Soybean Molecular Genetic Diversity

  • Perry B. Cregan
Part of the Plant Genetics and Genomics: Crops and Models book series (PGG, volume 2)


Simple Sequence Repeat Marker Simple Sequence Repeat Locus Soybean Cultivar Wild Soybean Soybean Genotype 
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  1. Abe, J., Xu, D.H., Suzuki, Y., Kanazawa, A., and Shimamoto, Y. (2003) Soybean germplasm pools in Asia revealed by nuclear SSRs. Theor. Appl. Genet. 106, 445–53.PubMedGoogle Scholar
  2. Akkaya, M.S., Bhagwat, A.A., and Cregan, P.B. (1992) Length polymorphisms of simple sequence repeat DNA in soybean. Genetics 132, 1131–9.PubMedGoogle Scholar
  3. Altshuler, D., Brooks, L.D., Chakravarti, A., Collins, F.S., Daly, M.J., and Donnelly, P. (2005) A haplotype map of the human genome. Nature 437, 1299–320.CrossRefGoogle Scholar
  4. Apuya, N.R., Frazier, B.L., Keim, P., Roth, E.J., and Lark, K.G. (1988) Restriction fragment length polymorphisms as genetic markers in soybean, Glycine max (L.) Merrill. Theoretical and Applied Genetics. 75, 889–901.Google Scholar
  5. Barrett, J.C., Fry, B., Maller, J., and Daly, M.J. (2005) Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21, 263–5.PubMedCrossRefGoogle Scholar
  6. Boerma, H.R., and Specht, J.E. (2004) Soybeans: Improvement, Production, and Uses. 3rd ed. American Society of Agronomy, Crop Science Society of America, Soil Science Society of America, Madison, WI.Google Scholar
  7. Brown-Guedira, G.L., Thompson, J.A., Nelson, R.L., and Warburton, M.L. (2000) Evaluation of genetic diversity of soybean introductions and North American ancestors using RAPD and SSR markers. Crop Sci. 40, 815–823.Google Scholar
  8. Carter, T.E., Nelson, R., Sneller, C.H., and Cui, Z. (2004) Genetic diversity in soybean:In: H. R. Boerma and J. E. Specht (Eds), Soybeans: Improvement, Production, and Uses. American Society of Agronomy, Crop Science Society of America, Soil Science Society of America, Madison, WI, pp. 303–416.Google Scholar
  9. Choi, I.-Y., Hyten, D.L., Matukumalli, L.K., Song, Q.-J., Chaky, J.M., Quigley, C.V., Chase, K., Lark, K.G., Reiter, R.S., Yoon, M.-S., Hwang, E.-Y., Yi, S.-I., Young, N.D., Shoemaker, R.C., van Tassell, C.P., Specht, J.E., and Cregan, P.B. (2007) A soybean transcript map: gene distribution, haplotype and SNP analysis. Genetics 176, 685–696.PubMedCrossRefGoogle Scholar
  10. Cregan, P.B., Jarvik, T., Bush, A.L., Shoemaker, R.C., Lark, K.G., Kahler, A.L., Kaya, N., VanToai, T.T., Lohnes, D.G., and Chung, J. (1999) An integrated genetic linkage map of the soybean genome. Crop Sci. 39, 1464–1490.Google Scholar
  11. Daly, M.J., Rioux, J.D., Schaffner, S.F., Hudson, T.J., and Lander, E.S. (2001) High-resolution haplotype structure in the human genome. Nat Genet 29, 229–32.PubMedCrossRefGoogle Scholar
  12. Diwan, N., and Cregan, P.B. (1997) Automated sizing of fluorescent-labeled simple sequence repeat (SSR) markers to assay genetic variation in soybean. Theor. Appl. Genet. 95, 723–733.CrossRefGoogle Scholar
  13. Feltus, F.A., Wan, J., Schulze, S.R., Estill, J.C., Jiang, N., and Paterson, A.H. (2004) An SNP resource for rice genetics and breeding based on subspecies indica and japonica genome alignments. Genome Res. 14, 1812–9.PubMedCrossRefGoogle Scholar
  14. Flint-Garcia, S.A., Thornsberry, J.M., and Buckler, E.S., IV. (2003) Structure of linkage disequilibrium in plants. Annu. Rev. Plant Biol. 54, 357–74.PubMedCrossRefGoogle Scholar
  15. Gabriel, S.B., Schaffner, S.F., Nguyen, H., Moore, J.M., Roy, J., Blumenstiel, B., Higgins, J., DeFelice, M., Lochner, A., Faggart, M., Liu-Cordero, S.N., Rotimi, C., Adeyemo, A., Cooper, R., Ward, R., Lander, E.S., Daly, M.J., and Altshuler, D. (2002) The structure of haplotype blocks in the human genome. Science 296, 2225–9.PubMedCrossRefGoogle Scholar
