Identifying genomic regions associated with key agro‐morphological traits in soft red winter wheat using genome‐wide association study

Abstract Agro‐morphological traits play a significant role in the adaptation of wheat to diverse agroecosystems. Genetic understanding of these traits is crucial to develop cultivars adapted to specific environments and maximize their productivity. This is a comprehensive genome‐wide association study (GWAS) of 230 diverse lines of soft red winter wheat for identifying quantitative trait loci (QTLs) related to eight key agro‐morphological traits. The diversity panel was evaluated in two locations for three consecutive years (2020–2023). A total of 150 significant marker–trait associations were detected, including 65 for three flag leaf traits, 35 for peduncle length, 33 for plant height, 16 for heading date, and one for plant vigor using 27,466 single nucleotide polymorphism (SNP) markers. Eleven high‐confidence major‐effect QTLs explaining greater than 10% phenotypic variance were detected, of which seven were stable, and one showed an association with plant height and peduncle length. QTLs possibly allelic for important dwarfing ( Rht23 ) and vernalization ( Vrn‐B1 ) genes were identified. Six QTLs, QFlw.uga‐1A , QPdl.uga‐1A , QFlw.uga‐2B.2 , QPdl.uga‐5A , QPdl.uga‐7A , and QPht.uga‐7B , are presumed to be novel, and nearby candidate gene(s) were identified for all except QPdl.uga‐1A . The pyramiding of favorable alleles from major‐effect QTLs was found to have significant improvement in peduncle length (shortened by 5 cm), flag leaf width (increased by 0.18 cm), and plant height (shortened by 11 cm). This study has improved our genetic understanding of important agro‐morphological traits. These results, upon further validation, can be used in breeding for desirable plant architecture to improve wheat yield potential.