Genome-wide association mapping for isolate-specific resistance to Ascochyta rabiei in chickpea (Cicer arietinum L.)

Ascochyta blight caused by Ascochyta rabiei is one of the most important foliar diseases of chickpea that can lead to significant yield losses worldwide. A genome-wide association study (GWAS) was applied on a panel of 165 chickpea genotypes against A. rabiei isolates belonging to six different pathotypes. Large phenotypic variation in disease reaction was observed, as the frequency of resistance to pathotypes-I and III was comparatively higher than resistance to other pathotypes. Overall, among the all genotype × pathotype interactions, 259 resistance responses were identified and genotypes were grouped into four clusters based on their phenotypic reactions. The chickpea panel genotyped using DArTseq assay was used for genome-wide association mapping (GWAS). The GWAS revealed 30 marker-trait associations (MTAs) representing 17 quantitate trait loci (QTL) across all chickpea chromosomes. Among them, 11 R-QTLs were associated with resistance to specific pathotype, and 6 R-QTLs were associated with resistance to two or more pathotypes. Most of these R-QTLs overlapped with the previously reported R-QTLs for resistance to A. rabiei, whereas identified R-QTLs on chromosomes Ca1, Ca2, Ca6 and Ca7 are most likely novel. Meanwhile, annotation within the R-QTL intervals revealed genes involved in salicylic acid (SA) and jasmonic acid (JA) regulation pathways as well as cell death programming. The known and novel R-QTL identified in this study may be targeted for use in future chickpea breeding programs to recombine different loci to improve the durability of resistance to multiple A. rabiei isolates/pathotypes.