Molecular Mapping, Chromosomal Assignment, and Genetic Diversity Analysis of Phytochrome Loci in Barley (Hordeum Vulgare)

Molecular Mapping, Chromosomal Assignment, and Genetic Diversity Analysis of Phytochrome Loci in Barley (Hordeum vulgare)

R. M. Biyashev, R. A. Ragab, P. J. Maughan, and M.A. Saghai Maroof

Phytochromes belong to a family of photoreceptors that perceive, interpret, and translate light signals that effect plant growth and development The objectives of Downloaded from https://academic.oup.com/jhered/article/88/1/21/2186575 by guest on 23 September 2021 this study were to use a heterologous phytochrome cDNA probe from oat to (1) identify phytochrome loci in barley, (2) determine the chromosomal and genomlc location of phytochrome gene(s) in barley, and (3) assess the extent of genetic variation at phytochrome loci In cultivated barley (Hordeum vulgare). Restriction fragment length polymorphism (RFLP) analysis detected four distinct phytochrome loci In barley, arbitrarily designated phyl, phy2, phy3, and phy4. Wheat-barley addition line analysis Indicated that phyl, phy2, and phy3 are located on barley chromosomes 7, 4, and 5, respectively, while phy4 represents duplicate loci located on barley chromosomes 2 and 7. Linkage mapping confirmed our results using wheat- barley addition line analysis and located the phyl and phy3 loci to the short arm of barley chromosome 7 and to the centromeric region of barley chromosome 5, respectively. Two to three alleles were detected at each of the five phytochrome loci examined. Genetic diversity values for the phytochrome loci were near previous estimates for RFLPs. Division of the barley samples based on spike morphology indicated that the level of diversity in two- and six-rowed barley is about equal, although significant differences in allellc frequencies were detected between the subgroups.

Light is a critical environmental factor in- ity of the two forms functions as a switch fluencing plant growth and development. that regulates gene expression (Quail Light provides the radiant energy neces- 1991). The exact molecular nature by sary for photosynthesis and is the pri- which phytochromes regulate signal path- mary stimulus for many changes in plant ways and gene expression is not known. growth patterns and developmental However, photoregulation by phytochro- events, such as leaf primordia formation, mes has been implicated in the expression plastid development, shade avoidance, of a number of nuclear genes, Including and flowering induction (Sage 1992). Per- the small subunit of rlbulosebisphosphate ception and interpretation of light stimuli carboxylase and chlorophyll a/b binding are modulated by several endogenous protein (Silverthorne and Tobin 1984), photoreceptors, including phytochromes protochlorophyllide reductase (Apel 1981), (red and far-red light receptors), blue light ribosomal RNA (Thien and Schopfer receptors, ultraviolet-A receptor(s), and 1982), and several unidentified mRNAs ultraviolet-B receptor(s). Of the different (Thompson et al. 1983). photoreceptor systems, the phytochro- Multiple phytochrome genes have been mes are the best characterized (Furuya identified, sequenced, and compared for 1993; Quail et al. 1995). several plant species using recombinant Phytochromes are cytosolically local- DNA technology [reviewed by Quail (1991) ized dimers composed of two polypep- and Quail et al. (1995)]. Complete phyto- tides, each containing a covalently at- chrome ami no acid sequences have been From the Department of Crop and Soil Environmental tached tetrapyrrole chromophore. The isolated from a variety of plant species, in- Sciences, Virginia Polytechnic Institute and State Uni- cluding oat, zucchini, pea, rice, and com. versity, Blacksburg, VA 24601. This research was sup- photosensory capacity of the molecule is ported In part by grants from the North American Bar- derived from its ability to exist in two Recently, Clack et al. (1994) and Sharrock ley Genome Mapping Project, VS. Department of Agri- known forms that are reversibly intercon- and Quail (1989) reported the isolation of culture NRI (93-3730f>8840), and the Rockefeller Foun- dation. R. A. Ragab Is a recipient of a postdoctoral vertible by red and far-red light: the red- five structurally distinct but related phy- fellowship from the Rockefeller Foundation. absorbing (Pr) form, and the far-red ab- tochrome genes from Ambidopsis, which Journal of Heredity 1997:88:21-26; 0022-1503/97/15.00 sorbing (Pfr) form. Photointerconvertibil- they designated as PhyA, PhyB, PhyQ

