Genetic Diversity of Wild Soybeans from Some Regions of Southern China Based on SSR and SRAP Markers


There are rich annual wild soybean (Glycine soja) resources in Southern China, which are the progenitor of cultivated soybean. To evaluate the genetic diversity and differentiation of G. soja in Southern China, we analyzed allelic profiles of 141 annual wild soybean accessions from Southern China and 8 core wild soybean accessions fromNorthern Chinaby using 41 simple sequence repeat (SSR) markers and 18 Sequence-related amplified polymorphism (SRAP) primer combinations. The 41 SSR markers produced a total of 421 alleles (10.27 per locus) with a mean of gene diversity of 0.825 (Simpson index) and 1.987 (Shannon-weaver index). The 18 SRAP primer combinations detected a total of 90 polymorphism bands (5 per primer combination) with a mean of gene diversity of 0.918 (Shannon-weaver index). SSR and SRAP markers detected 43 and 5 rare alleles in 149 wild soybeans, respectively. The wild soybeans from Fujian province showed the highest genetic diversity with Shannon-weaver index of 1.837 (by SSR) and 0.803 (by SRAP), and the highest allelic richness with an average of 8.8 alleles per locus and the most number of rare alleles of 0.68 per locus based on SSR data. An analysis of Molecular Variance (AMOVA) analysis showed that significant variance did exist amongHunan,Fujian, Guangxi andNorthern Chinasubpopulations based on SSR and SRAP data. The unweighted pair-group method of the arithmetic average (UPGMA) cluster analysis indicated that the wild soybeans fromFujianprovince occurred in different clusters based on both SSR and SRAP data. The above results indicated thatFujianprovince could be the major center of genetic diversity for annual wild soybean inSouthern China. In addition, Mantle test showed there was a weak positive linear correlation (r = 0.25) between SSR and SRAP analysis in the study.

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B. Sun, C. Fu, C. Yang, Q. Ma, D. Pan and H. Nian, "Genetic Diversity of Wild Soybeans from Some Regions of Southern China Based on SSR and SRAP Markers," American Journal of Plant Sciences, Vol. 4 No. 2, 2013, pp. 257-268. doi: 10.4236/ajps.2013.42034.

Conflicts of Interest

The authors declare no conflicts of interest.


