Exploring QTL genes contribute to chickpea ascochyta blight resistance across multiple environments using SSR, DArT and SNP assays

Chickpea (Cicer arietinum L.) occupies the third leading position among grain legumes in cultivated area around the world. Ascochyta blight (AB) caused by Ascochytarabiei (Pass.) Labr. is one of the most destructive foliar diseases of chickpea and can cause complete crop failure in many chickpea growing regions around the world. A recombinant inbred line (RIL) population, comprising 165 lines derived from the cross FLIP98-1065 (R) ILC1929 (S),were evaluated in six environments over three years (2008 – 2011) and three locations in Syria (field and greenhouse locations in Tel Hadya “TH“ and a field location at Lattakia “Lat“). The greenhouse experiments were conducted against AB pathotype II. ANOVA analysis indicated significant differences both among the RILs and among the environments. We produced a total of 1398 (134 SSR, 652 DArTseq and 612 SNP) markers and developed a high-resolution genetic map (1244 markers spanning 2503 cM on eight linkage groups). Three major conserved quantitative trait loci (QTLs) that confer AB resistance were identified: two on linkage group 2 (indicated as LG2-A and LG2-B) and one on linkage group 4 (indicated as LG4). These explain, respectively, a maximum of 18.5%, 11.1% and 25% of the total variation. In total, 18 predicted genes were located in LG4, and 9 and10 predicted genes, respectively, were located in LG2-A and LG2-B. This study presents a first set of SNP markers located within genes associated with AB resistance in chickpea, which could be applied in marker-assisted selection programs for breeding AB-resistant chickpeas.