21 PhyD, and PhyE. Analytical investigations cessions of cultivated barley (H. uulgare) the phytochrome loci were then combined of these phytochrome variants suggested representing all major barley growing ar- with the existing linkage data for the Step- that each phytochrome type has a spe- eas of the world. toe X Morex cross (Kleinhofs et al. 1993). cialized photosensory function, which Linkage analysis was performed using the may explain the diversity of responses at- RFLP Analysis computer program MapMaker 3.0b (Land- tributed to the phytochrome system DNA isolation and RFLP procedures were er et al. 1987) at LOD = 4.0, with a maxi- (Quail et aJ. 1995). as described by Saghai Maroof et al. mum Haldane distance of 50 cM. Despite significant biochemical, physio- (1984) and Zhang et al. (1993). An initial Diversity values (h) for each phytochro- logical, and molecular research efforts, in- screening of a subset of barley lines was me locus were calculated using the genie formation on the genomic location and ge- used to determine which restriction en- diversity index, h = 1 - Zp,2, where p, is netic diversity of the phytochrome zyme detected the highest level of poly- the frequency of the fth allele. Since the gene(s) in agronomic crops is limited. To morphism. Briefly, 8 (j.g of barley DNA was total sample of barley accessions can be date, the chromosomal location of only digested with each of six restriction en- divided between two groups based on the phytochrome PhyA locus has been zymes (Mndlll, £coRV, Xba\, Dral, Sst\, and spike morphology (two- or six-rowed), the identified in wheat and rice (Causse et al. £coRI) and electrophoresed on 0.8% aga- diversity values for the total sample were 1994; Ogihara et al. 1994). In this article rose gels, followed by standard Southern further partitioned into their respective Downloaded from https://academic.oup.com/jhered/article/88/1/21/2186575 by guest on 23 September 2021 we used a heterologous phytochrome transfer to nylon membranes. Blots were components as described by Nel (1973), cDNA probe from oat to (1) identify mul- hybridized overnight with a randomly HT = Hw + GJT, where HT is the total di- tiple phytochrome loci in barley, (2) de- primed ^-dCTP-labeled phytochrome probe versity, //w is the within-group diversity termine the chromosomal and genomic lo- (see following section). Following hybrid- component, and G^ is the between-group cation of phytochrome gene(s) in barley ization, blots were washed three times, differentiation. using linkage analysis and wheat-barley twice for 5 min at room temperature with chromosome addition lines, and (3) as- IX SSC and 0.1% SDS and once for 15 min sess the extent of genetic variation at phy- at 65°C with 0.5 x SSC and 0.1% SDS. After Results tochrome loci in cultivated barley (Hor- washing, blots were covered with plastic Chromosomal Assignment of deum uulgare). wrap and exposed to X-ray film for 7-10 Phytochrome Loci in Barley Using days. The restriction enzyme Xbal detect- Wheat-Barley Addition Lines ed the highest level of variation among the RFLP analysis using the phytochrome Materials and Methods barley lines, and was therefore used to probe detected four distinct DNA frag- Genetic Materials evaluate the level of genetic diversity ments (Figure 1). Initial mapping of the Three sets of genetic materials were stud- among all 96 barley accessions at the phy- these four fragments by wheat-barley ad- ied in this experiment. The first set of ma- tochrome loci. dition lines analysis