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Home , Chromoplast, Daylily

~1~ Summer 11 DJ Science

 ‘Pink Stripes’ (Derrow, 2006)  ‘Peppermint Ice’ (Lovell, 2004) — Photo courtesy of the hybridizer The unabridged version — Kyle Billadeau photo Genetics Part 3 Variegated or broken colors: Jumping ?

clonal and non-clonal patterns may be genet- some compound which affects pigmentation ic involving a change in DNA sequence or diffuses between cells By Maurice A. Dow, Ph.D. non-genetic. However, non-clonal patterns Region 4, Ontario, Canada are somewhat more likely to be environmen- Patterns help to identify possible causes Any characteristic can be variegated but tal or non-genetic. By looking at the patterns of pigmentation usually we think of variegated or flow- Clonal sectors (see glossary) can provide in individual cells we can get general clues ers and of differences in color. However, var- some information about when during devel- about the causes of the variegation. For iegation can be present in both and opment the event occurred. Large sectors example a pattern on the upper epidermis of and in any tissue and affect any char- indicate the event occurred early during a variegated flower or which is repeated acteristic. Variegation does not need to be development of the tissue or organ. Small and very similar to a pattern on its lower epi- obvious to the unaided human eye. It can be sectors indicate that the event occurred late dermis is unlikely to be genetic2. defined as any visible differences in the during development1. Few sectors indicate appearance or phenotype of the cells in a tis- that the event is infrequent or rare. Many Variegation can be genetic or non-genetic sue. The causes of variegation in are sectors indicate that the event is common. Finding that variegation is transmitted not known. Comparison to the causes of all The shape of a clonal sector is determined by from one generation to the next unfortunate- types of variegation found in any species may the location of the event and the time during ly does not necessarily indicate that the var- help explain those found in daylilies. development at which it occurred1. It pro- iegation is genetic. Variegation that is vides hints about how the tissue or organ induced by non-genetic factors can be trans- Clonal or non-clonal develops. mitted from parent to offspring3. A pheno- When we look at individual cells in a For more information about clonal analysis type, such as variegation, which is caused by flower or leaf and we measure the see http://www.jstor.org/stable/2443838. an environmental effect and which is identi- amount or concentration of pigment in each cal to a known genetically caused phenotype we find considerable variability. Some of Autonomous or Non-autonomous is called a phenocopy. this variability follows the same patterns as When the amount of pigment in a cell those of the cell divisions. We call those pat- depends only on the conditions in that cell, it Variegation can be Environmental terns clonal since cells are genetically identi- is autonomous. When the amount of pig- Variegation can be caused by environmen- cal, except in rare cases. Other times the vari- ment in a cell depends on conditions in the tal factors, for example, high temperatures ability does not follow the pat- surrounding cells, it is non-autonomous. A tern and these are non-clonal patterns. Both non-autonomous example would be when (See next page) ~2~ Glossary Allele – A variant of a . Alleles have one or more differ- ences in their DNA sequences. Natural genetic variation in populations is present as multiple alleles for most genes. An allele of a particular gene may have a very large effect on the phenotype, causing complete loss of the function of the gene or it may have a smaller effect or no effect on the phenotype. Few alleles will have large effects on a phenotype while most will have a small or no measurable effect. In a diploid individual each gene has two alle- les which may be the same or different. Angiosperm – species. In the gymnosperm, for example, coniferous trees, are predominantly inherited through the pollen parent. Chromoplast – A self-contained structure within a . Chromoplasts contain sufficient pigments to color the cell. Cytoplasmic genes – present in both the mitochondria and the plastids, small in cells. Mitochondria have 3 - 67 genes  ‘Doctor Strange Love’ (Cochenour, 2007) and plastids have 15 - 209 genes. The genes in these structures — Photo courtesy of the hybridizer show much less genetic variability than those in the nucleus. Dominant – The dominance component of a phenotype is the during growth and development. Mineral deficiencies due to environ- difference between the average of the two homozygous parental mental factors can cause symptoms which include variegation4. There phenotypes and that of the F1 offspring. When the dominance are mutations which affect the processing of the same minerals produc- component is exactly equal to the additive component the pheno- ing deficiencies with similar symptoms. As an example of the complex- type is completely dominant. When the dominance component is ities of variegation, in corn/maize (Zea mays) there is a stripes less than the additive component partial dominance is present or Mendelian (see glossary) mutation; iron deficiency can cause yellow the dominance is incomplete. When the dominance component is stripes; there is a yellow-stripe and there is a non-chromosomal zero the phenotype is perfectly additive. Few phenotypes will be (see glossary) stripe mutation. perfectly additive or completely dominant. At