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

Abstract

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.

Development and Application of Molecular Markers to Breed Common Bean (Phaseolus vulgaris L.) for Resistance to Common Bacterial Blight (CBB) — Current Status and Future Directions

“…The SU91 SCAR marker associated QTL tentatively positioned on LG 8 or chromosome 8 has been used the most often for MAS (Miklas et al 2005, Mutlu et al 2005b, Hou et al 2010, Navabi et al, unpublished results; Yu et al unpublished results). Epistatic interactions, however, between BC420 and SU91 CBB resistance QTL were detected (Vandemark et al, 2008), which would complicate the use of MMs in MAS. Epistatic interactions between other CBB resistance QTL were also reported in several other studies (Jung et al1997;Tar'an et al, 1998;O'Boyle et al, 2007,).…”

“…The expression of 6 putative genes with supported bean ESTs was assessed and verified by real time RT-PCR. For each putative gene, one or two primer pairs were designed and tested in the contrasting NILs (Near Isogenic Lines) (Vandemark et al 2008). Fifty-seven percent (8 of 14) of the primer pairs were polymorphic.…”

Interactions between QTL SAP6 and SU91 on resistance to common bacterial blight in red kidney bean and pinto bean populations

“…The real-time PCR primers and probe for amplifying SU91 (669 bp; GENBANK #EF553636) were as previously described (Vandemark et al 2008): forward primer SU91F2, 5 0 -d-CACATCGGTTAAC ATGAGTGATTTC-3 0 ; reverse primer SU91R86, 5 0 -d-CACACAAAGGAGGGATAAAAGAGATA A-3 0 ; and probe SU91P34, 5 0 -d-CATATATCATCG CCTATTGTGT-3 0 . The fluorochrome VIC (Applied Biosystems) was attached to the 5 0 terminus of the probe (TaqMan; Applied Biosystems) and a nonfluorescent minor groove binding quencher (MGB) was attached to the 3 0 terminus.…”

“…Reaction to CBB in BC 6 :F 2 plants was characterized by an epistatic interaction between BC420 and SU91. Plants that were homozygous recessive at both loci (bc420 bc420/su91 su91) and plants had at least a single copy of BC420 but were homozygous recessive for SU91 were susceptible to CBB; plants that had at least one copy of SU91 but were homozygous recessive for BC420 expressed an intermediate disease reaction, and the highest level of disease resistance was conferred by genotypes with at least a single resistance copy of both SU91 and BC420 (Vandemark et al 2008). Segregation for resistance among BC 6 :F 3 plants derived from BC 6 :F 2 plants that were heterozygous for both QTL did not deviate significantly from expected ratios of 9 resistant: 3 moderately resistant: 4 susceptible, which was consistent with a recessive epistatic model of inheritance between two loci.…”

“…Recently Vandemark et al (2008) examined the interaction between BC420 and SU91 in the expression of resistance to CBB in common bean using a near isogenic population derived from a cross between XAN 159 (resistant) and Teebus (susceptible). Plants were genotyped using an approach based on real-time PCR (Holland et al 1991;Heid et al 1996) that can be used to co-dominantly interpret plant genotypes for dominant SCAR markers Miklas 2002, 2005).…”