Development and identification of SCAR marker for heat tolerant in wheat via Bulk Segregant Analysis and Bioinformatics approaches

High temperature causes several biological changes in wheat and results in yield reduction. Use of DNA marker linked to heat resistance/tolerance attributes accelerates selection and expedites breeding for heat tolerance. In this study, heat-tolerant wheat var. Halna and heat-susceptible wheat var. K9006 were selected as donor and recipient, respectively, after phenotyping. In the F2 population, heat tolerant and susceptible Lines were bulked for the bulk segregant analysis. Parental polymorphism was studied by 32 RAPD primers, of which only six primers showed polymorphism between parents and used for the confirmation of F1crosses. The 10 tolerant and 10 susceptible F2 plants (F1 (K 9006 × Halna) were bulked and the tolerant bulk showing maximum membrane stability index (53.48%) and chlorophyll content (2.16 mg/g) were used for the molecular study. The RAPD primer (OPE 09) segregated susceptible and tolerant bulks and an unique band of 700 bp was observed in the tolerant parent (var. Halna) and the tolerant bulk was cloned and sequenced. A SCAR marker was developed from the cloned bands, and a primer pair was designed. The designed SCAR marker was successfully validated on the randomly selected heat-susceptible and heat-tolerant wheat varieties. The obtained sequence from the cloned unique bands of the tolerant bulk can be further utilized via bioinformatics tools. Further physicochemical, secondary structure prediction, transmembrane domain, tertiary structure prediction, active site prediction, and molecular docking were performed to analyze and elucidate the cloned sequence. The findings indicate that the identified sequence might be related to a specific biochemical pathway involving tolerance to heat stress in wheat.