Advertisement

Conservation Genetics

, Volume 12, Issue 5, pp 1145–1157 | Cite as

Genetic diversity and association mapping in a collection of selected Chinese soybean accessions based on SSR marker analysis

  • Ying-Hui Li
  • Marinus J. M. Smulders
  • Ru-Zhen Chang
  • Li-Juan QiuEmail author
Research Article

Abstract

For broadening the narrow genetic base of modern soybean cultivars, 159 accessions were selected from the Chinese soybean collection which contained at least one of seven important agronomic traits: resistance to soybean cyst nematode (SCN) or soybean mosaic virus (SMV), tolerance to salt, cold, or drought, high seed oil content or high protein content. Genetic diversity evaluation using 55 microsatellite loci distributed across the genome indicated that a large amount of genetic diversity (0.806) and allelic variation (781) were conserved in this selected set, which captured 65.6% of the alleles present in Chinese soybean collection (1,863 accessions). On average, 9.4 rare alleles (frequency <5%) per locus were present, which were highly informative. Using model-based Bayesian clustering in STRUCTURE we distinguished four main clusters and a set of accessions with admixed ancestry. The four clusters reflected different geographic regions of origin of the accessions. Since the clusters were also clearly different with respect to the seven agronomic traits, the inferred population structure was introduced when association analysis was conducted. A total of 21 SSR markers on 16 chromosomes were identified as significantly (P < 0.01) associated with high oil content (6), high protein content (1), drought tolerance (5), SCN resistance (6) and SMV resistance (3). Twelve of these markers were located in or near previously identified quantitative trait loci (QTL). The results for both genetic relationship and trait-related markers will be useful for effective conservation and utilization of soybean germplasm.

Keywords

Population structure Genetic diversity Association mapping Selected accessions Soybean 

Notes

Acknowledgments

This research was supported by National Key Technologies R&D Program in the 11th Five-Year Plan (No. 2006BAD13B05), the State Key Basic Research and Development Plan of China (973) (2010CB125900 and 2004CB117203), State High-tech (863) (No. 2006AA10A110, 2006AA10Z164), Crop Germplasm Conservation (NB08-2130315-(25-31)-06, NB08-2130315-(25-30)-06 and NB2010-2130135-25-05) the Academy and Institute Foundation for Basic Scientific Research in Institute of Crop Science, Chinese Academy of Agricultural Sciences.

