Uncovering genomic regions controlling plant architectural traits in hexaploid wheat using GWAS

Abstract

Background: Wheat is a staple food crop worldwide. Plant height is a key factor in plant architecture as it plays a crucial role in lodging and thus affects yield and quality. Genome-wide studies are mostly applied in crop plants, due to its advanced genotyping technologies, identification of novel loci, and improved statistical approaches. Results: In this study, the population was genotyped by using Illumina iSelect 90K single nucleotide polymorphism (SNP) assay and finally 22,905 high-quality SNPs were used to perform a genome-wide association study (GWAS) for plant architectural traits employing four multi-locus GWAS (ML-GWAS) and three single-locus GWAS (SL-GWAS) models. As a result, 174 and 97 significant SNPs controlling plant architectural traits were detected by four ML-GWAS and three SL-GWAS methods, respectively. Among these SNP makers, 43 SNPs were commonly detected, including seven across multiple environments and thirty-six across multiple methods. Interestingly, five most stable SNPs (Kukri_c34553_89, RAC875_c8121_1490, wsnp_Ex_rep_c66315_64480362, Ku_c5191_340, and tplb0049a09_1302) consistently detected across multiple environments and methods, possibly played a role in modulating plant height and flag leaf length. When comparing ML-GWAS methods, pLARmEB was the most powerful and accountable for the detection of 49 significant SNPs that mostly contributed to plant height (36 SNPs). However, in SL-GWAS the FarmCPU model detected most of the significant SNPs. Moreover, a total of 152 candidate genes were found that are likely to be involved in plant growth and development which may provide insightful information related to plant architectural traits.Conclusion: Altogether, our results reveal 174 and 97 significant SNPs controlling plant architectural traits using four ML-GWAS and three SL-GWAS methods, respectively. The detection of the stable loci across multiple environments and methods, possibly play a role in modulating plant architectural traits in hexaploid wheat, and finally will contribute to the discovery of valuable SNP loci for marker-assisted selection (MAS) in wheat molecular breeding.