GWAS identifies an ortholog of the rice D11 gene as a candidate gene for grain size in an international collection of hexaploid wheat

Honoré Tekeu,Martine Jean,Pierre F Djocgoué,Sébastien Bélanger,Patrick M Tsimi,Amina Abed,François Belzile,Eddy L M Ngonkeu,Davoud Torkamaneh,Wuletaw Tadesse,Brian Boyle

doi:10.1038/s41598-021-98626-0

Abstract

Grain size is a key agronomic trait that contributes to grain yield in hexaploid wheat. Grain length and width were evaluated in an international collection of 157 wheat accessions. These accessions were genetically characterized using a genotyping-by-sequencing (GBS) protocol that produced 73,784 single nucleotide polymorphism (SNP) markers. GBS-derived genotype calls obtained on Chinese Spring proved extremely accurate when compared to the reference (> 99.9%) and showed > 95% agreement with calls made at SNP loci shared with the 90 K SNP array on a subset of 71 Canadian wheat accessions for which both types of data were available. This indicates that GBS can yield a large amount of highly accurate SNP data in hexaploid wheat. The genetic diversity analysis performed using this set of SNP markers revealed the presence of six distinct groups within this collection. A GWAS was conducted to uncover genomic regions controlling variation for grain length and width. In total, seven SNPs were found to be associated with one or both traits, identifying three quantitative trait loci (QTLs) located on chromosomes 1D, 2D and 4A. In the vicinity of the peak SNP on chromosome 2D, we found a promising candidate gene (TraesCS2D01G331100), whose rice ortholog (D11) had previously been reported to be involved in the regulation of grain size. These markers will be useful in breeding for enhanced wheat productivity.

Highlights

Grain size is a key agronomic trait that contributes to grain yield in hexaploid wheat
Significant positive correlations were identified between grain yield and grain length (r = 0.50; p < 0.01) and between grain yield and grain width (r = 0.43; p < 0.01)
To assess the reproducibility and accuracy of genotypes called via the GBS approach, we genotyped 12 different plants of Chinese Spring (CS), which were added to the set of 288 wheat samples for single nucleotide polymorphism (SNP) calling and bioinformatics analysis

Summary

Introduction

Grain size is a key agronomic trait that contributes to grain yield in hexaploid wheat. Okamoto et al.[13] performed QTL analyses for grain size and shape-related traits using four synthetic wheat F2 populations to identify the genetic loci responsible for grain size and shape variation in hexaploid wheat and found QTLs for grain length and width on chromosomes 1D and 2D. This is interesting as the tenacious glume gene Tg-D1 on chromosome 2D is a well-known locus that has been recruited for the domestication of wheat grain size and shape. No studies have used GWAS based on GBS for economically important and essential grain yield components traits such as grain length and width in an international collection of hexaploid wheat. The present investigation aimed to identify QTLs and candidate genes governing grain length and width in an international collection of hexaploid wheat using a GBS-GWAS approach

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