  16. Gizlice, Z., Carter, T.E., Jr., and Burton, J.W. (1994) Genetic base for North American public soybean cultivars released between 1947 and 1988. Crop Sci. 34, 1143–1151.Google Scholar
  17. Hamblin, M.T., Mitchell, S.E., White, G.M., Gallego, J., Kukatla, R., Wing, R.A., Paterson, A.H., and Kresovich, S. (2004) Comparative population genetics of the panicoid grasses: sequence polymorphism, linkage disequilibrium and selection in a diverse sample of sorghum bicolor. Genetics 167, 471–83.PubMedCrossRefGoogle Scholar
  18. Hermann, A. 1962. A revision of genus Glycine and its immediate allies. USDA Tech. Bull. 1268, 1–79.Google Scholar
  19. Hymowitz, T. (2004) Speciation and cytogenetics:In: H. R. Boerma and J. E. Specht (Eds), Soybeans: Improvement, Production, and Uses. American Society of Agronomy, Crop Science Society of America, Soil Science Society of America, Madison, Wis., pp. 97–136.Google Scholar
  20. Hymowitz, T., and Newell, C.A. (1981) Taxonomy of the genus Glycine, domestication and uses of soybeans. Economic botany. 35, 272–288.Google Scholar
  21. Hyten, D.L., Choi, I.-Y., Song, Q., Shoemaker, R.C., Nelson, R.L., Costa, J.M., Specht, J.E., and Cregan, P.B. (2007a) Highly variable patterns of linkage disequilibrium in multiple soybean populations. Genetics 175, 1937–1944.Google Scholar
  22. Hyten, D.L., Song, Q., Zhu, Y., Choi, I.Y., Nelson, R.L., Costa, J.M., Specht, J.E., Shoemaker, R.C., and Cregan, P.B. (2006) Impacts of genetic bottlenecks on soybean genome diversity. Proc. Natl. Acad. Sci. U.S.A. 103, 16666–71.PubMedCrossRefGoogle Scholar
  23. Hyten, D.L., Choi, I.-Y., Yoon, M.-S., Song, Q.-J., Specht, J.E., Nelson, R.L., Chase, K., Young, N.D., Lark, K.G., Shoemaker, R.C., and Cregan, P.B. 2007b. An Assessment of Genome-wide Linkage Disequilibrium in Soybean. Plant & Animal Genome XV, San Diego, CA.Google Scholar
  24. Kanazin, V., Talbert, H., See, D., DeCamp, P., Nevo, E., and Blake, T. (2002) Discovery and assay of single-nucleotide polymorphisms in barley (Hordeum vulgare). Plant Mol Biol 48,529–37.PubMedCrossRefGoogle Scholar
  25. Keim, P., Shoemaker, R.C., and Palmer, R.G. (1989) Restriction fragment length polymorphism diversity in soybean. Theor. Appl. Genet. 77, 786–792.CrossRefGoogle Scholar
  26. Keim, P., Beavis, W., Schupp, J., and Freestone, R. (1992) Evaluation of soybean RFLP marker diversity in adapted germ plasm. Theor. Appl. Genet. 85, 205–212.CrossRefGoogle Scholar
  27. Kisha, T.J., Diers, B.W., Hoyt, J.M., and Sneller, C.H. (1998) Genetic diversity among soybean plant introductions and North American germplasm. Crop Sci. 38, 1669–1680.Google Scholar
  28. Kuroda, Y., Kaga, A., Tomooka, N., and Vaughan, D.A. (2006) Population genetic structure of Japanese wild soybean (Glycine soja) based on microsatellite variation. Mol. Ecol. 15, 959–74.PubMedCrossRefGoogle Scholar
  29. Li, Z., and Nelson, R.L. (2001) Genetic diversity among soybean accessions from three countries measured by RAPDs. Crop Sci. 41, 1337–1347.Google Scholar
  30. Li, Z., and Nelson, R.L. (2002) RAPD marker diversity among cultivated and wild soybean accessions from four Chinese provinces. Crop Sci. 42, 1737–1744.Google Scholar
  31. Li, Z., Qiu, L., Thompson, J.A., Welsh, M.M., and Nelson, R.L. (2001) Molecular genetic analysis of U.S. and Chinese soybean ancestral lines. Crop Sci. 41, 1330–1336.Google Scholar
  32. Lorenzen, L.L., and Shoemaker, R.C. (1996) Genetic relationships within old U.S. soybean cultivar groups. Crop Sci. 36, 743–752.Google Scholar
  33. Lorenzen, L.L., Boutin, S., Young, N., Specht, J.E., and Shoemaker, R.C. (1995) Soybean pedigree analysis using map-based molecular markers. I. Tracking RFLP markers in cultivars. Crop Science. 35, 1326–1336.Google Scholar
  34. Maughan, P.J., Saghai Maroof, M.A., and Buss, G.R. (1995) Microsatellite and amplified sequence length polymorphisms in cultivated and wild soybean. Genome 38, 715–723.PubMedGoogle Scholar