References

  1. Agrama HA, Eizenga GC, Yan W (2007) Association mapping of yield and its components in rice cultivars. Mol Breed 19:341–356CrossRefGoogle Scholar
  2. Beaumont M, Nichols R (1996) Evaluating loci for use in the genetic analysis of population structure. Proc R Soc Lond 263:1619–1626CrossRefGoogle Scholar
  3. Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633PubMedCrossRefGoogle Scholar
  4. Chang RZ, Sun JY (1991) Catalogues of Chinese soybean germplasm and resources: continuation I. China Agricultural Press, Beijing, ChinaGoogle Scholar
  5. Chang RZ, Sun JY, Qiu LJ, Chen YW (1996) Catalogues of Chinese soybean germplasm and resources: continuation II. China Agricultural Press, Beijing, China Google Scholar
  6. Chen Y, Wang D, Arelli P, Ebrahimi M, Nelson RL (2006) Molecular marker diversity of SCN-resistant sources in soybean. Genome 49:938–949PubMedCrossRefGoogle Scholar
  7. Chen QS, Zhang ZC, Liu CY, Xin DW, Shan DP, Qiu HM, Shan CY (2007) QTL analysis of major agronomic traits in soybean. Sci Agric Sin (China) 40:41–47Google Scholar
  8. Choi IY, Kang JH, Song HS, Kim NS (1999) Genetic diversity measured by simple sequence repeat variations among the wild soybean, Glycine soja, collected along the riverside of five major rivers in Korea. Genes Genetic Syst 74:169–177CrossRefGoogle Scholar
  9. Chung J, Babka HL, Graef GL, Staswick PE, Lee DJ, Cregan PB, Shoemaker RC, Specht JE (2003) The seed protein, oil, and yield QTL on soybean linkage group I. Crop Sci 43:1053–1067CrossRefGoogle Scholar
  10. Coordinative-Group-of-Evaluation-of-SCN (1993) Evaluation of soybean germplasn for resistance to races 1, 3 and 4 of the soybean cyst nematode. Soybean Science (China) 12:91–99Google Scholar
  11. Cregan PB, Jarvik T, Bush AL, Shoemaker RC, Lark KG, Kahler AL, Kaya N, VanToai TT, Lohnes DG, Chung J (1999a) An integrated genetic linkage map of the soybean genome. Crop Sci 39:1464–1490CrossRefGoogle Scholar
  12. Cregan PB, Mudge J, Fickus EW, Danesh D, Denny R, Young ND (1999b) Two simple sequence repeat markers to select for soybean cyst nematode resistance conditioned by the rhg1 locus. Theor Appl Genet 99:811–818CrossRefGoogle Scholar
  13. Csanadi G, Vollmann J, Stift G, Lelley T (2001) Seed quality QTLs identified in a molecular map of early maturing soybean. Theor Appl Genet 103:912–919CrossRefGoogle Scholar
  14. Cui Y, Qiu L (2004) A study of genetic diversity of Huanghuai summer sowing soybean in China. Sci Agric Sin (China) 37:15–22Google Scholar
  15. Cui Z, Carter TE, Burton JW (2000) Genetic base of 651 Chinese soybean cultivars released during 1923 to 1995. Crop Sci 40:1470–1481CrossRefGoogle Scholar
  16. Delannay X, Rogers DM, Palmer RG (1983) Relative genetic contributions among ancestral lines to North American soybean cultivars. Crop Sci 23:944–949CrossRefGoogle Scholar
  17. Du W, Yu D, Fu S (2009) Detection of quantitative trait loci for yield and drought tolerance traits in soybean using a recombinant inbred line population. J Integr Plant Biol 51:868–878PubMedCrossRefGoogle Scholar
  18. Gai J, Cui Z (1994) Ancestral analysis of soybean cultivars released in China. J Nanjing Agric Univ (China) 17:19–23Google Scholar
  19. Gai JY, Zhao TJ, Cui ZL, Qiu JX (1998) Nuclear and cytoplasmic contributions of germplasm from distinct areas to soybean cultivars released during 1923–1995 in China. Sci Agric Sin (China) 31:35–43Google Scholar
  20. Gizlice Z, Carter TE Jr, Burton JW (1994) Genetic base for North American public soybean cultivars released between 1947 and 1988. Crop Sci 34:1143–1151CrossRefGoogle Scholar
  21. Goudet J (2001) FSTAT, a program to estimate and test gene diversities and fixation indices (version 2.9. 3). http://wwwUnilCh/izea/softwares/fstatHtml
