Genetic loci underlying important shoot morphological traits of wild emmer wheat revealed by GWAS

Abstract Wild emmer wheat (WEW) played a central role in wheat evolution. During the long process of evolution, rapid alteration and sporadic genomic changes occurred in wheat resulting gene modifications and loss to some extent. WEW contains numerous genes that are absent in modern wheat gene pool, which might be useful for improving wheat. But, there is a lack of investigation in exploring genotype to phenotype associations in WEW. This study conducted genome wide association study (GWAS) on 19 shoot morphological traits and identified the genetic loci associated with several phenotypes from a collection of 263 WEW accessions using 90K SNP (single nucleotide polymorphism). A total of 11,393 SNP markers which passed the data quality screening, were used to conduct the GWAS analysis using a mixed linear model in TASSEL (Trait Analysis by Association, Evolution, and Linkage) software. A total of 857 significant MTAs (marker-trait association) were identified harbouring on all fourteen chromosomes, among which 81 were highly significant. On average, each significant MTA explained approximately 7% of phenotypic variance. The most significant MTAs were for tiller number, biomass, and some of yield related traits such as yield/plant and seed size. Putative candidate genes were also predicted for highly significant MTAs using the bioinformatics platform. The majority of the selected MTAs showed significant differences between alternative alleles for the corresponding phenotypes indicating their potential to be used in the breeding program. The genetic loci, contributing significantly to phenotypic variation, identified from this study will be useful in improving wheat morphological traits.