Genome-wide association studies reveal genomic regions for kernel-related traits in durum wheat

Kernel size and shape-related traits affect grain yield and semolina milling potential, both of which are important targets of durum wheat improvement programs. However, the genetic basis of these traits in durum wheat are largely unknown. In this study, we examined the genetic bases of kernel size and shape-related traits in a diverse panel of 170 genotypes, comprised mostly of Argentinian cultivars. Genotypes were characterized phenotypically in four field experiments in Argentina and genotypically using the 35K Axiom Wheat Breeder SNP Array. High phenotypic variability and heritability values were observed for all studied traits. Thousand kernel weight showed strong correlations with kernel area and factor form density, followed by kernel width, length and perimeter. Using genome-wide association mapping, a total of 80 marker-trait associations (MTAs) were identified over the FDR threshold (P < 0.00001). Of them, 23 MTAs were identified for best linear unbiased predictors (BLUPs) across the four environments or at least in two single environments, and ten SNPs located on 1B, 2A, 2B, 3B, 6A, and 7A chromosomes were identified by multiple mapping methods. Three of these SNPs, located on chromosome 2A, were selected as particularly interesting since they were identified by all three mapping methods tested. Two haplotype blocks (of 24.2 and 16.6 Mb) contain the SNPs of chromosome 2A, and both were strongly associated with most kernel traits. These haplotypes were not linked to Ppd-A1 gene and thus represent promising targets for further validation and implementation in molecular assisted breeding to improve kernel related traits in durum wheat.