  22. Gu H, Chen X, Zhu C, Li X, Zhang Z (1999) A facilitated technique for batch screening of soybean germplasm tolerant to photooxidation and drought. Jiangsu Agric Sci (China) 15:38–41Google Scholar
  23. Hallauer AR, Miranda JB (eds) (1988) Qualitative genetics in maize breeding, 2nd edn. Iowa State University Press, AmesGoogle Scholar
  24. Hisano H, Sato S, Isobe S, Sasamoto S, Wada T, Matsuno A, Fujishiro T, Yamada M, Nakayama S, Nakamura Y (2007) Characterization of the soybean genome using EST-derived microsatellite markers. DNA Res 14:271–281PubMedCrossRefGoogle Scholar
  25. Hyten DL, Pantalone VR, Sams CE, Saxton AM, Landau-Ellis D, Stefaniak TR, Schmidt ME (2004) Seed quality QTL in a prominent soybean population. Theor Appl Genet 109:552–561PubMedCrossRefGoogle Scholar
  26. Jun TH, Van K, Kim MY, Lee SH, Walker DR (2008) Association analysis using SSR markers to find QTL for seed protein content in soybean. Euphytica 162:179–191CrossRefGoogle Scholar
  27. Kuroda Y, Kaga A, Tomooka N, Vaughan DA (2006) Population genetic structure of Japanese wild soybean (Glycine soja) based on microsatellite variation. Mol Ecol 15:959–974PubMedCrossRefGoogle Scholar
  28. Levene H (1949) On a matching problem in genetics. Ann Math Stat 20:91–94 CrossRefGoogle Scholar
  29. Li SF, Shao GH (1992) The methods for identifying drought tolerance in soybean. Crops 1:30–31Google Scholar
  30. Li Y, Chang R, Zhao Y (1989) Studies on tolerance to cold in soybean II. Effect of low temperature treatment during germination on growth and development. Oil Crops China 6:41–43Google Scholar
  31. Li YJ, Zhao YT, Chang RZ, Liu F, Liang BW, Sun JY (1991) The study on cold tolerance in soybean? Identify soybean germplasms tolerant to cold in Northeast China. Oil Crops China 4:85–88Google Scholar
  32. Li Y, Chang R, Zhao Y, Sun J (1992) Laboratory screening on tolerance to cold in soybean and application in field. Soybean Sci (China) 11:49–57Google Scholar
  33. Li L, Qiu L, Chang R, He X (2005) Differentiation and genetic diversity of SSR molecular markers for Huanghuai and Southern summer sowing soybean in China. Acta Agron Sin (China) 31:777–783Google Scholar
  34. Li Y, Guan R, Liu Z, Ma Y, Wang L, Li L, Lin F, Luan W, Chen P, Yan Z, Guan Y, Zhu L, Ning X, Smulders M, Li W, Piao R, Cui Y, Yu Z, Guan M, Chang R, Hou A, Shi A, Zhang B, Zhu S, Qiu L (2008) Genetic structure and diversity of cultivated soybean (Glycine max (L.) Merr.) landraces in China. Theor Appl Genet 117:857–871PubMedCrossRefGoogle Scholar
  35. Li Y, Smulders MJM, Chang R, Qiu L (2010) Analysis of SSRs uncovers hierarchical structure and genetic diversity in Chinese soybean landraces. Agric Sci China 9:1739–1748Google Scholar
  36. Liang HZ, Wang SF, Yu YL, Lian Y, Wang TF, Wei YL, Gong PT, Liu XY, Fang HJ (2009) QTL mapping of isoflavone, oil and protein contents in soybean (Glycine max L. Merr.). Agri Sci China 9:1108–1116Google Scholar
  37. Liu K, Muse S (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21:2128–2129PubMedCrossRefGoogle Scholar
  38. Liu X, Zhang X (1993) Studies and evaluation on drought-tolerants of soybean germplasm from Hua-Huai-Hai valleys. J Shanxi Agric Sci (China) 21:19–24Google Scholar
  39. Luan W, Liu Z, Guan R, Chang R, He B, Qiu L (2005) Representativeness of Northeast China spring soybeans and their genetic diversity at SSR loci. Chin J Appl Ecol (China) 16:1469–1476Google Scholar
  40. Luan XL, Li ZF, Man WQ, Bai YN, Ma YS, Liu XL, Zheng BX, Du WG (2006) Identification of molecular markers linked to resistance for SMV3 in soybean. Mol Plant Breed 4:841–845Google Scholar
  41. Martin JM, Blake TK, Hockett EA (1991) Diversity among American spring barely cultivars based on coefficient of parentage. Crop Sci 31:1131–1137CrossRefGoogle Scholar
  42. Mi SJ, Qiu LJ, Chang RZ, Hao ZB, Guan RX (2004) Genetic diversity analysis of varieties of Glycine max (L.) Merr resistance to soybean mosaic virus by SSR fingerprints. Acta Phytopathol Sin 34:244–253Google Scholar
