Genome Wide Characterization of Resistance Genes Through Resequencing of Chickpea Genomes

Chickpea wilt disease, caused by Fusarium oxysporum f.sp. ciceri,(Foc) limits chickpea productivity worldwide. Eight physiological races of the pathogen are recognized based on the response of major disease resistance genes on linkage groups LG 2 and LG5. The focus of this study is an 8.2 cM region on LG2, containing numerous NB-LRR genes and conferring resistance to five of the Foc races.

            We re-sequenced the genomes of seven chickpea genotypes for which LG2 loci discriminate among five Foc races. JG 62 and WR 315 are universally susceptible and universally resistant genotypes, while the remaining five genotypes are RIL segregants from a cross of WR 315 and an unrelated susceptible parent. The five RIL sibling lineages differ in their responses to the five Foc races.

            For each of the seven chickpea genotypes, a single Nextera library composed of ~400bp inserts was prepared and barcoded. The universal wilt susceptible line (JG 62) and the universal resistant line (WR 315) were pooled together and sequenced separately in one lane to achieve ~10X coverage. The remaining five differential lines were pooled and sequenced in second lane to achieve coverage of ~4X.  We have previously annotated the chickpea CDC Frontier reference genome for NB-LRR disease resistance genes and identified a major extended cluster on LG2. The goal of this study is to broadly define the haplotypes on LG2 that correspond Foc resistance loci, and thus delimit a maximum set of candidate NB-LRR genes as one step towards functional analysis of these agronomically important genes.