A Genome-Wide Association Study Reveals a Rich Genetic Architecture of Flour Color-Related Traits in Bread Wheat.

Shengnan Zhai,Pingzhi Zhang,Wujun Ma,Shuanghe Cao,Jun Yan,Yuanfeng Hao,Yingxiu Wan,Weie Wen,Dengan Xu,Jindong Liu,Zhonghu He,Xianchun Xia

doi:10.3389/fpls.2018.01136

Abstract

Flour color-related traits, including brightness (L*), redness (a*), yellowness (b*) and yellow pigment content (YPC), are very important for end-use quality of wheat. Uncovering the genetic architecture of these traits is necessary for improving wheat quality by marker-assisted selection (MAS). In the present study, a genome-wide association study (GWAS) was performed on a collection of 166 bread wheat cultivars to better understand the genetic architecture of flour color-related traits using the wheat 90 and 660 K SNP arrays, and 10 allele-specific markers for known genes influencing these traits. Fifteen, 28, 25, and 32 marker–trait associations (MTAs) for L*, a*, b*, and YPC, respectively, were detected, explaining 6.5–20.9% phenotypic variation. Seventy-eight loci were consistent across all four environments. Compared with previous studies, Psy-A1, Psy-B1, Pinb-D1, and the 1B•1R translocation controlling flour color-related traits were confirmed, and four loci were novel. Two and 11 loci explained much more phenotypic variation of a* and YPC than phytoene synthase 1 gene (Psy1), respectively. Sixteen candidate genes were predicted based on biochemical information and bioinformatics analyses, mainly related to carotenoid biosynthesis and degradation, terpenoid backbone biosynthesis and glycolysis/gluconeogenesis. The results largely enrich our knowledge of the genetic basis of flour color-related traits in bread wheat and provide valuable markers for wheat quality improvement. The study also indicated that GWAS was a powerful strategy for dissecting flour color-related traits and identifying candidate genes based on diverse genotypes and high-throughput SNP arrays.

Highlights

Bread wheat (Triticum aestivum L.) is among the most important food crops and is one of the most traded commodities in world markets (Curtis and Halford, 2014)
To assess the pyramiding effect of favorable alleles of marker–trait associations (MTAs) for flour color-related traits, we examined the number of favorable alleles in each accession, and the best linear unbiased predictor (BLUP) value for each trait was regressed against the number of favorable alleles
Broad comparison of MTAs identified in this study with Quantitative trait loci (QTL) in previous reports indicated many common loci conditioning flour color-related traits, and four MTAs detected were new, including MTAs on chromosome 7A (2) for L∗, chromosome 2A (629,632,627–629,632,697 Mb) for a∗ and chromosome 7D (635,560,079–635,560,149 Mb) for yellow pigment content (YPC)

Summary

Introduction

Bread wheat (Triticum aestivum L.) is among the most important food crops and is one of the most traded commodities in world markets (Curtis and Halford, 2014). Flour color plays a significant role in the end-use quality of wheat, for Asian noodles and steamed bread, since it affects consumer acceptance, market value and human nutrition (Zhai et al, 2016a). Yellow pigment content (YPC) is the most important determinant of flour yellowness caused mainly by accumulation of carotenoids in the grain (Mares and Campbell, 2001). It is a very important quality criterion for pasta made from durum wheat. Understanding the genetic basis of flour color-related traits (L∗, a∗, b∗, and YPC) is necessary for improving wheat quality by marker-assisted selection (MAS)

Objectives

Methods

Results

Discussion

Conclusion