the molecular level of gene expression usually both alleles in a diploid will be Genetic mutations causing variegation expressed. can be located in any of three locations Expressivity – when individuals with the same genotype show Plant cells have genes in three different locations. Genes are present differences in some aspects of the phenotype this is known as vari- in the mitochondria. These are structures within cells associated with able expressivity. This can also occur when a genotype affects processes involving energy in the cell. Genes are present in plastids. structures in an individual that are produced in multiple copies Plastids are structures within cells associated with producing and stor- and these may show differences, for example, single and double ing the food manufactured by the cell. Genes are also present in the on the same plant. nucleus where they are packaged into . The genes in the Genotype – the sequence of the DNA making up the nuclear nucleus are described as Mendelian. Both the mitochondria and the genes of an individual. plastids reproduce within plant cells. Both also are typically primarily Heterozygous – in a diploid the presence of two different alle- transferred to the offspring through the seed parent (80% of angiosperm les for one gene, e.g. W/w individuals are heterozygous. The terms [see glossary] species)5. In a typical plant, such as a daylily, the plastids for a tetraploid are different. have about 110 to 120 genes, the mitochondria have about 50 genes Homozygous – in a diploid the presence of two identical alleles and the nucleus has about 40,000 genes8. Both the mitochondria and for one gene, e.g. both W/W and w/w individuals are homozygous. plastids require several thousand genes to function; nearly all of those Mendelian – Genes and their mutations which are similar in genes are present in the nucleus. The DNA in plastids and mitochon- inheritance to those studied by Gregor Mendel. These are found dria has been sequenced for a number of species and the identity and on the chromosomes in the nucleus of the cell. The inheritance of function of most of the genes has been analyzed. the phenotypes associated with these follow simple ratios, for Variegation can be caused by mutations in the mitochondrial genes, example 3:1 for dominant versus recessive phenotypes in the F2 the genes or the nuclear genes. In general, the number and generation. importance of each gene location is proportional to the number of genes Mutation – A change in the sequence of the DNA of a gene. present in that location. Most of the mutations which affect pigmenta- This results in a different allele. It may or may not result in a dif- tion, including variegation, occur in nuclear genes6. This is also true for ferent phenotype. Mutations may be selectively neutral and have the vast majority of the mutations which cause abnormally colored no measurable effect on a plant, or they may be deleterious and seedlings (e.g. white or albino)6. Perhaps even more interesting or con- lost by natural selection or be advantageous and increase by natu- fusing is that nuclear mutations are known that cause permanent non- ral selection to replace disadvantageous alleles. Some alleles may genetic changes in plastids and these can be inherited completely inde- form what are called balanced polymorphisms in which case two pendently of the original nuclear mutations and cause maternally (80% or more alleles have advantages and disadvantages in different cir- of the angiosperm species) transmitted variegation7. cumstances, none is consistently better and the alleles are main- (See next page) See Glossary, next page ~3~ cross-. Glossary Leaf Variegation A typical permanent (continued from page 2) Leaf variegation includes green versus change in plastids white or yellow sectors or as in Coleus leaves involves changes in tained in the population at intermediate frequencies. Mutations sectors of other colors such as red or purple. their , a with visible effects occur very rarely, roughly once in a million to It can have several different causes. The structure used for pro- once in a hundred thousand. same causes of leaf variegation may affect tein synthesis, or the Non-chromosomal – Genes and their mutations which do not flower, stem, etc., variegation, since loss of the ribosomes in follow Mendelian rules of inheritance and are not located on the these plant organs may contain one or more the plastids. This type chromosomes in the nucleus. They may be present in the mito- of various types of plastids e.g. proplastids, of variegation can chondria or in plastids. See also cytoplasmic genes. , , , chro- become independent Nuclear genes – present on the chromosomes in the nucleus. moplasts, etc at some times during their of the original nuclear They are what Mendel studied in his peas. There are approximate- development. Variegation which affects plas- genetic changes after ly 40,000 different genes in a typical diploid higher plant such as tids in organs other than the leaves will not specific types of cross- daylilies. They show a high level of genetic variability and affect all necessarily involve green colored sectors. pollinations. If the characteristics. Such variegation in might involve yel- original variegated Phenotype – the observed characteristics of an individual, for low, or versus white sectors or might plant is cross-pollinat- example, measured height or flower color. involve orange versus yellow sectors, etc. ed with a normal green – small structures within a cell. The mitochondria plant the F1 will be and plastids are examples of organelles. Variegation