Genetic diversity of Elymus sibiricus germplasm resources revealed by SRAP markers

doi:10.11686/cyxb20140125

Abstract

Abstract: SRAP markers were used to analyze genetic diversity and genetic relationship among eighty-four Elymus sibiricus accessions from Asia. A set of 23 primer combinations yielded 337 bands,of which 203 were polymorphic (60.24%). Genetic similarity values (GS) among the accessions ranged between 0.783 and 0.965 with a mean of 0.865. On the average,Mongolian and Russian accessions were the most similar while,Mongolian and Qinghai-Tibet Plateau accessions were the most distant ones. Cluster analysis grouped the 84 accessions into two clusters,which has quite a high fit (r=0.88) to the original similarity matrix. Results of cluster analysis which was supported strongly by the principal coordinate analysis. The molecular variance analysis (AMOVA) showed that the proportion of variation explained by within geographic group and between geographic groups diversity was 0.7962 and 0.2038,respectively. Similar results were obtained when genetic diversity was estimated using the Shannon’s index of diversity. Based on pairwise Φ_ST between geographic groups,cluster analysis showed a clear demarcation between accessions from Qinghai-Tibet Plateau and the others as separate groups. The clustering pattern was probably dependent on geographic origin and ecological adaptability of the accessions. The results of present study can be useful in collecting germplasm and the establishment of core collections of E. sibiricus. The results in this study will provide useful information for the use of E. sibiricus germplasm and variety breeding.

CLC Number:

S543.03

GU Xiao-yan,GUO Zhi-hui,ZHANG Xin-quan,ZHOU Yong-hong,BAI Shi-qie,ZHANG Chang-bing,JIANG Zong-rong,LIU Xin,ZHOU Chao-jie,MA Xiao. Genetic diversity of Elymus sibiricus germplasm resources revealed by SRAP markers[J]. Acta Prataculturae Sinica, 2014, 23(1): 205-216.