unambiguously as- terials was a barley mapping population signed each of these DNA fragments to consisting of 138 double haploid (DH) Phytochrome Clone separate barley chromosomes, indicating lines developed from the a cross between The oat cDNA phytochrome clone utilized that each of these DNA fragments repre- the barley cultivars Steptoe and Morex. in this experiment was kindly donated by sents a distinct barley phytochrome locus. The mapping population used in this ex- S. Kay (University of Virginia) and has Hence, we will refer to each fragment as a periment has a well-developed molecular been fully described by Hershey et al. specific phytochrome locus and label map consisting of 434 molecular markers, (1984). The phytochrome probe was pre- them phyl, phy2, phy3, and phy4, where spanning 1430 cM, and is one of the prin- pared by digesting the cDNA clone with phyl represents the largest restriction cipal mapping populations of the North the restriction enzymes Kpnl and SsA, fragment detected and phy4 represents American Barley Genome Mapping Project which yielded a 3.0 kbp fragment repre- the smallest restriction fragment detected. (Kleinhofs et al. 1993). The second set in- senting the phytochrome coding region. Figure 1 shows the RFLP banding pattern cluded a series of wheat-barley chromo- This fragment was purified from agarose produced in the wheat-barley addition line some addition lines (Islam 1983). These gel slices and labeled with ^P-dCTP by a analysis when probed with the phytochro- materials included a barley cultivar (Betz- random primer protocol (Feinberg and Vo- me probe. The barley parent of the addi- es), a wheat cultivar (Chinese Spring), and gelstein 1983). Since multiple phytochro- tion lines (Betzes, lane 8) shows four dis- six addition lines representing chromo- me loci were detected with this probe, tinct DNA fragments (phyl, phy2, phy3, somes 1, 2, 3, 4, 6, and 7 of barley. Each each phytochrome locus was arbitrarily and phyf), and is completely different addition line contains the 21 pairs of designated with an arabic numeral corre- from the banding pattern observed in the wheat chromosomes from Chinese Spring sponding to the decreasing size of the re- wheat parent (Chinese Spring, lane 1). plus one pair of barley chromosomes from striction fragment containing each phyto- Analysis of the wheat-barley addition lines the barley cultivar Betzes. The wheat-bar- chrome locus (e.g., phyl > phy2 > phy3 > (lanes 2-7) show that the phyl and phy2 ley addition lines were used to confirm the phy4; see also Figure 1). loci are located on barley chromosome 7 chromosomal location of phytochrome (lane 7) and 4 (lane 5), respectively. Two loci and to determine chromosomal loca- Data Analysis bands corresponding to the phy4 fragment were detected on barley chromosomes 2 tions of phytochrome loci that did not seg- Segregation ratios for each polymorphic (lane 3) and 7 (lane 7), suggesting that the regate between the parents of the map- phytochrome locus in the double haploid phy4 gene is represented as a duplicate lo- ping population. The third set of genetic barley population were tested for good- cus in the barley genome. None of the six materials was used to determine genetic ness-of-fit to an expected 1:1 genotypic ra- wheat-barley addition lines showed a cor- diversity levels at phytochrome loci; this tio using the computer program linkage-1 responding band for the phy3 locus. Since was composed of a broad sample of 96 ac- (Suiter et al. 1983). Segregation data for

