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

Conservation Genetics

Volumn 12, Issue 5, 2011, Pages 1145-1157

  Li, Ying Hui ^a   Smulders, Marinus J M ^b   Chang, Ru Zhen ^a   Qiu, Li Juan ^a  

^a INSTITUTE OF PLANT PROTECTION   (China)

^b WAGENINGEN UNIVERSITY   (Netherlands)

Author keywords

Association mapping; Genetic diversity; Population structure; Selected accessions; Soybean

Indexed keywords

AGRONOMY; ALLELE; ASSORTATIVE MATING; BAYESIAN ANALYSIS; CHROMOSOME; CONSERVATION GENETICS; DROUGHT STRESS; GENETIC MARKER; GENETIC VARIATION; GERMPLASM; NEMATODE; POPULATION STRUCTURE; PROTEIN; SOYBEAN; VIRUS;

GLYCINE MAX; HETERODERA GLYCINES; SOYBEAN MOSAIC VIRUS;

EID: 80052531220     PISSN: 15660621     EISSN: 15729737     Source Type: Journal    
DOI: 10.1007/s10592-011-0216-y     Document Type: Article

References (79)

1. Agrama HA, Eizenga GC, Yan W (2007) Association mapping of yield and its components in rice cultivars. Mol Breed 19: 341-356.
2. Beaumont M, Nichols R (1996) Evaluating loci for use in the genetic analysis of population structure. Proc R Soc Lond 263: 1619-1626.
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: 2633.
4. Chang RZ, Sun JY (1991) Catalogues of Chinese soybean germplasm and resources: continuation I. China Agricultural Press, Beijing, China.
5. Chang RZ, Sun JY, Qiu LJ, Chen YW (1996) Catalogues of Chinese soybean germplasm and resources: continuation II. China Agricultural Press, Beijing, China.
6. Chen Y, Wang D, Arelli P, Ebrahimi M, Nelson RL (2006) Molecular marker diversity of SCN-resistant sources in soybean. Genome 49: 938-949.
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: 41-47.
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: 169-177.
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: 1053-1067.
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: 91-99.
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: 1464-1490.
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: 811-818.
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: 912-919.
14. Cui Y, Qiu L (2004) A study of genetic diversity of Huanghuai summer sowing soybean in China. Sci Agric Sin (China) 37: 15-22.
15. Cui Z, Carter TE, Burton JW (2000) Genetic base of 651 Chinese soybean cultivars released during 1923 to 1995. Crop Sci 40: 1470-1481.
16. Delannay X, Rogers DM, Palmer RG (1983) Relative genetic contributions among ancestral lines to North American soybean cultivars. Crop Sci 23: 944-949.
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: 868-878.
18. Gai J, Cui Z (1994) Ancestral analysis of soybean cultivars released in China. J Nanjing Agric Univ (China) 17: 19-23.
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: 35-43.
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: 1143-1151.
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: 38-41.
23. Hallauer AR, Miranda JB (eds) (1988) Qualitative genetics in maize breeding, 2nd edn. Iowa State University Press, Ames.
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: 271-281.
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: 552-561.
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: 179-191.
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: 959-974.
28. Levene H (1949) On a matching problem in genetics. Ann Math Stat 20: 91-94.
29. Li SF, Shao GH (1992) The methods for identifying drought tolerance in soybean. Crops 1: 30-31.
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: 41-43.
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: 85-88.
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: 49-57.
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: 777-783.
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: 857-871.
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: 1739-1748.
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: 1108-1116.
37. Liu K, Muse S (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21: 2128-2129.
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: 19-24.
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: 1469-1476.
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: 841-845.
41. Martin JM, Blake TK, Hockett EA (1991) Diversity among American spring barely cultivars based on coefficient of parentage. Crop Sci 31: 1131-1137.
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: 244-253.
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: 1452-1458.
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: 834-839.
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: 2015-2022.
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: 435-440.
47. Pritchard J, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
48. Qiu L, Chang R (eds) (2006) Descriptors and data standard for soybean (Glycine spp.). China Agriculture Press, Beijing.
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): 34-39.
50. Rohlf F (2000) NTSYS-pc. Numerical taxonomy and multivariate analysis system (version 2. 1). State University of New York, New York.
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: 920-930.
52. Shao G, Song J (1986) Preliminary studies on the evaluation of salt tolerance in soybean varieties. Sci Agric Sin (China) 6: 31-35.
53. Shao GH, Chang RZ, Chen YW (1993) The development of salt tolerance in soybean. Soybean Sci 12: 244-248.
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: 250-256.
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: 361-366.
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: 122-128.
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: 1950-1960.
58. Thompson JA, Nelson RL, Vodkin LO (1998) Identification of diverse soybean germplasm using RAPD markers. Crop Sci 38: 1348-1355.
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: 1617-1630.
60. Wang GX (1982) Catalogues of Chinese soybean germplasm and resources. China Agricultural Press, Beijing, China.
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: 1032-1038.
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: 215-223.
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: 777-787.
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: 1339-1349.
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: 1093-1105.
66. 2 population. DNA Res 14: 257-269.
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: 360-366.
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: 526-535.
69. Xiong D, Zhao T, Gai J (2008) Parental analysis of soybean cultivars released in China. Sci Agric Sin (China) 41: 2589-2598.
70. Xu DH, Gai JY (2003) Genetic diversity of wild and cultivated soybeans growing in China revealed by RAPD analysis. Plant Breed 122: 503-506.
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: 69-77.
73. Yue P, Arelli PR, Sleper DA (2001a) Molecular characterization of resistance to Heterodera glycines in soybean PI 438489B. Theor Appl Genet 102: 921-928.
74. Yue P, Sleper DA, Arelli PR (2001b) Mapping resistance to multiple races of Heterodera glycines in soybean PI 89772. Crop Sci 41: 1589-1595.
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): 908-916.
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: 251-255.
77. Zheng CM, Chang RZ, Qiu LJ, Wu DP, Gao FL (2000) Identification the resistance of soybean germplasm to SMV3. Soybean Sci (China) 19: 299-306.
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: 1794-1802.
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: 1331-1342.