Genotyping with real-time PCR reveals recessive epistasis between independent QTL conferring resistance to common bacterial blight in dry bean.

Resistance to common bacterial blight in common bean is a complex trait that is quantitatively inherited. Combining QTL is the current strategy for improving resistance, but interactions among different QTL are unknown. We examined the interaction between two independent QTL present in dry bean breeding line XAN 159. The QTL were studied in a near isogenic population consisting of 120 BC6:F2 plants. Each BC6:F2 plant was evaluated for disease reaction at several time points after pathogen inoculation and the dominant SCAR markers linked with QTL on linkage groups B6 (BC420 approximately QTL) and B8 (SU91 approximately QTL) were interpreted as codominant markers using real time PCR assays. This enabled assignment of BC6:F2 plants to all nine possible genotypes. Reaction to CBB in BC6:F2 plants was characterized by an epistatic interaction between BC420 and SU91 such that: 1) the expression of BC420 was epistatically suppressed by a homozygous recessive su91//su91 genotype; 2) SU91//SU91 and SU91//su91 genotypes conditioned an intermediate disease reaction when homozygous recessive for bc420//bc420; and 3) the highest level of disease resistance was conferred by genotypes with at least a single resistance allele at both QTL (BC420//-; SU91//-). Segregation for resistance among BC6:F3 plants derived from BC6:F2 plants that were heterozygous for both QTL did not deviate significantly from expected ratios of 9 resistant: 3 moderately resistant: 4 susceptible. This is consistent with a recessive epistatic model of inheritance between two loci. These results indicate breeders will realize greatest gains in resistance to CBB by selecting breeding materials that are fixed for both QTL. This is a first report of a qualitative digenic model of inheritance discerning an interaction between two QTL conditioning disease resistance in plants.