Identification and expression analysis of putative genomic regions disseminating biotic stress tolerance in chickpea (Cicer arietinum).

Chickpea (Cicer arietinum L.) productivity is heavily constrained by major biotic stresses, particularly Fusarium wilt, Ascochyta blight and Botrytis gray mold, which collectively cause significant annual yield losses worldwide. To develop a refined understanding of the genetic architecture underlying resistance to these pathogens, a comprehensive meta-analysis was conducted using 113 QTLs taken from 24 independent studies, including diverse mapping populations. This analysis led to the identification of 27 MQTLs, which represent both novel genomic regions and, crucially, refined positions of previously known QTLs with reduced confidence intervals. Four robust Breeders' MQTLs were identified on the basis of high phenotypic variance (PVE ≥ 10%), a low confidence interval (CI ≤ 2 cM) and the involvement of multiple initial QTLs. Among these breeder MQTLs, 229 candidate genes, including key players in plant defense, such as receptor-like kinases (RLKs), resistance gene analogues (RGAs) and genes for RML1A, HSPRO2 and endochitinase A, were identified. These genes were validated through qRT‒PCR expression profiling in contrasting genotypes (WR-315 and JG-62). These refined genomic regions and their associated markers provide a direct pathway for pyramiding multiple resistance QTLs through marker-assisted selection and provide a direct pathway to breed chickpea varieties with durable, broad-spectrum resistance to key fungal diseases. The integrated meta-genomic framework significantly enhances precision and utility and paves the way for the functional characterization of the underlying resistance mechanisms. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-026-04698-y.