大麦SSR标记遗传多样性及其与农艺性状关联分析

doi:10.3864/j.issn.0578-1752.2013.02.002

Abstract

Abstract: 【Objective】In order to provide useful information for hybridization combination of parent materials and molecular assisted breeding, the genetic diversity of parent materials was determined by using SSR markers and their association with some agronomic traits were detected. 【Method】 A total of 86 SSR markers were screened for polymorphism among parent materials, and then the analysis on genetic diversity of these materials were detected. Population structure was analyzed through 57 selected markers, and then association analysis between SSR markers and 5 agronomic traits were performed using TASSEL GLM (General Linear Model) and MLM (Mixed Linear Model) programs.【Result】A total of 200 alleles were found from 113 materials, ranged from 1 to 5. Allele frequency ranged from 0.0088 to 1.0000 and Shannon index ranged from 0.0000 to 1.2236. The genetic similarity ranged from 0.5504 to 0.9897, with the mean of 0.7477. Genetic structure analysis showed that the population of these parent materials was composed of 4 subpopulations. There were 9 SSR markers associated with plant height, spike length, awn length, grain number per spike and Spikelet Compactness under GLM program, and the rate of explanation on the phenotype of related marker ranged from 0.0507 to 0.2766. There were 6 SSR markers associated with plant height, awn length and spikelet compactness under MLM program, and the rate of explanation on the phenotype of related marker ranged from 0.0238 to 0.1999.【Conclusion】Genetic diversity and population structure of 113 materials were analyzed through SSR markers and their association with phenotypes were detected. Nine markers, associated with plant height, spike length, awn length, grain number per spike and spikelet compactness, were determined under GLM program. And 6 markers associated with plant height, awn length and spikelet compactness were determined under MLM program. These markers were on chromosomes 1H, 2H, 3H, 4H and 7H, respectively.

Key words: SSR , genetic diversity , population structure , association analysis

LAI Yong, WANG Peng-Xi, FAN Gui-Qiang, SI Er-Jing, WANG Jin, YANG Ke, MENG Ya-Xiong, LI Bao-Chun, MA Xiao-Le, SHANG Xun-Wu, WANG Hua-Jun. Genetic Diversity and Association Analysis Using SSR Markers in Barley[J].Scientia Agricultura Sinica, 2013, 46(2): 233-242.

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References

[1]Tanksley S D, McCouch S R. Seed banks and molecular maps: Unlocking genetic potential from the Wild. Science, 1997, 277(2): 1063-1064.

[2]Tinker N A, Fortin M G, Mather D E. Random amplified polymorphic DNA and pedigree relationship in spring barley. Theoretical and Applied Genetics, 1993, 85: 976-984.

[3]Russell J, Fuller J, Young G, Thomas B, Macaulay M, Waugh R, Powell W, Taramino G. Discriminating between barley genotypes using microsatellite markers. Genome, 1997, 40: 442-450.

[4]Struss D, Plieske J. The use of microsatellite markers for detection of genetic diversity in barley populations. Theoretical and Applied Genetics, 1998, 97: 308-315.

[5]Vanhala T K, Rijn C P E, Buntjer J, Stam P, Nevo E, Poorter H, Van Eeuwijk F A. Environmental, phenotypic and genetic variation of wild barley (Hordeum spontaneum) from Israel. Euphytica, 2004, 137: 297-309.

[6]Bhagwat A A, Cregan P B, Akkaya M S. Length polymorphisms of simple sequence repeat DNA in soybean. Genetics, 1992, 132: 1131-1139.

[7]Saghai-Maroof M A, Biyashev R M, Yang G P, Zhang Q, Allard R W. Extraordinarily polymorphic microsatellite DNA in barley: Species diversity, chromosomal locations, and population dynamics. Proceedings of the National Academy of Sciences of the United States of America, 1994, 91: 5466-5470.

[8]Weber J L. Informativeness of human (dC-dA)n.(dG-dT)n polymorphism. Genomics, 1990, 7: 524-530.

[9]Wang Z, Weber J L, Zhong G, Tanksley S D. Survey of plant short tandem DNA repeats. Theoretical and Applied Genetics, 1994, 88: 1-6.

[10]Nordborg M. Linkage disequilibrium, gene trees and sel?ng: An ancestral recombination graph with partial self-fertilization. Genetics, 2000, 154: 923-929.

[11]Flint-Garcia S A, Thornsberry J M, Buckler I V. Structure of linkage disequilibrium in plants. Annual Review of Plant Biology, 2003, 54: 357-374.