References

Reference:
[1]Moreno González J, Cubero J I. Selection strategies and choice of breeding methods[A]. In: Hayward M D, Bosemark N O, Romagosa I. Plant Breeding, Principles and Prospects[M]. London: Chapman & Hall, 1993: 281-313.
[2]Dewey D R. Cytogenetics of Elymus sibiricusand its hybrids with Agropyron tauri, Elymus canadensis, and Agropyron caninu[J]. Botanical Gazette, 1974, 135: 80-87. 
[3]Bowden W M, Cody W J. Recognition of Elymus sibiricus L. from Alaska and the district of Mackenzie[J]. Bulletin of the Torrey Botanical Club, 1961, 88: 153-155. 
[4]Dao L T, Mai L. Domestication of Elymus sibiricus in Xinjiang[J]. Grassland of China, 1988, (4): 48-50.
[5]Wang Y F, Pan C B, Yang Z Y. Breeding report of Elymus sibiricus L. cv. Chuancao No.1[J]. Journal of Sichuan Grassland, 1994, (4): 7-13.
[6]Zhang Z, Wang B D, Wu J L, et al. Selection and extention of Elymus sibiricus L. cv. nongmu[J]. Grassland of China, 1995, (4): 29-32.
[7]Yuan Q H, Zhang J Y, Zhang W S, et al. Biodiversity of native populations of Elymus dahuricus and Elymus sibiricus[j]. Acta Prataculturae Sinica, 2003, 12(5): 44-49.
[8]Melchinger A E, Graner A, Singh M, et al. Relationships among winter and spring cultivars revealed by RFLP’s[J]. Crop Science, 1994, 34: 1191-1199.
[9]Li G, Quiros C F. Sequence-related amplified polymorphism (SRAP), a new marker system based on a simple PCR reaction: its application to mapping and gene tagging in Brassica[J]. Theoretical and Applied Genetics, 2001, 103: 455-461.
[10]Williams J G K, Kubelik A R, Livak K J, et al. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers[J]. Nucleic Acids Research, 1990, 18: 6531-6535.
[11]Vos P, Hogers R, Bleeker M, et al. AFLP: A new technique for DNA finger printing[J]. Nucleic Acids Research, 1995, 23: 4407-4414.
[12]Ferriol M, Pico B, Nuze F. Genetic diversity of a germplasm collection of Cucurbita pepo using SRAP and AFLP markers[J]. Theoretical and Applied Genetics, 2003, 107: 271-282.
[13]Budak H, Shearman R C, Parmaksiz I, et al. Molecular characterization of buffalograss germplasm using sequence-related amplified polymorphism markers[J]. Theoretical and Applied Genetics, 2004, 108: 328-334.
[14]Vandemark G J, Ariss J J, Bauchan G A, et al. Estimating genetic relationships among historical sources of alfalfa germplasm and selected cultivars with sequence related amplified polymorphisms[J]. Euphytica, 2006, 152: 9-16.
[15]Li J Q, Wang L H,Zhan Q W, et al. Genetic diversity of 20 ryegrass accessions by SRAP markers[J]. Acta Prataculturae Sinica, 2013, 22(2): 158-164.
[16]Han X Y, Wang L S, Shu Q Y, et al. Molecular characterization of tree peony germplasm using sequence-related amplified polymorphism markers[J]. Biochemical Genetics, 2008, 46: 162-179.
[17]Budak H, Shearman R C, Parmaksiz I, et al. Comparative analysis of seeded and vegetative biotype buffalograsses based on phylogenetic relationship using ISSRs, SSRs, RAPDs, and SRAPs[J]. Theoretical and Applied Genetics, 2004, 109: 280-288.
[18]Doyle J J. DNA protocols for plants-CTAB total DNA isolation[A]. In: Hewitt G M, Johnston A. Molecular Techniques in Taxonomy[M]. Berlin, Germany： Springer-Verlag， 1991: 283-293.
[19]Nei M, Li W H. Mathematical model for studying genetic variation in terms of restriction endonucleases[J]. Proceedings of the National Academy of Sciences, 1979, 76: 5269-5273.
[20]Mantel N. The detection of disease clustering and a generalized regression approach[J]. Cancer Research, 1967, 27: 209-220. 
[21]Yap I, Nelson R J. WinBoot: a program for performing bootstrap analysis of binary data to determine the confidence limits of UPGMA-based dendrograms[C]. Manila, Philippines: International Rice Research Institute (IRRI), 1995.
[22]Felsenstein J. Confidence limits on phylogenesis: an approach using the bootstrap[J]. Evolution, 1985, 39: 783-791.
[23]Rolf J F. NTSYS-pc: Numerical Taxonomy and Multivariate Analysis System, Version 2.1[M]. New York, USA：Exeter Software, Setaukel, 2000.
[24]Powell W, Morgante M, Andre C, et al. The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) marker for germplasm analysis[J]. Molecular Breeding, 1996, 2: 225-238.