can be caused by genetically heterozy- Recessive – A phenotype that is completely masked by an alter- Simple (Mendelian) Nuclear Mutations gous for the typically native phenotype. In these cases, variegation appears when recessive variegation Sector – Part of a tissue or organ with an unexpected or differ- the plant has a specific genotype9. All cells in mutation and there- ent appearance. Each stripe of white in a leaf with green and white the plant have the same genotype. Whether fore not genetically stripes is a sector. In a flower with white petals showing splashes of a cell is green or not green is dependent on variegated. However, blue each splash is a sector. other non-genetic factors and some sort of at least some of the off- Somatic recombination – Cells which are genetically heterozy- threshold effect. Threshold effects are typi- spring may inherit the gous, e.g. A/a should produce two daughter cells which are genet- cally present whenever a characteristic is - permanently changed ically identical. However, sometimes during cell division the two egorized as being present or absent and the abnormal mitochon- chromosomes of a pair ‘break’ and are rejoined incorrectly. This assumption is that there is an underlying con- dria or plastids from can result in one daughter cell which is AA and the other daugh- tinuous factor. This type of variegation is not the seed parent and be ter cell which is aa and is called somatic recombination. When maternally transmitted. For variegation variegated. If one of both daughter cells survive to produce visible clonal sectors and which is completely recessive it will be pres- these variegated indi- the phenotype of AA cells is different from that of the Aa cells, vis- ent in the F1 generation of seedlings only if viduals is again cross- ibly obvious twin sectors are produced. the original variegated plant is self-pollinated pollinated with a nor- and self-compatible. If the plant is cross-pol- mal green individual then half of the iegation with any certainty. linated with pollen from a normal green plant seedlings will be homozygous normal. the seedlings of the F1 generation will not However, some of those individuals may have Variegation can be caused by show any variegation. The variegation will inherited abnormal organelles from their var- Mutations in the Organelles re-appear in the F2 generation of sibling iegated seed parent and be variegated them- Mutations in the genes within the mito- crosses of the normal green F1 seedlings. This selves. The variegation would then be inde- chondria or plastids can cause variegation by sort of variegation has not yet been identified pendent of the original Mendelian mutation. creating genetically and phenotypically dif- 12 in daylilies. These sorts of variegation have been found in ferent types of plastids , (e.g. green versus barley (four different genes), corn/maize (two white or yellowish). Often these genetic Variegation can be caused by Nuclear different genes) and Pennisetum. It has not changes involve the deletions of many genes Mutations with Permanent Non-Genetic yet been found in daylilies. from the organellesee glossary DNA. This Effects in Plastids type of variegation is inherited maternally The initial variegation which appears in Variegation can be caused by when organelles are inherited maternally and these cases is due to the nuclear genotype of Nuclear Mutations which change the not paternally or biparentally. the initial plant10. However, the mutation DNA in Organelles causes a permanent non-genetic change in This type of variegation follows the same Variegation can be caused by some of, either the mitochondria or the plas- pattern as when nuclear mutations cause per- Environmental Effects which make tids. This permanent change cannot be manent non-genetic changes in organelles11. Permanent Changes to Plastids repaired and is reproduced when the mito- It requires microscopic analysis, DNA Just as mutations can make permanent chondria or plastids divide. This type of var- sequencing and observations of the results of non-genetic changes to the plastids so can iegation can be maternally transmitted. It is various crosses to distinguish between these some environmental effects. For example, a also inherited as a normal Mendelian charac- two types of causes. In both cases, if the orig- plastid may lose its ribosomes because of teristic. For recessive mutations variegation inal plant showing the variegation is no extreme temperatures or because of the will appear in the F2 generation of sibling longer available it may not be possible to effects of various chemicals, such as antibi- 13,3 crosses of normal green F1 seedlings from determine the true original cause of the var- otics . Plastids without ribosomes can (See next page) ~4~ are active. Genes must be approximately 75-90% of the gametes on switched on and switched off at average; layer 1 is responsible for approxi- the correct times during devel- mately 10-25% of the gametes17. Layer 1 also opment in the flower bud before forms the epidermal layer in the petals and it opens. Since all cells in a plant . The epidermis contains the antho- are usually genetically identical cyanin pigments. Somatic mutations visible but phenotypically may differ, as sectors of changed cyanic color in petals the ultimate causes of the differ- and sepals can be inherited if they occurred ences in gene expression are early enough in the floral . We can non-genetic. In modern terms identify such mutations by a change in the  ‘Willy Nilly’ (Saxton,  ‘Willy Nilly’ (Saxton, developmental processes are pigments which