Genetic analysis of grain protein content and dough quality traits in elite spring bread wheat (Triticum aestivum) lines through association study

Wheat quality parameters are complex traits predominantly influenced by the genetic background of varieties. A total of 802 spring bread wheat breeding lines were tested at Marchouch station, Morocco in 2018 aimed at mining invaluable QTNs for grain protein content (PR), gluten content (GL), alveograph strength (W) and zeleny sedimentation test (Z). A single-locus (MLM) and multi-locus (FarmCPU) GWAS models were implemented using 5,095 SNP markers generated from the genotyping-by-sequencing (GBS) platform. A total of 36 and 92 QTNs were detected for the four quality traits from the MLM and FarmCPU GWAS models, respectively. The FarmCPU model detected markers on homoeologous chromosome group one having highly significant QTNs with PR, GL, W and Z traits. The two implemented GWAS models detected significant QTNs on the short arm of homoeologous chromosome groups 2 and 6 for GL, PR, W and Z traits. FarmCPU model detected SNP_615302 marker on chromosome 3B with highly significant MTAs and concurrent effect for PR, GL and W traits. Moreover, significant MTAs were detected on chromosomes 3D, 4A, 4B, 5A, 5B, 7A, 7B and 7D for the four studied quality traits across the two GWAS models. The in-silico gene annotation for QTNs using the high confidence gene models detected genes involved in numerous functions including regulating plant growth, development and tolerance to biotic and abiotic stresses. The identified markers could potentially be useful tool for quality improvement through marker-assisted selection in future breeding programs.