22 The Journal of Heretfity 1997.88(1) 3 4 5 6 7 8 somes 2 and 7 of barley (Figure 1, Table

Linkage Analysis of Phytochrome Loci The linkage relationships for two of the four phytochrome loci were determined using segregation data for 434 molecular marker loci from a double haploid mapping population. The parents of the mapping population (Steptoe and Morex) differed in phytochrome alleles for only two (phyl and phyJ) of the four phytochrome loci (Figure 2). Chi-square tests revealed that the segregation of the phy3 locus fit

the expected 1:1 segregation ratio, while Downloaded from https://academic.oup.com/jhered/article/88/1/21/2186575 by guest on 23 September 2021 the phyl locus deviated significantly from the expected 1:1 ratio (chi-square values were 8.83 and 0.26 for phyl and phy3, respectively). Interestingly, Causse et al. (1994) reported significant distortion of several molecular marker loci mapping near a phytochrome (PhyA) locus on rice chromosome 3 and suggested that the segregation distortion observed in this genomic region in rice may be associated with the presence of a closely linked genetic factor(s) regulating fertility. Whether a similar genetic phenomenon is affecting the segregation of this phytochrome locus in barley is not known. Linkage analysis located the phytochrome locus phyl to the short arm of barley chromosome 7 at 21.6 cM from marker ABG316B and 10.1 cM from ABG705 (Fig- ure 2). Phytochrome locus phy3 mapped near the centromeric region on the long arm of barley chromosome 5, 9.2 cM from Figure 1. The RFLP banding pattern for wheat (lane 1; Chinese Spring), barley (lane 8; Betzes), and wheat-barley marker ABC 160 and 11.3 cM from ABG464 addition lines 1, 2, 3, 4, 6, and 7 (lanes 2-7) used to map phytochrome loci to barley chromosomes using wheat- (Figure 2). The genetic mapping of phyl barley addition line analysis. The letters a, b, c, and d Indicate the positions of the lour phytochrome loci, phyl. and phy3 to barley chromosomes 7 and 5, phy2, phy3, and phy4, respectively. respectively, confirmed the inferences ob- tained from wheat-barley addition lines. the wheat-barley addition line that carries addition lines analysis indicates that phy- The map location of these two phytochro- barley chromosome 5 is sterile and is not tochrome loci phyl, phy2, and phy3 are lo- me loci are of particular interest because represented in the analysis, we infer that cated on chromosomes 7,4, and 5, respec- both loci are positioned in relatively large the phy3 locus is located on barley chro- tively, while phy4 represents a duplicate gaps within the barley molecular map mosome 5. In summary, the wheat-barley locus presumably located on chromo- (Figure 2). For example, previous to the

Table 1. Sample size, number of alleles, diversity values, and differentiation component for each locus In the total sample and In each subgroup of calUvated barley

Spike morphology Total sample Two-rowed group Six-rowed group Chromo- some No. of No. of No. of Locus location* alleles Diversity alleles Diversity alleles Diversity

Phyl 7 3 0.573 67 2 0.308 21 3 0.628 46 45 Phy2 4 2 0.366 83 2 0.497 26 2 0.188 57 8.0 phy3 3- 3 0.549 S3 3 0560 27 3 0523 56 1.4 phy4 2.7 2 0.323 89 2 0500 24 2 0.123 61 82

• Chromosomal locations were determined by wheat-barley addition line analysis and/or linkage analysis. * Differentiation component between the two- and six-rowed barley groups. ' Only those samples that could be scored unambiguously were used in the diversity analysis.

