The genetic architecture of seed composition in soybean is refined by genome-wide association scans across multiple populations.

Justin N Vaughn,Randall L Nelson,Zenglu Li,Perry B Cregan,Qijian Song

doi:10.1534/g3.114.013433

Abstract

Soybean oil and meal are major contributors to world-wide food production. Consequently, the genetic basis for soybean seed composition has been intensely studied using family-based mapping. Population-based mapping approaches, in the form of genome-wide association (GWA) scans, have been able to resolve loci controlling moderately complex quantitative traits (QTL) in numerous crop species. Yet, it is still unclear how soybean’s unique population history will affect GWA scans. Using one of the populations in this study, we simulated phenotypes resulting from a range of genetic architectures. We found that with a heritability of 0.5, ∼100% and ∼33% of the 4 and 20 simulated QTL can be recovered, respectively, with a false-positive rate of less than ∼6×10−5 per marker tested. Additionally, we demonstrated that combining information from multi-locus mixed models and compressed linear-mixed models improves QTL identification and interpretation. We applied these insights to exploring seed composition in soybean, refining the linkage group I (chromosome 20) protein QTL and identifying additional oil QTL that may allow some decoupling of highly correlated oil and protein phenotypes. Because the value of protein meal is closely related to its essential amino acid profile, we attempted to identify QTL underlying methionine, threonine, cysteine, and lysine content. Multiple QTL were found that have not been observed in family-based mapping studies, and each trait exhibited associations across multiple populations. Chromosomes 1 and 8 contain strong candidate alleles for essential amino acid increases. Overall, we present these and additional data that will be useful in determining breeding strategies for the continued improvement of soybean’s nutrient portfolio.

Highlights

Soybeans are a primary contributor to the worldwide production of culinary oils and animal feed
Many methods have been developed to account for these biases, and genome-wide association (GWA) scans have identified known genes in numerous crops and model organisms, including maize (Buckler et al 2009), rice (Atwell et al 2010; Huang et al 2010), Arabidopsis (Atwell et al 2010), and foxtail millet (Jia et al 2013)
We aim to explore the utility of GWA scans in soybean, to refine quantitative trait loci (QTL) for assorted seed composition traits, and to assess the relationship between population structure and genetic architecture with regard to these traits

Summary

Introduction

Soybeans are a primary contributor to the worldwide production of culinary oils and animal feed. Many methods have been developed to account for these biases, and genome-wide association (GWA) scans have identified known genes in numerous crops and model organisms, including maize (Buckler et al 2009), rice (Atwell et al 2010; Huang et al 2010), Arabidopsis (Atwell et al 2010), and foxtail millet (Jia et al 2013) This collection of species has a broad range of mating systems and population histories, soybean represents an extreme case of inbreeding (Hyten et al 2006; Chung et al 2013). We aim to explore the utility of GWA scans in soybean, to refine QTL for assorted seed composition traits, and to assess the relationship between population structure and genetic architecture with regard to these traits

Objectives

Methods

Results

Conclusion