B, illustrates producing a number of fragments. homologous DNA sequences in a heterozygous person containing one chromosome a are distinguished by the letters a and b. In the region of © Jones & Bartlett Learning, withLLC two copies of the repeat ©and Jones another & chromosome Bartlett Learning, LLC interest, chromosome a contains two cleavage sites and NOT FOR SALE OR DISTRIBUTIONb with five copies of the repeat.NOT When FOR cleaved SALE and sepa OR- DISTRIBUTION chromosome b contains three. On the right is shown rated in a gel, chromosome a yields a shorter fragment the position of the DNA fragments produced by cleav- than that from chromosome b, because a contains fewer age after separation in an electric field. Each fragment copies of the repeat. A genetic polymorphism resulting appears as a discrete band in the gel. The fragment from a tandemly repeated short DNA sequence is called from chromosome a migrates more slowly than those © Jones & Bartlett Learning, LLC a simple sequence© Jones repeat & Bartlett (SSR). AnLearning, example of LLC an from chromosome b because it is longer, and longer NOT FOR SALE OR DISTRIBUTION SSR is the repeatingNOT FOR sequence SALE OR DISTRIBUTION fragments move more slowly through the gel. In this example, DNA from a person heterozygous for the a 59-...TGTGTGTGTGTG...-39

© Jones &(A) Bartlett Learning, LLC © Jones(B) & Bartlett Learning,Mutated LLC site NOT FOR SALEG AATT ORC DISTRIBUTIONGAATTC GAATTCNOT FORGAAT SALETC OR DISTRIBUTIONGAACTC GAATTC CTT AAG CTT AAG CTTAAG CTTAAG CTTGAG CTTAAG

5' 3' 5' 3' 3' 5' 3' 5'

No cleavage

FIGURE 4.20 A minor difference in the DNA sequence of two molecules can be detected if the difference eliminates a restriction site. (A) This molecule contains three restriction sites for EcoRI, including one at each end. It is cleaved into two fragments by the enzyme. (B) This molecule has a mutant base sequence in the EcoRI site in the middle. It changes 59-GAATTC-39 into 59-GAACTC-39, which is no © Jones &longer Bartlett cleaved byLearning, EcoRI. Treatment LLC of this molecule with EcoRI results© Jones in one larger & Bartlettfragment. Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION 4.4 Polymorphic DNA Sequences Are Used in Human Genetic Mapping 131 4TH PAGES © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. (A) DNA in chromosomes Direction of current Longer DNA Shorter DNA © Jones & Bartlett Learning, LLC © Jones &fragments Bartlett Learning, LLCfragments NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION 5’ 3’ a 3’ 5’ Supporting gel 5’ 3’ b 3’ © Jones & Bartlett Learning,5’ LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION DNA band from DNA bands from Positions of cleavage sites chromosome a chromosome b

(B) DNA in chromosomes Direction © Jones & Bartlett Learning, LLC © Jonesof ¤t Bartlett Learning, LLC Longer DNA Shorter DNA NOT FOR SALE OR DISTRIBUTION fragmentsNOT FOR SALE ORfragments DISTRIBUTION 12 5’ 3’ a 3’ 5’ Supporting gel © Jones & Bartlett Learning, LLC12345 © Jones & Bartlett Learning, LLC 5’ 3’ b NOT FOR SALE3’ OR DISTRIBUTION NOT5’ FOR SALE OR DISTRIBUTION

Positions of Tandem repeats DNA band from DNA band from cleavage sites of DNA sequence chromosome b chromosome a

FIGURE 4.21 Two types© Jones of genetic & variation Bartlett that areLearning, widespread inLLC most natural populations of animals© Jonesand plants. & (A) Bartlett RFLP (restriction Learning, LLC fragment length polymorphism), in which alleles differ in the presence or absence of a cleavage site in the DNA. The different alleles yield different fragmentNOT lengths FOR (shown SALE in the gel OR pattern DISTRIBUTION at the right) when the molecules are cleaved withNOT a restriction FOR SALEenzyme. (B)OR SSR DISTRIBUTION (simple sequence repeat), in which alleles differ in the number of repeating units present between two cleavage sites.

and© theJones polymorphism & Bartlett consists Learning, of differences LLC in the © Jones & Bartlett Learning, LLC TABLE 4.3 numberNOT ofFOR TG repeats.SALE AOR particular DISTRIBUTION “allele” of the SSR NOT FOR SALE OR DISTRIBUTION is defined by the number of TG repeats it includes. One source of the utility of SSRs in human genetic Some Simple Sequence Repeats in the mapping is the high density of SSRs across the genome. Human Genome There is an average of one SSR per 2 kb of human SSR repeat unit Number of SSRs in the human genome © Jones & BartlettDNA. Some Learning, examples areLLC shown in TABLE 4.3. The© Jones59-AC-3 & Bartlett9 Learning, LLC 80,330 prevalence of different SSRs differs. Some dinucleo- NOT FOR SALE OR DISTRIBUTION NOT FOR9 SALE9 OR DISTRIBUTION tide repeats, such as 59-AC-39 and 59-AT-39, are far 5 -AT-3 56,260 more frequent than others, such as 59-GC-39. Overall, 59-AG-39 23,780 dinucleotide repeats are much more abundant than 59-GC-39 290 trinucleotide repeats. The second source of utility of 59-AAT-39 11,890 SSRs in genetic mapping© Jones is the & large Bartlett number Learning, of alleles LLC © Jones & Bartlett Learning, LLC 59-AAC-39 7,540 that can be presentNOT in anyFOR human SALE population. OR DISTRIBUTION The NOT FOR SALE OR DISTRIBUTION large number of alleles also implies that most people 59-AGG-39 4,350 will be heterozygous, and so their DNA will yield two 59-AAG-39 4,060 bands upon cleavage with the appropriate restriction 59-ATG-39 2,030 endonuclease. Because of their high degree of variation 9 9 among© Jones people, & DNABartlett polymorphisms Learning, are LLC also widely 5 -CGG-3 © Jones & Bartlett Learning, 1,740 LLC usedNOT in DNAFOR typing SALE in criminalOR DISTRIBUTION investigations. 59-ACC-39 NOT FOR SALE OR DISTRIBUTION 1,160 In genetic mapping, the phenotype of a person with 59-AGC-39 870 respect to a DNA polymorphism is a pattern of bands 59-ACT-39 580 in a gel. As with any other type of genetic marker, the genotype of a person with respect to the polymorphism Data from International Human Genome Sequencing Consortium, Nature 409 (2001): © Jones & Bartlettis inferred, Learning,insofar as it isLLC possible, from the phenotype.© Jones860–921. & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION 132 CHAPTER 4 Gene Linkage and Genetic Mapping 4TH PAGES © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. I 4, 5 4, 6 1, 2 3, 4 © Jones & Bartlett Learning, LLCII © Jones & Bartlett Learning, LLC 4, 6 1, 3 NOT FOR SALE OR DISTRIBUTIONIII NOT FOR SALE OR DISTRIBUTION DNA bands are 1, 4 1, 6 3, 4 1, 6 3, 6 3, 4 1, 4 observed in gel.

1 1 © Jones2 & Bartlett Learning, LLC © Jones &2 Bartlett Learning, LLC 3 3 Position of DNANOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION fragment in gel 4 4 5 5 6 6

FIGURE 4.22 Human pedigree showing segregation of SSR alleles. Six alleles (1–6) are present in the pedigree, but any one person can have© onlyJones one allele & Bartlett (if homozygous) Learning, or two alleles LLC (if heterozygous). © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