Biyashev et al • Phytoctvome Loci in Barley 23 123456789 10 11 me gene family in Arabidopsis that con- sists of at least five structurally related phytochrome genes (PhyA, PhyB, PhyC, PhyD, and PhyE). Quail et al. (1995) suggested that the large diversity of responses attributed to the phytochrome system is the result of photosensory spe- cialization of individual phytochrome variants. Indeed, photomorphogenic mutant analysis indicates that phytochromes PhyA and PhyB have contrasting and specific photosensory functions in controlling hypocotyl elongation in etiolated Arabi- dopsis seedlings (Dehesh et al. 1993; McCormac et al. 1993). While the identification of five distinct Downloaded from https://academic.oup.com/jhered/article/88/1/21/2186575 by guest on 23 September 2021 ••*»••. phytochrome loci in barley supports the c conclusion that phytochrome genes are m t» encoded as small multigene families in higher plants, the photosensory special- ization of these particular loci in barley is d not known. Equally unclear is the relationship among the barley phytochrome loci and the phytochrome loci identified in Ar- abidopsis (which has become the model Figure 2. Segregation patterns for two phytochrome loci phyl and phy3 (labeled a and c, respectively) In 11 DH system for the study of photoreceptors in lines. Phytochrome loci phy2 (labeled b) and phyt (labeled d) are not polymorphic In this cross higher plants) and other plant species. In- terestingly, however, since several specific positioning of phyl, the molecular map of the phytochrome loci between the groups, homologous chromosomes are conserved barley contained a 31.7 cM gap on chro- the overall difference was not significant among barley, wheat, and rice (Kurata et mosome 7. After the addition of phyto- and is largely the result of different sample al. 1994; Saghai Maroof et al. 1996), and chrome locus phyl the size of this gap has sizes between the groups. However, parti- since previous genetic mapping has local- been reduced to 21.6 cM. tioning of the barley accessions showed ized a phytochrome locus {PhyA) to wheat that the frequency of the alleles at specific chromosome 4 (Ogihara et al. 1994) and Genetic Diversity phytochrome loci differed dramatically two phytochrome loci (Phya and Phyb) to Ninety-six accessions of cultivated barley between the two subgroups. For example, rice chromosome 3 (Causse et al. 1994; Lin were assayed for genetic diversity at each the most frequent allele (number 2) de- et al. 1995), one might infer that the barley phytochrome locus. Polymorphism was tected at the phy2 locus (P = .54) in the phytochrome phy2 locus on barley chro- detected at all four phytochrome loci. two-rowed group was rarely observed (P mosome 4 represents a homolog of one of Three distinct allelic variants were detect- = .11) In the six-rowed barley group. The these phytochrome loci, based solely on ed for phytochrome loci phyl and phy3, Gsr statistic, which measures the amount chromosomal homologies among these while two variants were detected for phy- of differentiation between groups, had an grass species (barley chromosome 4, tochromes phy2 and phy4 among all the average value of 5.53%, ranging from 1.4% wheat chromosome 4, and rice chromo- barley accessions examined. The predom- at the phy3 locus to 8.2% at the phy2 locus some 3 are homologous chromosomes). inant allele for phyl, phy2, phy3, and phy4 (Table 1). An equally intriguing observation is the had frequencies of 0.55, 0.57, 0.60, and similarity In the chromosomal location of 0.64, respectively. A total of 10 alleles were the phytochrome phy3 locus and a major observed in the entire sample of 96 barley Discussion photoperiod response gene {Ppd3) in barley (Blake T, personal communication). accessions for all four phytochrome loci. We used a heterologous phytochrome The phytochrome phy3 locus maps to a Phytochrome locus phyl exhibited the cDNA probe from oat to detect five barley genomic region of chromosome 5 flanked highest level of genie diversity (0.57) fol- phytochrome loci, arbitrarily designated by the same RFLP markers as the photo- lowed by the phy3 locus (0.55), while phy2 as phyl, phy2, phy3, and phy4 (duplicate period response gene Ppd3 (Blake T, per- and phy4 showed the lowest diversity val- locus). The identification of five phyto- sonal commincatlon). A more detailed ues (0.37 and 0.32, respectively, Table 1). chrome loci suggests that phytochrome is mapping study will be necessary to deter- The 96 accessions of cultivated barley represented as a small multigene family in mine the exact genetic relationship be- can be partitioned into two groups on the barley. This is consistent with previous tween this phytochrome locus (phyS) and basis of the possession of two- or six- studies by Hershey et al. (1985) who re- the photoperiod response gene Ppd3 and rowed spikes. The number of alleles and ported the existence of a small family of to determine the relationships among the diversity values calculated for each barley at least four phytochrome genes in oat phytochrome loci identified in this study group are presented in Table 1. Although (Aoena satiod) and by Clack et al. (1994) and those reported in other plant species. the number of alleles and the diversity val- and Sharrock and Quail (1989) who re- ues appeared to be different at many of ported the existence of a small phytochro- In addition to identifying the chromo-

24 The Journal of Heredity 1997:88(1) dicated that the level of polymorphism be- • - MWG502 tween the two groups is not significantly ABC164 different. This finding was not unexpected £uF2A because these barley groups are interfer- - - ABR313 ABC152B tile and have no mechanism to separate RisBPP16 them into different gene pools. It is inter- " " MWG920-1 Pcr2 esting to note, however, that the phyto- - - ABR337 - - ABG316B chrome locus (phyf) that exhibits the CDO105B greatest differentiation (G^ = 8.2%) be- Dor2 tween the two- and six-rowed barley 10 CM groups is located on one of the chromosomes (chromosome 2) where genes influ- encing the number of rows in the spike - - ABC160 have been identified (Shin et al. 1990). In this investigation we have identified Downloaded from https://academic.oup.com/jhered/article/88/1/21/2186575 by guest on 23 September 2021 five phytochrome loci that represent a small multigene family in barley. These Phy3 loci have been described by their chromosomal and genomic locations and genetic diversity levels. The identification and description of phytochrome loci are Phyl - - ABG464 important steps in the understanding of the photosensory circuitry of higher plants and in the eventual manipulation of - - His3B the photosynthetic system at the molecu- - - ABC307A lar level.

