The transferability of SSR and EST-SSR markers of different origins in Elymus and Roegneria in the Triticeae (Poaceae)

doi:10.11686/cyxb2015324

Abstract

Abstract: Elymus and Roegneria, two important genera in the tribe Triticeae, include many important forage grasses, and also carry elite genes for improving cereal crops. However, there is ongoing dispute on the species boundaries and interspecific systematic relationships in the two genera. The biosystematic relationships in the group are of keen interest to agrostologists around the world. Based on known SSR markers in Triticeae, the objective of this study was to screen out the high transferability markers for Elymus and Roegneria, which would provide important information for understanding the biosystematic relationships of the two genera. A total of 230 simple sequence repeats (SSR) and SSR based on expressed sequence tags (EST-SSR) markers from 5 different genera including wheat, barley, Elymus, Pseudoroegneria and Leymus, were used to study the transferability to 23 species containing the St, H, and Y genomes. Among the 230 SSR markers, 163 (70.87%) markers could generate clear bands, which showed a high transferability for those markers. The EST-SSR markers (87.60%) showed a higher transferability than genomic SSR markers (49.50%), but the genomic SSR markers showed a higher polymorphism (85.98%) than the EST-SSR markers (79.37%). A total of 579 bands were amplified from the 163 SSR markers able to generate clear bands, of which 533 bands were polymorphic. The number of amplified bands of each of these 163 SSR markers ranged from 1 to 11 with an average of 3.55 bands. Cluster analysis using the unweighted pair group method with arithmetic average (UPGMA) showed that the species with same or similar genome could be grouped together. Additionally, the H genome showed a rather distant phylogenetic relationship with St genome, and distant phylogenetic relationships were also revealed between the diploid species containing the H genome and other species in the study. The selected SSR markers from 5 genera could be amplified successfully in Elymus and Roegneria. To summarise, a total of 163 high transferability SSR markers were found to be suitable for the further phylogeny analysis, which also revealed the phylogenetic relationships among the species. The results from this study provide important information for improving understanding of biosystematic relationships between Elymus and Roegneria.

CHEN Shi-Yong, MA Xiao, ZHANG Xin-Quan, CHEN Zhi-Hua, ZHOU Kai. The transferability of SSR and EST-SSR markers of different origins in Elymus and Roegneria in the Triticeae (Poaceae)[J]. Acta Prataculturae Sinica, 2016, 25(2): 132-140.