Linkage between different polymorphic loci is detected human genome can be duplicated or deleted in much through lack of independent assortment of the alleles in larger but still submicroscopic chunks ranging from © Jones &pedigrees, Bartlett and Learning, recombination LLC and genetic mapping are © Jones1 kb to & 1 BartlettMb (Mb standsLearning, for megabase LLC pairs, or one NOT FORcarried SALE out OR using DISTRIBUTION the same principles as apply in other NOTmillion FOR baseSALE pairs). OR This DISTRIBUTION type of variation is known as organisms, except that in human beings, because of the copy-number variation (CNV). The extra or miss- small family size, different pedigrees are pooled for anal- ing copies of the genome in CNVs can be detected ysis. Primarily through the use of DNA polymorphisms, by means of hybridization with oligonucleotides in genetic mapping in humans has progressed rapidly. DNA microarrays. Since each spot on the microarray To give an example© Jonesof the type& Bartlett of data usedLearning, in consistsLLC of millions of identical© Jones copies of& aBartlett particular Learning, LLC human genetic mapping,NOT a three-generation FOR SALE ORpedigree DISTRIBUTION of oligonucleotide sequence, theNOT number FOR of SALE these ORthat DISTRIBUTION a family segregating for several alleles of an SSR is illus- undergo hybridization depends on how many cop- trated in FIGURE 4.22. In this example, each of the par- ies of the complementary sequence are present in ents is heterozygous, as are all of the children. Yet every genomic DNA. A typical region is present in two person can be assigned his or her genotype because the copies (one inherited from the mother and the other SSR alleles© Jones are codominant. & Bartlett At Learning, present, DNA LLC polymor- from the father).© Jones If an individual& Bartlett has Learning, an extra copy LLC of phismsNOT are FORthe principal SALE types OR ofDISTRIBUTION genetic markers used the region, NOTthe ratio FOR of SALEhybridization OR DISTRIBUTION and, therefore, in genetic mapping in human pedigrees. Such polymor- fluorescence intensity is 3 : 2, while if an individual phisms are prevalent, are located in virtually all regions has a missing copy, the ratio of hybridization and, of the chromosome set, and have multiple alleles and therefore, fluorescence intensity is 1 : 2. These differ- so yield a high proportion of heterozygous genotypes. ences can readily be detected with DNA microarrays. © Jones &Furthermore, Bartlett Learning,only a small amount LLC of biological material © JonesMoreoever, & Bartlett since CNVs Learning, are relatively LLC large, a microar- NOT FORis SALEneeded ORto perform DISTRIBUTION the necessary tests. NOTray FOR typically SALE has ORmany DISTRIBUTION different oligonucleotides that One feature of the human genetic map is that there are complementary to sequences at intervals across the is about 60 percent more recombination in females than CNV; hence, the CNV results in a increase or decrease in males, so the female and male genetic maps differ in in signal intensity of all the oligonucleotides included length. The female map is about 4400 cM, the male map in the CNV. Current SNP chips also include about about 2700 cM. Averaged© Jones over both & sexes,Bartlett the length Learning, of aLLC million oligonucleotide probes© Jones designed & Bartlett to detect Learning, LLC the human genetic mapNOT for all FOR 23 pairs SALE of chromosomes OR DISTRIBUTION known CNVs. NOT FOR SALE OR DISTRIBUTION is about 3500 cM. Because the total DNA content per CNVs by definition exceed 1 kb in size, but haploid set of human chromosomes is 3200 million base many are much larger. In one study of about 300 pairs, there is, very roughly, 1 cM per million base pairs individuals with their ancestry in Africa, Europe, in the human genome. or Asia, approximately 1500 CNVs were discovered © Jones & Bartlett Learning, LLC by hybridization© Jones with µarrays. Bartlett Learning, These averaged LLC GeneNOT dosage FOR SALEcan differ OR DISTRIBUTION owing to 200 to 300 NOTkb in length.FOR SALE In the aggregate,OR DISTRIBUTION the CNVs copy-number variation (CNV). included 300 to 450 million base pairs, or 10 to 15 percent of the nucleotides in the entire genome. In addition to the small-scale variation in copy num- Many of the CNVs were located in regions near ber represented by such genomic features as simple- known mutant genes associated with hereditary © Jones &sequence Bartlett repeats Learning, (SSRs), aLLC substantial portion of the © Jonesdiseases. & BartlettCNVs in Learning, alpha and LLC beta hemoglobin NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION 4.4 Polymorphic DNA Sequences Are Used in Human Genetic Mapping 133 4TH PAGES © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. © Jones & Bartlettthe Learning,human LLC connection© Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Starch Contrast proteinaceous resources (for example, meats and blood) and simple saccharides (for example, from fruit, © Jones & Bartlett Learning, LLC honey,© and Jones milk). .& . .Bartlett We estimated Learning, LLC George H. Perry1,2, NOTNathaniel FOR J. SALEincludes OR DISTRIBUTION macaques and mangabeys, [salivaryNOT amylase FOR gene] SALE AMY1 OR copy DISTRIBUTION Dominy3, Katrina G. Claw1, Arthur produces even more salivary amylase number in three high-starch and S. Lee2, Heike Fiegler4, Richard than humans. Cercopithecines are 4 1 four low-starch population sam- Redon , John Werner , and 6 other unique among primates in storing ples. . . . Notably, the proportion authors 2007 starchy foods, such as the seeds of 1Arizona State University, Tempe, AZ; of individuals from the combined 2Brigham© Jones and Women’s & Bartlett Hospital, Boston, Learning, MA; unripe LLC fruits, in a cheek pouch,© andJones high-starch & Bartlett sample Learning, with at LLC least 3University of California, Santa Cruz, CA; it is a plausible hypothesis that the six AMY1 copies (70 percent) was 4TheNOT Wellcome FOR Trust SangerSALE Institute, OR Hinxton DISTRIBUTION UK. NOT FOR SALE OR DISTRIBUTION increased amylase facilitates diges- nearly two times greater than that Diet and the Evolution of Human Amylase Gene tion of the starch. It is not known Copy Number Variation for low-starch populations (37 whether the increased amylase pro- percent). . . . Diet more strongly duction in cercopithecines is due to predicts AMY1 copy number than © Jones & Bartlett Learning, LLC copy-number ©variation Jones or & toBartlett some Learning,geographic LLCproximity. . . . We favor other mechanism. NOT FOR SALEWe ORfavor DISTRIBUTION a model in which NOT FOR SALE OR DISTRIBUTIONa model in which AMY1 copy num- AMY1 copy number has ber has been subject to positive or been subject to positive directional selection in at least some or directional selection in Hominin evolution is characterized high-starch populations but has at least some high-starch by significant dietary shifts, facili- evolved neutrally (that is, through populations© Jones. . . & Bartletttated Learning, in part by LLCthe development genetic© drift) Jones in low-starch & Bartlett popula Learning,- LLC NOT FOR SALEof OR stone DISTRIBUTION tool technology, the con- tions. .NOT . . Comparisons FOR SALE with OR other DISTRIBUTION Evolution of increased enzyme activ- trol of fire and, most recently, the great apes suggest that AMY1 copy ity can occur through regulatory domestication of plants and ani- number was probably gained in mutations that increase transcription mals. . . . Starch, for instance, has the human lineage. . . . The initial of a single gene or through increases become an increasingly prominent human-specific increase in AMY1 in ©gene Jones copy & number. Bartlett This Learning, study component LLC of the human diet,© par Jones- copy & Bartlett number mayLearning, have been LLC coin- reportsNOT a FORstrong SALEcorrelation OR between DISTRIBUTION ticularly among agricultural NOTsocie- FORcident SALE with OR a dietary DISTRIBUTION shift early in amount of starch in the diets of ties. . . . A distinction can be made hominin evolutionary history. For human populations and the number between “high-starch” populations example, it is hypothesized that of copies of a gene encoding salivary for which starchy food resources starch-rich plant underground amylase, a starch-degrading enzyme. comprise a substantial portion of storage organs such as bulbs, © Jones & BartlettHumans are Learning, not alone among LLC primates the diet and© “low-starch”Jones & Bartlett popu- Learning,corms and LLCtubers were a critical NOT FOR SALEin having OR evolved DISTRIBUTION higher amylase lations with NOTtraditional FOR dietsSALE that OR DISTRIBUTIONfood resource for early hominins. activity. A group of Old World Mon- incorporate relatively few starchy keys called cercopithecines, which foods [but] instead emphasize Source: Science 328: 710–722.

genes are known to be associated with resistance to Copy-number variation has helped malaria, and CNVs in an HIV-1 receptor gene CCL3 human populations adapt to are© associatedJones & withBartlett resistance Learning, to AIDS. LLC The preva- © Jones & Bartlett Learning, LLC a high-starch diet. lenceNOT of FORCNVs SALE has prompted OR DISTRIBUTION the inclusion of CNV NOT FOR SALE OR DISTRIBUTION oligonucleotides onto DNA microarrays to be able Increased copy number is sometimes beneficial, with to assess what effects CNVs may have on the risk the result that natural selection operates to gradually of complex diseases such as autism or Alzheimer’s increase copy number throughout an entire population disease. of organisms. An excellent example in human evolution © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION 134 CHAPTER 4 Gene Linkage and Genetic Mapping 4TH PAGES © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC 5.2 NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR6. 6DISTRIBUTION 6.8

Average amylase-gene copy number per © Jones & Bartlett Learning, LLC individual© Jones differs & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION accordingNOT to theFOR amount SALE OR DISTRIBUTION of starch in the diet.

5.5 5.4 5.1 © Jones & Bartlett Learning, LLC6.9 © Jones & Bartlett Learning, LLC Low-starch diet NOTHigh-starch FOR SALE diet OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

Amylase copy number is greater in populations with a high-starch diet even when © Jones & Bartlett Learning, LLC the populations are © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION geographically close.NOT FOR SALE OR DISTRIBUTION

FIGURE 4.23 Amylase copy number varies with the amount of starch in human diets. [Data from G. H. Perry, et al. Nat. Genet. 39 (2007): 1256–1260.]

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC is copy-number variationNOT in FOR the gene SALE for ORthe starch-DISTRIBUTIONamylase results from copy-numberNOT variation. FOR SALE The results OR DISTRIBUTION degrading enzyme amylase, which is produced in the of one study of amylase gene copy number are shown in salivary gland and pancreas. FIGURE 4.23. Seven populations were assayed for amy- As anatomically modern humans left their original lase gene copy number, four with low-starch diets (blue) homes in Southern Africa about 200,000 years ago and and three with high-starch diets (red). On average, migrated© Jones first north & Bartlett to populate Learning, all of Africa LLC and then, individuals in© Jonespopulations & Bartlett with a low-starch Learning, diet LLChad aboutNOT 60,000 FOR years SALE ago, into OR the DISTRIBUTION Middle East and then an average ofNOT 5.4 copiesFOR ofSALE the amylase OR DISTRIBUTION gene, whereas other parts of the world, the migrating populations those with a high-starch diet had an average of 6.7 cop- had to cope with different climates, soil types, water ies of the gene. The comparisons exclude geography as availability, and native plants and animals. Some of the an explanation for the difference. Note, for example, the novel conditions were accommodated by changes in contrasting populations in Tanzania in East Africa at the © Jones &diet. Bartlett Traditional Learning, hunter-gatherer LLC populations in humid © Joneslower right& Bartlett and the Learning,contrasting populations LLC in Siberia NOT FORclimates SALE such OR asDISTRIBUTION tropical forests typically eat a diet rich NOTand FOR Japan SALE at the ORupper DISTRIBUTION right. Our nearest primate rela- in meat or fish and relatively low in starch. Pastoralists, tives, chimpanzees and gorillas, have only one copy of who follow herds like reindeer or bison as they migrate the amylase gene; therefore, amylase gene copy number during the year, also have diets rich in meat and rela- apparently has increased generally in human evolution, tively low in starch. In contrast, hunter-gatherer popu- perhaps beginning at a time when our ancestors left the lations in arid climates© rely Jones more &on Bartlett roots and Learning, tubers humidLLC forests for the arid savannahs© Jones and & began Bartlett to eat Learning, LLC for food and increase theirNOT intake FOR of SALEstarch. Populations OR DISTRIBUTION more starchy roots and tubers.NOT FOR SALE OR DISTRIBUTION that switch to agriculture also have a dramatic increase in dietary starch because cultivated staple foods like 4.5 Tetrads contain all four wheat, rice, potatoes, and corn are rich in starch. One consequence of copy-number variation is that products of meiosis. the amount© Jones of protein & Bartlett produced Learning, from any gene LLC included In some species© Jones of fungi, & Bartletteach meiotic Learning, tetrad is LLCcon- in theNOT region FOR is usually SALE proportional OR DISTRIBUTION to the copy number. tained in a sac-likeNOT FORstructure, SALE called OR an ascusDISTRIBUTION, and can be Increased gene copy number usually implies increased recovered as an intact group. Each product of meiosis is protein level. In human populations with high-starch included in a reproductive cell called an ascospore, and diets, it might be expected that increased amylase is all of the ascospores formed from one meiotic cell remain beneficial because more calories can be absorbed as together in the ascus FIGURE 4.24. The advantage of © Jones &the Bartlett starch is digested.Learning, In human LLC populations, increased © Jonesthese organisms& Bartlett for Learning,the study of LLCrecombination is the NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION 4.5 Tetrads Contain All Four Products of Meiosis 135 4TH PAGES © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. A The 2 A : 2 a segregation means that the Mendelian ratio of 1 : 1 is realized in the © Jones & Bartlett Learning, LLC a © Jones & Bartlettproducts Learning, of each individual LLC meiotic division NOT FOR SALE OR DISTRIBUTION ChromosomeNOT FOR SALEand OR is DISTRIBUTIONnot merely an average over a large duplication number of meioses. Two other features of ascus-producing A organisms are especially useful for genetic analysis: (1) They are haploid, so dominance © Jones & Bartlett Learning,A LLC is not a complicating© Jones factor & Bartlett because Learning,the LLC Meiosis I NOT FOR SALE OR DISTRIBUTIONa genotype is expressedNOT FOR directly SALE in the ORpheno DISTRIBUTION- type. (2) They produce very large numbers a of progeny, making it possible to detect rare events and to estimate their frequencies accurately. Furthermore, the life cycles of © Jones & BartlettSegregation Learning, of chromosomes LLC in meiosis I © Jonesthe organisms & Bartlett tend to Learning, be short. The LLC only NOT FOR SALE OR DISTRIBUTION NOTdiploid FOR stage SALE is the ORzygote, DISTRIBUTION which undergoes meiosis soon after it is formed; the resulting a A haploid meiotic products (which form the a A ascospores) germinate to regenerate the vegetative stage FIGURE 4.25. In most of © Jones & Bartlett Learning, LLC © Jones & Bartlettthe organisms, Learning, the LLCmeiotic products, or their NOT FOR SALE OR DISTRIBUTIONSegregation of chromosomes in meiosisNOT II FOR SALEderivatives, OR DISTRIBUTION are not arranged in any particular order in the ascus. However, bread molds of the genus Neurospora and related organ- a A Meiosis II isms have the useful characteristic that the a A meiotic products are arranged in a definite © Jones & Bartlett Learning, LLC order directly ©related Jones to the& Bartlett planes of Learning,the LLC Spore NOT FOR SALE ORformation DISTRIBUTION meiotic divisions.NOT In NeurosporaFOR SALE, each OR of the DISTRIBUTION four products of meiosis also undergoes a mitotic division, with the result that each Ascospores member of the tetrad yields a pair of genetically identical ascospores. We will examine © Jones & Bartlett Learning, LLC © Jonesthe ordered & Bartlett system afterLearning, first looking LLC at A NOT FOR SALE OR DISTRIBUTION NOTunordered FOR SALE tetrads. OR DISTRIBUTION

