Genome-wide insights into seed morphometry and breeding ideotypes in durum wheat

Durum wheat ( Triticum turgidum ssp. durum ) is a staple cereal crop that is widely cultivated in the Mediterranean and semi-arid areas. The morphology of the grain plays an important role in determining yield, milling quality, and the suitability for various end-use applications. Although seed size and shape hold economic significance, the genetic basis of these traits has been less extensively studied in durum wheat compared to bread wheat. The current study evaluated a panel of 185 accessions for various seed morphometric and weight traits using digital image-based phenotyping. Substantial genetic variation was detected, with high levels of heritability for major traits, including single seed weight (84.1%) and grain perimeter (78.9%), indicating a high possibility of selection. Genome-wide association analysis (GWAS) using 25,019 high-quality SNPs on the wheat 90 K Infinium iSelect SNP array with eight GWAS models detected 47 significant marker-trait associations (MTAs) across all 14 chromosomes, with the sub-genome B having the most significant associations. Five MTAs co-located with previously reported loci for grain size, shape and weight, while the remaining 42 were putatively novel. Putative candidate genes located near associated loci included genes encoding F-box proteins, transporters, and metabolic enzymes, which have previously been implicated in grain development and nutrient allocation. The stage-specific regulation of candidate genes and their in silico expression profiling during early and mid-grain development was also examined, with some of these genes continuing to be expressed during seed maturation. The Multi-trait Genotype-Ideotype Distance Index (MGIDI) analysis identified slender (IC0535876, IC0128512) and bold (UAS12, UAS38) grain ideotypes as promising accessions. This study reveals substantial genetic variation and polygenic architecture underlying seed morphometric traits in durum wheat. The results suggest that these accessions and associated loci may serve as useful resources for future validation and breeding applications. The identified MTAs and candidate genes may further support marker-assisted selection for grain size and shape.