appears to start at the base of 1963) 1963) considered epigenetics. petals or sepals. The larger such sectors are, — Jane M. Carson photo — Coral Kincaid photo Epigenetic effects have an ele- the earlier during flower development the Note the streak at a petal's edge in both flowers. ment of randomness in their mutation occurred and the more likely the occurrence which can result in mutation has affected some of the gametes. reproduce and cannot repair the loss. One variegation38. Some developmental changes A somatic mutation, visible as a colored might think that such chemical factors might can be transmitted through somatic cell divi- sector, that affects only a small fraction of one be unlikely in natural environments; that is sions (mitosis) and others can be transmitted petal is less likely to have affected tissues in not necessarily the case as some antibiotics through gamete production (meiosis). Such the or the pistil and less likely to be are produced by soil microorganisms14. Plant ‘inheritance’ does not necessarily follow present in any gametes. On the other hand, a cells are also capable of making antibiotic- Mendelian rules/ratios and may be inconsis- somatic mutation which affects at least part like compounds and these are known to tent39. of one and of one petal is more likely to cause effects similar to antibiotics15. Plants also affect the associated stamens and part of also produce -inactivating proteins Somatic mutations the pistil. Somatic mutations in plants can be in response to various stresses and infections. Mutations or sports can occur in any cell inherited18. If the phenotypes of appropriate- One current hypothesis is that albino plants within a plant. When mutations occur at any ly early and large sectors are found to be not may often be due to stress causing plants to time in cells which are part of the germ line inheritable, when tested in genetic crosses, produce these sorts of compounds, for exam- (the cell lineage which will produce the male this suggests that the variegation was non- ple, during micropropagation13 which then and female gametes) they can be inherited. genetic. act on their own cellular structures. Plastids When mutations occur in cells which are not without ribosomes may be very frequent in part of the germ line (the somatic lineage) Somatic Recombination variegated plants; for example, five variegat- they can be inherited if they occur early Sectors of a changed color have sometimes ed Pelargonium were examined and enough in an appropriate tissue layer in a been used to predict whether a plant is het- all were found to lack ribosomes in their meristem or growing point18. Plants, unlike erozygous for a mutation in a pigment deter- chloroplasts40. animals do not separate their germ line from mining gene. The assumption is that a somat- The inheritance of variegation can be very their somatic line until very late in develop- ic mutation in the remaining normal allele complex. This makes genetic analysis more ment. will produce a sector with the appropriate vis- than a simple case of finding a variegated In daylilies there are vegetative ibly altered color. However, phenotypically plant and crossing it as pod and pollen parent which later become inflorescence (or scape) different sectors may not be genetically differ- with a normal plant. Even if variegation in meristems, inflorescence branch meristems ent from the rest of the plant. Even if the sec- the offspring from such crosses indicates and floral meristems. In plants, somatic tor is genetically different from the rest of the maternal transmission, the involvement of a mutations in mature individuals can be plant the phenotype of the sector does not recessive nuclear gene in creating the original inherited, depending on when and where the necessarily provide information which helps variegation is not disproved. To test for that mutation occurred. This is the basis for the correctly determine the genotype of the possibility, the phenotypically normal inheritance of mutations produced when plant. seedlings from the normal X variegated cross seeds are treated with mutagenic chemicals Let’s look at an example. A plant has a red- need to be self-pollinated or sib-crossed to or radiation. This is also the basis for the use colored flower. On one petal there is a pink produce the F2 generation. Enough offspring of pollen from converted diploid cultivars sector on the normal red background. If we need to be grown to check for an approxi- with tetraploid cultivars as pod parents. know or assume that pink is recessive to red mately 3:1 segregation of normal to variegat- Treatment of the vegetative growing point then the appearance of the pink sector sug- ed offspring. Nor is leaf variegation that is not (shoot apical meristem or SAM) with various gests that the sector is homozygous for the nuclear/Mendelian necessarily due to chloro- chemicals (e.g. colchicine) produces somatic pink mutation. That conclusion is the basis plasts; changes in the mitochondria can changes in ploidy in the vegetative meristem for assuming that the plant is heterozygous cause leaf variegation16. that can be inherited when the meristem for the pink mutation. Unfortunately, becomes a reproductive meristem and even- although this may sometimes be the case it is Variable expressivity tually produces gametes. by no means necessary or likely. Mutations Variegation can be produced by develop- For more information about meristems see occur more or less at random. There is a low mental errors or problems. For example, in a http://www.public.iastate.edu/~bot.512/lec- probability that