Unordered tetrads have no relation to the geometry a A © Jones & Bartlett Learning, LLC © Jones & Bartlettof meiosis. Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALEIn OR the DISTRIBUTIONtetrads when two pairs of alleles are segregating, three patterns of segregation are possible. For example, in the cross A B a 3 a b, the three types of tetrads are © Jones & Bartlett Learning, LLC AB AB ab ab© Jonesreferred &to Bartlettas parental Learning, LLC NOT FOR SALE OR DISTRIBUTION NOTditype FOR, or SALE PD. Only OR two DISTRIBUTION Ascus genotypes are represented, and their alleles FIGURE 4.24 Formation of an ascus containing all of the four products of a have the same combi- single meiosis. Each ascospore present in the ascus is a reproductive cell formed nations found in the from© oneJones of the products& Bartlett of meiosis. Learning, LLC © Jones & Bartlettparents. Learning, LLC NOT FOR SALE OR DISTRIBUTION NOTAb FORAb aB SALE aB referredOR DISTRIBUTION to as nonpa- potential for analyzing all of the products from each rental ditype, or NPD. meiotic division. For example, one can see immediately Only two genotypes are from the diagram in Figure 4.24 that a tetrad containing represented, but their the products of a single meiosis in a heterozygous Aa alleles have nonparental © Jones & Bartlettorganism containsLearning, 2 A ascosporesLLC and 2 a ascospores.© Jones & Bartlett Learning,combinations. LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION 136 CHAPTER 4 Gene Linkage and Genetic Mapping 4TH PAGES © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. Conjugation and nuclear fusion produce diploid © Jones & Bartlett Learning, LLC zygote. © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Zygote (2n) α a αa © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FORα SALEConjugation OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION α a αa Mitosis a a α © Jones & Bartlett Learning,Haplophase LLC © Jones & Bartlett Learning, LLC mitosis Meiosis and NOT FOR SALE OR DISTRIBUTION sporulation NOT FOR SALE OR DISTRIBUTION a Ascospore αa α germination α Diploid cells a a (2n) a © Jones & Bartlett Learning, LLC a© Jonesa & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION α α NOT FOR SALE OR DISTRIBUTION α α Meiosis and sporulation produce Ascus with four haploid spores. © Jones & Bartlett Learning,ascospores LLC(n) © Jones & Bartlett Learning, LLC

FIGURE 4.25 Life cycle NOTof the yeast FOR Saccharomyces SALE OR cerevisiae DISTRIBUTION. Mating type is determined by the alleles NOTa and a .FOR Both haploid SALE and OR DISTRIBUTION diploid cells normally multiply by mitosis (budding). Depletion of nutrients in the growth medium induces meiosis and sporulation of cells in the diploid state. Diploid nuclei are shown in red, haploid nuclei in yellow.

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC AB AbNOT aB FORab referredSALE toOR as tetratypeDISTRIBUTION, or TT. All 2. The exchangeNOT processFOR SALE consists OR of the DISTRIBUTION breaking and four of the possible genotypes are rejoining of the two chromatids, resulting in the present. reciprocal exchange of equal and corresponding segments. Tetratype tetrads demonstrate this point Tetratype tetrads demonstrate that because they contain the reciprocal products (A b and a B if the parental alleles were in coupling, A B © Jones &crossing-over Bartlett Learning, takes LLC place at the © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FORand aSALE b if they OR were DISTRIBUTION in repulsion). four-strand stage of meiosis and is reciprocal. Tetrad analysis affords a convenient We noted earlier that tetrads from heterozygous test for linkage. organisms regularly contain© Jones 2 A &and Bartlett 2 a ascospores, Learning, TetradLLC analysis is an effective ©way Jones to determine & Bartlett whether Learning, LLC which implies that Mendelian segregation takes place two genes are linked, because in each meiosis. TheNOT existence FOR of SALE tetratype OR tetrads DISTRIBUTION NOT FOR SALE OR DISTRIBUTION for linked genes demonstrates two features about KEY CONCEPT crossing-over that we have assumed, so far without proof. When genes are unlinked, the parental ditype © Jones & Bartlett Learning, LLC tetrads and© theJones nonparental & Bartlett ditype tetradsLearning, are LLC 1. The exchange of segments between parental chro- expected in equal frequencies (PD 5 NPD). matidsNOT takesFOR place SALE in the OR first DISTRIBUTION meiotic prophase, NOT FOR SALE OR DISTRIBUTION after the chromosomes have duplicated. Tetratype tetrads demonstrate this assertion because only The reason for the equality PD 5 NPD for unlinked two of the four products of meiosis show recombi- genes is shown in part A of FIGURE 4.26, where the nation. This would not be possible unless crossing- two pairs of alleles A, a and B, b are located in different © Jones & Bartlettover took Learning,place at the four-strand LLC stage. © Joneschromosomes. & Bartlett In the Learning, absence of crossing-over LLC between NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION 4.5 Tetrads Contain All Four Products of Meiosis 137 4TH PAGES © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. (A) No crossing-over genes, meiotic cells with no crossovers always Ascus outnumber those with four-strand double cross- A B Ascospore © Jones & Bartlett Learning, LLC © Jones overs.& Bartlett Therefore, Learning, LLC AB NOT FOR SALE OR DISTRIBUTIONA B NOT FOR SALE OR DISTRIBUTION abAB a b KEY CONCEPT ab Linkage is indicated when nonparental ditype a b Parental tetrads appear with a much lower frequency than ditype parental ditype tetrads (NPD ,, PD). © Jones & Bartlett Learning,tetrad LLC © Jones & Bartlett Learning, LLC ANOT FOR SALE bOR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Ab A b The relative frequencies of the different types aBAb of tetrads can be used to determine the map dis- a B aB tance between two linked genes. The simplest case a B Nonparental is one in which the genes are sufficiently close © Jones & Bartlett Learning, LLC ditype that double© Jones and higher& Bartlett levels ofLearning, crossing-over LLC can NOT FOR SALE OR DISTRIBUTION tetrad be neglected.NOT FOR In this SALE case, OR tetratype DISTRIBUTION tetrads arise (B) Crossing-over between one of the genes and its centromere only from meiotic cells in which a single crossover occurs between the genes (Figure 4.27, part A and A B part B). As we saw in Figure 4.6, the genetic map AB Ab B distance across an interval is defined as one-half AbaB © Jones & Bartlett Learning,a LLC b © Jones the& Bartlettproportion Learning, of cells with LLC a crossover in the ab NOT FOR SALE OR DISTRIBUTIONa NOT FORinterval, SALE so OR the mapDISTRIBUTION distance implied by the tetrads b Tetratype is given by tetrad A Map distance 5 b 1 Number of tetratype tetrads A Ab × × 100 (4.1) b 2 Total number of tetrads © Jones & Bartlett Learning, abAB LLC © Jones & Bartlett Learning, LLC a B NOT FOR SALE OR DISTRIBUTIONaB To take a specific example,NOT suppose FOR SALE100 tetrads OR are DISTRIBUTION B a Tetratype analyzed from the cross A B 3 a b, and the result is tetrad that 91 are PD and 9 TT. The finding that NPD ,, PD means that the genes are linked, and the fact FIGURE 4.26 Types of unordered asci produced with two genes that NPD 5 0 means that the genes are so closely in different© Jones chromosomes. & Bartlett (A) In the Learning, absence of a crossover,LLC random linked© that Jones double & Bartlettcrossing-over Learning, does not LLC occur arrangementNOT FOR of chromosome SALE ORpairs atDISTRIBUTION metaphase I results in two different betweenNOT them. FOR The SALE map distance OR DISTRIBUTION between A and B combinations of chromatids, one yielding PD tetrads and the other NPD tetrads. (B) When a crossover takes place between one gene and its is calculated as follows: centromere, the two chromosome arrangements yield TT tetrads. If both 1 9 genes are closely linked to their centromeres (so that crossing-over is rare), Mapdistancec=× ×=100 45. M few TT tetrads are produced. 2 100 © Jones & Bartlett Learning, LLC © JonesWe &must Bartlett emphasize Learning, that Equation LLC (4.1) is valid only NOT FOR SALE OR DISTRIBUTION NOT FORwhen SALENPD 5 OR 0, so DISTRIBUTION that interference across the region prevents the occurrence of double crossing-over. When either gene and its centromere, the two chromosomal double crossovers do take place in the interval, then configurations are equally likely at metaphase I, and so NPD  0, and the formula for map distance has to be PD 5 NPD. When there is a crossover between either modified to take the double crossovers into account. gene and its centromere© Jones (Figure & 4.26,Bartlett part B),Learning, a tetra- LLC The mapping procedure© usingJones tetrads & Bartlett differs from Learning, LLC type tetrad results, NOTbut this FOR does SALE not change OR DISTRIBUTION the fact that presented earlier in theNOT chapter FOR in SALE that the OR map DISTRIBUTION that PD 5 NPD. distance is not calculated directly from the number of In contrast, when genes are linked, parental ditypes recombinant and nonrecombinant chromatids. Instead, are far more frequent than nonparental ditypes. To see the map distance is calculated directly from the tetrads why, assume that the genes are linked and consider and the inferred crossovers that give rise to each type the© eventsJones required & Bartlett for the Learning, production LLC of the three of tetrad.© However, Jones it& is Bartlettnot necessary Learning, to carry out LLC a full typesNOT of FORtetrads. SALE FIGURE OR 4. DISTRIBUTION27 shows that when no tetrad analysisNOT FORfor estimating SALE ORlinkage. DISTRIBUTION The alternative crossing-over takes place between the genes, a PD is to examine spores chosen at random after allow- tetrad is formed. Single crossover between the genes ing the tetrads to break open and disseminate their results in a TT tetrad. The formation of a two-strand, spores. This procedure is called random-spore analysis, three-strand, or four-strand double crossover results and the linkage relationships are determined exactly as © Jones & Bartlettin a PD, TT, Learning, or NPD tetrad, LLC respectively. With linked© Jonesdescribed & Bartlett earlier forLearning, Drosophila LLC and corn. In particular, NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION 138 CHAPTER 4 Gene Linkage and Genetic Mapping 4TH PAGES © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. (A) No crossing-over the frequency of recombination equals the number of A B spores that are recombinant for the genetic markers © Jones & Bartlett Learning, LLC © Jonesdivided & by Bartlett the total numberLearning, of spores. LLC AB NOT FOR SALE OR DISTRIBUTIONA B NOT FOR SALE OR DISTRIBUTION abAB a b The geometry of meiosis is revealed ab in ordered tetrads. a b Parental ditype (PD) In the bread mold Neurospora crassa, the products of © Jones & Bartlett Learning, LLCmeiosis are contained in an ordered© Jones array & of Bartlett ascospores Learning, LLC (B) Single crossoverNOT FOR SALE OR DISTRIBUTION(FIGURE 4.28). A zygote nucleus,NOT contained FOR SALE in a sac-like OR DISTRIBUTION A B ascus, undergoes meiosis almost immediately after it is AB formed. The four nuclei produced by meiosis are in a A Bb linear, ordered sequence in the ascus, and each of them a aBAb b undergoes a mitotic division to form two genetically iden- ab © Jones & Bartlett Learning, LLC tical and adjacent© Jones ascospores. & Bartlett Each mature Learning, ascus contains LLC a b NOT FOR SALE OR DISTRIBUTIONTetratype (TT) eight ascosporesNOT arranged FOR SALEin four pairs, OR eachDISTRIBUTION pair derived from one of the products of meiosis. The ascospores can (C) 2-strand double crossover be removed one by one from an ascus and each germi- A B nated in a culture tube to determine its genotype. AB Ordered asci also can be classified as PD, NPD, or TT A B © Jones & Bartlett Learning, LLC abAB © Joneswith respect & Bartlett to two pairsLearning, of alleles, LLC which makes it pos- a b NOT FOR SALE OR DISTRIBUTION ab NOTsible FOR to assessSALE the OR degree DISTRIBUTION of linkage between the genes. a b The fact that the arrangement of meiotic products is Parental ordered also makes it possible to determine the recom- ditype (PD) bination frequency between any particular gene and its (D) 3-strand double crossover centromere. The logic of the mapping technique is based © Jones & Bartlett Learning, LLC © JonesFIGURE & 4.Bartlett29 Learning, LLC A B on the feature of meiosis shown in . NOT FOR SALEAb OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION A B aBAB KEY CONCEPT a b ab Homologous centromeres of parental chromo- a b somes separate at the first meiotic division; the Tetratype (TT) © Jones & Bartlett Learning, LLC centromeres© Jonesof sister chromatids& Bartlett separate Learning, at the LLC second meiotic division. NOT(E) 3-strand FOR double SALE crossover OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION A B AB Thus, in the absence of crossing-over between a gene A B and its centromere, the alleles of the gene (for example, A a abAb b and a) must separate in the first meiotic division; this sep- aB © Jones & Bartlett Learning,a LLCb © Jonesaration &is calledBartlett first-division Learning, segregation LLC . If, instead, a NOT FOR SALE OR DISTRIBUTION Tetratype (TT) NOTcrossover FOR SALE is formed OR between DISTRIBUTION the gene and its centromere, the A and a alleles do not become separated until the (F) 4-strand double crossover second meiotic division; this separation is called second- division segregation. The distinction between first-divi- A B Ab sion and second-division segregation is shown in Figure A © JonesB & Bartlett Learning, 4.29.LLC As shown in part A, only© Jones two possible & Bartlett arrange -Learning, LLC a aBAb b ments of the products of meiosis can yield first-division NOT FOR SALEaB OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION a b segregation—A A a a or a a A A. However, four patterns Nonparental of second-division segregation are possible because of the ditype (NPD) random arrangement of homologous chromosomes at FIGURE 4.27 Types of tetrads produced with two linked metaphase I and of the chromatids at metaphase II. These genes.© (A) Jones In the absence & Bartlett of a crossover, Learning, a PD tetrad LLC is produced. four arrangements,© Jones which & are Bartlett shown in Learning, part B, are LLC (B) WithNOT a single FOR crossover SALE between OR the DISTRIBUTION genes, a TT tetrad is NOT FOR SALE OR DISTRIBUTION produced. (C2F) Among the four possible types of double A a A a, a A a A, A a a A, and a A A a crossovers between the genes, only the four-strand double The percentage of asci with second-division segre- crossover in part F yields an NPD tetrad. gation patterns for a gene can be used to map the gene with respect to its centromere. For example, let us assume © Jones & Bartlett Learning, LLC © Jonesthat 30 & percent Bartlett of a Learning,sample of asci LLC from a cross have a NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION 4.5 Tetrads Contain All Four Products of Meiosis 139 4TH PAGES © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. Asexual Cross fertilization Asexual cycle cycle Conidia (n) Conidia (n) © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Haploid nuclei fuse to form diploid nucleus. © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Diploid cell Hyphae of forms in the Hyphae of mating-type A protoperithecium. mating-type a

