Korean soybean core collection: Genotypic and phenotypic diversity population structure and genome-wide association study

Autoři: Namhee Jeong aff001;  Ki-Seung Kim aff002;  Seongmun Jeong aff003;  Jae-Yoon Kim aff003;  Soo-Kwon Park aff001;  Ju Seok Lee aff005;  Soon-Chun Jeong aff005;  Sung-Taeg Kang aff006;  Bo-Keun Ha aff007;  Dool-Yi Kim aff001;  Namshin Kim aff003;  Jung-Kyung Moon aff008;  Man Soo Choi aff001
Působiště autorů: National Institute of Crop Science, Rural Development Administration, Wanju-gun, Jeollabuk-do, Republic of Korea aff001;  FarmHannong, Ltd., Daejeon, Republic of Korea aff002;  Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea aff003;  Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon, Republic of Korea aff004;  Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungcheongbuk-do, Republic of Korea aff005;  Department of Crop Science & Biotechnology, Dankook University, Cheonan, Chungcheongnam-do, Republic of Korea aff006;  Division of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Republic of Korea aff007;  National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, Jeollabuk-do, Republic of Korea aff008
Vyšlo v časopise: PLoS ONE 14(10)
Kategorie: Research Article
doi: https://doi.org/10.1371/journal.pone.0224074


A core collection is a subset that represents genetic diversity of the total collection. Soybean (Glycine max (L.) Merr.) is one of major food and feed crops. It is the world’s most cultivated annual herbaceous legume. Constructing a core collection for soybean could play a pivotal role in conserving and utilizing its genetic variability for research and breeding programs. To construct and evaluate a Korean soybean core collection, genotypic and phenotypic data as well as population structure, were analyzed. The Korean soybean core collection consisted of 430 accessions selected from 2,872 collections based on Affymetrix Axiom® 180k SoyaSNP array data. The core collection represented 99% of genotypic diversity of the total collection. Analysis of population structure clustered the core collection into five subpopulations. Accessions from South Korea and North Korea were distributed across five subpopulations. Analysis of molecular variance indicated that only 2.01% of genetic variation could be explained by geographic origins while 16.18% of genetic variation was accounted for by subpopulations. Genome-wide association study (GWAS) for days to flowering, flower color, pubescent color, and growth habit confirmed that the core collection had the same genetic diversity for tested traits as the total collection. The Korean soybean core collection was constructed based on genotypic information of the 180k SNP data. Size and phenotypic diversity of the core collection accounted for approximately 14.9% and 18.1% of the total collection, respectively. GWAS of core and total collections successfully confirmed loci associated with tested traits. Consequently, the present study showed that the Korean soybean core collection could provide fundamental and practical material and information for both soybean genetic research and breeding programs.

Klíčová slova:

Crop genetics – Crops – Genetic polymorphism – Genome-wide association studies – Phenotypes – Plant growth and development – Population genetics – Soybean


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