Physical map of QTLs for some agronomic traits across many environments, identification of related candidate genes, and development of KASP markers with emphasis on terminal heat stress tolerance in common wheat

Abstract To understand the genetic architecture of important agronomic traits under heat stress, we used a doubled-haploid (DH) mapping population (177 lines) derived from a heat sensitive cultivar (PBW343) and a heat tolerant genotype (KSG1203). This population was evaluated for 11 agronomic traits under timely (optimum), late (mild heat stress), and very late sown (heat stress) environments over two locations and three years totalling 15 environments. Best linear unbiased estimates for each trait and a sequencing based genotyping (SBG) SNP genetic map comprising 5,710 markers were used for composite interval mapping of QTLs. The identified 66 QTLs were integrated into a physical map (5,710 SNPs; 14,263.4 Mb) of wheat. The 66 QTLs (20 novel QTLs) each explained 5.3–24.9% of the phenotypic variation. Thirteen stable QTLs each with high PVE were recommended for marker-assisted recurrent selection (MARS) for optimum and heat stress environments. Selected QTLs were validated by their presence in high yielding DH lines. Three QTLs for 1000-grain weight were co-localized with known genes TaERF3-3B, TaFER-5B, and TaZIM-A1; a QTL for grain yield was co-localized with TaCol-B5, and gene TaVRT-2 was associated with traits related with some of the QTLs for spike traits. Specific known genes for several traits including thermostability, enhanced grain yield etc. were co-located with the QTLs. Furthermore, 61 differentially expressed candidate genes for heat tolerance in plants that encode 28 different proteins were identified. KASP markers for three major/stable QTLs were developed for MARS focussing on the development of heat tolerant wheat varieties and germplasm.