Zygote A aAa Zygote nucleus (2n) nucleus (2n)

First meiotic division © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION A aANOT FOR SALE ORa DISTRIBUTION

Second meiotic division

Mitotic divisions

NOT FOR SALE OR DISTRIBUTIONAscus with eight AscusNOT with FOR eight SALE OR DISTRIBUTION ascospores (n) ascospores (n) in ordered array in ordered array

FIGURE 4.28 The life cycle of Neurospora crassa. The vegetative body consists of partly segmented filaments called hyphae. Conidia are asexual spores that function in the fertilization of organisms of the opposite mating type. A protoperithecium develops into a structure in which numerous cells undergo meiosis. © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC second-division segregationNOT FOR pattern SALE for the AOR and DISTRIBUTION a alleles. Equation (4.2) is valid asNOT long FORas the SALE gene isOR close DISTRIBUTION This means that 30 percent of the cells undergoing meiosis enough to the centromere for us to neglect multiple had a crossover between the A gene and its centromere. crossovers. Reliable linkage values are best deter- Because the map distance between two genes is, by defi- mined for genes that are near the centromere. The nition, equal to one-half times the proportion of cells with location of more distant genes is then accomplished a crossover© Jones between & Bartlett the genes, Learning, the map distance LLC between by mapping© Jones these genes & Bartlett relative Learning,to genes nearer LLC the a geneNOT and FOR its centromere SALE OR is given DISTRIBUTION by the equation centromere.NOT FOR SALE OR DISTRIBUTION If a gene is far from its centromere, crossing-over Map distance 5 between the gene and its centromere will be so fre- Number of asci with quent that the A and a alleles become randomized with 1 second division segregation × × 100 (4.2) respect to the four chromatids. The result is that the six © Jones & Bartlett2 Learning,Total number LLC of asci © Jonespossible & Bartlett spore arrangements Learning, shown LLC in Figure 4.29 are NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION 140 CHAPTER 4 Gene Linkage and Genetic Mapping 4TH PAGES © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. (A) First-division segregation (B) Second-division segregation A © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLCA Homologous NOT FOR SALE OR DISTRIBUTIONcentromeres of NOTA FOR SALE OR DISTRIBUTIONAb parental a a chromosomes a a © JonesNo crossing-over & Bartlett Learning, LLC Single crossover © Jones & Bartlett Learning, LLC between gene and Meiosis I between gene and Meiosis I NOTcentromere FOR SALE occurs. OR DISTRIBUTION centromere occurs. NOT FOR SALE OR DISTRIBUTION

A A

© Jones & Bartlett Learning, LLC A © Jones & Bartlett Learning,a LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Homologous centromeres A and a separated A and a not yet separated separate.

a A © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOTa FOR SALE OR DISTRIBUTIONa

Meiosis II Meiosis II

A A © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION A andNOT a separated FOR SALE OR DISTRIBUTION Centromeres split A a and separate. a A

A and a separated © Jones & Bartlett Learning, LLC a © Jones & Bartlett Learning,a LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Mitosis Mitosis

A AAAaaaa AAaaAAaa

© Jones & BartlettPossible Learning, spore patterns LLC or © Jones & Bartlett Learning,or LLC NOT FOR SALE ORwith DISTRIBUTION first-division NOT FOR SALE OR DISTRIBUTION segregation aaaaAAAA aaA AAAaa

FIGURE 4.29 First- and second-division segregation in Neurospora. (A) First-division segregation patterns are found in the ascus when a crossover© Jones between & the Bartlett gene and centromereLearning, does LLC not take place. The alleles separate© (segregate)Jones &in meiosisBartlett I. Two Learning, spore patterns LLC are possible,NOT dependingFOR SALE on the ORorientation DISTRIBUTION of the pair of chromosomes on the first-divisionNOT spindle. FOR The SALE orientation OR shown DISTRIBUTION results in the pattern in the upper ascus. (B) Second-division segregation patterns are found in the ascus when a crossover between the gene and the centromere delays separation of A from a until meiosis II. Four patterns of spores are possible, depending on the orientation of the pair of chromosomes on the first-division spindle and that of the chromatids of each chromosome on the second-division spindle. The orientation shown results in the pattern in the top ascus. © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION 4.5 Tetrads Contain All Four Products of Meiosis 141 4TH PAGES © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. all equally frequent. Therefore, when the chromatids meiosis can be recovered in a four-spore (yeast) or participating in each cross over are chosen at random, eight-spore (Neurospora) ascus. As we have noted, most © Jones & Bartlett Learning, LLC © Jonesasci &from Bartlett heterozygous Learning, Aa diploids LLC contain ratios of NOT FOR SALEKEY CONCEPT OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION The maximum frequency of second-division segre- 2 A : 2 a in four-spored asci, or gation asci is 2/3. 4 A : 4 a in eight-spored asci

demonstrating normal Mendelian segregation. Occa- © Jones & Bartlett Learning, LLCsionally, however, aberrant© ratios Jones are also & Bartlettfound, such Learning, as LLC Gene conversionNOT suggests FOR SALE a molecular OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION mechanism of recombination. 3 A : 1 a or 1 A : 3 a in four-spored asci, and 5 A : 3 a or 3 A : 5 a in eight-spored asci Genetic recombination may be regarded as a process of breakage and repair between two DNA molecules. Different types of aberrant ratios can also occur. The In ©eukaryotes, Jones & the Bartlett process takesLearning, place early LLC in meiosis aberrant ©asci Jones are said & to Bartlett result from Learning, gene conversion LLC afterNOT each FOR molecule SALE has OR replicated, DISTRIBUTION and with respect because itNOT appears FOR as ifSALE one allele OR has DISTRIBUTION “converted” the to genetic markers, it results in two molecules of the other allele into a form like itself. Gene conversion is parental type and two recombinants. For genetic stud- frequently accompanied by recombination between ies of recombination, fungi such as yeast or Neurospora genetic markers on either side of the conversion event, are particularly useful, because all four products of any even when the flanking markers are tightly linked. This © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Region containing a mismatched base pair

G AGTCG AAT C © Jones & Bartlett Learning,C TCAG LLCT TTA G © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

One or the other © Jones & Bartlett Learning, LLC strand is chosen © Jones & Bartlett Learning, LLC G AGTCG AAT C to be repaired. G NOT FOR SALEC TC OR DISTRIBUTIONA G NOT FOR SALEAACT OR DISTRIBUTION

AGT TT GAG CT T GATTGACTC A segment of the strand to be repaired is excised © Jones & Bartlett Learning, LLC and ©discarded. Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

G AGTCG AAT C GAG CT C TC A G T GATTGACTC © Jones & Bartlett Learning,The gap remaining LLC is © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTIONfilled in by repair NOT FOR SALE OR DISTRIBUTION synthesis using the other strand as a template.

