Comprehensive Genome‐Wide Association Study Reveals Genomic Regions Associated With Agro‐Morphological Traits Under Heat Stress in Indian Mustard [ <scp> <i>Brassica juncea</i> </scp> (L.) Czern. and Coss.]

ABSTRACT Elevated temperatures adversely affect the growth and productivity of Brassica juncea at various developmental stages. Breeding heat‐tolerant varieties presents an economically viable strategy to reduce the impacts of heat stress. Therefore, a genome‐wide association study was conducted, focusing on agro‐morphological traits under late‐sown conditions, exerting heat stress at the reproductive phase. A diverse panel of 142 genotypes was used for phenotyping and SNP genotyping. During late‐sown conditions of 2020–2021, 2021–2022 and 2022–2023, a total of 59 significant marker–trait associations were identified. Among these, 11 SNPs were consistently associated with key traits across the seasons. These stable SNPs were further analysed through gene annotation and in silico expression profiling. The SNPs were linked to several important agro‐morphological traits affected by heat stress. In silico analysis of SNPs revealed important candidate genes directly involved in stress response and trait regulation. Expression profiling confirmed predominant expression of these genes in corresponding tissues, indicating their functional relevance. The identified candidate genes will be subsequently used for the development of heat‐tolerant B. juncea varieties through molecular breeding approaches.