a new mutation, even in the plant genetically capable of producing antho- tures/SAM.htm appropriate gene will be the same and pro- cyanins, developmental processes control Daylily meristems have three tissue layers. when those genes are active and where they Cells derived from layer 2 ultimately form (See next page) ~5~ duce an identical mutant phenotype as the that the plant is heterozygous for the light red more consistent, for example, by reducing the previous mutation. In the above example, the mutation when in fact it is heterozygous for a range. Those changes result in what is called plant could be heterozygous for an allele white mutation at a different gene. canalization and developmental stability. which would cause a recessive white-colored There are situations in which a sector of a They affect the expression of the mutation. flower (null or knock-out mutation). The changed color occurs in a plant which is het- When individuals with a history of such new mutation, even if it is at the same gene, erozygous for a pigment mutation and the selection for a characteristic, for example could have produced a partially active prod- same mutation is homozygous in the sector. from a red-flowered species, population or uct and a pink appearance when associated In these cases recombination may have line – selection for stable uniform cyanic pig- with the white allele. The plant would be occurred in the somatic tissues and an origi- mentation) are crossed with those without heterozygous for the ‘white’ allele and het- nally heterozygous cell has produced one such a history for example from a yellow- erozygous for the ‘pink’ allele in the sector but daughter cell which is homozygous normal flowered species, population or line, the sta- actually heterozygous for the ‘white’ allele and one daughter cell which is homozygous bility will break down. Each individual off- elsewhere not heterozygous for a ‘pink’ allele mutant20. If the homozygous normal sector is spring of the crosses will be more variable in elsewhere as would be assumed because the phenotypically different from the heterozy- color; the amount of pigment in each cell will sector was pink. gous petal background then there will be two vary more widely, or the range in the amount There are other circumstances, in which a visibly different twin sectors. Twin sectors of pigment will be larger than in the parent. plant heterozygous for a mutation at one may not be visible as such if the mutation is They will also, on average, have a lower con- gene is apparently normal in appearance and completely recessive, in which case only the centration of pigment per cell than the a sector of a different color appears on a homozygous mutant sector is visibly obvious. parental populations since they are heterozy- petal. It might be assumed that the plant was Twin sectors will not occur when one of the gous. The combination of a lower average heterozygous for a particular flower color. daughter cells dies for any reason before amount of pigment in each cell with a wider However an apparently recessive mutation reproducing and thus does not create a clon- range in the amount of pigment in each cell may have occurred in a completely different al sector. Single sectors may also be pro- may result in patchiness or variegation in gene. Although the plant is now heterozy- duced20 when the recombination occurred color, for example, there may be more cells gous for mutations at two different genes and through somatic gene conversion rather than with no pigment. is expected to be normal in appearance it can somatic crossing over. Figure 1 provides an example of the mean actually be mutant. This can occur when the and variability in the amount of pigment per phenotypes of plants heterozygous for one Chimeras cell for one parent and one offspring individ- mutation are only apparently dominant (for Variegation can be produced in individuals ual from a cross of a yellow line with a red example, they produce 80% of the normal which are mixtures of two or more different line. amount of pigment and we cannot distin- cell types, whether those cell types are initial- Figure 1. The frequency distributions of the guish 80% from 100% with the unaided eye). ly caused by genetic or non-genetic factors, as amount of pigment per cell within individual A heterozygous individual at one gene with long as the different types are repro- 80% of the normal pigment which suffers a duced when the cells divide. These Figure 1 new mutation (heterozygous) at a different sorts of individuals are called mosaics gene that results in say 85% of the normal or chimeras. amount of pigment, will have only 68% (80% See reference 21 for a more X 85%) of the normal pigment and may now detailed discussion of chimeras. be visibly mutant19. The plant may have a mutant colored sector on a normal back- Developmental instability and ground but not be heterozygous at any specif- canalization ic gene for the mutant flower color. As an When a new mutation occurs its example a plant may be heterozygous for a effects on the phenotype are often mutation ‘a’ which causes white flowers when highly variable. For example, to the homozygous but red flowers when heterozy- unaided eye the amount of pigment gous. Plants which are Aa are red flowered in each cell of an apparently uni- and apparently identical to plants which are formly colored petal may vary widely AA to the unaided eye but actually produce when viewed with a microscope. The only 70% of the normal amount of pigment. amount of variability or the range in A somatic mutation occurs at another gene the amount of