Genome-wide association study for protein and color content in a tetraploid wheat collection

Grain protein content (GPC) and yellow index (YI) are the most important quality traits to measure the quality of tetraploid wheats that benefit the pasta consumers. The main objective of this study was to characterize GPC and YI using 144 different accessions of tetraploid wheats ( Triticum turgidum L., 2 n = 4x = 28; AABB genome) constituted by several subspecies and evaluated in southern Italy for 2 years (2019 and 2022) and in central Chile during 2021 in order to identify new useful superior alleles. SNPs marker, suitable for genome-wide association study (GWAS) were 3924. GWAS was carried out using the Mixed Linear Model (Q+K) which identified 22 marker-trait associations for both traits analyzed, representing 10 and 12 regions associated with grain protein content and yellow index, respectively. QTL linked to GPC were detected on chromosomes 2 A, 3 A, 5 A, and 7 A, while QTL for YI were localized on chromosomes 1B, 2B, 3 A, 4B, 6 A, 6B, 7 A, reflecting their complex genetic nature. The phenotypic variation (R 2 ) explained, ranking from 8.1 % to 8.6 % for GPC and from 8.2 % to 11.6 % for YI content. In addition, one gene involved in nitrogen metabolism, the glutamine synthetase 2 ( GS2 ) on chromosome 2 A, and the main gene involved in the synthesis of carotenoid pigments, the phytoene synthase 1 ( Psy-A1 ) on chromosome 7 A were identified as key candidate genes regulating these two quality traits. Finally, the identification of new haplotypes improves our understanding of the genetic mechanisms controlling protein and color traits in tetraploid wheat and facilitate the development of superior wheat varieties in the future. • Protein and color traits in tetraploid wheat linked to specific genetic regions. • Newly identified wheat alleles may enhance grain quality and pasta color. • Candidate genes for nitrogen metabolism and carotenoid synthesis found. • Genetic variation in wheat offers targets for breeding superior varieties. • Environment impacts traits, but strong genetic control enables targeted selection.