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New Phytol. 2016 Jan;209(2):871-84. doi: 10.1111/nph.13626. Epub 2015 Oct 19.

Domestication footprints anchor genomic regions of agronomic importance in soybeans.

Author information

1
Key Laboratory of Soybean Biology in Chinese Education Ministry, Northeast Agricultural University, Harbin, 150030, China.
2
Bioinformatics Division, Biomarker Technologies Corporation, Beijing, 101300, China.
3
Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
4
Illinois Soybean Center for Excellence in Soybean Research, Southern Illinois University, Carbondale, IL, 62901, USA.
5
Department of Crop and Soil Science, Washington State University, Pullman, WA, 99164-6420, USA.

Abstract

Present-day soybeans consist of elite cultivars and landraces (Glycine max, fully domesticated (FD)), annual wild type (Glycine soja, nondomesticated (ND)), and semi-wild type (semi-domesticated (SD)). FD soybean originated in China, although the details of its domestication history remain obscure. More than 500 diverse soybean accessions were sequenced using specific-locus amplified fragment sequencing (SLAF-seq) to address fundamental questions regarding soybean domestication. In total, 64,141 single nucleotide polymorphisms (SNPs) with minor allele frequencies (MAFs) > 0.05 were found among the 512 tested accessions. The results indicated that the SD group is not a hybrid between the FD and ND groups. The initial domestication region was pinpointed to central China (demarcated by the Great Wall to the north and the Qinling Mountains to the south). A total of 800 highly differentiated genetic regions and > 140 selective sweeps were identified, and these were three- and twofold more likely, respectively, to encompass a known quantitative trait locus (QTL) than the rest of the soybean genome. Forty-three potential quantitative trait nucleotides (QTNs; including 15 distinct traits) were identified by genome-wide association mapping. The results of the present study should be beneficial for soybean improvement and provide insight into the genetic architecture of traits of agronomic importance.

KEYWORDS:

divergence of soybean species; genome-wide association mapping; origin; selective sweeps; sequencing

PMID:
26479264
DOI:
10.1111/nph.13626
[Indexed for MEDLINE]
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