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Nat Biotechnol. 2015 Apr;33(4):408-14. doi: 10.1038/nbt.3096. Epub 2015 Feb 2.

Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean.

Author information

1
State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
2
1] State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China. [2] College of Animal Science and Technology, Northwest A&F University, Yangling, China.
3
1] State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China. [2] University of Chinese Academy of Sciences, Beijing, China.
4
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
5
Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
6
1] State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. [2] University of Chinese Academy of Sciences, Beijing, China.
7
Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, Korea.

Abstract

Understanding soybean (Glycine max) domestication and improvement at a genetic level is important to inform future efforts to further improve a crop that provides the world's main source of oilseed. We detect 230 selective sweeps and 162 selected copy number variants by analysis of 302 resequenced wild, landrace and improved soybean accessions at >11× depth. A genome-wide association study using these new sequences reveals associations between 10 selected regions and 9 domestication or improvement traits, and identifies 13 previously uncharacterized loci for agronomic traits including oil content, plant height and pubescence form. Combined with previous quantitative trait loci (QTL) information, we find that, of the 230 selected regions, 96 correlate with reported oil QTLs and 21 contain fatty acid biosynthesis genes. Moreover, we observe that some traits and loci are associated with geographical regions, which shows that soybean populations are structured geographically. This study provides resources for genomics-enabled improvements in soybean breeding.

PMID:
25643055
DOI:
10.1038/nbt.3096
[Indexed for MEDLINE]

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