  35. Maughan, P.J., Saghai-Maroof, M.A., Buss, G.R., and Huestis, G.M. (1996) Amplified fragment length polymorphism (AFLP) in soybean: species diversity, inheritance, and near-isogenic line analysis. Theor. Appl. Genet. 93, 392–401.CrossRefGoogle Scholar
  36. Morgante, M., and Olivieri, A.M. (1993) PCR-amplified microsatellites as markers in plant genetics. Plant J. 3, 175–82.PubMedCrossRefGoogle Scholar
  37. Narvel, J.M., Fehr, W.R., Chu, W.C., Grant, D., and Shoemaker, R.C. (2000) Simple sequence repeat diversity among soybean plant introductions and elite genotypes. Crop Sci. 40,1452–1458.Google Scholar
  38. National Research Council. Committee on Genetic Vulnerability of Major Crops. (1972) Genetic Vulnerability of Major Crops National Academy of Sciences, Washington.Google Scholar
  39. Palmer, R.G., Pfeiffer, T.W., Buss, G.R., and Kilen, T.C. (2004) Qualitative genetics:In: H. R. Boerma and J. E. Specht (Eds), Soybeans: Improvement, Production, and Uses. American Society of Agronomy, Crop Science Society of America, Soil Science Society of America, Madison, WI, pp. 137–233.Google Scholar
  40. Powell, W., Morgante, M., Doyle, J.J., McNicol, J.W., Tingey, S.V., and Rafalski, A.J. (1996) Genepool variation in genus Glycine subgenus Soja revealed by polymorphic nuclear and chloroplast microsatellites. Genetics 144, 793–803.PubMedGoogle Scholar
  41. Rafalski, A., and Morgante, M. (2004) Corn and humans: recombination and linkage disequilibrium in two genomes of similar size. Trends Genet. 20, 103–11.PubMedCrossRefGoogle Scholar
  42. Risch, N., and Merikangas, K. (1996) The future of genetic studies of complex human diseases. Science 273, 1516–7.PubMedCrossRefGoogle Scholar
  43. Rongwen, J., Akkaya, M.S., Bhagwat, A.A., Lavi, U., and Cregan, P.B. (1995) The use of microsatellite DNA markers for soybean genotype identification. Theor. Appl. Genet. 90, 43–48.CrossRefGoogle Scholar
  44. Roth, E.J., and Lark, K.G. (1984) Isopropyl-N(3-chlorophenyl) carbamate (CIPC) induced chromosomal loss in soybean: a new tool for plant somatic cell genetics. Theoretical and Applied Genetics. 68, 421–431.CrossRefGoogle Scholar
  45. Scallon, B.J., Dickinson, C.D., and Nielsen, N.C. (1987) Characterization of a null-allele for the Gy4 glycinin gene from soybean. Mol. Gen. Genet. 208, 107–113.CrossRefGoogle Scholar
  46. Schneider, K., Weisshaar, B., Borchardt, D.C., and Salamini, F. (2001) SNP frequency and allelic haplotype structure of Beta vulgaris expressed genes. Molecular Breeding: New Strategies in Plant Improvement. 8, 63–74.Google Scholar
  47. Skorupska, H.T., Shoemaker, R.C., Warner, A., Shipe, E.R., and Bridges, W.C. (1993) Restriction fragment length polymorphism in soybean germplasm of the southern USA. Crop Sci. 33, 1169–1176.Google Scholar
  48. Sneller, C.H., Miles, J.W., and Hoyt, J.M. (1997) Agronomic performance of soybean plant introductions and their genetic similarity to elite lines. Crop Sci. 37, 1595–1600.Google Scholar
  49. Song, Q.-J., Choi, I.-Y., Heo, N.-K., and Kim, N.-S. (1998) Genotype fingerprinting, differentiation and association between morphological traits and SSR loci of soybean landraces. Plant Res. 1, 81–91.Google Scholar
  50. Song, Q.J., Quigley, C.V., Nelson, R.L., Carter, T.E., Boerma, H.R., Strachan, J.L., and Cregan, P.B. (1999) A selected set of trinucleotide simple sequence repeat markers for soybean cultivar identification. Plant Varieties and Seeds 12, 207–220.Google Scholar
  51. Tajima, F. (1983) Evolutionary relationship of DNA sequences in finite populations. Genetics 105, 437–60.PubMedGoogle Scholar
  52. Tenaillon, M.I., U’Ren, J., Tenaillon, O., and Gaut, B.S. (2004) Selection versus demography: a multilocus investigation of the domestication process in maize. Mol. Biol. Evol. 21,1214–25.PubMedCrossRefGoogle Scholar
