Genomic consequences of selection and genome-wide association mapping in soybean

BMC Genomics

Research Article

Zixiang Wen¹  John F. Boyse¹  Dechun Wang¹  Qijian Song²  Perry B. Cregan² 

[1] Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 Bogue St., Rm. A384-E, 48824-1325, East Lansing, MI, USA;Soybean Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, 20705, Beltsville, MD, USA;

关键词: Selective sweep;    Single nucleotide polymorphisms;    GWAS;    Soybean;   

DOI  :  10.1186/s12864-015-1872-y

 received in 2015-03-02, accepted in 2015-08-21,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundCrop improvement always involves selection of specific alleles at genes controlling traits of agronomic importance, likely resulting in detectable signatures of selection within the genome of modern soybean (Glycine max L. Merr.). The identification of these signatures of selection is meaningful from the perspective of evolutionary biology and for uncovering the genetic architecture of agronomic traits.ResultsTo this end, two populations of soybean, consisting of 342 landraces and 1062 improved lines, were genotyped with the SoySNP50K Illumina BeadChip containing 52,041 single nucleotide polymorphisms (SNPs), and systematically phenotyped for 9 agronomic traits. A cross-population composite likelihood ratio (XP-CLR) method was used to screen the signals of selective sweeps. A total of 125 candidate selection regions were identified, many of which harbored genes potentially involved in crop improvement. To further investigate whether these candidate regions were in fact enriched for genes affected by selection, genome-wide association studies (GWAS) were conducted on 7 selection traits targeted in soybean breeding (grain yield, plant height, lodging, maturity date, seed coat color, seed protein and oil content) and 2 non-selection traits (pubescence and flower color). Major genomic regions associated with selection traits overlapped with candidate selection regions, whereas no overlap of this kind occurred for the non-selection traits, suggesting that the selection sweeps identified are associated with traits of agronomic importance. Multiple novel loci and refined map locations of known loci related to these traits were also identified.ConclusionsThese findings illustrate that comparative genomic analyses, especially when combined with GWAS, are a promising approach to dissect the genetic architecture of complex traits.

【 授权许可】

CC BY   
© Wen et al. 2015