Hostname: page-component-78c5997874-fbnjt Total loading time: 0 Render date: 2024-11-14T17:27:55.505Z Has data issue: false hasContentIssue false
  • English
  • Français

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

Published online by Cambridge University Press:  16 July 2014

Kil Hyun Kim ,
Seukki Lee ,
Min-Jung Seo ,
Gi-An Lee ,
Kyung-Ho Ma ,
Soon-Chun Jeong ,
Suk-Ha Lee ,
Eui Ho Park ,
Young-Up Kwon  and
Jung-Kyung Moon
Kil Hyun Kim
Affiliation:
National Institute of Crop Science, Rural Development Administration, Suwon, Republic of Korea
Seukki Lee
Affiliation:
Technology Cooperation Bureau, Rural Development Administration, Suwon, Republic of Korea
Min-Jung Seo
Affiliation:
National Institute of Crop Science, Rural Development Administration, Suwon, Republic of Korea
Gi-An Lee
Affiliation:
National Academy of Agricultural Science, Rural Development Administration, Suwon, Republic of Korea
Kyung-Ho Ma
Affiliation:
National Academy of Agricultural Science, Rural Development Administration, Suwon, Republic of Korea
Soon-Chun Jeong
Affiliation:
Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Chungbuk, Republic of Korea
Suk-Ha Lee
Affiliation:
Plant Genomics and Breeding Institute, Seoul National University, Seoul, Republic of Korea Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
Eui Ho Park
Affiliation:
School of Biotechnology, Yeungnam University, Gyeongbuk, Republic of Korea
Young-Up Kwon
Affiliation:
National Institute of Crop Science, Rural Development Administration, Suwon, Republic of Korea
Jung-Kyung Moon*
Affiliation:
National Institute of Crop Science, Rural Development Administration, Suwon, Republic of Korea
*
* Corresponding author. E-mail: [email protected]
Get access Rights & Permissions [Opens in a new window]

Abstract

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.

Keywords

genetic diversityKoreapopulation structurerare alleleswild soybean
Type
Research Article
Information
Plant Genetic Resources , Volume 12 , Issue S1: Special issue on the 3rd International Symposium on “Genomics of Plant Genetic Resources” , July 2014 , pp. S45 - S48
Copyright
Copyright © NIAB 2014 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

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. 303–416.Google Scholar
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: 169–177.CrossRefGoogle Scholar
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: 2611–2620.Google Scholar
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: 47–50.Google Scholar
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. 23–48.Google Scholar
Keim, P, Olson, TC and Shoemaker, RC (1988) A rapid protocol for isolating soybean DNA. Soybean Genetics Newsletter 15: 150–154.Google Scholar
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: 22032–22037.Google Scholar
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: 1045–1055.Google Scholar
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: 606–616.Google Scholar
Liu, K and Muse, SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21: 2128–2129.Google Scholar
Nei, M (1973) Analysis of gene diversity in subdivided populations. Proceedings of the National Academy of Sciences of the United States of America 70: 3321–3323.Google Scholar
Nei, M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89: 583–590.Google Scholar
Peakall, R and Smouse, PE (2012) GenAlEX 6.5: genetic analysis in Excel. Population genetic software for teaching and research – an update. Bioinformatics 28: 2537–2539.CrossRefGoogle ScholarPubMed
Pimentel, D and Patzek, TW (2005) Ethanol production using corn, switchgrass, and wood; biodiesel production using soybean and sunflower. Natural Resources Research 14: 65–76.Google Scholar
Pritchard, JK, Stephens, M and Donnelly, P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945–959.Google Scholar
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: 178–183.Google Scholar
Schuelke, M (2000) An economic method for the fluorescent labeling of PCR fragments. Nature Biotechnology 18: 233–234.Google Scholar
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. 13–50.Google Scholar
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: 122–128.Google Scholar
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: 371–381.Google Scholar
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.Google Scholar
Yu, H and Kiang, YT (1993) Genetic variation in South Korean natural populations of wild soybean (Glycine soja). Euphytica 68: 213–221.Google Scholar
Supplementary material: File

Kim Supplementary Material

Table S1

Download Kim Supplementary Material(File)
File 25.1 KB
Supplementary material: File

Kim Supplementary Material

Table S2

Download Kim Supplementary Material(File)
File 11.8 KB
Supplementary material: File

Kim Supplementary Material

Table S3

Download Kim Supplementary Material(File)
File 10.4 KB
Supplementary material: File

Kim Supplementary Material

Table S4

Download Kim Supplementary Material(File)
File 66.2 KB