[25]Schneider S, Roessli D, Excoffier L. ARLEQUIN version 3.1: A Software for Population Genetics Data Analysis[M]. Switzerland：Genetics and Biometry Laboratory, University of Geneva, 2006.
[26]Excoffier L, Smouse P E, Quattro J M. Analysis of molecular variance inferred from metric distances among DNA haplotypes: applications to human mitochondrial DNA restriction data[J]. Genetics, 1992, 131:479-491.
[27]Mizianty M. Variability and structure of natural populations of Elymus caninus(L.) L. based on morphology[J]. Plant Systematics and Evolution, 2005, 251: 199-216.
[28]Díaz O, Sun G L, Salomon B, et al. Levels and distribution of allozyme and RAPD variation in populations of Elymus fibrosis (Schrenk) Tzvel. (Poaceae)[J]. Genetic Resources and Crop Evolution, 2000, 47: 11-24. 
[29]Ma X, Zhou Y H, Yu H Q, et al. Genetic Diversity of Gliadin in Wild Germplasm of Elymus nutans Griseb.[J]. Hereditas(Beijing), 2006, 28(6): 699-706.
[30]Ruiz M, Aguiriano E. Analysis of duplication in the Spanish durum wheat collection maintained in the CRF-INIA on the basis of agro-morphological traits and gliadin proteins[J]. Genetic Resources and Crop Evolution, 2004, 51: 231-235.
[31]Zhang X Q, Salomom B, von Bothmer R. Application of random amplified polymorphic DNA markers to evaluate intraspecific genetic variation in the Elymus alaskanus complex (Poaceae)[J]. Genetic Resources and Crop Evolution, 2002, 49: 397-407.
[32]Sun G L, Díaz O, Salomon B, et al. Genetic diversity in Elymus caninus as revealed by isozyme, RAPD and microsatellite markers[J]. Genome, 1999, 42: 420-431.
[33]Agafonov A V, Baum B R, Bailey L G, et al. Differentiation in the Elymus dahuricus complex (Poaceae): evidence from grain proteins, DNA, and crossability[J]. Hereditas, 2002, 135: 277-289.
[34]Xu D H, Ban T. Phylogenetic and evolutionary relationships between Elymus humidusand other Elymus species based on sequencing of non-coding regions of cpDNA and AFLP of nuclear DNA[J]. Theoretical and Applied Genetics, 2004, 108: 1443-1448.
[35]Zeng B, Zhang X Q, Lan Y, et al. Evaluation of genetic diversity and relationships in orchardgrass（Dactylis glomerataL.) germplasm based on SRAP markers[J]. Canadian Journal of Plant Science, 2008, 88: 53-60. 
[36]Yan J J, Bai S J, Zhang X Q, et al. Genetic diversity of wild Elymus sibiricus germplasm from the Qinghai-Tibetan Plateau in China detected by SRAP markers[J]. Acta Prataculturae Sinica, 2010, 19(1): 173-183.
[37]Hamrick J L, Godt M J W. Conservation genetics of endemic plant species[A]. In: Avise J C, Hamrick J L. Conservation Genetics, Case Histories from Nature[M]. New York: Chapman and Hall, 1996: 281-304.
[38]Sun T, Liu Z J, Liu F M, et al. Analysis of genetic diversity in Anemone obtusiloba populations with ISSR markers[J]. Acta Prataculturae Sinica, 2013, 22(3): 259-265.
[39]Max K H, William C S, Bruce W. The origin of isolating mechanism in flowing plants[A]. In: Max K H. Evolutionary Biology[M]. New York: Plenum Press, 1978: 185-317.
[40]Zeng L, Yuan Q H, Wang F, et al. Genetic diversity analysis of Agropyron germplasm resources by ISSR[J]. Acta Prataculturae Sinica, 2013, 22(1): 260-267.
[41]Johnson R C, Johnston W J, Golob C T, et al. Characterization of the USDA Poa pratensiscollection using RAPD markers and agronomic descriptors[J]. Genetic Resources and Crop Evolution, 2002, 49: 349-361. 
[42]Zhang Y L, Li B Y, Zheng D. A discussion on the boundary and area of the Tibetan Plateau in China[J]. Geographical Research, 2002, 21(1): 1-8.
[43]Chen S Y, Ma X, Zhang X Q,et al. Genetic variation and geographical divergence in Elymus nutans Griseb. (Poaceae: Triticeae) from West China[J]. Biochemical Systematics and Ecology, 2009, 37: 716-722.
[44]Chen Z H, Miao J M, Zhong J C, et al. Genetic diversity of wild Elymus nutans germplasm detected by SRAP markers[J]. Acta Prataculturae Sinica, 2009, 18(5): 192-200.
[45]Miao J M, Zhang X Q, Chen Z H, et al. SRAP and RAPD analysis of Elymus nutans Griseb.germplasm from the Qinghai-Tibetan Plateau and Xinjiang[J]. Acta Agrectir Sinica, 2011, 19(2): 127-134.
[46]Fu Y B, Peterson G W, Williams D, et al. Patterns of AFLP variation in a core subset of cultivated hexaploid oat germplasm[J]. Theoretical and Applied Genetics, 2005, 530: 530-539.

