Development of SNP based functional marker for anthracnose resistant Co-2 gene in common bean (Phaseolus vulgaris L.)

Abstract

Abstract Background Anthracnose caused by the fungus Colletotrichum lindemuthianum is one of the most devastating diseases of common beans resulting in catastrophic yield loss. Among the various disease control management techniques, genetic resistance in the host is the most efficient and sustainable strategy for its control. In common bean, the single dominant Co-2 gene confers broad-spectrum resistance against a large number of Colletotrichum isolates. Functional markers (FMs) derived from polymorphic regions in gene sequences influencing phenotypic variation are very effective in marker assisted selection (MAS) of target gene for host plant resistance. Methods and results The present study was undertaken to develop a FM from the promoter region of the Co-2 gene that could enhance its incorporation in breeding programmes. The diverse common bean genotypes were evaluated for anthracnose resistance under controlled conditions. The identified resistant and moderately resistant genotypes were further screened for the presence of the Co-2 gene, a broad-spectrum disease resistance gene using the SCAreoli marker. The promoter regions of the genes of anthracnose resistant and susceptible genotypes were amplified, cloned and sequenced. The SNPs within the regulatory motifs of the promoter region were identified and 14 out of 23 SNPs were found to be strongly associated with disease resistance using genotypic and phenotypic data. The allele-specific CAPS marker was developed and further validated in 43 common bean genotypes with varying anthracnose resistance. The genotype of the CAPS marker and the observed phenotype were perfectly correlated, thereby can be utilized in breeding projects in poorer nations where anthracnose is a common problem. Conclusions The identified allelic marker can be used for transferring anthracnose resistance from highly resistant genotypes into susceptible cultivated varieties of common beans using MAS.