Allele-specific amplification for the detection of ascochyta blight resistance in chickpea

A new co-dominant molecular marker, CaETR, was developed based on allelic sequence length polymorphism in an ethylene receptor-like gene located in the genomic region of a QTL (QTL(AR1)) conferring ascochyta blight resistance in chickpea. This marker not only discriminated resistance and susceptible phenotypes of chickpea to ascochyta blight, but also easily detected heterozygous genotypes. Using the CaETR marker in combination with a previously developed co-dominant SCAR marker (SCY17(590)) linked to another QTL (QTL(AR2)) it was possible to detect resistance alleles in 90 % of resistant accessions in a collection of landraces, advances breeding lines and cultivars, and also detected susceptible alleles in all cases. The results of this study offer a scope for improving the efficiency of conventional chickpea breeding by carrying out negative selection for QTL(AR1) and QTL(AR2) in early generations without relaying directly on the phenotype. This PCR-based approach using both co-dominant markers is proposed as an efficient tool for selecting blight-resistant genotypes in breeding programs.