参考文献：
[1]Moreno-González J, Cubero J I. Selection strategies and choice of breeding methods[A]. In: Hayward M D, Bosemark N O, Romagosa I. Plant Breeding, Principles and Prospects[M]. London: Chapman & Hall, 1993: 281-313.
[2]Dewey D R. Cytogenetics of Elymus sibiricus and its hybrids with Agropyron tauri, Elymus canadensis, and Agropyron caninu[J]. Botanical Gazette, 1974, 135: 80-87. 
[3]Bowden W M, Cody W J. Recognition of Elymus sibiricus L. from Alaska and the district of Mackenzie[J]. Bulletin of the Torrey Botanical Club, 1961, 88: 153-155. 
[4]道来提, 麦耒. 新疆老芒麦的驯化[J]. 中国草地, 1988, (4): 48-50.
[5]王元富, 盘朝邦, 杨智永. 川草1号老芒麦选育报告[J]. 四川草原, 1994, (4): 7-13.
[6]张众, 王比德, 吴渠来, 等. 农牧老芒麦的选育推广及其栽培利用[J]. 中国草地, 1995, (4): 29-32.
[7]袁庆华, 张吉宇, 张文淑, 等. 披碱草和老芒麦野生居群生物多样性研究[J]. 草业学报, 2003, 12(5): 44-49.
[8]Melchinger A E, Graner A, Singh M,et al. Relationships among winter and spring cultivars revealed by RFLP’s[J]. Crop Science, 1994, 34: 1191-1199.
[9]Li G, Quiros C F. Sequence-related amplified polymorphism (SRAP), a new marker system based on a simple PCR reaction: its application to mapping and gene tagging in Brassica[J]. Theoretical and Applied Genetics, 2001, 103: 455-461.
[10]Williams J G K, Kubelik A R, Livak K J,et al. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers[J]. Nucleic Acids Research, 1990, 18: 6531-6535.
[11]Vos P, Hogers R, Bleeker M,et al. AFLP: A new technique for DNA finger printing[J]. Nucleic Acids Research, 1995, 23: 4407-4414.
[12]Ferriol M, Pico B, Nuze F. Genetic diversity of a germplasm collection of Cucurbita pepousing SRAP and AFLP markers[J]. Theoretical and Applied Genetics, 2003, 107: 271-282.
[13]Budak H, Shearman R C, Parmaksiz I,et al. Molecular characterization of buffalograss germplasm using sequence-related amplified polymorphism markers[J]. Theoretical and Applied Genetics, 2004, 108: 328-334.
[14]Vandemark G J, Ariss J J, Bauchan G A,et al. Estimating genetic relationships among historical sources of alfalfa germplasm and selected cultivars with sequence related amplified polymorphisms[J]. Euphytica, 2006, 152: 9-16.
[15]李杰勤, 王丽华, 詹秋文, 等. 20个黑麦草品系的SRAP遗传多样性分析[J]. 草业学报, 2013, 22(2): 158-164.
[16]Han X Y, Wang L S, Shu Q Y,et al. Molecular characterization of tree peony germplasm using sequence-related amplified polymorphism markers[J]. Biochemical Genetics, 2008, 46: 162-179.
[17]Budak H, Shearman R C, Parmaksiz I,et al. Comparative analysis of seeded and vegetative biotype buffalograsses based on phylogenetic relationship using ISSRs, SSRs, RAPDs, and SRAPs[J]. Theoretical and Applied Genetics, 2004, 109: 280-288.
[18]Doyle J J. DNA protocols for plants-CTAB total DNA isolation[A]. In: Hewitt G M, Johnston A. Molecular Techniques in Taxonomy[M]. Berlin, Germany： Springer-Verlag， 1991: 283-293.
[19]Nei M, Li W H. Mathematical model for studying genetic variation in terms of restriction endonucleases[J]. Proceedings of the National Academy of Sciences, 1979, 76: 5269-5273.
[20]Mantel N. The detection of disease clustering and a generalized regression approach[J]. Cancer Research, 1967, 27: 209-220. 
[21]Yap I, Nelson R J. WinBoot: a program for performing bootstrap analysis of binary data to determine the confidence limits of UPGMA-based dendrograms[C]. Manila, Philippines: International Rice Research Institute (IRRI), 1995.
[22]Felsenstein J. Confidence limits on phylogenesis: an approach using the bootstrap[J]. Evolution, 1985, 39: 783-791.
[23]Rolf J F. NTSYS-pc: Numerical Taxonomy and Multivariate Analysis System, Version 2.1[M]. New York, USA：Exeter Software, Setaukel, 2000.
[24]Powell W, Morgante M, Andre C,et al. The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) marker for germplasm analysis[J]. Molecular Breeding, 1996, 2: 225-238.