[1] F. S. Li, “Geographical Distribution and Ecological Diffusing of Wild Soybean Germplasm in China,” In: F. S. Li, Ed., Researching Progress on Wild Soybean of China, Chinese Agricultural Press, Beijing, 1994, pp. 40-48.
[2] Y. L. Ding, T. J. Zhao and J. Y. Gai, “Genetic Diversity and Ecological Differentiation of Chinese Annual Wild Soybean (Glycine soja),” Biodiversity Science, Vol. 16, No. 2, 2008, pp. 133-142.
[3] B. C. Zhuang, H. Xu and Y. M. Wang, “Polymorphism and Geographical Distribution of the Stem and Leaf Characters of Wild Soybean (Glycine soja) in China,” Acta Agronomica Sinica, Vol. 22, No. 5, 1996, pp. 583-586.
[4] Y. S. Dong, B. C. Zhuang, L. M. Zhao, H. Sun and M. Y. He, “The Genetic Diversity of Annual Wild Soybeans Grown in China,” Theoretical and Applied Genetics, Vol. 103, No. 1, 2001, pp. 98-103. doi:10.1007/s001220000522
[5] K. J. Wang, X. H. Li and F. S. Li, “Phenotypic Diversity of the Big Seed Type Subcollection of Wild Soybean (Glycine soja Zucc.) in China,” Genetic Resources and Crop Evolution, Vol. 55, No. 8, 2008, pp. 1335-1346. doi:10.1007/s10722-008-9332-z
[6] J. Li, Y. Tao, S. Z. Zheng and J. L. Zhou, “Isozymatic Differentiation in Local Population of Glycine soja Sieb & Zucc,” Acta Botanica Sinica, Vol. 37, 1995, pp. 669-676.
[7] Z. A. Hu, M. Zhong, W. Wei and H. X. Wang, “Detection of DNA Diversity of Wild Soybean (Glycine soja) in Natural Populations by New Procedure of RAPD and RFLP,” Soybean Genetics Newsletter, Vol. 24, 1997, pp. 37-38.
[8] J. Abe, A. Hasegawa, H. Fukushi, T. Mikami, M. Ohara and Y. Shimamoto, “Introgression between Wild and Cultivated Soybeans of Japan Revealed by RFLP Analysis of Chloroplast DNAs,” Economic Botany, Vol. 53, No. 3, 1999, pp. 285-291. doi:10.1007/BF02866640
[9] Z. L. Li and R. L. Nelson, “RAPD Marker Diversity among Cultivated and Wild Soybean Accessions from Four Chinese Provinces,” Crop Science, Vol. 42, No. 5, 2002, pp. 1737-1744. doi:10.2135/cropsci2002.1737
[10] Y. W. Chen and R. L. Nelson, “Genetic Variation and Relationships among Cultivated, Wild, and Semiwild Soybean,” Crop Sciences, Vol. 44, No. 1, 2004, pp. 316- 325. doi:10.2135/cropsci2004.0316
[11] Z. X. Wen, Y. L. Ding, T. J. Zhao and J. Y. Gai, “Genetic Diversity and Peculiarity of Annual Wild Soybean (G. soja Sieb. et Zucc.) from Various Eco-Regions in China,” Theoretical and Applied Genetics, Vol. 119, No. 2, 2009, pp. 371-381. doi:10.1007/s00122-009-1045-y
[12] J. Yan, T. H. He and B. R. Lu, “Genetic Spatial Clustering: Significant Implications for Conservation of Wild Soybean (Glycine soja: Fabaceae),” Genetica, Vol. 128, No. 1-3, 2006, pp. 41-49. doi:10.1007/s10709-005-4823-8
[13] D. H. Xu and J. Y. Gai, “Genetic Diversity of Wild and Cultivated Soybeans Growing in China Revealed by RAPD Analysis,” Plant Breeding, Vol. 122, No. 6, 2003, pp. 503-506. doi:10.1046/j.0179-9541.2003.00911.x
[14] D. L. Hyten, Q. J. Song, Y. L. Zhu , I. Y. Choi, R. L. Nelson, J. M. Costa, J. E. Specht, R. C. Shoemaker and P. B. Cregan, “Impacts of Genetic Bottlenecks on Soybean Genome Diversity,” Proceedings of the National Academy of Sciences of the United States of America, Vol. 103, No. 45, 2006, pp. 16666-16671. doi:10.1073/pnas.0604379103
[15] Y. Fukuda, “Cytogenetical Studies on the Wild and Cultivated Manchurian Soybeans (Glycine L.),” Japanese Journal of Botany, Vol. 6, 1933, pp. 489-506.
[16] F. S. Li, “Study on Origin and Evolution of Soybean,” Soybean Science, Vol. 13, No. 1, 1994, pp. 61-66.
[17] T. Hymowitz and C. A. Newell, “Taxonomy of Genus Glycine, Domestication and Uses of Soybeans,” Economic Botany, Vol. 35, No. 3, 1981, pp. 272-288. doi:10.1007/BF02859119
[18] B. Xu, H. Xu, B. C. Zhuang, Q. H. Lu, Y. M. Wang and F. S. Li, “The Genetic Diversity and Geographic Distribution of Kernel Traits of G. soja in China,” Acta Agronomica Sinica, Vol. 21, No. 6, 1995, pp.733-739.
[19] B. C. Zhuang, D. W. Hui, Y. M. Wang, J. Gu, B. Xu and S. Y. Chen, “RAPD Analysis of Different Evolutionary Types in Different Latitude in China,” Chinese Science Bulletin, Vol. 39, No. 23, 1994, pp. 2178-2180.
[20] J. Y. Gai, D. H. Xu and Z. Gao, “Studies on the Evolutionalry Relasionship among Eco-Types of G. max and G. soja in China,” Acta Agronomica Sinica, Vol. 26, No. 5, 2000, pp. 513-520.
[21] S. L. Lv, “Discussion on the Original Region of Cultivated Soybean in China,” Scientia Agricultura Sinica, No. 4, 1978, pp. 90-94.
[22] D. H. Xu, Z. Gao, Q. Z. Tian, J. Y. Gai, H. Fukushi, S. Kitajma, J. Abe and Y. Shimamoto, “Genetic Diversity of the Annual Wild Soybean (Glycine soja) in China,” Chinese Journal of Applied & Environmental Biology, Vol. 5, No. 5, 1999, pp. 439-443.
