Novel Genomic Regions linked to Ascochyta blight Resistance in two differentially resistant cultivars of chickpea

Ascochyta blight (AB) caused by the fungal pathogen Ascochyta rabiei is a devastating foliar disease of chickpea (Cicer arietinum L.). Genotyping-by-sequencing (GBS) has been used in the current study for the identification of AB associated quantitative trait loci (QTLs) and their gene(s). We evaluated genotyping-by-sequencing (GBS)-based approach for mapping QTLs associated with AB resistance in chickpea using two recombinant inbred lines populations (AB3279 and AB482) derived from two crosses ILC 1929 X ILC 3279 and ILC 1929 X ILC 482, under six different environments. In total, twenty-one different genomic regions were identified on linkage groups CalG02 and CalG04 pertaining to AB resistance in both populations AB3279 and AB482. Four genomic regions were detected on CalG02 in the population AB3279 and nine major genomic regions were associated with AB resistance on CaLG04, five out of them were common to both resistant parents ‘ILC3279’ and ‘ILC482’, and eight minor genomic regions with two out of them common between both populations. These regions contain 1,118 SNPs significantly associated (p ≤ 0.001) with AB resistance. Gene ontology (GO) assigned these QTLs to 319 genes, many of which were associated with stress and disease resistance, with most important genes belonging to resistance gene families including Leucine-Rich Repeat (LRR), and transcription factors families. Our results may refer to the flowering-associated gene GIGANTEA as a possible key factor in AB resistance in chickpea. The results have narrowed the AB resistance associated regions on the chickpea physical map and the associated markers will help in breeding programs for chickpea improvement.