Two 24-mer SCAR primers (SW13) were developed from a previously identified 10-mer RAPD primer (OW13(690)) linked to the I gene, which conditions resistance to bean common mosaic virus (BCMV) in common bean. Linkage between SW13 and the I gene was tested in three F2 populations segregating for both SW13 and the I gene: N84004/Michelite (1.0 +/- 0.7 cM), Seafarer/UI-114 (1.3 +/- 0.8 cM), and G91201/Alpine (5.0 +/- 2.2 cM). SW13 proved to be more specific and reproducible than the OW13(690) RAPD marker. Using different heat-stable DNA polymerases, SW13 amplified a single 690-bp fragment linked to the I gene that more consistently permitted the identification of resistant plants. In addition, the presence of the I gene was detected using SW13 in genotypes originating from different gene pools of Phaseolus vulgaris L., indicating a broad utility of this marker for bean breeding programs.

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The development and use of RAPD markers for applications in crop improvement has recently generated considerable interest within the plant breeding community. One potential application of RAPDs is their use for "tagging" simply-inherited (monogenic) pest-resistance genes and enabling more efficient identification and selection of genotypes carrying specific combinations of resistance genes. In this report, we propose and describe the use of heterogeneous inbred populations as sources of near-isogenic lines (NILs) for targeting RAPD markers linked to major pest resistance genes. The development of these NILs for RAPD marker analyses involved a sequence of line and mass selection during successive generations of inbreeding. DNA bulks derived from the NILs were used to identify a RAPD marker (designated OK14620, generated by 5'-CCCGCTACAC-3' decamer) that was tightly linked (2.23±1.33 centiMorgans) to an important rust [Uromyces appendiculatus (Pers.) Unger var. appendiculatus] resistance gene (Ur-3) in common bean (Phaseolus vulgaris L.). The efficiency of this approach was demonstrated by a low rate of false-positives identified, the tightness of the linkage identified, and the ability to detect polymorphism between genomic regions that are representative of the same gene pool of common bean. This method of deriving NILs should find application by researchers interested in utilizing marker-assisted selection for one or more major pest resistance genes. The identification of OK14620 should help to facilitate continued use of the Ur-3 resistance source and will now enable marker-assisted pyramiding of three different bean rust resistance sources (two previously tagged) to provide effective and stable resistance to this important pathogen.

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.