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

Zixiang Wen,Qijian Song,John F Boyse,Perry B Cregan,Dechun Wang

doi:10.1186/s12864-015-1872-y

Abstract

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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1872-y) contains supplementary material, which is available to authorized users.

Highlights

Crop 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
Effect of selection on diversity and linkage disequilibrium To better understand the patterns of genomic modification imposed by selection, profiles of 52,041 single nucleotide polymorphisms (SNPs) were characterized in 342 soybean landraces and 1062 improved lines
To evaluate the degree to which genetic diversity throughout the genome has been impacted by selection, we further quantified variation in nucleotide diversity, linkage disequilibrium (LD) and haplotype block structure for the two populations

Summary

Introduction

Crop 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 The cultivated soybean, Glycine max (L.) Merr., was domesticated in China from its wild ancestor, G. soja Sieb. The exact series of steps by which soybean was domesticated is still unknown, the divergence between G. max and G. soja likely happened ~0.8 million years ago based on inter-genomic comparison analysis [1]. The long time period since divergence and probably multiple domestication events resulted in a multitude of localized Glycine max landraces [2], which are adapted to different environments. Quantitative trait locus (QTL) mapping has been used to localize genomic regions underlying phenotypic variation. Genomewide association study (GWAS) has been used to dissect various traits, such as disease resistance, yield and quality related traits [10,11,12]

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