Superior haplotypes for haplotype‐based breeding for drought tolerance in pigeonpea (Cajanus cajan L.)

Abstract

Haplotype‐based breedin g, a recent promising breeding approach to develop tailored made crop varieties deals with identification of superior haplotypes and their deployment in breeding programs. In this context, whole genome re‐sequencing data of 292 genotypes from pigeonpea reference set was mined to identify the superior haplotypes for 10 drought‐responsive candidate genes. A total of 83, 132 and 60 haplotypes were identified in breeding lines, landraces and wild species, respectively. Candidate gene‐based association analysis of these 10 genes on a subset of 137 accessions of the pigeonpea reference set revealed 23 strong marker‐trait associations (MTAs) in five genes influencing seven drought responsive component traits. Haplo‐pheno analysis for the strongly associated genes resulted in the identification of most promising haplotypes for three genes regulating five component drought traits. Gene C. cajan_23080 ‐H2 was found to be the superior most haplotype in terms of plant weight (PW), fresh weight (FW) and turgid weight (TW), C.cajan_30211‐ H6 for PW, FW, TW and dry weight (DW), C.cajan_26230 ‐H11 for FW and DW and C.cajan_26230 ‐H5 for relative water content (RWC) under drought stress condition. The identified donor genotypes possessing superior haplotype combinations may be utilized in haplotype‐based breeding to develop next‐generation tailor‐made better drought responsive pigeonpea cultivars.