Genome-wide association study identifies candidate genes for agronomic traits under heat- and combined recurrent drought-and heat-stress in wheat

Combined heat and drought stress, mainly during sensitive growth stages, considerably limits wheat yields. Herein, we report on an experiment conducted to analyze and predict the phenology, architecture, and kernel yield component (PAKyC) traits of a diverse bread wheat population grown under heat stress and fully irrigated conditions (HSFIC), and combined recurrent drought and heat stress (CRDHS). 17,711 high-quality single-nucleotide polymorphisms (SNPs) were used to perform a GWAS for 13 PAKyC traits on 187 genotypes, a subset of 234 genotypes, using the BLINK model. Nine constitutive SNPs, 24 marker-trait associations (MTAs), broad-effect pleiotropic SNPs, conditional pleiotropic SNPs, adaptive pleiotropic SNPs under CRDHS, and two robust SNPs were identified. Furthermore, 35 candidate genes were associated with cellular components, biological processes, and molecular functions under CRDHS and HSFIC. Among these genes, 12 were highly expressed (> 0.5 TPM) in response to drought, heat, and combined stresses. Nine genes were identified to be transcription factors regulating drought and heat responses, while the functions of the other three genes remain unclear. Overall, HSFIC and CRDHS environments enabled the dissection of heritable and strongly correlated traits, MTAs, and pleiotropy types: constitutive, adaptive, and conditional. They also helped identify robust SNPs and candidate genes that are important for bread wheat breeding.