Landscape of genomic diversity and trait discovery in soybean.

Babu Valliyodan,Yanjun Li,Henry T Nguyen,Gunvant Patil,Lu Dai,Dong Xu,Xin Liu,Chengxuan Chen,Theresa A Musket,Cheng Shifeng,Li Song,Peng Zeng,Tri D Vuong,Dan Qiu Dan Qiu,Trupti Joshi,Jiaying Huang,J Grover Shannon

doi:10.1038/srep23598

Babu Valliyodan, Yanjun Li + Show 15 more

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https://doi.org/10.1038/srep23598

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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.

Highlights

We provided a significant genomic variation data set for wild, landrace, and elite soybean lines
High-quality data, and millions of SNPs in the representative soybean lines provide an unprecedented opportunity for us to understand the landscape of soybean diversity and domestication
Our findings showed that the SNP variation and PAV between the wild and elite lines were 43% and 50%, respectively; and this finding explains the diversification of elite lines after domestication based on climatic zones, plant architecture, and agronomic traits

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Introduction

Natural genetic variation analysis of soybean germplasm using the genome sequence information of individuals will greatly help to identify genes and rare alleles that are associated with major traits and components for soybean improvement. We provided a significant genomic variation data set for wild, landrace, and elite soybean lines. High-quality data, and millions of SNPs in the representative soybean lines provide an unprecedented opportunity for us to understand the landscape of soybean diversity and domestication.

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