A Genome-Wide Association Study of Highly Heritable Agronomic Traits in Durum Wheat.

Shubin Wang,Shuwei Liu,Qun Sun,Shiaoman Chao,Steven Xu,Guangmin Xia

doi:10.3389/fpls.2019.00919

Abstract

Uncovering the genetic basis of key agronomic traits, and particularly of drought tolerance, addresses an important priority for durum wheat improvement. Here, a genome-wide association study (GWAS) in 493 durum wheat accessions representing a worldwide collection was employed to address the genetic basis of 17 agronomically important traits and a drought wilting score. Using a linear mixed model with 4 inferred subpopulations and a kinship matrix, we identified 90 marker-trait-associations (MTAs) defined by 78 markers. These markers could be merged into 44 genomic loci by linkage disequilibrium (r2 > 0.2). Based on sequence alignment of the markers to the reference genome of bread wheat, we identified 14 putative candidate genes involved in enzymes, hormone-response, and transcription factors. The GWAS in durum wheat and a previous quantitative trait locus (QTL) analysis in bread wheat identified a consensus QTL locus.4B.1 conferring drought tolerance, which was further scanned for the presence of potential candidate genes. A haplotype analysis of this region revealed that two minor haplotypes were associated with both drought tolerance and reduced plant stature, thought to be the effect of linkage with the semi-dwarfing gene Rht-B1. Haplotype variants in the key chromosome 4B region were informative regarding evolutionary divergence among durum, emmer and bread wheat. Over all, the data are relevant in the context of durum wheat improvement and the isolation of genes underlying variation in some important quantitative traits.

Highlights

The bulk of the wheat cropped across the world is represented by either hexaploid bread wheat (Triticum aestivum ssp. aestivum) or tetraploid durum wheat (Triticum turgidum ssp. durum)
We identified 44 chromosome loci associated with 17 agronomic traits and a drought wilting score using genome-wide association studies (GWAS) on a durum wheat panel
A possible explanation for this unexpected result, which was observed in a similar analysis of the genetic basis of awn type in bread wheat (Liu Y. et al, 2017), is that GWAS imposes genetic stratification on the population, which masks the effect of major genes

Summary

Introduction

The bulk of the wheat cropped across the world is represented by either hexaploid bread wheat (Triticum aestivum ssp. aestivum) or tetraploid durum wheat (Triticum turgidum ssp. durum). A core subset has been assembled from this collection, comprising 493 entries with spring growth habit, of which 235 are classed as landraces, 77 as breeding lines, 55 as released cultivars, leaving 126 of unknown breeding status (Aoun et al, 2016; Chao et al, 2017) The size of this panel is appropriate for conducting genome-wide association studies (GWAS), a method which has been applied with some success to reveal the genetic basis of some key agronomic traits in bread wheat (e.g., Liu Y. et al, 2017; Sun et al, 2017; Würschum et al, 2017, 2018). The application of GWAS in durum wheat has to date been more limited, with most of these studies focused on geographically specific diversity and associated with limited sample size (e.g., Maccaferri et al, 2010; Mengistu et al, 2016; Kidane et al, 2017; Soriano et al, 2017; Mangini et al, 2018; Sukumaran et al, 2018)

Methods

Results

Discussion

Conclusion