© Jones & Bartlett Learning, LLCThe two possible types of© Jones & Bartlett Learning, LLC G AGTCG AAT C G AGTCA AAT C NOT FOR SALEC TC ORAG DISTRIBUTIONC T T A G repair result in different NOT FORC TC SALEAGT T TORA G DISTRIBUTION DNA sequences.

FIGURE 4.30 Mismatch repair consists of the excision of a segment of a DNA strand containing a base mismatch followed by repair © Jones & Bartlettsynthesis. Either Learning, strand can be LLC excised and corrected. In this example,© Jones the G 2&T mismatchBartlett is correctedLearning, to either LLC G2C (left) or A2T (right). NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION 142 CHAPTER 4 Gene Linkage and Genetic Mapping 4TH PAGES © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. implies that gene conversion can be one conse- A a quence of the recombination process. Gene conversion results from a normal DNA © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC G T C G A A T G T C A A A T NOT FORrepair SALE process OR DISTRIBUTIONin the cell known as mismatch NOT FORC A GSALEC T T A OR DISTRIBUTIONC A G T T T A repair. In this process, an enzyme recognizes any base pair in a DNA duplex in which the paired bases are mismatched—for example, G paired with T, or A paired with C. When such a mismatch is found in a molecule of© duplexJones DNA, & Bartlett a small segLearning,- LLC © Jones & Bartlett Learning, LLC ment of one strand isNOT excised FOR and SALE replaced OR with DISTRIBUTION NOT FOR SALE OR DISTRIBUTION a new segment synthesized using the remaining G A strand as a template. In this manner the mis- G T C A A T G T C A A T C A G T T T A C A G C T T A matched base pair is replaced. FIGURE 4.30 shows an example in which a mismatched G2T pair is being© repaired. Jones The & Bartlettstrand that Learning, is excised could LLC be © Jones & Bartlett Learning, LLC Heteroduplex Heteroduplex eitherNOT the strand FOR containing SALE OR T or DISTRIBUTION the one contain- NOT FOR SALE OR DISTRIBUTION ing G, and the newly synthesized (repaired) segment, shown in red, would contain either a C or an A, respectively. The two possible products of repair CT G T C G A A T AAGA G T C G A A T differ in DNA sequence. C A G C T T A C A G C T T A © Jones & BartlettThe role ofLearning, mismatch LLCrepair in gene conver- © Jones & Bartlett Learning, LLC NOT FORsion SALE is illustrated OR DISTRIBUTION in FIGURE 4.31. The pair of DNA NOT FOR SALEResult: OR DISTRIBUTION aA conversion duplexes across the top represents the DNA molecules of two alleles in a cell undergoing meiosis. One duplex contains a G2C base pair highlighted G A G T C A A A T aaTC G T C A A A T in color; this corresponds to the A allele. The other C A G T T T A C A G T T T A duplex contains an A©2 TJones base pair& Bartlett at the same Learning, LLC © Jones & Bartlett Learning, LLC position, which correspondsNOT FORto the SALEa allele. OR In the DISTRIBUTION Result: A aNOT conversion FOR SALE OR DISTRIBUTION process of recombination, the participating DNA duplexes can exchange pairing partners. The result is shown in the second row. The exchange of pair- G A G T C A A A T aAGA G T C G A A T ing partners creates a heteroduplex region in C A G T T T A C A G C T T A which© any Jones bases &that Bartlett are not identical Learning, in the LLCparen- © Jones & Bartlett Learning, LLC tal duplexesNOT FOR become SALE mismatched. OR DISTRIBUTION In this example, NOT Result:FOR NoSALE conversion OR DISTRIBUTION one heteroduplex contains a G2T base pair and the other an A2C base pair. At this point, the mismatch repair system comes into play and corrects CT G T C G A A T AaTC G T C A A A T the mismatches. Each mismatch can be repaired C A G C T T A C A G T T T A © Jones &in Bartletteither of twoLearning, ways, so LLCthere are four possible © Jones & Bartlett Learning, LLC NOT FORways SALE in whichOR DISTRIBUTION the mismatches can be repaired. NOT FOR SALE ORResult: DISTRIBUTION No conversion One type of repair results in gene conversion of a to A, another results in gene conversion of A to FIGURE 4.31 Mismatch repair resulting in gene conversion. Only a a, and the remaining two restore the sequences of small part of the heteroduplex region is shown. the original duplexes and so do not result in gene conversion. © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTIONThe crossovers needed forNOT the FORchiasmata SALE to formOR DISTRIBUTION 4.6 Recombination is initiated by a are initiated by programmed double-stranded breaks in DNA (FIGURE 4.32, part A). In a double-stranded double-stranded break in DNA. break, the size of the gap is usuallly increased by In prophase I of meiosis, chiasmata are the physi- nuclease digestion of the broken ends, with greater cal manifestations© Jones & Bartlettof crossing-over Learning, between LLC DNA degradation© of Jones the 59 ends & Bartlett leaving overhanging Learning, 39 endsLLC molecules.NOT FORThese SALEstructures OR bridge DISTRIBUTION between pairs of as shown inNOT the illustration.FOR SALE These OR gaps DISTRIBUTION are repaired sister chromatids in a bivalent and are important in the using the unbroken homologous DNA molecule as a proper alignment of the bivalent at the metaphase plate template, but in meiosis the repair process can result in preparation for anaphase I. Bivalents that lack chias- in crossovers that yield chiasmata between nonsister mata to help hold them together are prone to undergo chromatids. These crossovers are also the physical basis © Jones &nondisjunction. Bartlett Learning, LLC © Jonesof what & is Bartlett observed geneticallyLearning, as LLCrecombination. NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION 4.6 Recombination Is Initiated by a Double-Stranded Break in DNA 143 4TH PAGES © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. AB

ab ab © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALEElongating OR DISTRIBUTIONstrand ejected D loop NOTexpands FOR and SALE OR DISTRIBUTION serves as template for the AB remaining free 3Ј end.

ab AB © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC ab NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

Ejected end pairs with Synthesis across gaps correct partner. completes repair © Jones & Bartlett Learning,Dark blue LLC ©Light Jones blue & Bartlett Learning, LLC ABand red ABand pink NOT FOR SALE OR DISTRIBUTIONstrands NOTstrands FOR SALE OR DISTRIBUTION abbreak and abbreak and rejoin. rejoin.

Holliday © Jones & BartlettNew synthesis Learning, completes LLC Strand breakage© Jones and & Bartlettjunctions Learning, LLC NOT FOR SALErepair ORof DSB; DISTRIBUTION products rejoining separatesNOT FOR duplexes; SALE OR DISTRIBUTION are nonrecombinant for products are recombinant for markers A and B. markers A and B.

AB AB

FIGURE 4.32 (A) Double-strand break in a duplex DNA molecule with overhanging 39 ends facing the gap. Repair of the break makes use of the nonbroken homologous duplex. (B) Repair pathway that does not result in crossing-over, although the heteroduplex regions can undergo gene conversion. (C) Repair pathway that does result in crossing-over, also with possible gene conversion in heteroduplex regions. [Adapted from© D. JonesK. Bishop and& Bartlett D. Zickler, Cell Learning, 117 (2004): 9–15.]LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

A double-stranded break does not necessarily result plex region is the region where the light blue strand is in a crossover, however. Repair of the double-stranded paired with the red strand. Because it is a heteroduplex, break by the noncrossover pathway is illustrated in Fig- any base-pair mismatches in this region could be cor- ure© 4.32, Jones part &B. BartlettThe first step Learning, in repair is LLC that a broken rected by© mismatch Jones &repair Bartlett in such Learning, a way as to LLC result 39NOT end invades FOR theSALE homologous OR DISTRIBUTION unbroken DNA duplex, in gene NOTconversion. FOR SALESuch heteroduplex OR DISTRIBUTION regions are forming a short heteroduplex region with one strand typically only a few hundred base pairs in length. They and a looped-out region of the other strand called are much shorter than a gene and vastly shorter than a a D loop. (Specific proteins are required to mediate chromosome, and so gene conversions are rare events strand invasion; in E. coli the strand-invasion protein except for short regions very near the site of a double- © Jones & Bartlettis known asLearning, RecA.) In LLCthe illustration, the heterodu©- Jonesstranded & Bartlett break. Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION 144 CHAPTER 4 Gene Linkage and Genetic Mapping 4TH PAGES © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. At one end of the heteroduplex, the free 39 end of the double-stranded break, but note that the resulting the broken DNA strand is extended (brown), but after structure includes two places where the strands have © Jones a& time Bartlett it is ejected Learning, from the LLCtemplate, and the strands of © Jonesexchanged & Bartlett pairing Learning,partners. Each LLC of the structures NOT FORthe SALE unbroken OR duplexDISTRIBUTION are able to come together again. NOTwhere FOR pairing SALE partners OR DISTRIBUTION are switched is called a Hol- At this point, the extension of the 39 end is long enough liday junction, named after Robin Holliday, who first that pairing can take place with the complementary predicted that such structures would be involved in strand in the broken duplex. At the same time, this recombination. pairing provides a template for the 39 end of the other The problem with Holliday junctions is that they broken strand. Extension© Jones of the & 3 9Bartlett ends across Learning, the LLCare places where DNA strands© Jones from different & Bartlett duplex Learning, LLC remaining gaps completesNOT theFOR repair SALE of the OR double- DISTRIBUTIONmolecules are interconnected.NOT How FOR the SALEstrands OR are DISTRIBUTION stranded break. Note that although gene conversion interconnected is shown for the DNA double helices can occur in the noncrossover pathway, the resulting in FIGURE 4.33, part A. Resolution of the Holliday duplex DNA molecules are nonrecombinant. junctions is necessary for the DNA molecules to The crossover pathway for repairing a double- become free of one another. This requires breakage and stranded© Jones break is& illustratedBartlett Learning,in Figure 4.32, LLC part C. rejoining of ©one Jones pair of &DNA Bartlett strands Learning, at each Holliday LLC AgainNOT invasion FOR of SALE the unbroken OR DISTRIBUTION duplex forms a D junction. TheNOT breakage FOR and SALE rejoining OR DISTRIBUTIONis an enzymatic loop and a short heteroduplex region in which gene function carried out by an enzyme called the Holliday conversion can occur. As in the noncrossover path- junction-resolving enzyme. way, the free 39 end of the broken DNA strand is Parts B and C in Figure 4.33 show two ways in extended (brown), but in this case it continues until which the Holliday structures can be resolved. Break- © Jones &it displacesBartlett the Learning, partner strand LLC (pink) of the template © Jonesage and & rejoiningBartlett of Learning, the strands LLCindicated by the red NOT FORstrand SALE (red). OR The DISTRIBUTION displaced strand can then serve as a NOTarrows FOR results SALE in ORa crossover DISTRIBUTION at the site of the left-hand template for the elongation of the 39 end of the other Holliday junction, whereas breakage and rejoining of broken strand. Eventually, the extensions of the broken the strands indicated by the blue arrows results in a strands become long enough that they can be attached crossover at the site of the right-hand Holliday junc- to the broken 59 ends. This completes the repair of tion. In both cases, the resulting DNA molecules have © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

Holliday © Jones & Bartlett Learning, LLCjunctions © Jones & Bartlett Learning, LLC NOT FOR SALE AOR DISTRIBUTION NOT FORB SALE OR DISTRIBUTION

