Abstract
Key messageA high-density linkage map of chickpea using 3430 SNPs was constructed and used to identify QTLs and candidate genes for ascochyta blight resistance in chickpea.Chickpea cultivation in temperate conditions is highly vulnerable to ascochyta blight infection. Cultivation of resistant cultivars in combination with fungicide application within an informed disease management package is the most effective method to control ascochyta blight in chickpeas. Identifying new sources of resistance is critical for continued improvement in ascochyta blight resistance in chickpea. The objective of this study was to identify genetic loci and candidate genes controlling the resistance to ascochyta blight in recombinant inbred lines derived from crossing cultivars Amit and ICCV 96029. The RILs were genotyped using the genotyping-by-sequencing procedure and Illumina® GoldenGate array. The RILs were evaluated in the field over three site-years and in three independent greenhouse experiments. A genetic map with eight linkage groups was constructed using 3430 SNPs. Eight QTLs for resistance were identified on chromosomes 2, 3, 4, 5 and 6. The QTLs individually explained 7–40% of the phenotypic variations. The QTLs on chromosomes 2 and 6 were associated with the resistance at vegetative stage only. The QTLs on chromosomes 2 and 4 that were previously reported to be conserved across diverse genetic backgrounds and against different isolates of Ascochyta rabiei were confirmed in this study. Candidate genes were identified within the QTL regions. Their co-localization with the underlying QTLs was confirmed by genetic mapping. The candidate gene-based SNP markers would lead to more efficient marker-assisted selection for ascochyta blight resistance and would provide a framework for fine mapping and subsequent cloning of the genes associated with the resistance.
Highlights
Chickpea (Cicer arietinum L.) is the world’s second most important grain legume
74.6% of the reads were aligned to the CDC Frontier reference genome sequence (v2.6) and the remaining 25.4% reads were removed from further analysis
14,531 SNPs were physically mapped on the eight chickpea chromosomes, whereas the remaining 1050 SNPs were mapped on 188 unplaced scaffolds
Summary
Chickpea (Cicer arietinum L.) is the world’s second most important grain legume. Multiple pests and diseases significantly affect chickpea productivity. Ascochyta blight caused by the necrotrophic fungal pathogen. Ascochyta rabiei (Pass.) Lab. is one of the most devastating fungal diseases of chickpea. A. rabiei can infect the chickpea plant at any growth stage from plant emergence to seed maturity and produces blight-like symptoms on all aboveground plant parts. The ascochyta blight infection results in lower yield and poor seed quality. In North America, management of ascochyta blight is heavily dependent on fungicide applications. This practice has resulted in insensitivity of A. rabiei isolates against certain fungicides such as strobilurin (Chang et al 2007; Wise et al 2009).
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