Population structure and domestication revealed by high-depth resequencing of Korean cultivated and wild soybean genomes

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Title
Population structure and domestication revealed by high-depth resequencing of Korean cultivated and wild soybean genomes
Author(s)
Won Hyung Chung; Namhee Jeong; Jiwoong Kim; Woo Kyu Lee; Yun Gyeong Lee; Sang Heon Lee; Woongchang Yoon; J H Kim; I Y Choi; H K Choi; J K Moon; Namshin Kim; Soon Chun Jeong
Bibliographic Citation
DNA Research, vol. 21, no. 2, pp. 153-167
Publication Year
2014
Abstract
Despite the importance of soybean as a major crop, genome-wide variation and evolution of cultivated soybeans are largely unknown. Here, we catalogued genome variation in an annual soybean population by high-depth resequencing of 10 cultivated and 6 wild accessions and obtained 3.87 million high-quality single-nucleotide polymorphisms (SNPs) after excluding the sites with missing data in any accession. Nuclear genome phylogeny supported a single origin for the cultivated soybeans. We identified 10-fold longer linkage disequilibrium (LD) in the wild soybean relative to wild maize and rice. Despite the small population size, the long LD and large SNP data allowed us to identify 206 candidate domestication regions with significantly lower diversity in the cultivated, but not in the wild, soybeans. Some of the genes in these candidate regions were associated with soybean homologues of canonical domestication genes. However, several examples, which are likely specific to soybean or eudicot crop plants, were also observed. Consequently, the variation data identified in this study should be valuable for breeding and for identifying agronomically important genes in soybeans. However, the long LD of wild soybeans may hinder pinpointing causal gene(s) in the candidate regions.
Keyword
DomesticationResequencingSoybeanVariation
ISSN
1340-2838
Publisher
Oxford Univ Press
DOI
http://dx.doi.org/10.1093/dnares/dst047
Type
Article
Appears in Collections:
Synthetic Biology and Bioengineering Research Institute > Genome Editing Research Center > 1. Journal Articles
Ochang Branch Institute > 1. Journal Articles
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