Appraising the Genetic Architecture of Kernel Traits in Hexaploid Wheat Using GWAS.

Ali Muhammad,Weicheng Hu,Lingqiang Wang,Jianguo Li,Guosheng Xie,Zhaoyang Li,Jibin Wang

doi:10.3390/ijms21165649

Abstract

Kernel morphology is one of the major yield traits of wheat, the genetic architecture of which is always important in crop breeding. In this study, we performed a genome-wide association study (GWAS) to appraise the genetic architecture of the kernel traits of 319 wheat accessions using 22,905 single nucleotide polymorphism (SNP) markers from a wheat 90K SNP array. As a result, 111 and 104 significant SNPs for Kernel traits were detected using four multi-locus GWAS models (mrMLM, FASTmrMLM, FASTmrEMMA, and pLARmEB) and three single-locus models (FarmCPU, MLM, and MLMM), respectively. Among the 111 SNPs detected by the multi-locus models, 24 SNPs were simultaneously detected across multiple models, including seven for kernel length, six for kernel width, six for kernels per spike, and five for thousand kernel weight. Interestingly, the five most stable SNPs (RAC875_29540_391, Kukri_07961_503, tplb0034e07_1581, BS00074341_51, and BobWhite_049_3064) were simultaneously detected by at least three multi-locus models. Integrating these newly developed multi-locus GWAS models to unravel the genetic architecture of kernel traits, the mrMLM approach detected the maximum number of SNPs. Furthermore, a total of 41 putative candidate genes were predicted to likely be involved in the genetic architecture underlining kernel traits. These findings can facilitate a better understanding of the complex genetic mechanisms of kernel traits and may lead to the genetic improvement of grain yield in wheat.

Highlights

Bread wheat (Triticum aestivum L.) is a staple food crop worldwide, providing 20% of the caloric intake of humans [1,2]
Phenotypic variations of kernel traits among the 319 wheat accessions were evaluated at the experimental field in Wuhan during the winter seasons of 2017 and 2018
We found 24 significant single nucleotide polymorphism (SNP) co-detected by at least two ML-genome-wide association study (GWAS) methods, whereas three SNPs were consistently repeated in both years

Summary

Introduction

Bread wheat (Triticum aestivum L.) is a staple food crop worldwide, providing 20% of the caloric intake of humans [1,2]. Food production needs to be increase by an estimated 50% in order to keep pace with the increasing demands projected for 2050. This requires continuing genetic gains in yield improvement by approximately 1.1% per annum [3]. Enhancing the yield by evaluating grain traits is a common target for genetic improvement in wheat breeding. Grain yield is governed by multiple genes, which are greatly influenced by environmental factors [4]. The total grain yield depends on multiple yield components, such as grain number per spike, thousand kernel weight, kernel length, and kernel width, where each component is quantitatively inherited [5]

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