  43. Narvel JM, Fehr WR, Chu W, Grant D, Shoemaker RC (2000) Simple sequence repeat diversity among soybean plant introductions and elite genotypes. Crop Sci 40:1452–1458CrossRefGoogle Scholar
  44. Nichols DM, Glover KD, Carlson SR, Specht JE, Diers BW (2006) Fine mapping of a seed protein QTL on soybean linkage group I and its correlated effects on agronomic traits. Crop Sci 46:834–839CrossRefGoogle Scholar
  45. Panthee DR, Pantalone VR, West DR, Saxton AM, Sams CE (2005) Quantitative trait loci conditioning protein concentration and quality, and other seed characteristics in soybean [Glycine max (L.) Merrill]. Crop Sci 45:2015–2022CrossRefGoogle Scholar
  46. Piao R, Liu Z, Guan R, Chang R, Hao Z, Qiu L (2005) Genetic diversity of southern summer soybean in Chinese coastal revealed by SSR markers. J Agric Biotechnol (China) 13:435–440Google Scholar
  47. Pritchard J, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959PubMedGoogle Scholar
  48. Qiu L, Chang R (eds) (2006) Descriptors and data standard for soybean (Glycine spp.). China Agriculture Press, BeijingGoogle Scholar
  49. Qiu LJ, Chang RZ, Chen KM, Li XH, Guan RX, Sun JY (2002) Analysis of conserving and renewal status for Chinese soybean germplasm. J Plant Genet Resour (China), 3(2):34–39Google Scholar
  50. Rohlf F (2000) NTSYS-pc. Numerical taxonomy and multivariate analysis system (version 2.1). State University of New York, New YorkGoogle Scholar
  51. Roussel V, Koenig J, Beckert M, Balfourier F (2004) Molecular diversity in French bread wheat accessions related to temporal trends and breeding programmes. Theor Appl Genet 108:920–930PubMedCrossRefGoogle Scholar
  52. Shao G, Song J (1986) Preliminary studies on the evaluation of salt tolerance in soybean varieties. Sci Agric Sin (China) 6:31–35Google Scholar
  53. Shao GH, Chang RZ, Chen YW (1993) The development of salt tolerance in soybean. Soybean Sci 12:244–248Google Scholar
  54. Shi A, Chen P, Zhang B, Hou A (2010) Genetic diversity and association analysis of protein and oil content in food-grade soybeans from Asia and the United States. Plant Breed 129:250–256CrossRefGoogle Scholar
  55. Shibata M, Takayama K, Ujiie A, Yamada T, Abe J, Kitamura K (2008) Genetic relationship between lipid content and linolenic acid concentration in soybean seeds. Breed Sci 58:361–366CrossRefGoogle Scholar
  56. Song QJ, Marek LF, Shoemaker RC, Lark KG, Concibido VC, Delannay X, Specht JE, Cregan PB (2004) A new integrated genetic linkage map of the soybean. Theor Appl Genet 109:122–128PubMedCrossRefGoogle Scholar
  57. Song Q, Jia G, Zhu Y, Grant D, Nelson RT, Hwang EY, Hyten DL, Cregan PB (2010) Abundance of SSR motifs and development of candidate polymorphic SSR markers (BARCSOYSSR_1. 0) in soybean. Crop Sci 50:1950–1960CrossRefGoogle Scholar
  58. Thompson JA, Nelson RL, Vodkin LO (1998) Identification of diverse soybean germplasm using RAPD markers. Crop Sci 38:1348–1355CrossRefGoogle Scholar
  59. Vigouroux Y, Mitchell S, Matsuoka Y, Hamblin M, Kresovich S, Smith J, Jaqueth J, Smith O, Doebley J (2005) An analysis of genetic diversity across the maize genome using microsatellites. Genetics 169:1617–1630PubMedCrossRefGoogle Scholar
  60. Wang GX (1982) Catalogues of Chinese soybean germplasm and resources. China Agricultural Press, Beijing, ChinaGoogle Scholar
  61. Wang L, Guan R, Zhangxiong L, Chang R, Qiu L (2006a) Genetic diversity of Chinese cultivated soybean revealed by SSR markers. Crop Sci 46:1032–1038CrossRefGoogle Scholar
  62. Wang L, Guan Y, Guan R, Li Y, Ma Y, Dong Z, Liu X, Zhang H, Zhang Y, Liu Z (2006b) Establishment of Chinese soybean Glycine max core collections with agronomic traits and SSR markers. Euphytica 151:215–223CrossRefGoogle Scholar