[25]Schneider S, Roessli D, Excoffier L. ARLEQUIN version 3.1: A Software for Population Genetics Data Analysis[M]. Switzerland：Genetics and Biometry Laboratory, University of Geneva, 2006.
[26]Excoffier L, Smouse P E, Quattro J M. Analysis of molecular variance inferred from metric distances among DNA haplotypes: applications to human mitochondrial DNA restriction data[J]. Genetics, 1992, 131:479-491.
[27]Mizianty M. Variability and structure of natural populations of Elymus caninus (L.) L. based on morphology[J]. Plant Systematics and Evolution, 2005, 251: 199-216.
[28]Díaz O, Sun G L, Salomon B,et al. Levels and distribution of allozyme and RAPD variation in populations of Elymus fibrosis (Schrenk) Tzvel. (Poaceae)[J]. Genetic Resources and Crop Evolution, 2000, 47: 11-24. 
[29]马啸, 周永红, 于海清, 等. 野生垂穗披碱草种质的醇溶蛋白遗传多样性分析[J]. 遗传, 2006, 28(6): 699-706.
[30]Ruiz M, Aguiriano E. Analysis of duplication in the Spanish durum wheat collection maintained in the CRF-INIA on the basis of agro-morphological traits and gliadin proteins[J]. Genetic Resources and Crop Evolution, 2004, 51: 231-235.
[31]Zhang X Q, Salomom B, von Bothmer R. Application of random amplified polymorphic DNA markers to evaluate intraspecific genetic variation in the Elymus alaskanus complex (Poaceae)[J]. Genetic Resources and Crop Evolution, 2002, 49: 397-407.
[32]Sun G L, Díaz O, Salomon B,et al. Genetic diversity in Elymus caninus as revealed by isozyme, RAPD and microsatellite markers[J]. Genome, 1999, 42: 420-431.
[33]Agafonov A V, Baum B R, Bailey L G,et al. Differentiation in the Elymus dahuricuscomplex (Poaceae): evidence from grain proteins, DNA, and crossability[J]. Hereditas, 2002, 135: 277-289.
[34]Xu D H, Ban T. Phylogenetic and evolutionary relationships between Elymus humidusand other Elymus species based on sequencing of non-coding regions of cpDNA and AFLP of nuclear DNA[J]. Theoretical and Applied Genetics, 2004, 108: 1443-1448.
[35]Zeng B, Zhang X Q, Lan Y,et al. Evaluation of genetic diversity and relationships in orchardgrass（Dactylis glomerataL.) germplasm based on SRAP markers[J]. Canadian Journal of Plant Science, 2008, 88: 53-60. 
[36]鄢家俊，白史且，张新全, 等. 青藏高原老芒麦种质基于SRAP标记的遗传多样性研究[J]. 草业学报, 2010, 19(1): 173-183.
[37]Hamrick J L, Godt M J W. Conservation genetics of endemic plant species[A]. In: Avise J C, Hamrick J L. Conservation Genetics, Case Histories from Nature[M]. New York: Chapman and Hall, 1996: 281-304.
[38]孙涛, 刘左军, 刘凤梅, 等. 钝裂银莲花不同居群遗传多样性的ISSR分析[J]. 草业学报, 2013, 22(3): 259-265.
[39]Max K H, William C S, Bruce W. The origin of isolating mechanism in flowing plants[A]. In: Max K H. Evolutionary Biology[M]. New York: Plenum Press, 1978: 185-317.
[40]曾亮, 袁庆华, 王方, 等. 冰草属植物种质资源遗传多样性的ISSR分析[J]. 草业学报, 2013, 22(1): 260-267.
[41]Johnson R C, Johnston W J, Golob C T,et al. Characterization of the USDA Poa pratensis collection using RAPD markers and agronomic descriptors[J]. Genetic Resources and Crop Evolution, 2002, 49: 349-361. 
[42]张镱锂, 李炳元, 郑度. 论青藏高原范围与面积[J]. 地理研究, 2002, 21(1): 1-8.
[43]Chen S Y, Ma X, Zhang X Q,et al. Genetic variation and geographical divergence in Elymus nutans Griseb. (Poaceae: Triticeae) from West China[J]. Biochemical Systematics and Ecology, 2009, 37: 716-722.
[44]陈智华, 苗佳敏, 钟金城, 等. 野生垂穗披碱草种质遗传多样性的SRAP研究[J]. 草业学报, 2009, 18(5): 192-200.
[45]苗佳敏, 张新全, 陈智华, 等. 青藏高原和新疆地区垂穗披碱草种质的SRAP及RAPD分析[J]. 草地学报, 2011, 19(2): 127-134.
[46]Fu Y B, Peterson G W, Williams D,et al. Patterns of AFLP variation in a core subset of cultivated hexaploid oat germplasm[J]. Theoretical and Applied Genetics, 2005, 530: 530-539.
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