Selection for Monogenic Pest Resistance Traits with Coupling‐ and Repulsion‐Phase RAPD Markers

Abstract

The random amplified polymorphic DNA (RAPD) assay has recently provided a marker system that may be useful for indirect selection and pyramiding of monogenic pest resistance traits in crop species. Our objective was to investigate the efficiency of marker‐assisted selection with RAPD markers linked in coupling and in repulsion with a single resistance allele. Common bean (Phaseolus vulgaris L.) near‐isogenic lines differing for the recessive bean common mosaic virus (BCMV) resistance allele bc‐3 were screened to identify linked RAPD markers. Two cosegregating RAPD markers were identified and scored across an F2 population of 103 individuals segregating for the bc‐3 allele. One RAPD marker was linked in coupling (1.9. ± 1.4 cM) and one in repulsion (7.1 ± 2.6 cM) with the bc‐3 allele. Categorization of the bc‐3 genotypes in the F2 population revealed that selection against the repulsion‐phase RAPD, as opposed to selection for the coupling‐phase RAPD, provided a greater proportion of homozygous resistant (81.8 versus 26.3%) selections, and a lower proportion of both segregating (18.2 versus 72.5%) and homozygous susceptible (0.0 versus 1.2%) selections. Selection of individuals based on the phenotype of both RAPD markers (i.e., the plus form of the coupling‐phase RAPD and simultaneous with the minus form of the repulsion‐phase RAPD) was identical to selection based solely on the repulsion‐phase RAPD alone. The selection results obtained in our case study were consistent with the theoretical expectations, and both demonstrated that repulsion‐phase linkages provided greater selection efficiency than coupling‐phase linkages, even when the former have greater linkage distances from the pest resistance allele. Because repulsion‐phase RAPD markers are more useful in marker‐assisted selection for monogenic pest resistance traits, researchers will want to design their screening experiments in ways that will optimize the discovery of these.