Landscape of genomic diversity and trait discovery in soybean.
Sci Rep, 2016/3/31;6:23598.
Valliyodan B[1], Dan Qiu[1], Patil G[1], Zeng P[2], Huang J[2], Dai L[2], Chen C[2], Li Y[2], Joshi T[3, 4], Song L[1], Vuong TD[1], Musket TA[1], Xu D[3], Shannon JG[5], Shifeng C[2], Liu X[2], Nguyen HT[1]
Affiliations
PMID: 27029319DOI: 10.1038/srep23598
Impact factor: 4.996
Abstract
Cultivated soybean [Glycine max (L.) Merr.] is a primary source of vegetable oil and protein. We report a landscape analysis of genome-wide genetic variation and an association study of major domestication and agronomic traits in soybean. A total of 106 soybean genomes representing wild, landraces, and elite lines were re-sequenced at an average of 17x depth with a 97.5% coverage. Over 10 million high-quality SNPs were discovered, and 35.34% of these have not been previously reported. Additionally, 159 putative domestication sweeps were identified, which includes 54.34 Mbp (4.9%) and 4,414 genes; 146 regions were involved in artificial selection during domestication. A genome-wide association study of major traits including oil and protein content, salinity, and domestication traits resulted in the discovery of novel alleles. Genomic information from this study provides a valuable resource for understanding soybean genome structure and evolution, and can also facilitate trait dissection leading to sequencing-based molecular breeding.
MeSH terms
Alleles; Chromosome Mapping; Genetic Variation; Genome, Plant; Genome-Wide Association Study; High-Throughput Nucleotide Sequencing; Plant Breeding; Polymorphism, Single Nucleotide; Quantitative Trait Loci; Quantitative Trait, Heritable; Sequence Analysis, DNA; Soybean Oil; Glycine max
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