Genome-Wide Association Study Reveals the Genetic Basis of Five Quality Traits in Chinese Wheat.

Shuiyuan Hao,Min Wu,Baogerile Baogerile,Mingming Xin,Jianguang Tao,Jinchao Dong,Jinghong Shi,Dan Liu,Liangliang Yu,Sanming Miao,Qunce Pei,Haiwei Wang,Ming Gao,Hongyao Lou,Mingshan You,Naihu Zhao

doi:10.3389/fpls.2022.835306

Abstract

Bread wheat is a highly adaptable food crop grown extensively around the world and its quality genetic improvement has received wide attention. In this study, the genetic loci associated with five quality traits including protein content (PC), gluten content (GC), baking value (BV), grain hardness (HA), and sedimentation value (SV) in a population of 253 Chinese wheat grown in Inner Mongolia were investigated through genome wide association mapping. A total of 103 QTL containing 556 SNPs were significantly related to the five quality traits based on the phenotypic data collected from three environments and BLUP data. Of these QTL, 32 QTL were continuously detected under at least two experiments. Some QTL such as qBV3D.2/qHA3D.2 on 3D, qPC5A.3/qGC5A on 5A, qBV5D/qHA5D on 5D, qBV6B.2/qHA6B.3 on 6B, and qBV6D/qHA6D.1 on 6D were associated with multiple traits. In addition, distribution of favorable alleles of the stable QTL in the association panel and their effects on five quality traits were validated. Analysis of existing transcriptome data revealed that 34 genes were specifically highly expressed in grains during reproductive growth stages. The functions of these genes will be characterized in future experiments. This study provides novel insights into the genetic basis of quality traits in wheat.

Highlights

Bread wheat (Triticum aestivum L.), which is a highly adaptable food crop cultivated globally, supplies approximately 20% of the total calories consumed by humans (Shiferaw et al, 2013; Shewry and Hey, 2015)
The present study was undertaken to identify genes/quantitative trait loci (QTL) related to wheat quality traits across different environments in Inner Mongolia using an association mapping approach combined with a high-density SNP marker assay
A total of 30,729 high-quality SNP markers were identified across all 21 wheat chromosomes (Table 1 and Supplementary Figure 1), of which 10,879, 12,142, and 7,771 markers were located in the A, B, and D subgenomes, respectively

Summary

INTRODUCTION

Bread wheat (Triticum aestivum L.), which is a highly adaptable food crop cultivated globally, supplies approximately 20% of the total calories consumed by humans (Shiferaw et al, 2013; Shewry and Hey, 2015). With the rapid development of genome sequencing technology and high-density SNP arrays for genotyping (e.g., 9, 35, 55, 90, 660, and 820), the genome-wide association study (GWAS) has become an increasingly popular and promising alternative to linkage mapping for elucidating the genetic basis of complex traits, especially quality traits (Yu et al, 2006; Zhu et al, 2008; Ji et al, 2021). This method enables the use of natural populations without interbreeding to produce progeny, making it convenient for phenotype and genotype identifications. The present study was undertaken to identify genes/QTL related to wheat quality traits across different environments in Inner Mongolia using an association mapping approach combined with a high-density SNP marker assay

MATERIALS AND METHODS

RESULTS

DISCUSSION

DATA AVAILABILITY STATEMENT