Resolution of the Holliday Resolution of the Holliday junctions by breakage and junctions by breakage and reunion at the sites of the reunion at the sites of the red arrows. © Jones & Bartlett Learning, LLC blue arrows. © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION A b A b

Site of Site of a crossover B a crossover B © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Recombinant products A b and a B Recombinant products A b and a B

FIGURE 4.33 (A) Two Holliday junctions in a pair of DNA molecules undergoing recombination (the parental chromosomes are AB and ab); (B and C) two modes of resolution depending on which strands are broken and rejoined. Part D is an electron micrograph showing a single Holliday junction between a pair of DNA molecules. [Illustration modified from B. Alberts. Essential Cell Biology. Garland Science, © Jones &1997. Bartlett Illustration Learning, reproduced with LLC permission of Huntington Potter,© Johnnie Jones B. Byrd, & Bartlett Sr., Alzheimer’s Learning, Center & Research LLC Institute.] NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION 4.6 Recombination Is Initiated by a Double-Stranded Break in DNA 145 4TH PAGES © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. a crossover that yields reciprocal recombinant A b and attaches methyl (2CH3) groups to the amino acid a B products. (In principle, resolution could also take lysine of an abundant protein called histone H3 that, © Jones & placeBartlett at the Learning, red arrows in LLC one Holliday junction and the© Jonestogether & Bartlett with other Learning, histone LLC proteins, binds with NOT FOR SALEblue arrows OR DISTRIBUTIONin the other, but these resolutions result NOTin FORDNA SALEto form OR a chain DISTRIBUTION of small DNA-protein beads noncrossover products. It is unclear how often these known as nucleosomes. DNA is usually packaged in noncrossover types of resolution take place.) the form of nucleosomes containing histone H3, and hence wherever the target 13-mer of PRDM9 occurs, Recombination tends to take place at nucleosomes containing histone H3 are also pres- preferred positions© Jones in & the Bartlett genome. Learning, LLCent. Evidently, methylation© ofJones histone & H3Bartlett by PRDM9 Learning, LLC NOT FOR SALE OR DISTRIBUTIONpredispposes the DNA toNOT undergo FOR a double-stranded SALE OR DISTRIBUTION In some organisms, including humans and other mam- break, but the molecular details of break formation mals, programmed double-stranded DNA breaks are still unknown. More than 30 alleles of the gene are much more likely to occur at certain positions encoding PRDM9 have been identified, which differ in the genome than others. Crossovers resulting in in their propensity to recognize the 13-mer target recombination© Jones & are Bartlett much more Learning, likely to occurLLC at these and to methylate© Jones histone & Bartlett H3. Variation Learning, in the LLCalleles positions,NOT FOR which SALE are referred OR DISTRIBUTIONto as hotspots of recom- encodingNOT PRDM9 FOR accounts SALE for OR the DISTRIBUTIONdiffering efficiency bination. The human genome contains about 30 thou- of PRDM9-associated hotspots. sand hotspots of recombination, spaced an average of Although recombination tends to be initiated by 100 kb apart. These hotspots are often located in the means of double-stranded breaks at hotspots of recom- spaces between genes, and they differ greatly from one bination, it should be emphasized that there are so © Jones & Bartlettto the next Learning,in the likelihood LLC of a double-stranded break.© Jonesmany & hotspotsBartlett relative Learning, to number LLC of crossover events NOT FOR SALEOne particular OR DISTRIBUTION protein has been implicated in aboutNOT FORthat the SALE sites ofOR recombination DISTRIBUTION in any particular meiotic 40 percent of hotspots across the human genome. cell show a great deal of randomness. In the human The protein is known as PRDM9, and it is known to genome, for example, there are about 30 thousand bind with double-stranded DNA at sites that match or hotspots of recombination and about 60 crossover nearly match the 13-mer sequence events per meiosis. Roughly speaking, each crossover © Jones & Bartlett Learning, LLCcould take place at any of© aboutJones 500 & hotspots Bartlett in Learning,the LLC 5-CCGCCGTMWCCWC-3 NOT FOR SALE OR DISTRIBUTIONvicinity. The relatively smallNOT number FOR of SALE crossovers OR per DISTRIBUTION where M means A or C, and W means T or A. The meiosis means that crossovers occur essentially at ran- protein does not cause the double-stranded break dom sites chosen from among the very large number of directly. PRDM9 is actually a methyl transferase that hotspots that occur across the genome. © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

n Genes that are located in the same chromosome and that do n Variations in DNA sequence among individuals (polymor- not show independent assortment are said to be linked. phisms) serve as genetic markers along the genome that are n The alleles of linked genes present together in the same used for genetic mapping, tracing the genetic ancestry of chromosome tend to© be Jones inherited & as Bartletta group. Learning, LLCindividuals, and many other purposes.© Jones & Bartlett Learning, LLC n Crossing-over between homologous chromosomes results n Among the most useful types of DNA polymorphisms are in recombination, whichNOT breaks FOR up SALEcombinations OR of DISTRIBUTION linked single-nucleotide polymorphismsNOT (SNPs), FOR restriction SALE fragment OR DISTRIBUTION alleles. length polymorphisms (RFLPs), simple-sequence repeats (SSRs), and copy-number polymorphisms (CNPs). n The frequency of recombination serves as a measure of distance between linked genes along a chromosome, providing n Tetrads are sensitive indicators of linkage because they include a genetic map of the relative positions of the genes. all the products of meiosis. n ©The Jones map distance & Bartlett between genes Learning, in a genetic LLC map is related to n At the DNA© Jones level, recombination & Bartlett is initiated Learning, by a double- LLC the frequency of crossing-over between the genes in meiosis. stranded break in a DNA molecule. Use of the homolo- NOT FOR SALE OR DISTRIBUTION gous DNANOT molecule FOR as aSALE template OR for repair DISTRIBUTION can result in a n Physical distance along a chromosome is often, but not crossover, in which both strands of the participating DNA always, correlated with map distance. molecules are broken and rejoined.

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION 146 CHAPTER 4 Gene Linkage and Genetic Mapping 4TH PAGES © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. © Jones LEARNING& Bartlett Learning,OUTCOMES LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION n Given a genetic map with two genes, predict the kinds and n Explain how linkage is detected between two genes in an relative frequencies of gametes that would be produced by an organism with unordered tetrads and estimate the distance in individual of a specified genotype. the genetic map between the genes. n Analyze the results of a genetic cross with three linked genes n Explain how linkage between a gene and its centromere is to deduce the genotypes© ofJones the parents, & Bartlett the order of Learning, the genes LLCdetected in an organism with ordered© Jones tetrads and& Bartlett estimate the Learning, LLC along the chromosome,NOT the map FOR distances SALE between OR the DISTRIBUTION genes, map distance between the gene NOTand its centromere.FOR SALE OR DISTRIBUTION and the degree of interference between crossovers. n Distinguish between a single-nucleotide polymorphism (SNP), a restriction fragment length polymorphism (RFLP), and copy-number variation (CNV). Describe one experimental method© Jones by which & each Bartlett type of polymorphism Learning, can LLC be detected. © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

ISSUES AND IDEAS

© Jones &n BartlettDistinguish betweenLearning, genetic LLC recombination and genetic © Jonesn What & is Bartlettmeant by the Learning, term chromosome LLC interference? complementation. Is it possible for two mutant genes to NOT FOR SALE OR DISTRIBUTION NOTn FORIn human SALE genetics, OR why DISTRIBUTION are molecular variations in DNA show complementation but not recombination? Is it pos- sequence, rather than phenotypes such as eye color or sible for two mutant genes to show recombination but not blood-group differences, used for genetic analysis? complementation? n In genetic analysis, what is so special about the ability to n In genetic analysis, why is it important to know the position examine tetrads in certain fungi? of a gene along a chromosome? n Explain how tetratype tetrads demonstrate that recombina- n What is the maximum ©frequency Jones of recombination& Bartlett between Learning, LLCtion takes place at the four-strand© Jones stage of meiosis & Bartlett and is Learning, LLC two genes? Is there a maximum map distance between reciprocal. two genes? NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION n Explain why the observation PD .. NPD with respect to n Why is the frequency of recombination over a long interval tetrads is a sensitive indicator of linkage. of a chromosome always smaller than the map distance over the same interval?

Problem 1 Solution. To determine which, if any, genes are linked, consider the mutants in pairs, and sum the data to find the In Drosophila, the recessive mutant allele spineless (ss) results in total number of parental types and recombinant types for each thin bristles, cinnabar (cn) results in bright red eyes, and ebony © Jones & Bartlett Learning, LLC © Jonespair. For & ss Bartlettand cn, the parentalLearning, types are LLC 241 1 212 1 25 1 (e) results in a black body color. A cross is carried out between 35 5 513 and the recombinant types are 223 1 202 1 31 1 NOT FORfemales SALE of genotypeOR DISTRIBUTION ss cn e / 1 1 1 and males of genotype NOT FOR SALE OR DISTRIBUTION 31 5 487. These numbers are close enough to 500 : 500 that one ss cn e / ss cn e. In this type of symbolism, each 1 denotes the may infer that ss and cn are unlinked. Similarly, for cn and e, the nonmutant allele of the gene written at the corresponding posi- parental types sum to 515 and the recombinant types to 485, tion. From this cross, the following 1000 progeny were obtained: hence cn and e are unlinked. For ss and e, however, the parental ss cn e / ss cn e 241 types sum to 878 and the recombinant types to 122, and this ss 1 e / ss cn© e Jones &223 Bartlett Learning, resultLLC implies that ss and e are linked.© Jones The estimated & Bartlett frequency Learning, LLC 1 cn 1 / ss cnNOT e FOR202 SALE OR DISTRIBUTIONof recombination is 122/1000 5 0.122NOT or 12.2 FOR percent. SALE OR DISTRIBUTION 1 1 1 / ss cn e 212 ss cn 1 / ss cn e 25 ss 1 1 / ss cn e 31 1 cn e / ss cn e 31 1 1 © Jones e / &ss Bartlettcn e Learning,35 LLC © Jones & Bartlett Learning, LLC DetermineNOT which, FOR if any,SALE of the OR genes DISTRIBUTION are linked, and for NOT FOR SALE OR DISTRIBUTION those that are linked, estimate the frequency of recombination between the genes.

