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Title: Genotyping with Real-time PCR Reveals Recessive Epistasis Between Independent QTL Conferring Resistance to Common Bacterial Blight in Dry Bean

item Vandemark, George
item Fourie, Diedre
item Miklas, Phillip - Phil

Submitted to: Journal of Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/5/2008
Publication Date: 8/1/2008
Citation: Vandemark, G.J., Fourie, D., Miklas, P.N. 2008. Genotyping with Real-time PCR Reveals Recessive Epistasis Between Independent QTL Conferring Resistance to Common Bacterial Blight in Dry Bean. Journal of Theoretical and Applied Genetics.117:513-522.

Interpretive Summary: Molecular markers are DNA sequences that can be useful for selecting plants with desired attributes for traits that are difficult to evaluate, such as disease resistance. However, many traits are not controlled by a single gene, but rather by an interaction between several genes, each of which may have different amounts of influence on trait expression. One of the most severe diseases of bean is a leaf and pod disease caused common bacterial blight (CBB). Up to 22 different genes have been implicated in the expression of resistance in bean to CBB. Historically, molecular markers associated with these resistance genes have only been able to determine if the gene of interest is present, but have not been able to distinguish plants with one copy of the gene from plants with two copies of the gene. Breeders need to be able to identify plants that have two copies of a gene of interest in order to assure that a variety produced from these plants uniformly expresses the trait. In addition, previously available molecular markers have not been useful for determining how different genes interact to confer resistance to CBB. Two important genes for resistance to CBB are referred to as BC420 and SU91. This paper describes the development of “real-time fluorescent PCR” assays that were used to determining whether plants have zero, one, or two copies of both BC420 and SU91 and to establish how these two genes interact to confer resistance to CBB. We observed the following relationships between these two genes: 1. Plants with no copies of SU91 are susceptible to CBB even if they have two copies of BC420; 2. Plants that have no copies of BC420 but at least one copy of SU91 express moderate disease resistance, and 3. The highest level of resistance occurs in plants that have at least one copy of both BC420 and SU91. These results indicate that bean breeders must pick plants that have copies of both of these genes in order to realize the highest levels of resistance possible. In addition, the PCR assay can be used to identify plants with desired gene combinations as seedlings. This will result in savings of thousands of dollars per breeding cycle in labor and facilities costs. These results will also make it possible to develop resistant varieties much faster than could be done using previously available molecular markers.

Technical 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 in, 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~QTL) and B8 (SU91~QTL) were interpreted as codominant markers using real time PCR assays. This enabled assignment of BC6F2 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: i) the expression of BC420 was epistatically suppressed by a homozygous recessive su91//su91 genotype; ii) SU91//SU91 and SU91//su91 genotypes conditioned an intermediate disease reaction when homozygous recessive for bc420//bc420; and iii) the highest level of disease resistance was conferred by genotypes with at least a single copy of both QTL (BC420//-; SU91//-). Segregation for resistance among BC6F3 plants derived from BC6F2 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 duplicate 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.