mQTL-seq and classical mapping implicates the role of an AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED (AHL) family gene in ascochyta blight resistance of chickpea

Abstract

Ascochyta blight (AB) caused by the fungal pathogen Ascochyta rabiei is a serious foliar disease of the legume crop chickpea (Cicer arietinum L.). Despite many genetic studies on chickpea-Ascochyta interaction, genome-wide scan of chickpea for the identification of AB associated QTLs and their gene(s) has not been accomplished. To elucidate narrow QTLs for AB resistance, here we report the use of multiple QTL-sequencing (mQTL-seq) approach on two sets of extreme AB phenotype bulks derived from Cicer intraspecific and interspecific crosses. Two major QTLs qABR4.1 and qABR4.2, and a minor QTL qABR4.3 were identified on assembled pseudomolecule 4 (Ca4). We narrowed qABR4.1 to a ‘robust ~50 kb region’ through mapping on a larger intraspecific RIL population and comparative analysis. Among four genes, the CaAHL18 gene showed higher expression under Ascochyta stress in AB resistant parent suggesting that it is the candidate gene under ‘robust qABR4.1’. Dual-luciferase assay with CaAHL18 polymorphic cis-regulatory sequences showed that higher expression is associated with an allelic variation. Thus, our findings on chickpea-Ascochyta interaction have narrowed down AB resistance associated QTLs on chickpea physical map and identified a novel QTL qABR4.3. The narrowed QTL and gene associated markers will help in biotechnological and breeding programs for chickpea improvement.