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Solutions: Step by Step 147 4TH PAGES © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. © Jones & ProblemBartlett 2 Learning, LLC © Jonesrecombinants & Bartlett with thoseLearning, of the nonrecombinants. LLC If the gene order is correct, then it will require two recombination events NOT FOR SALEIn Drosophila OR, theDISTRIBUTION recessive mutant allele cinnabar (cn) resultsNOT FOR SALE OR DISTRIBUTION in bright red eyes, curved (c) results in curved wings, and (one in each interval) to derive the double-recombinant plexus (px) results in extra wing veins. All three genes are chromosomes from the nonrecombinants. If this is not the linked. In a cross between cn c px / 1 1 1 females and cn c case, rearrange the order of the genes. (The “odd man out” px / cn c px males, the following progeny were counted: in comparing the double recombinants with the nonrecombinants is always the gene in the middle.) In this particular cn c px / cn© c Jonespx & Bartlett296 Learning, LLCexample, the gene order is correct© Jones as given. &Finally, Bartlett with this Learning, LLC cn c 1 / cnNOT c px FOR SALE63 OR DISTRIBUTIONpreliminary bookkeeping done,NOT we can FOR proceed SALE to tackle OR the DISTRIBUTION cn 1 1 / cn c px 119 questions. (a) The frequency of recombination between cn cn 1 px / cn c px 10 and c is given by the totals of all classes of progeny show- 1 c px / cn c px 86 ing recombination in the cn 2 c interval, in this case (205 1 1 c 1 / cn c px 15 25)/1000 5 0.23. (b) The frequency of recombination between 1 1 1 / cn c px 329 c and px equals (145 1 25)/1000 5 0.17. (c) The frequency of ©1 Jones 1 px &/ cnBartlett c px Learning,82 LLC © Jones & Bartlett Learning, LLC recombination between cn and px equals (145 1 205)/1000 5 Total 1000 NOT FOR SALE OR DISTRIBUTION 0.35. (NoteNOT that the FOR double SALE recombinants OR DISTRIBUTION are not included in this total, because the double recombinants are not recom- (a) What is the frequency of recombination between cn and c? bined for cn and px; their allele combinations for cn and px are (b) What is the frequency of recombination between c and px? the same as in the parents.) (d) The frequency of recombina- (c) What is the frequency of recombination between cn and px? tion between cn and px (0.35) is smaller than the sum of that (d) Why is the frequency of recombination between cn and px © Jones & Bartlett Learning, LLC © Jonesbetween & Bartlett cn and c and Learning, that between LLCc and px (0.23 1 0.17 5 smaller than the sum of that between cn and c and that between 0.40) because of double crossovers. (e) The coefficient of coin- NOT FOR SALEc and px ?OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION cidence equals the observed number of double recombinants (e) What is the coefficient of coincidence across this region? divided by the expected number. The observed number is 25 What is the value of the interference? and the expected number is 0.23 3 0.17 3 1000 5 39.1; the (f) Draw a genetic map of the region, showing the locations of coefficient of coincidence therefore equals 25/39.1 5 0.64. cn, c, and px and the map distances between the genes. © Jones & Bartlett Learning, LLCThe interference equals 1 2 coefficient© Jones of coincidence, & Bartlett and Learning,so LLC Solution. Do not try to hurry through linkage problems! You will be the interference equals 1 2 0.64 5 0.36. (f) The genetic map rewarded by taking timeNOT to organize FOR the informationSALE OR in the DISTRIBUTION optimal is shown in the accompanyingNOT diagram. FOR The distancesSALE areOR in DISTRIBUTION manner. First, group the progeny types into reciprocal pairs—cn c px map units (centimorgans). However, the map distances of 23 with 1 1 1, cn c 1 with 1 1 px, and so forth—and make a new list and 17 map units are based on the 23 percent and 17 percent organized as shown here. (Ignore the cn c px chromosome from the recombination observed between cn and c and between c and father because it contributes no information about recombination.) px, respectively; the actual distances in map units are probably © Jones & Bartlett Learning, LLC a little greater© Jones than these & estimates Bartlett because Learning, of a small amountLLC cn c px 296 625 of double recombination within each of the intervals. NOT1 1 FOR 1 SALE329 OR  DISTRIBUTION NOT FOR SALE OR DISTRIBUTION cn c px cn c 1 63 145 1 1 px 82  23 17 cn 1 1 119 205 © Jones & Bartlett1 c px Learning, 86 LLC  © Jones & Bartlett Learning, LLC Problem 3 NOT FOR SALEcn OR1 px DISTRIBUTION 10 NOT FOR SALE OR DISTRIBUTION 25 In Neurospora, the gene arg12 encodes the enzyme needed 1 1  c 15 to convert ornithine to citrulline in the pathway of arginine Total 1000 biosynthesis. The gene was discovered in the experiments of Beadle and Tatum discussed in Chapter 1. In a cross between arg12 and ARG12 strains, where arg12 denotes the mutant In this tabulation, a space© Jones has been &inserted Bartlett between Learning, the pairs LLC © Jones & Bartlett Learning, LLC of reciprocal products in order to keep the groups separate. allele and ARG12 the nonmutant allele, two-thirds of the The number next to eachNOT brace FOR is the SALEtotal number OR of DISTRIBUTION chromo- resulting asci show second-divisionNOT segregation. FOR SALE What does OR this DISTRIBUTION somes in the group. The most numerous group of reciprocal observation imply about the map distance between arg12 and chromosomes (in this case, cn c px and 1 1 1) consists of the the centromere? nonrecombinants, and the least numerous group of recipro- Solution. Two-thirds is the maximum proportion of second- cal chromosomes (in this case, cn 1 px and 1 c 1) consists of division segregation that can occur. This value is observed for the© double Jones recombinants. & Bartlett Rearrange Learning, the order LLCof the groups, any gene that© Jones is so far from & Bartlettthe centromere Learning, that one or moreLLC if necessary,NOT FOR so that SALE the nonrecombinants OR DISTRIBUTION are at the top crossovers NOTare almost FOR certain SALE to take OR place DISTRIBUTION between the gene of the list and the double recombinants are at the bottom. and the centromere. Hence, we can deduce that arg12 is at least (In the present example, rearrangement is not necessary.) 50 map units from the centromere. This map distance is a mini- At this point, also make sure that the order of the genes is mum, and the true map distance could be greater. correct as given, by comparing the genotypes of the double © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION 148 CHAPTER 4 Gene Linkage and Genetic Mapping 4TH PAGES © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. © JonesCONCEPTS & Bartlett Learning,IN ACTION: LLC PROBLEMS FOR SOLUTION© Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION 4.1 A double heterozygote has the repulsion configuration 4.9 Two genes in chromosome 7 of corn are identified by the A b / a B of two linked genes that have a frequency of recombi- recessive alleles gl (glossy), determining glossy leaves, and ra nation of 0.20. If a randomly chosen gamete carries A, what is (ramosa), determining branching of ears. When a plant hetero- the probability that it also carries B? zygous for each of these alleles was crossed with a homozygous © Jones & Bartlett Learning, LLCrecessive plant, the progeny consisted© Jones of the following & Bartlett geno- Learning, LLC 4.2 What gametes, and inNOT what FORfrequencies, SALE are produced OR DISTRIBUTION types with the numbers of each indicated:NOT FOR SALE OR DISTRIBUTION by a female Drosophila of genotype A B / a b when the genes are present in the same chromosome and the frequency of Gl ra/gl ra 98 gl Ra/gl ra 91 recombination between the genes is 8 percent? What gametes, Gl Ra/gl ra 7 gl ra/gl ra 4 and in what frequencies, are produced by a male of the same Calculate the frequency of recombination between these genes. genotype? © Jones & Bartlett Learning, LLC 4.10 In the yellow-fever© Jones mosquito, & Bartlett Aedes aegyptiLearning,, a dominant LLC 4.3 ANOT cell undergoing FOR SALE meiosis ORin an DISTRIBUTIONorganism with unordered gene DDT for NOTDDT resistance FOR SALE(DDT is dichlorodiphenyltrichloOR DISTRIBUTION- tetrads undergoes a double crossover between two markers. roethane, a long-lasting insecticide) and a dominant gene Dl for If the ratio of 2-strand : 3-strand : 4-strand doubles is 1 : 2 : 1, Dieldrin resistance (Dieldrin is another long-lasting insecticide) what is the ratio of PD : TT : NPD tetrads? (PD stands for are known to be in the same chromosome. A cross was carried parental ditype tetrad, TT for tetratype, and NPD for nonparen- out between a DDT-resistant strain and a Dieldrin-resistant © Jones &tal ditype.)Bartlett Learning, LLC © Jonesstrain, and & Bartlettfemale progeny Learning, resistant to bothLLC insecticides were testcrossed with wildtype males. Among the progeny, 99 were NOT FOR4.4 SALE A coefficient OR DISTRIBUTION of coincidence of 0.36 implies which one or NOTresistant FOR toSALE both insecticides, OR DISTRIBUTION 88 were resistant to DDT only, 89 more of the following statements are true: were resistant to Dieldrin only, and 106 were sensitive to both (a) The frequency of double crossovers was 36 percent. insecticides. (b) The frequency of double crossovers was 36 percent of the (a) Are DDT and Dl alleles of the same gene? How can you tell? number that would be expected© Jones if there & were Bartlett no interference. Learning, LLC (b) Are DDT and Dl linked? © Jones & Bartlett Learning, LLC (c) There were 0.36 times as many single crossovers as double (c) What can you deduce about the genetic positions of DDT crossovers. NOT FOR SALE OR DISTRIBUTIONand Dl along the chromosome? NOT FOR SALE OR DISTRIBUTION (d) There were 0.36 times as many single crossovers in one region as there were in an adjacent region. 4.11 Two pure-breeding strains of mice are crossed to produce (e) There were 0.36 times as many parental as recombinant F1 mice that are heterozygous for three linked genes with alleles progeny. Aa, Bb, and Dd. Numerous triply heterozygous F1 mice are © Jones & Bartlett Learning, LLC testcrossed, and© theJones genotypes & Bartlettand numbers Learning, of the resulting LLC 4.5 A gene in Neurospora, a fungus with ordered tetrads, progeny are as follows: showsNOT 10% second-division FOR SALE segregation. OR DISTRIBUTION What is the map dis- NOT FOR SALE OR DISTRIBUTION A2 B2 D2 10 tance between the gene and the centromere? A2 B2 dd 350 4.6 In Drosophila pseudoobscura, the eye-color mutation A2 bb D2 100 purple (pr) and the wing mutation crossveinless (cv) are located A2 bb dd 40 aa B2 D2 60 © Jones &in chromosomeBartlett Learning, 3 at a distance LLCof 18 map units. What phe- © Jones & Bartlett Learning, LLC notypes, and in what proportions, would you expect in the aa B2 dd 120 NOT FORprogeny SALE from OR the DISTRIBUTION mating of pr+ cv+ / pr cv females with pr cv / NOT FOR SALEaa bb ORD 2DISTRIBUTION 320 pr cv males? Total 1000 (a) Which gene is in the middle? 4.7 Construct a genetic map of a chromosome from the (b) Specify the genotype of the F triple heterozygote as following recombination frequencies between individual pairs of 1 completely as possible, with the genes in the correct order and genes: r2c, 10; c2p, 12; p2r, 3; s2c, 16; s2r, 8. You will discover © Jones & Bartlett Learning, theLLC correct alleles on each chromosome.© Jones & Bartlett Learning, LLC that the distances are not strictly additive. Why aren’t they? NOT FOR SALE OR DISTRIBUTION (c) Which two genes are closest together?NOT FOR SALE OR DISTRIBUTION 4.8 A Drosophila cross is carried out with a female that is (d) What is the map distance between the two closest genes? heterozygous for both the y (yellow body) and bb (bobbed Assume that interference is complete between these two genes. bristles) mutations. Both genes are located in the X chromo- (e) If interference is not complete, how will the true map some. Among 200 male progeny, there were 49 wildtype for distance differ from the value you calculated in part (d)? Briefly both traits,© Jones 51 with &yellow Bartlett body, 41 Learning, with bobbed bristles, LLC and explain why this© Jonesis so. & Bartlett Learning, LLC 59 mutantNOT for FOR both genes. SALE Do theseOR genesDISTRIBUTION show evidence for 4.12 In corn,NOT the genes FOR v (virescent SALE seedlings), OR DISTRIBUTION pr (red aleu- linkage? [Note: The appropriate chi-square test is a test for a rone), and bm (brown midrib) are all on chromosome 5, but not 1 : 1 ratio of parental : recombinant gametes.] necessarily in the order given. The cross v1 pr bm/v pr1 bm 1 3 v pr bm/v pr bm © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Concepts in Action: Problems for Solution 149 4TH PAGES © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. © Jones & produBartlettces 1000 Learning, progeny with LLCthe following phenotypes: © Jones (c) Suggest& Bartlett a genetic Learning, hypothesis that LLC can explain the data in panel C. v1 pr bm 226 NOT FOR SALE OR DISTRIBUTION NOT FOR (d) Are SALE the data OR consistent DISTRIBUTION with your hypothesis? v pr1 bm1 229 v1 pr bm1 153 Number v pr1 bm 185 of each v1 pr1 bm 59 v pr bm1 71 1 1 © Jones1 & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC v pr bm 36 ABC 65 70 240 25 v pr NOTbm FOR SALE OR41 DISTRIBUTION NOT FOR SALE OR DISTRIBUTION (a) Determine the gene order, the recombination frequencies between adjacent genes, the coefficient of coincidence, and the interference. Phenotypes observed Phenotypes Phenotypes observed (b)© Explain Jones why, & in Bartlettthis example, Learning, the recombination LLC frequencies in population© Jones &of Bartlettparents inLearning, progeny LLC are not good estimates of map distance. NOT FOR SALE OR DISTRIBUTION 4.15 The NOTfollowing FOR classes SALE and frequencies OR DISTRIBUTION of ordered tetrads 4.13 The male I-2 in the accompanying pedigree is affected were obtained from the cross a1 b1 3 a b in Neurospora. (Only with Huntington disease, a type of neuromuscular degeneration one member of each pair of spores is shown.) What is the order caused by a rare autosomal dominant mutation HD with com- of the genes in relation to the centromere? plete penetrance. The wildtype, nonmutant allele is denoted hd. Spore pair © Jones & BartlettThe woman Learning,II-1 is also affected. LLC The RFLP alleles A and a © Jones & Bartlett Learning, LLC Number of yielding the bands in the gel are linked to the Huntington locus 1–2 3–4 5–6 7–8 asci NOT FOR SALEwith a recombination OR DISTRIBUTION frequency of 10 percent. NOT FOR SALE OR DISTRIBUTION a1 b1 a1 b1 a b a b 1766 (a) Is the genotype of II-1 HD A/hd a or is it HD a/hd A? a1 b1 a b a1 b1 a b 220 (b) Given the pattern of bands in the gel, what is the probability that III-1 will be affected? a1 b1 a b1 a1 b a b 14 (c) Given the pattern of bands in the gel, what is the probability © Jones & Bartlett Learning, LLC4.16 A portion of the linkage© map Jones of chromosome & Bartlett 2 in the Learning, LLC that III-2 will be affected? NOT FOR SALE OR DISTRIBUTIONtomato is illustrated here. The NOToblate phenotype FOR SALE is a flattened OR DISTRIBUTION I fruit, the peach phenotype is hairy fruit (like a peach), and com- 1 2 pound influorescence means clustered flowers. II o (oblate) ci (compound influorescence) p (peach) 1 2 © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC III 15 cM 20 cM NOT FOR SALE1 OR DISTRIBUTION2 NOT FOR SALE OR DISTRIBUTION Among 1000 gametes produced by a plant of genotype o ci 1/1 A 1 p, what types of gametes would be expected, and what number would be expected of each? Assume that the chromosome a interference across this region is 80 percent but that interference within each region is complete. © Jones & Bartlett4.14 A human Learning, geneticist discovers LLC the molecular variation in© Jones & Bartlett Learning, LLC 4.17 The yeast Saccharomyces cerevisiae has unordered tetrads. NOT FOR SALEDNA sequence OR DISTRIBUTION illustrated in the accompanying diagrams of NOT FOR SALE OR DISTRIBUTION In a cross carried out to study the linkage relationships among electrophoresis gels. In the human population as a whole, she three genes, the tetrads in the accompanying table were finds any of four phenotypes, shown in panel A. She believes obtained. The cross was between a strain of genotype 1 b c and that this may be a simple genetic polymorphism with three one of genotype a 1 1. alleles, like the ABO blood groups. There are two alleles that yield DNA fragments of© different Jones sizes, & fastBartlett (F) or slow Learning, (S) LLC (a) From these data determine© which, Jones if any, & of Bartlettthe genes are Learning, LLC migration, and a “null”NOT allele (FORO) in which SALE the DNA OR fragment DISTRIBUTION is linked. NOT FOR SALE OR DISTRIBUTION deleted. The genotypes in panel A would therefore be, from left (b) For any linked genes, determine the map distances. to right, FF or FO, SS or SO, FS, and OO. In the population as a Tetrad Genotypes of Number whole, the putative OO genotype is extremely common, and the type spores in tetrads of tetrads FS genotype is quite rare. To investigate this hypothesis further, 1 a 1 1 a 1 1 1 b c 1 b c 132 the geneticist studies offspring of matings between parents who 2 a b 1 a b 1 1 1 c 1 1 c 124 have© theJones putative & FS Bartlett genotype (panelLearning, B). The types LLC of progeny, © Jones & Bartlett Learning, LLC 3 a 1 1 a 1 c 1 b 1 1 b c 64 andNOT their numbers,FOR SALE are shown OR in panelDISTRIBUTION C. NOT FOR SALE OR DISTRIBUTION 4 a b 1 a b c 1 1 1 1 1 c 80 (a) What result would be expected from the three-allele Total 400 hypothesis? (b) Are the observed data consistent with this result? Why or why not? © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION 150 CHAPTER 4 Gene Linkage and Genetic Mapping 4TH PAGES © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. © Jones 4.18& Bartlett A small portion Learning, of the genetic LLC map of Neurospora crassa © Jones & Bartlett Learning, LLC chromosome VI is illustrated here. The cys-1 mutation blocks A A MOMENT TO THINK NOT FORcysteine SALE synthesis, OR DISTRIBUTION and the pan-2 mutation blocks pantothenic NOT FOR SALE OR DISTRIBUTION acid synthesis. Assuming complete chromosome interference, Answer to Problem: The coincidence is equal to the determine the expected frequencies of the following types of observed number of double crossovers divided by the expected number, but the observed and expected fre asci in a cross of cys-1 pan-2 3 CYS-1 PAN-2. quencies (proportions) can be used as well, because in the (a) First-division segregation© Jones of cys-1 and & first-divisionBartlett Learning, LLCconversion to frequencies, both numerator© Jones and & denominator Bartlett Learning, LLC are divided by the same number. Set r 5 0.32 and r 5 segregation of pan-2. NOT FOR SALE OR DISTRIBUTION NOT1 FOR SALE2 OR DISTRIBUTION (b) First-division segregation of cys-1 and second-division 0.25. We know that r1 includes the proportion of gametes with single recombination in region 1 (call this s ) plus the segregation of pan-2. 1 proportion of gametes with double recombination (call this d ). (c) Second-division segregation of cys-1 and first-division Hence r1 5 s1 1 d. Similarly, r2 5 s2 1 d, where s2 is the segregation of pan-2. proportion of gametes with single recombination in region 2. (d) Second-division segregation of cys-1 and second-division © Jones & Bartlett Learning, LLC In the two-point© Jonescross between & Bartlett w and r, the Learning, observed LLC segregation of pan-2. frequency of recombination, 0.45, equals s1 1 s2 because (e) ParentalNOT ditFORype, tetratype, SALE andOR nonparental DISTRIBUTION ditype tetrads. none of the doubleNOT recombinantsFOR SALE are detected.OR DISTRIBUTION Now we can solve for d because r1 1 r2 5 (s1 1 d ) 1 (s2 1 d ) 5 s1 1 s2 1

