Four haplotype blocks linked to Ascochyta blight disease resistance in chickpea under Mediterranean conditions

Abstract

Ascochyta blight, caused by the fungal pathogen Ascochyta blight, caused by the fungal pathogen Ascochyta rabiei, is a devastating biotic stress that poses a significant threat to chickpea cultivation worldwide. To combat this disease, breeding programs have focused on developing cultivars with resistance to Ascochyta blight. However, a comprehensive understanding of the underlying plant defense mechanism is still lacking. To identify genomic regions associated with resistance, a recombinant inbred line (RIL) population was created by crossing ILC3279 (kabuli, resistant) and WR315 (desi, susceptible), which was then phenotyped and sequenced using a tuneable genotyping-by-sequencing (tGBS) protocol to obtain single nucleotide polymorphisms (SNPs). We further validated the association of genomic regions with Ascochyta blight resistance in a second recombinant inbred line\population derived from the cross between JG62 (desi, susceptible) and ILC72 (kabuli, resistant). Our analysis identified four genomic regions associated with Ascochyta blight resistance in chromosomes 2 and 4, among which a region spanning from 3.52 to 8.20 Mb in chromosome 4 was the most robust candidate for resistance, being associated with resistance in both years and populations. A total of 30 genes from the identified regions were selected as robust candidates, and LOC101507066, which encodes a leucine-rich repeat receptor-like protein kinase, was the most robust candidate gene, as it plays critical roles in plant stress responses and immunity. Our findings have potential to accelerate marker-assisted genetic improvement and facilitate the development of integrated strategies for crop protection.