pigment in each cell, ‘r’ which also causes white flowers when is a measure of the developmental homozygous. Plants which are Rr are appar- stability of pigment production in ently identical to the unaided eye to plants each individual. Selection, both arti- which are RR and are red-flowered but pro- ficial by the hybridizer and natural duce only 80% of the normal pigment. The can act to make the phenotypic cells in the sector with the somatic mutation effects of the mutation more uniform and plants of a cross involving a developmentally sta- are Aa Rr. Those cells only produce 56% of also more resistant to environmental distur- ble red line with a developmentally stable yellow the normal amount of pigment (70% X 80%) bances. That is, selection will act to reduce line. The area under the curve colored green indi- and are light red. The observer sees a light the variability within each individual or to cates the total number of cells with no apparent red sector on a red background and assumes make the amounts of pigment in each cell pigment. The F1 will show variegated color. (See next page) ~6~ 3a) To create a new flwer first select the while the original remains in place and past- Virus Infection can cause Variegation appropriate parents. Deletion ed into a new location29 (a ). The story of broken flower colors caused by 3b) To create select the appropriate par- differ from one type of virus infections in tulips is well known. Cases ents. Deletion virus by only one gene30 and are thought to of virus infections causing variegated flower 4a) To create a new xflower first select the have evolved from that type of virus or vice colors are known from camellia22, abutilon23, appropriate parents. Insertion versa. Both transposons and retrotransposons and other plant species24. are known 4b) To create a new flower first select the are apparently able to move laterally between to infect daylilies and any new cases of bro- zopg appropriate parents. Insertion species31 somewhat like infections. ken flower color must be considered as 5a) To create a neww flower first select the Insertions, duplications and other muta- potentially caused by a virus infection. appropriate parents. Duplication tions can cause variegation due to gene Although, it should not be assumed that bro- 5b) To create a new flower first select select silencing32. Transposons can cause variega- ken flower color necessarily means a virus the appropriate parents. Duplication tion due to genetic changes (clonal sectors), infection is present, plant pathologists do 6a) To create a new flower first tceles the for example, when they excise from a gene. consider flower color breaking as a good diag- appropriate parents. Inversion Transposons, retrotransposons, viruses and nostic feature of virus infection25. 6b) To create a new flower etairporppa eht some mutations are similar enough that The patterns created by virus infection can tceles tsrif parents. Inversion plants react to them with similar mecha- be very similar to those created by several dif- 7) To create a new [cut this & paste else- nisms. This can make it next to impossible to ferent genetic causes. The symptoms of infec- where] flower first select the appropriate par- distinguish between the causes of variegation tion can vary from no visibly obvious abnor- ents. Transposon outside of a molecular genetics laboratory. mal effects (‘symptomless’, although poten- 8) To create a new [copy this & paste else- The important difference between a trans- tially with effects on growth, height, yield, where] flower first select the appropriate par- poson and other insertion mutations is that a etc.) to plant death and will depend on the ents. Retrotransposon transposon can be removed from the gene in both the genotype of the virus and of the cul- which it is inserted. A mutation which has tivar25. For example, all Easter lilies are prob- A mutation may have no effect on the been created by the insertion of a transposon ably virus infected26. Viruses can become function of the gene, or the effect may vary is not necessarily a permanent mutation. integrated into chromosomes and be inherit- from slight to completely destroying the Such mutations are described as unstable or ed27. Some viruses can be transmitted entire gene’s function (e.g. a knock-out mutable. This creates a pattern in the expect- through seed or pollen and passed to off- mutation). The same gene may have some ed changes in phenotype (variegation) when spring25. It is not simple to determine recessive mutations and some dominant an active transposon is involved. The pattern whether a new case of broken flower color is mutations, although the majority of new is a distinguishing and a somewhat diagnostic caused by a virus infection and it requires lab- mutations are more or less recessive. Most feature of transposon insertions and their oratory testing to be confident about whether new mutations cause a loss of function; a few excision. any viruses are present or not. cause a gain in function. The average gene28 has approximately the equivalent of 1350 Variegation Patterns caused Different types of Nuclear (Mendelian) ‘letters’ which code for 450 ‘words’ using the by Transposons Mutations can cause Variegation sentence analogy from above. Mutations can We begin with a normal gene functioning Variegation can be caused by mutations, occur at any of the ‘letters’ approximately in to produce its normal product – the wild-type inherited equally from both the pod and a random manner. The effect a mutation has phenotype. The transposon, which typically pollen parent9. There are many different