References

[1] Chen M J, Jia S X. China Forage Plant[M]. Beijing: China Agricultural Press, 2002.
[2] Gu X Y, Guo Z H, Zhang X Q, et al . Phenotypic variation in seven ex-situ conservation populations of Elymus breviaristatus . Acta Prataculturae Sinica, 2015, 24(5): 141-152.
[3] Leigh F, Lea V, Law J, et al . Assessment of EST- and genomic microsatellite markers for variety discrimination and genetic diversity studies in wheat. Euphytica, 2003, 133: 359-366.
[4] Han Z G, Guo W Z, Song X L, et al . Genetic mapping of EST-derived microsatellites from the diploid Gossypium arboreum in allotetraploid cotton. Molecular Genetics and Genomics, 2004, 272: 308-327.
[5] Zhang W, Tang Z X, Fu S L, et al . Genetic diversity and phylogenetic relationships among triticeae species as revealed by wheat microsatellite markers. Southwest China Journal of Agricultural Sciences, 2008, 2: 267-271.
[6] Saha M C, Mian M A, Eujayl I, et al . Tall fescue EST-SSR markers with transferability across several grass species. Theoretical Applied Genetics, 2004, 109: 783-791.
[7] Eujayl I, Sledge M K, Wang L, et al . Medicago truncatula EST-SSRs reveal cross- species genetic markers for Medicago spp. Theoretical and Applied Genetics, 2004, 108: 414-422.
[8] Gupta P K, Rustgi S, Sharma S, et al . Transferable EST-SSR markers for the study of polymorphism and genetic diversity in bread wheat. Molecular Genetics and Genomics, 2003, 270: 315-323.
[9] Che Y H, Li H J, Yang Y P, et al . On the use of SSR markers for the genetic characterization of the Agropyron cristatum (L.) Gaertn. in Northern China. Genetic Resources and Crop Evolution, 2008, 55(3): 389-396.
[10] Sun G L, Salomon B, Bothmer von R. Analysis of tetraploid Elymus species using wheat microsatellite markers and RAPD markers. Genome, 1997, 40: 806-814.
[11] Li Y X, Li S S, Li L H, et al . Comparison of genetic diversity of twelve Elymus species using ISSR and SSR markers. Scientia Agricultura Sinica, 2005, 38(8): 1522-1527.
[12] Sun G L, Salomon B, Bothmer von R. Characterization and analysis of microsatellite loci in Elymus caninus (Triticeae: Poaceae). Theoretical Applied Genetics, 1998, 96: 676-682.
[13] Sun G L, Salomon B, Bothmer von R. Characterization of microsatellite loci from Elymus alaskanus and length polymorphism in several Elymus species (Triticeae: Poaceae). Genome, 1998, 41: 455-463.
[14] Mott I W, Larson S R, Jones T A, et al . A molecular genetic linkage map identifying the St and H subgenomes of Elymus (Poaceae: Triticeae) wheatgrass. Genome, 2011, 54: 819-828.
[15] Röder M S, Korzun V, Wendehake K, et al . A microsatellite map of wheat. Genetics, 1998, 149: 2007-2023.
[16] Liu Z W, Biyashev R M, Saghai-Maroof M A. Development of simple sequence repeat DNA markers and their integration into a barley linkage map. Theoretical and Applied Genetics, 1996, 93: 869-876.
[17] Peng J H, Lapitan N L V. Characterization of EST-derived microsatellites in the wheat genome and development of eSSR markers. Functional and Integrative Genomics, 2005, 5(2): 80-96.
[18] Castillo A, Budak H, Varshney R, et al . Transferability and polymorphism of barley EST-SSR markers used for phylogenetic analysis in Hordeum chilense . BMC Plant Biology, 2008, 8: 97.
[19] Bushman B S, Larson S R, Mott I W, et al . Development and annotation of perennial Triticeae ESTs and SSR markers. Genome, 2008, 51: 779-788.
[20] Rohlf F J. NTSYSpc: Numerical Taxonomy and Multivariate Analysis System, Version 2.1 Exeter Software[M]. New York: Applied Biostatics Inc, 2000.
[21] Nei M, Li W. A mathematical model for studying genetic variation in the terms of restriction endonucleases. Proceedings of the National Academy of Sciences, 1979, 17: 5269-5273.
[22] Yap I V, Nelson R J. Winboot: a program for performing bootstrap analysis of binary data to determine the confidence limits of UPGMA-based dendrograms[C]. Manlia: International Rice Research Institute, 1996.
[23] Guo W Z, Wang W, Zhou B L, et al . Cross-species transferability of G. arboretum -derived EST-SSRs in the diploid species of Gossypium . Theoretical and Applied Genetics, 2006, 112: 1573-1581.
[24] Hernández P, Laurie D A, Martin A, et al . Utility of barley and wheat simple sequence repeat (SSR) markers for genetic analysis of Hordeum chilense and tritordeum. Theoretical and Applied Genetics, 2002, 104: 735-739.
[25] MacRitchie D, Sun G. Evaluating the potential of barley and wheat microsatellite markers or genetic analysis of Elymus trachycaulus complex species. Theoretical and Applied Genetics, 2004, 108: 720-724.
[26] Eufayl I, Sorrells M E, Baum M, et al . Isolation of EST-derived microsatellite markers for genotyping the A and B genome of wheat. Theoretical and Applied Genetics, 2002, 104: 399-407.
[27] Liu Q L, Ge S, Tang H, et al . Phylogenetic relationships in Elymus (Poaceae: Triticeae) based on the nuclear ribosomal transcribed spacer and chloroplast trnL-F sequences. New Phytologist, 2006, 170: 411-420.
[28] Lu B R. A study on systematic relationships between Elymus and Hordeum (Poaceae). Acta Phytoaxonomica Sinica, 1997, 35(3): 193-207.
[29] Baum B R, Yang J L, Yen C, et al . A taxonomic synopsis of the genus Campeiostachys Drobov. Journal of Systematics and Evolution, 2011, 42(9): 146-159.
[30] Yan J, Yang J L. Triticeae Biosystematics (Volume IV)[M]. Beijing: China Agricultural Press, 2011.
[1] 陈默君, 贾慎修. 中国饲用植物[M]. 北京: 中国农业出版社, 2002.
[2] 顾晓燕, 郭志慧, 张新全, 等. 短芒披碱草异位保护群体的表型多样性研究. 草业学报, 2015, 24(5): 141-152.
[5] 张炜, 唐宗祥, 符书兰, 等. 利用小麦微卫星引物分析小麦及其近缘种遗传多样性. 西南农业学报, 2008, 2: 267-271.
[11] 李永祥, 李斯深, 李立会, 等. 披碱草属12个物种遗传多样性的ISSR和SSR比较分析. 中国农业科学, 2005, 38(8): 1522-1527.
[28] 卢宝荣. 披碱草属与大麦属系统关系的研究. 植物分类学报, 1997, 35(3): 193-207.
[30] 颜济, 杨俊良. 小麦族生物系统学(第四卷)[M]. 北京: 中国农业出版社, 2011.