Genome-wide association analysis uncovers stable QTLs for yield and quality traits of spring bread wheat (Triticum aestivum) across contrasting environments

Abstract Heat and drought are the foremost abiotic stress factors that significantly diminish both grain yield and quality parameters of bread wheat. Genetic improvement of varieties withstanding such stresses and able to give sufficient grain yield with appropriate quality is very essential. A Genome-wide association study was conducted with 15 K wheat SNP assay for grain yield and quality traits of 189 spring bread wheat genotypes from ICARDA tested at two heat-stressed locations of Dongula and Wad Medani (Sudan) and the drought-stressed location at Marchouch (Morocco). Analysis of variance revealed a significant variation among genotypes for grain yield and quality traits. GWAS with a mixed linear model (MLM) revealed 192 marker-trait associations (MTAs) across the three environments on 17 chromosomes. Highest MTAs were scored for grain yield (50) followed by zeleny sedimentation test (39) and grain protein content (37). Gluten content and alveograph strength scored 29 and 25 MTAs, respectively. The SNP markers RAC875_c24504_119 and BS00063946_51 on chromosome 3B exhibited highly significant and stable MTAs for zeleny sedimentation test across the three environments. The BS00063624_51 marker on chromosome 3B had also revealed a robust and stable MTA for both zeleny sedimentation test and alveograph strength. Highly significant multi-MTAs were detected for grain yield on chromosome 5A and for both grain protein content and gluten content on the short arm of chromosome 1A across the three contrasting environments. The high confidence gene models identified for SNP markers with significant MTAs were involved in encoding genes for various functions including regulating plant growth, development and resistance to both biotic and abiotic stresses. The identified SNP markers with strong MTAs for grain yield and quality traits could potentially applicable for marker-assisted breeding.