*Corresponding/Presenting authors’ email: sachinkpsingh@gmail.com

Development of heat tolerant wheat varieties has assumed importance due to frequent episodes of high temperature stress. To understand the genetic architecture of important agronomic traits under heat stress, we used a doubled-haploid (DH) mapping population (177 lines) derived from the cross of a heat-sensitive cultivar (PBW343) and a heat-tolerant genotype (KSG1203).

This population was evaluated in alpha-lattice design with three replication for 11 agronomic traits under timely (optimum), late (mild heat stress), and very late sown (heat stress) environments at two locations namely Meerut (latitude 28° 58' 19.8588'' N; longitude 77° 44' 30.678'' E) and Lucknow (latitude 26° 53' 48.9696'' N; longitude 81° 5' 54.8268'' E) located in Indo-Gangetic Plain (IGP) region for three years (2018-2020); 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. Each of the 66 QTLs (20 novel QTLs) 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 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.

The RT-qPCR analysis for 13 genes exhibited their role in heat tolerance at three grain development stages (10, 15, and 20 days post anthesis) in parental genotypes grown under normal and heat stress conditions. Further, Kompetitive allele specific PCR (KASP) markers for three major/stable QTLs were developed for exercising MARS.

Noteworthy aspect of the current study is the endeavour to validate the QTLs identified for MARS by examining their marker allele composition in the five top yielding DH lines each in timely, late and very late sowing environments.

Overall, present study reported stable QTLs, promising candidate genes, novel KASP markers and superior DH lines for heat tolerance, providing genomic resources to assist breeding for the development of high-yielding and heat-tolerant wheat germplasm and varieties.