  53. Thompson, J.A., and Nelson, R.L. (1998a) Utilization of diverse germplasm for soybean yield improvement. Crop Sci. 38, 1362–1368.Google Scholar
  54. Thompson, J.A., and Nelson, R.L. (1998b) Core set of primers to evaluate genetic diversity in soybean. Crop Sci. 38, 1356–1362.Google Scholar
  55. Thompson, J.A., Nelson, R.L., and Vodkin, L.O. (1998) Identification of diverse soybean germplasm using RAPD markers. Crop Sci. 38, 1348–1355.Google Scholar
  56. Ude, G.N., Kenworthy, W.J., Costa, J.M., Cregan, P.B., and Alvernaz, J. (2004) Genetic diversity of soybean cultivars from China, Japan, North America, and North American ancestral lines determined by amplified fragment length polymorphism. Crop Sci. 43, 1858–1867.Google Scholar
  57. Vos, P., Hogers, R., Bleeker, M., Reijans, M., van de Lee, T., Hornes, M., Frijters, A., Pot, J., Peleman, J., Kuiper, M., and et al. (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23, 4407–14.PubMedCrossRefGoogle Scholar
  58. Wang, L., Guan, R., Zhangxiong, L., Chang, R., and Qui, L. (2006) Genetic diversity of Chinese cultivated soybean revealed by SSR markers. Crop Sci. 46, 1032–1038.CrossRefGoogle Scholar
  59. Wang, N., Akey, J.M., Zhang, K., Chakraborty, R., and Jin, L. (2002) Distribution of recombination crossovers and the origin of haplotype blocks: the interplay of population history, recombination, and mutation. Am J Hum Genet 71, 1227–34.PubMedCrossRefGoogle Scholar
  60. Watterson, G.A. (1975) On the number of segregating sites in genetical models without recombination. Theor. Popul. Biol. 7, 256–76.PubMedCrossRefGoogle Scholar
  61. Weir, B.S. (1990) Genetic Data Analysis. Sinauer Associates, Sunderland, MA.Google Scholar
  62. Welsh, J., and McClelland, M. (1990) Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res. 18, 7213–8.PubMedCrossRefGoogle Scholar
  63. Williams, J.G., Kubelik, A.R., Livak, K.J., Rafalski, J.A., and Tingey, S.V. (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res. 18, 6531–5.PubMedCrossRefGoogle Scholar
  64. Wright, S.I., Bi, I.V., Schroeder, S.G., Yamasaki, M., Doebley, J.F., McMullen, M.D., and Gaut, B.S. (2005) The effects of artificial selection on the maize genome. Science 308, 1310–4.PubMedCrossRefGoogle Scholar
  65. Xu, D.H., and Gai, J.Y. (2003) Genetic diversity of wild and cultivated soybeans growing in China revealed by RAPD analysis. Plant Breeding 122, 503–506.CrossRefGoogle Scholar
  66. Yoon, M.S., Song, Q.J., Choi, I.Y., Specht, J.E., Hyten, D.L., and Cregan, P.B. (2007) BARCSoySNP23: a panel of 23 selected SNPs for soybean cultivar identification. Theor. Appl. Genet. 114, 885–99.PubMedCrossRefGoogle Scholar
  67. Zakharova, E.S., Epishin, S.M., and Vinetski, Y.P. (1989) An attempt to elucidate the origin of cultivated soybean via comparison of nucleotide sequences encoding glycinin B4 polypeptide of cultivated soybean, Glycine max, and its presumed wild progenitor, Glycine soja. Theoretical and Applied Genetics. 78 (6), 852–856.CrossRefGoogle Scholar
  68. Zhu, T., Shi, L., Doyle, J.J., and Keim, P. (1995) A single nuclear locus phylogeny of soybean based on DNA sequence. Theor. Appl. Genet. 90, 991–999.CrossRefGoogle Scholar
  69. Zhu, Y.L., Song, Q.J., Hyten, D.L., Van Tassell, C.P., Matukumalli, L.K., Grimm, D.R., Hyatt, S.M., Fickus, E.W., Young, N.D., and Cregan, P.B. (2003) Single-nucleotide polymorphisms in soybean. Genetics 163, 1123–34.PubMedGoogle Scholar

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© Springer Science+Business Media, LLC 2008

Authors and Affiliations

  • Perry B. Cregan
    • 1
  1. 1.Soybean Genomics and Improvement Laboratory, U.S. Department of AgricultureAgricultural Research ServiceBeltsville

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