  63. Wang J, McClean PE, Lee R, Goos RJ, Helms T (2008) Association mapping of iron deficiency chlorosis loci in soybean (Glycine max L. Merr.) advanced breeding lines. Theor Appl Genet 116:777–787PubMedCrossRefGoogle Scholar
  64. Wen ZX, Zhao TJ, Zheng YZ, Liu SH, Wang CE, Wang F, Gai JY (2008) Association analysis of agronomic and quality traits with SSR markers in Glycine max and Glycine soja in China: II. Exploration of elite alleles. Acta Agron Sin (China) 34:1339–1349Google Scholar
  65. Wu X, Blake S, Sleper DA, Shannon JG, Cregan P, Nguyen HT (2009) QTL, additive and epistatic effects for SCN resistance in PI 437654. Theor Appl Genet 118:1093–1105PubMedCrossRefGoogle Scholar
  66. Xia Z, Tsubokura Y, Hoshi M, Hanawa M, Yano C, Okamura K, Ahmed T, Anai T, Watanabe S, Hayashi M (2007) An integrated high-density linkage map of soybean with RFLP, SSR, STS, and AFLP markers using a single F2 population. DNA Res 14:257–269PubMedCrossRefGoogle Scholar
  67. Xie H, Chang R, Cao Y, Zhang M, Feng Z, Qiu L (2003) Selection of core SSR loci by using Chinese autumn soybean. Sci Agric Sin (China) 36:360–366Google Scholar
  68. Xie H, Guan R, Chang R, Qiu L (2005) Genetic diversity of Chinese summer soybean germplasm revealed by SSR markers. Chin Sci Bull 50:526–535Google Scholar
  69. Xiong D, Zhao T, Gai J (2008) Parental analysis of soybean cultivars released in China. Sci Agric Sin (China) 41:2589–2598Google Scholar
  70. Xu DH, Gai JY (2003) Genetic diversity of wild and cultivated soybeans growing in China revealed by RAPD analysis. Plant Breed 122:503–506CrossRefGoogle Scholar
  71. Yeh F, Yang R, Boyle T (1999) POPGENE Version 131: Microsoft Window-based freeware for population genetic analysis. University of Alberta and Center for International Forestry Research. http://www.ualberta.ca/~fyeh/index.htm
  72. Yoon MS, Lee J, Kim CY, Kang JH, Cho EG, Baek HJ (2009) DNA profiling and genetic diversity of Korean soybean (Glycine max (L.) Merrill) landraces by SSR markers. Euphytica 165:69–77CrossRefGoogle Scholar
  73. Yue P, Arelli PR, Sleper DA (2001a) Molecular characterization of resistance to Heterodera glycines in soybean PI 438489B. Theor Appl Genet 102:921–928CrossRefGoogle Scholar
  74. Yue P, Sleper DA, Arelli PR (2001b) Mapping resistance to multiple races of Heterodera glycines in soybean PI 89772. Crop Sci 41:1589–1595CrossRefGoogle Scholar
  75. Zhao J, Artemyeva A, Pino Del Carpio D, Kumar Basnet R, Zhang N, Gao J, Li F, Bucher J, Wang X, Visser RGF, Bonnema G (2010) Design of a Brassica rapa core collection for association mapping studies. Genome 53(11):908–916Google Scholar
  76. Zhang HY, Guan RX, Li YH, Wang LX, Luan WJ, Chang RZ, Liu ZX, Qiu LJ (2005) Genetic diversity analysis and marker assisted identification of salt tolerant soybean by using SSR marker. J Plant Genet Resour (China) 6:251–255Google Scholar
  77. Zheng CM, Chang RZ, Qiu LJ, Wu DP, Gao FL (2000) Identification the resistance of soybean germplasm to SMV3. Soybean Sci (China) 19:299–306Google Scholar
  78. Zhou X, Carter T Jr, Cui Z, Miyazaki S, Burton J (2000) Genetic base of Japanese soybean cultivars released during 1950 to 1988. Crop Sci 40:1794–1802CrossRefGoogle Scholar
  79. Zhou XL, Carter TE Jr, Cui ZL, Miyazaki S, Burton JW (2002) Genetic diversity patterns in Japanese soybean cultivars based on coefficient of parentage. Crop Sci 42:1331–1342CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  • Ying-Hui Li
    • 1
  • Marinus J. M. Smulders
    • 2
  • Ru-Zhen Chang
    • 1
  • Li-Juan Qiu
    • 1
    Email author
  1. 1.The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA), Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijingPeople’s Republic of China
  2. 2.Plant Research InternationalWageningen UR Plant BreedingWageningenThe Netherlands

Personalised recommendations