[12]Zondervan K T, Cardon L R. The complex interplay among factors that influence allelic association. Nature Reviews Genetics, 2004, 5: 89-100.

[13]Gupta P K, Rustgi S, Kulwal P L. Linkage disequilibrium and association studies in higher plants: Present status and future prospects. Plant Molecular Biology, 2005, 57: 461-485.

[14]Matus I A, Hayes P M. Genetic diversity in three groups of barley germplasm assessed by simple sequence repeats. Genome, 2002, 45: 1095-1106.

[15]Brantestam A K, Bothmer R, Dayteg C, Rashal I, Tuvesson S, Weibull J. Genetic diversity changes and relationships in spring barley (Hordeum vulgare L.) germplasm of Nordic and Baltic areas as shown by SSR markers. Genetic Resources and Crop Evolution, 2007, 54: 749-758.

[16]Sun D F, Ren W B, Sun G L, Peng J H. Molecular diversity and association mapping of quantitative traits in Tibetan wild and worldwide originated barley (Hordeum vulgare L.) germplasm. Euphytica, 2011, 178: 31-43.

[17]Malysheva-Otto L V, Ganal M W, Röder M S. Analysis of molecular diversity, population structure and linkage disequilibrium in a worldwide survey of cultivated barley germplasm (Hordeum vulgare L.). BMC Genetics, 2006, 7: 6.

[18]Kraakman A T W, Martnez F, Mussiraliev B, Eeuwijk F A, Niks R E. Linkage disequilibrium mapping of morphological, resistance, and other agronomically relevant traits in modern spring barley cultivars. Molecular Breeding, 2006, 17: 41-58.

[19]Ivandic V, Hackett C A, Nevo E, Keith R, Thomas W T B, Forster B P. Analysis of simple sequence repeats (SSRs) in wild barley from the Fertile Crescent: Associations with ecology, geography and ?owering time. Plant Molecular Biology, 2002, 48: 511-527.

[20]Ivandic V, Thomas W T B, Nevo E, Zhang Z, Forster B P. Associations of simple sequence repeats with quantitative trait variation including biotic and abiotic stress tolerance in Hordeum spontaneum. Plant Breeding, 2003, 4: 300-304.

[21]Paterson A H, Brubaker C L, Wendel J F. A rapid method for extraction of cotton (Gossypium spp.) genomic DNA suitable for RFLP or PCR analysis. Plant Molecular Biology Reporter, 1993, 11: 122-127.

[22]Porebski S, Bailey L G, Baum B R. Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components. Plant Molecular Biology Reporter, 1997, 15: 8-15.

[23]Korff M, Wang H, Léon J, Pillen K. Development of candidate introgression lines using an exotic barley accession (Hordeum vulgare ssp. spontaneum) as donor. Theoretical and Applied Genetics, 2004, 109: 1736-1745.

[24]Evanno G, Regnaut S, Goudet J. Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study. Molecular Ecology, 2005, 14, 2611-2620.

[25]洪棋斌, 侯磊, 罗小英, 李德谋, 肖月华, 裴炎, 杨开俊, 甲错. 应用RAPD分析西北高原青稞的遗传背景. 中国农业科学, 2001, 34(2): 133-138.

Hong Q B, Hou L, Luo X Y, Li D M, Xiao Y H, Pei Y, Yang K J, Jia C. Using RAPD for evaluating genetic background among naked barley varieties in sichuan northwestern region. Scientia Agricultura Sinica, 2001, 34(2): 133-138. (in Chinese)

[26]Guo H, Wei Y M, Chen F, Zheng Y L. Genetic diversity of Hordeum bogdanii wilensky native to Xinjiang, China, based on STS_PCR markers. Acta Botanica Sinica, 2002, 44(11): 1327-1332.

[27]施永泰, 边红武, 韩凝, 潘建伟, 童微星, 朱睦元. 中国江、浙地区栽培大麦遗传资源的RAPD研究. 作物学报, 2004, 30(3): 258-265.

Shi Y T, Bian H W, Han N, Pan J W, Tong W X, Zhu M Y. Genetic variation analysis by RAPD of some barley cultivars in China. Acta Agronomica Sinica, 2004, 30(3): 258-265. (in Chinese)

[28]张赤红, 张京. 大麦品种资源遗传多样性的SSR标记评价. 麦类作物学报, 2008, 28(2): 214-219.

Zhang C H, Zhang J. Genetic diversity assessment of barley germplasm resources using SSR markers. Journal of Triticeae Crops, 2008, 28(2): 214-219. (in Chinese)

[29]刘志敏, 金能, 吕超, 黄祖六, 许如根. 大麦种质资源的SSR遗传多样性分析. 麦类作物学报, 2011, 31(5): 839-846.