on the function of the gene is determined by is a large piece of DNA, becomes inserted types of mutations which change the DNA where in the gene the mutation occurs and into the gene. It disrupts the gene’s function sequence of the genes. Simple English sen- the type and characteristics of the mutation. causing a mutation. The mutation may tences can be used as an analogy to illustrate become homozygous by appropriate crosses. these mutation types. In the following exam- Active Transposons (Jumping Genes) This causes a change in phenotype from wild- ples, sentence 1 is the equivalent of one nor- can cause Variegation type to mutant as most mutations are reces- mal gene and each letter is part of the One particular type of mutation, an inser- sive21. When, occasionally, the transposon is sequence of instructions coded in the DNA tion, occurs when a piece of extraneous cut out of the gene in a particular cell then of the gene. Sentences 2 to 8 are examples of DNA is inserted into a gene. Sometimes the there is a chance that the gene returns to its particular types of mutations. piece of inserted DNA is large and contains normal function, for example, when the complete gene sequences. When a large entire transposon is removed. The phenotype 1) To create a new flower first select the piece of DNA is inserted into a gene the will no longer be mutant in all the descen- appropriate parents. Normal or wild- usual result is a knock-out mutation and the dents of that original cell. Their phenotype type gene no longer functions at all. will be normal or near-normal. This is called 2a) To creyte a new flower first select the One specific type of insertion is called a a reversion. A clonal sector will be created appropriate parents. Point mutation popularly known as a with the normal phenotype. Since the trans- 2b) To cremte a new flower first select the ‘jumping gene’. Transposable elements are poson is not excised from all cells, some of the appropriate parents. Point mutation able to move or transpose about the DNA in cells will have the original mutant phenotype 2c) To preate a new flower first select the a cell. Transposable elements can be cut out while others will have the reverted pheno- appropriate parents. Point mutation from their current location and pasted into a type. Once the transposon has been cut from 2d) To create a new flower lirst select the new location (a transposon) or they can be the gene it may be lost or it may be inserted appropriate parents. Point mutation simply copied from their current location into any gene. This causes a new somatic (See next page) ~7~ mutation in some characteristic although it transposon might excise in pollen mother active transposons. In plants, when geneti- will not be obviously visible since it will be cells directly in germ line tissues which do not cists do not have active transposons in a par- heterozygous. produce but do produce the ticular species they transfer active trans- The expected pattern that is present in the pollen. posons from other species. Thus plant species vast majority of transposon-based variega- are not thoroughly surveyed for active trans- tion, is for the basic characteristic of the plant Distinguishing Types of Sectoring Patterns posons. Much of genetics research in one to be mutant with sectors of reverted normal For tentative identification of transposon species is directly applicable to other species or near normal appearance. Since most based variegation one would look for sectors – that is one reason why particular species mutations are recessive this can also be of a dominant phenotype on a recessive phe- have been chosen for specific types of genet- described as sectors of the dominant pheno- notype background or sectors of near normal ics research. One of the best genetically type on a recessive phenotypic background. phenotype (wild-type) on mutant back- researched group of species are mammals, For those studying variegation without grounds. Usually this is fairly easy to do, for including humans. Geneticists have searched molecular genetic techniques this is one of example, in daylilies a pattern of reddish sec- very hard to find active transposons in mam- the basic rules to help identify potential tors on a whitish or yellowish background fits mals but have been unable to find any cur- transposon-based variegation33. These sorts the expected pattern. However, the frequen- rently active37 transposons. As has been typ- of variegation are genetic, and clonal. cy and size of sectors differs among different ically found in other species, there is evi- Typically the phenotype of the sectors is types of transposons. Some may excise very dence that active transposons were once autonomous but this depends on the normal early in development and create large sectors. present but they were inactivated in the dis- characteristics of the gene in which the inser- Some may excise very frequently and create tant prehistoric past. Variegation in mammals tion occurred. many sectors. Sometimes, there may be so cannot be caused by active transposons. Just Transposons are one of many factors which many and such large sectors that they may as active transposons are absent from some can cause mutations. In homozygous mutant overlap and create the appearance of sectors species, such as mammals, one cannot individuals with active transposons the occa- of a recessive pheno- sional excision of the transposon causes type on a dominant A Figure 2 somatic mutations which may be visible as phenotype back- variegation. Some of the somatic mutations ground. Such sector- The flowers of morning glory