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Genetic diversity and population structure of wild soybean (Glycine soja Sieb. and Zucc.) accessions in Korea

  • Kil Hyun Kim (a1), Seukki Lee (a2), Min-Jung Seo (a1), Gi-An Lee (a3), Kyung-Ho Ma (a3), Soon-Chun Jeong (a4), Suk-Ha Lee (a5) (a6), Eui Ho Park (a7), Young-Up Kwon (a1) and Jung-Kyung Moon (a1)...


Genetic variation in wild soybean (Glycine soja Sieb. and Zucc.) is a valuable resource for crop improvement efforts. Soybean is believed to have originated from China, Korea, and Japan, but little is known about the diversity or evolution of Korean wild soybean. Therefore, in this study, we evaluated the genetic diversity and population structure of 733 G. soja accessions collected in Korea using 21 simple sequence repeat (SSR) markers. The SSR loci produced 539 alleles (25.7 per locus) with a mean genetic diversity of 0.882 in these accessions. Rare alleles, those with a frequency of less than 5%, represented 75% of the total number. This collection was divided into two populations based on the principal coordinate analysis. Accessions from population 1 were distributed throughout the country, whereas most of the accessions from population 2 were distributed on the western side of the Taebaek and Sobaek mountains. The Korean G. soja collection evaluated in this study should provide useful background information for allele mining approach and breeding programmes to introgress alleles into the cultivated soybean (G. max (L). Merr.) from wild soybean.


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Carter, TE Jr, Nelson, R, Sneller, CH and Cui, Z (2004) Genetic diversity in soybean. In: Boerma, HR and Specht, JE (eds) Soybeans: Improvement, Production, and Uses. Madison, WI: American Society of Agronomy, pp. 303416.
Choi, IY, Kang, JH, Song, HS and Kim, NS (1999) Genetic diversity measured by simple sequence repeat variations among the wild soybean, Glycine soja, collected along the riverside of five rivers in Korea. Genes & Genetic Systems 74: 169177.
Evanno, G, Regnaut, S and Goudet, J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 14: 26112620.
Excoffier, L, Laval, G and Schneider, S (2005) Arelequin (version 3.0): an integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online 1: 4750.
Hymowitz, T and Singh, RJ (1987) Taxonomy and speciation. In: Wilcox, JR (ed.) Soybeans: Improvement, Production, and Uses, 2nd edn. Madison, WI: American Society of Agronomy, pp. 2348.
Keim, P, Olson, TC and Shoemaker, RC (1988) A rapid protocol for isolating soybean DNA. Soybean Genetics Newsletter 15: 150154.
Kim, MY, Lee, S, Van, K, Kim, TH, Jeong, S-C, Choi, I-Y, Kim, DS, Lee, YS, Park, D, Ma, J, Kim, WY, Kim, BC, Park, S, Lee, KA, Kim, D-H, Kim, K-H, Shin, JH, Jang, YE, Kim, KD, Liu, WX, Chaisan, T, Kang, YJ, Lee, YH, Kim, KH, Moon, JK, Schmutz, J, Jackson, SA, Bhak, J and Lee, S-H (2010) Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome. Proceedings of the National Academy of Sciences of the United States of America 107: 2203222037.
Kuroda, Y, Tomooka, N, Kaga, A, Wanigadeva, SMSW and Vaughan, D (2009) Genetic diversity of wild soybean (Glycine soja Sieb. and Zucc.) and Japanese cultivated soybeans [G. max (L.) Merr.] based on microsatellite (SSR) analysis and the selection of a core collection. Genetic Resources and Crop Evolution 56: 10451055.
Lee, JD, Yu, JK, Hwang, YH, Blake, S, So, YS, Lee, GJ, Nguyen, HT and Shannon, JG (2008) Genetic diversity of wild soybean (Glycine soja Sieb. and Zucc.) accessions from South Korea and other countries. Crop Science 48: 606616.
Liu, K and Muse, SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21: 21282129.
Nei, M (1973) Analysis of gene diversity in subdivided populations. Proceedings of the National Academy of Sciences of the United States of America 70: 33213323.
Nei, M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89: 583590.
Peakall, R and Smouse, PE (2012) GenAlEX 6.5: genetic analysis in Excel. Population genetic software for teaching and research – an update. Bioinformatics 28: 25372539.
Pimentel, D and Patzek, TW (2005) Ethanol production using corn, switchgrass, and wood; biodiesel production using soybean and sunflower. Natural Resources Research 14: 6576.
Pritchard, JK, Stephens, M and Donnelly, P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945959.
Schmutz, J, Cannon, SB, Schlueter, J, Ma, J, Mitors, T, Nelson, W, Hyten, DL, Song, Q, Thelen, JJ, Cheng, J, Xu, D, Hellsten, U, May, GD, Yu, Y, Sakurai, T, Umezawa, T, Bhattacharyya, MK, Sandhu, D, Valliyodan, B, Lindquist, E, Peto, M, Grant, D, Shu, S, Goodstein, D, Barry, K, Griggs, MF, Abernathy, B, Du, J, Tian, Z, Zhu, L, Gill, N, Joshi, T, Libault, M, Sethuranman, A, Zhang, XC, Shinozake, K, Nguyen, HT, Wing, RA, Cregan, P, Specht, J, Grimwood, J, Rokhsar, D, Stacey, G, Shoemaker, RC and Jackson, SA (2010) Genome sequence of the palaeopolyploid soybean. Nature 463: 178183.
Schuelke, M (2000) An economic method for the fluorescent labeling of PCR fragments. Nature Biotechnology 18: 233234.
Singh, RJ, Nelson, RL and Chung, GH (2007) Soybean (Glycine max (L.) Merr.). In: Singh, RJ (ed.) Genetic Resources, Chromosome Engineering, and Crop Improvement: Oilseed Crops, vol. 4. Boca Raton, FL: CRC Press, pp. 1350.
Song, QJ, Marek, LF, Shoemaker, RC, Lark, KG, Concibido, VC, Delannay, X, Specht, JE and Cregan, PB (2004) A new integrated genetic linkage map of the soybean. Theoretical and Applied Genetics 109: 122128.
Wen, Z, Diang, Y, Zhao, T and Gai, J (2009) Genetic diversity and peculiarity of annual wild soybean (G. soja Sieb. and Zucc.) from various eco-regions in China. Theoretical and Applied Genetics 119: 371381.
Yeh, FC, Yang, R and Boyle, T (1999) POPGENE VERSION 1.31: Microsoft Window-based freeware for population genetic analysis. University of Alberta, Edmonton, AB, Canada.
Yu, H and Kiang, YT (1993) Genetic variation in South Korean natural populations of wild soybean (Glycine soja). Euphytica 68: 213221.


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