Liu Z M, Jin N, Lü C, Huang Z L, Xu R G. Genetic diversity analysis of barley varieties by SSR. Journal of Triticeae Crops, 2011, 31(5): 839-846. (in Chinese)

[30]Harris B P, Stokesbury K D E. The spatial structure of local surficial sediment characteristics on Georges Bank, USA. Continental Shelf Research, 2010, 30(17): 1840-1853.

[31]Wang M L, Zhu C S, Barkley N A, Chen Z B, Erpelding J E, Murray S C, Tuinstra M R, Tesso T, Pederson G A, Yu J M. Genetic diversity and population structure analysis of accessions in the US historic sweet sorghum collection. Theoretical and Applied Genetics, 2009, 120: 13-23.

[32]Kline J B, Moore D J, Clevenger C V. Activation and association of the Tec tyrosine kinase with the human prolactin receptor: Mapping of a Tec/Vav-receptor binding site. Molecular Endocrinology, 2001, 15: 832-841.

[33]Hansen M, Kraft T, Ganestam S, Sall T, Nilsson N O. Linkage disequilibrium mapping of the bolting gene in sea beet using AFLP markers. Genetical Research, 2001, 77: 61-66.

[34]Cockram J, White Jon, Leigh F J, Lea V J, Chiapparino E, Laurie D A, Mackay I J, Powell W, O'Sullivan D M. Association mapping of partitioning loci in barley. BMC Genetics, 2008, 9: 16.

[35]Zhang Z W, Ersoz E, Lai C Q, Todhunter R J, Tiwari H K, Gore M A, Bradbury P J, Yu J M, Arnett D K, Ordovas J M, Buckler E S. Mixed linear model approach adapted for genome-wide association studies. Nature Genetics, 2010, 4: 355-360.

[36]Price A L, Zaitlen N A, Reich D, Patterson N. New approaches to population stratification in genome-wide association studies. Nature Reviews Genetics, 2010, 7: 459-463.

[37]Roy J K, Smith K P, Muehlbauer G J, Chao S M, Close T J, Steffenson B J. Association mapping of spot blotch resistance in wild barley. Molecular Breeding, 2010, 26: 243-256.

[38]Kicherer S, Backes G, Walther U and Jahoor A. Localising QTLs for leaf rust resistance and agronomic traits in barley (Hordeum vulgare L.). Theoretical and Applied Genetics, 2000, l00: 881-888.

[39]Marquez-Cedillo L A, Hayes P M, Kleinhofs A, Legge W G, Rossnagel B G, Sato K, Ullrich S E, Wesenberg D M. QTL analysis of agronomic traits in barley based on the doubled haploid progeny of two elite North American varieties representing different germplasm groups. Theoretical and Applied Genetics, 2001, 103: 625-637.

[40]Teulat B, Borries C, This D. New QTLs identified for plant water status, water-soluble carbohydrate and osmotic adjustrnent in a barley population grown in a growth-chamber under two water regimes. Theoretical and Applied Genetics, 2001, 103: 161-170.

[41]Korff M, Wang H, Léon J, Pillen K. AB-QTL analysis in spring barley: II. Detection of favourable exotic alleles for agronomic traits introgressed from wild barley (H. vulgare ssp. spontaneum). Theoretical and Applied Genetics, 2006, 112: 1221-1231.

[42]Baghizadeh A, Taleei A R, Naghavi M R. QTL analysis for some agronomic traits in barley (Hordum vulgare L.). International Journal of Agriculture and Biology, 2007, 9: 372-374.

[43]Hori K, Kobayashi T, Shimizu A, Sato K, Takeda K, Kawasaki S. Ef?cient construction of a high-density linkage map and its application to QTL analysis in barley. Theoretical and Applied Genetics, 2003, 107: 806-813.

[44]Sameri M, Takeda K, Komatsuda T. Quantitative trait loci controlling agronomic traits in recombinant inbred lines from a cross between oriental- and occidental-type barley cultivars. Breeding Science, 2006, 56: 243-252.

[45]Shahinnia F, Druka A, Franckowiak J, Morgante M, Waugh R, Stein N. High resolution mapping of dense spike-ar (dsp.ar) to the genetic centromere of barley chromosome 7H. Theoretical and Applied Genetics, 2012, 124: 373-384.

[46]Wang J, Yang J, McNeil D L, Zhou M. Identi?cation and molecular mapping of a dwar?ng gene in barley (Hordeum vulgare L.). Euphytica, 2010, 175: 331-342.

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