show- are complete reversions back to the normal ing is most likely pro- ing broken colors due to different wild-type but others may only be partial duced by non-trans- causes. reversions and have phenotypes which differ poson based causes. A) Variegation due to the excision of from both the normal and the mutant. For However, to help dis- a transposon. The colored sectors example, if the normal is red-flowered and tinguish between the show where the transposon has been the transposon based mutation is to white- causes one would cut out of the gene in which it was located. The cells in the flowered, a homozygous mutant individual need to know the colored sectors are genetically different from those in the would have white flowers with red sectors. parentage of the phe- uncolored sectors. Sometimes a sector might be light red or notypically mutable B), C) and D) Non-clonal variegation due to three different pink, etc. Red sectors would be complete or variegated individ- types of gene silencing. The cells in the darker colored sectors reversions; light red or pink sectors would be ual and one might are genetically identical to those in the lighter colored sectors. examples of partial reversions. In both cases have to carefully of reversions the affected gene would no examine many sec- B C D longer contain the transposon and the phe- tored tissues looking notype would be stable. Somatic mutations in for the rare occur- plants can be inherited18. It is possible to pro- rence of few and small duce individuals, by appropriate crosses, with sectors. the stable partially reverted phenotypes and corresponding genotypes (in the example, Transposons are not individuals with stable completely light red or always active Figure 1 A, B, C and D reproduced with permission from The Science of edited by pink flowers). Although muta- E. Grotewold, 2006, Springer, New York. The mutations caused by transposons can tions due to trans- be inherited in two different ways. posons are not initially stable when they first assume that active transposons are present in Transposons may excise in tissues which per- appear, they can become permanently stable daylilies. We cannot simply assume that var- mit visibly obvious phenotypes to appear, when the transposon is inactivated. iegation in daylilies is caused by active trans- such as variegation in anthocyanin pigments Transposons are inactivated by mutations posons. in the epidermis of flower petals. Those which occur within the transposon sequence somatic mutations which occur early enough or by epigenetic processes. Mutations can Gene Silencing to be present in a meristem of any sort can be also become permanently stable if the trans- Variegation can be caused by gene silenc- inherited in the same manner as any poson leaves a small portion of DNA in the ing38. Gene silencing occurs when the chimeric ‘sport’ can be inherited. gene when it is excised. expression of a gene is interrupted or sup- Transposons may also independently excise Most species do not have currently active pressed and is an epigenetic effect. Some in any tissue without visibly obvious pheno- transposons. Most individuals of those viruses affect gene expression, for example, types appearing. For example, an active species with active transposons do not have producing broken flower color. Geneticists (See next page) ~8~ use deliberate virus infections to learn how consistent spotted or similar type patterns. Van de Peer, (2007). How many genes are differences in gene expression may affect par- Transposons are not implicated in the causes there in plants (… and why are they there)? ticular phenotypes. of spots or dots, etc. in plant species in which Current Opinion in Plant Biology 10: 199- Infections caused by certain viruses can all or almost all individuals are spotted. For 203. induce gene silencing where none was pres- example, the genetic basis for patterns such ent before. Infections caused by other viruses as the dots or spots in has not been 9) Dominic Rosso, Rainer Bode, Wenze Li, can turn-off gene silencing when it was pre- completely defined but current research indi- Marianna Krol, Diego Saccon, Shelly Wang, viously present. These sorts of epigenetic cates that they are not due to transposons36. Lori A. Schillaci, Steven R. Rodermel, Denis effects may show random differences P. Maxwell, and Norman P.A. 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If an individual heterozygous for such a silencing of chalcone synthase in petunia iojap (ij), a pattern striping gene of maize The dominant white mutation is infected with a using a geminivirus-based episomal vector. EMBO Journal 11: 4037-4046. virus capable of switching-off gene silencing The Plant Journal 15: 593–604. the result is variegation with white and pig- Richard Jorgensen, The germinal inheri- 11) J. M. Martinez-Zapater, P. Gil, J. Capel mented sectoring34. tance of epigenetic information in plants. and C. R. Somerville (1992) Mutations at Another phenotype with an epigenetic (1993) Phil. Trans. R. Soc. Lond. B 339: 173- the Arabidopsis CHM Locus Promote component is the star pigmentation pattern 181. Rearrangements of the Mitochondrial in petunia flowers. If an individual with a Que, Q., H.-Y. Wang, and R.A. Jorgensen. . The Plant Cell, 4: 889-899. star-type pattern is infected with a virus (1998). 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36) Masumi Yamagishi (2010) Oriental hybrid lily Sorbonne homologue of LhMYB12 regulates anthocyanin biosynthe- ses in flower and spots Mol Breeding DOI: 10.1007/s11032-010-9490-5.

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