- - ABG705 References - - CMWG706A Apel K, 1981. The protochlorophyllldae holochromeof barley: phytochrome-lnduced Increase of translatable CD0669B mRNA coding for the NADPH protochlorophyllldae ox- ABG708 - \- ABC257 idoreductase. Eur J Blochem 120:89-93. Adh6 iPgd2 Causse MA, Fulton TM, Cho YG, Ann SN, Chunwongse ABG497 - - CMWG733 J, Wu K, Xiao J, Yu Z, Ronald PC, Harrington SE, Second ABG395 G, McCouch SR, and Tanksley SD, 1994 Saturated mo- CD0749 lecular map of the rice genome based on an Interspe- Rrn2 cific backcross population. Genetics 138.1251-1274. Ubi2 - " AtpbA Clack T, Mathews S, and Sharrock RA, 1994. The phy- B12DB • - ABG702 tochrome apoproteln family In Arabidopsis Is encoded by five genes: the sequences and expression of PHYD Ltpl and PHYE Plant Mol Blol 25:413-427. - - ABC322B Dehesh K, Francl C, Parks BM, Seeley KA, Short TW, - - ABC261 Tepperman JM, and Quail PH, 1993. Arabidopsis HY8 - - WG541 - - MWG635C locus encodes phytochrome A. Plant Cell 5:1081-1088. - - Cab2 Felnberg AP and Vogelsteln B, 1983. A technique for WG530 radlolabelling DNA restriction endonuclease fragments ABA001 - - Aga7 to high specific activity. Anal Blochem 132:6-13. - \- ABG373 Furuya M, 1993. Phytochromes: their molecular species, gene families, and functions. Annu Rev Plant Phys- ABG055 lol Plant Mol Blol 44:617-645. - |- ABG387A Hershey HP, Barker RF, Idler KB, Ussemore JL, and Quail PH, 1985. Analysis of cloned cDNA and genomic sequences for phytochrome: complete amlno add se- Chromosome 7 Chromosome 5 quences for two gene products expressed In etiolated Figure 3. Genomlc location of phytochrome loci phyl and phy3 on chromosomes 7 and 5 of barley, respectively. Aoena. Nucleic Adds Res 13*543-8559 Only a portion of the chromosomes containing the phytochrome loci are shown. Scale Is shown at the left In Hershey HP, Gilbert JT, Ussemore JL, and Barker RF, centiMorgans. The approximate location of centromere regions are Indicated by the C. 1984. Molecular donlng of cDNA for Aoena phytochrome. Proc Nat! Acad Sd USA 81:2332-2336. Islam AKMR, 1983. DUelosomlc additions of barley somal and genomic location of phytochro- for the phytochrome loci fell within the chromosomes to wheat. In: Proceedings of the 6th In- ternational Wheat Genetics Symposium, Kyoto (Saka- me loci in barley, we surveyed the level of range of previous estimates for isozymes moto S, ed). Kyoto: Kyoto University Press; 233-238. genetic variation at each phytochrome lo- and random RFLPs within cultivated bar- Klelnhofs A, KUIan A, Saghai Maroof MA, Btyashev RM, cus in a sample of 96 accessions of culti- ley, that is, between 0.10 and 0.74 (Saghai Hayes PM, Chen R, Lapltan N, Fenwlck A, Blake TK, vated barley. Genetic variation was de- Maroof et al. 1995). Kanazin V, Ananlev E, Oahleen L, Kudrna D, Skadsen R, and Steffenson BJ, 1993. A molecular, Isozyme and mor- tected at all four (five) phytochrome loci The partitioning of the 96 barley lines phological map of the barley {Hordeum aulgare) ge- surveyed. The diversity values calculated into two- and six-rowed barley groups in- nome. Theor Appl Genet 86:705-712.

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26 The Journal of Heredity 1997:88(1)