[23] P. Awadalla and K. Ritland, “Microsatellite Variation and Evolution in the Mimulus guttatus Species Complex with Contrasting Mating Systems,” Molecular Biology and Evolution,” Vol. 14, No. 10, 1997, pp. 1023-1034. doi:10.1093/oxfordjournals.molbev.a025708
[24] Q. J. Song, L. F. Marek, R. C. Shoemaker, K. G. Lark, V. C. Concibido, X. Delannay, J. E. Specht and P. B. Cregan, “A New Integrated Genetic Linkage Map of the Soybean,” Theoretical and Applied Genetics, Vol. 109, No. 1, 2004, pp. 122-128. doi:10.1007/s00122-004-1602-3
[25] G. Li and C. F. Quiros, “Sequence-Related Amplified Polymorphism (SRAP), a New Marker System Based on a Simple PCR Reaction: Its Application to Mapping and Gene Tagging in Brassica,” Theoretical and Applied Genetics, Vol. 103, No. 2-3, 2001, pp. 455-461. doi:10.1007/s001220100570
[26] Y. C. Wen, H. Z. Wang, J. X. Shen, G. H. Liu and S. F. Zhang, “Analysis of Genetic Diversity and Genetic Basis of Chinese Rapeseed Cultivars (Brassica napus L.) by Sequence-Related Amplified Polymorphism Markers,” Scientia Agricultura Sinica, Vol. 39, No. 2, 2006, pp. 246-256.
[27] C. Li, X. X. Lu, Z. E. Zhang, X. L. Chen, F. Lin, X. Y. Zhang and C. J. Liu, “Genetic Integrity Analysis of Cotton (Gossypium hirsutum Linn.) Accessions Using SRAP and SSR Markers,” Journal of Plant Genetic Resources, Vol. 8, No. 1, 2007, pp. 21-25.
[28] F. Zhao, Z. J. Cai, T. Z. Hu, H. G. Yao, L. Wang, N. Dong, B. Wang, Z. G. Ru and W. X. Zhai, “Genetic Analysis and Molecular Mapping of a Novel Gene Conferring Resistance to Rice Stripe Virus,” Plant Molecular Biology Reporter, Vol. 28, No. 3, 2010, pp. 512-518. doi:10.1007/s11105-009-0178-0
[29] N. Mutlu, F. H. Boyac?, M. G??men and K. Abak, “Development of SRAP, SRAP-RGA, RAPD and SCAR Markers Linked with a Fusarium Wilt Resistance Gene in Eggplant,” Theoretical and Applied Genetics, Vol. 117, No. 8, 2008, pp. 1303-1312. doi:10.1007/s00122-008-0864-6
[30] S. P. Gai, W. L. Gai and J. Y. Huang, “Comparison of SSR and SRAP Marker for Varieties Identification in Maize (Zea mays L.),” Journal of Plant Genetic Resources, Vol. 12, No. 3, 2011, pp. 468-472.
[31] O. Gulsen, S. Karagul and K. Abak, “Diversity and Relationships among Turkish Okra Germplasm by SRAP and Phenotypic Marker Polymorphism,” Biologia, Vol. 62, No. 1, 2006, pp. 41-45. doi:10.2478/s11756-007-0010-y
[32] H. Xie, “Genetic Diversity on Representative Samples from Primary Core Collection of Soybean (G. max) in China,” Ph.D. Thesis, Chinese Academy of Agricultural Sciences, Beijing, 2002.
[33] M. Nei, “Estimation of Average Heterozygosity and Genetic Distance from a Small Number of Individuals,” Genetics, Vol. 89, 1978, pp. 583-590.
[34] R. Peakall and P. E. Smouse, “GENALEX 6: Genetic Analysis in Excel. Population Genetic Software for Teaching and Research,” Molecular Ecology Notes, Vol. 6, No. 1, 2006, pp. 288-295. doi:10.1111/j.1471-8286.2005.01155.x
[35] L. Excoffier, P. Smouse and J. M. Quattro, “Analysis of Molecular Variance Inferred from Metric Distances among DNA Haplotypes: Application to Human Mitochondrial DNA Restriction Data,” Gentics, Vol. 131, No. 2, 1992, pp. 479-491.
[36] N. A. Mantel, “The Detection of Disease Clustering and a Generalized Regression Approach,” Cancer Research, Vol. 27, 1967, pp. 209-220.
[37] W. Y. Zeng, J. Liang, Y. Chen, Q. Y. Wei, F. Y. Tang, K. Z. Zhong and W. J. Chen, “Genetic Diversity Analysis of New Wild Soybean Collection in Guangxi,” Soybean Science, Vol. 30, No. 3, 2011, pp. 379-383.
[38] H. Y. Liu, H. Zhang, X. Zhou, K. J. Wang and X. H. Li, “Preliminary Report on Distribution Status and Character Identification of Wild Soybean in Hunan,” Hunan Agricultural Sciences, No. 5, 2008, pp. 20-21.
[39] C. M. Cheng, C. Y. Yang, Q. B. Ma and H. Nian, “Genetic Diversity Analysis of Wild Soybean Resources in Jiang-xi,” Journal of Plant Genetic Resources, Vol. 12, No. 6, 2011, pp. 928-933.
[40] G. B. Xu, “Plant Population Genetics,” 2th Edition, Science Press, Beijing, 2009.
[41] M. Kimura, “Rare Variant Alleles in the Light of the Neutral Theory,” Molecular Biology and Evolution, Vol. 1, No. 1, 1984, pp. 84-93.
[42] R. Lande, “Adaptation to an Extraordinary Environment by Evolution of Phenotypic Plasticity and Genetic Assimilation,” Journal Evolutionary Biology, Vol. 22, No. 7, 2009, pp. 1435-1446. doi:10.1111/j.1420-9101.2009.01754.x
[43] D. J. Liu and S. C. Xu, “The Ecological Distribution and Classification on Wild Soybean in Fujian,” Journal of Fujian Academy of Agricultural Sciences, Vol. 6, No. 2, 1991, pp. 18-24.
[44] M. Agarwal, N. Shrivastava and H. Padh, “Advances in Molecular Marker Techniques and Their Applications in Plant Sciences,” Plant Cell Reports, Vol. 27, No. 4, 2008, pp. 617-631. doi:10.1007/s00299-008-0507-z

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