cys-1 pan-2 2d 5 0.57, whereas s1 1 s2 5 0.45. Subtracting, we obtain 2d 5 0.57 2 0.45 5 0.12, or d 5 0.06. This is the “observed” 7 cM 3 cM (inferred in this case) frequency of double recombinants. The

expected frequency of double recombinants equals r1 3 r2 5 © Jones &4.19 Bartlett The accompanying Learning, gel diagram LLC shows the positions of © Jones0.32 3 & 0.25 Bartlett 5 0.08. Thus Learning, the coincidence LLC across the region NOT FORDNA SALE bands OR associated DISTRIBUTION with the A, a and B, b allele pairs for NOT isFOR 0.06/0.08 SALE 5 0.75, OR and DISTRIBUTIONthe interference equals 1 2 0.75 5 two linked genes. On the left are the phenotypes of the parents, 0.25. In other words, there is about a 25% deficit in double recombinants from the frequency that would be expected and on the right are the phenotypes of the progeny and the with independence. number of each observed. Is the linkage phase of A and B in the doubly heterozygous parent coupling or repulsion? What is the frequency of recombination© betweenJones these & Bartlettgenes? Learning, LLC © Jones & Bartlett Learning, LLC NOT FORProgeny SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Parents 155 44 36 165 GENETICS on the web GeNETics on the Web will introduce you to some of the A a most important sites for finding genetics information on the © Jones & Bartlett Learning, LLC Internet. To© explore Jones these & sites, Bartlett visit the Learning, Jones & Bartlett LLC B companion site to accompany Essential Genetics: A Genomic NOTb FOR SALE OR DISTRIBUTION Perspective,NOT Sixth FOREdition ,SALE at http://biology.jbpub.com/ OR DISTRIBUTION Hartl/EssentialGenetics.

There you will find a chapter-by-chapter list of highlighted 4.20 Janet is performing a test cross to determine the linkage keywords. When you select one of the keywords, you will be relationships between three Drosophila genes, dpy, unc and dor. linked to a Web site containing information related to that © Jones &Her Bartlett entire grade Learning, depends on getting LLC this right! She testcrosses © Joneskeyword. & Bartlett Learning, LLC NOT FORfemales SALE heterozygous OR DISTRIBUTION for the recessive alleles: NOT FOR SALE OR DISTRIBUTION dpy (dumpy body) / dpy1 (normal body) unc (uncoordinated) / unc1 (coordinated) dor (deep orange eye) / dor1 (red eye). The cross yields the following© Jones results: & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC normal body, red eye, coordinatedNOT FOR SALE OR DISTRIBUTION75 NOT FOR SALE OR DISTRIBUTION normal body, red eye, uncoordinated 348 normal body, deep orange eye, uncoordinated 96 dumpy body, red eye, coordinated 110 dumpy body, deep orange eye, coordinated 306 dumpy© body, Jones deep orange& Bartlett eye, uncoordinated Learning, LLC 65 © Jones & Bartlett Learning, LLC (a) WhatNOT is the FOR genotype SALE of the OR F1 heterozygous DISTRIBUTION female? NOT FOR SALE OR DISTRIBUTION (b) Construct a map of the region indicating the order of the genes and the distances (in map units) between them. (c) What is the interference in this region?

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Concepts in Action: Problems for Solution 151 4TH PAGES © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION.