Understanding the genomic associations among disease resistance loci will facilitate breeding of multiple disease resistant cultivars. We constructed a genetic linkage map in common bean (Phaseolus vulgaris L.) containing six genes and nine quantitative trait loci (QTL) comprising resistance to one bacterial, three fungal, and two viral pathogens of bean. The mapping population consisted of 79 F5:7 recombinant inbred lines (RILs) derived from a `Dorado'/XAN 176 hybridization. There were 147 randomly amplified polymorphic DNA (RAPD) markers, two sequence characterized amplified region (SCAR) markers, one intersimple sequence repeat (ISSR) marker, two seedcoat color genes R and V, the Asp gene conditioning seed brilliance, and two rust [Uromyces appendiculatus var. appendiculatus (Pers.:Pers) Unger] resistance genes: one conditioning resistance to Races 53 and 54 and the other conditioning resistance to Race 108. These markers mapped across eleven linkage groups, one linked triad, and seven linked pairs for an overall map length of 930 cM (Kosambi). Genes conditioning resistance to anthracnose (Co-2) [Colletotrichum lindemuthianum (Sacc. and Magnus) Lams.-Scrib.], bean rust (Ur-5), and bean common mosaic virus (I and bc-3) (BCMV) did not segregate in this population, but were mapped by inference using linked RAPD and SCAR markers identified in other populations. Nine previously reported quantitative trait loci (QTL) conditioning resistance to a variety of pathogens including common bacterial blight [Xanthomonas campestris pv. phaseoli (Smith) Dye], ashy stem blight [Macrophomina phaseolina (Tassi) Goid.], and bean golden mosaic virus (BGMV), were located across four linkage groups. Linkage among QTL for resistance to ashy stem blight, BGMV, and common bacterial blight on linkage group B7 and ashy stem blight, BGMV, and rust resistance loci on B4 will complicate breeding for combined resistance to all four pathogens in this population.

The Up 2 gene of common bean (Phaseolus Vulgaris L.) is an important source of dominant genetic resistance to the bean rust pathogen [Uromyces appendiculatus (Pers. ex Pers.) Unger var 'appendiculatus' [syn U. Phaseoli (Reben) Wint.]. Up 2 in combination with other rust resistance genes may be used to obtain potentially stable genetic resistance. It is difficult, however, to combine rust resistance genes effective against a single race due to epistatic interactions that frequently occur between them. A strategy that employed bulked DNA samples formed separately from the DNA of three BC6F2 individuals with Up 2 and three without Up 2 as contrasting near-isogenic lines (NILs) was used to identify random amplified polymorphic DNA fragments (RAPDs) tightly linked to the Up 2 locus. Only 1 of 931 fragments amplified by 167 10-mer primers of arbitrary sequence in the polymerase chain reaction (PCR) was polymorphic. The RAPD marker (OA141100) amplified by the 5'-TCTGTGCTGG-3' primer was repeatable and its presence and absence easy to score. No recombination was observed between OA141100 and the dominant Up 2 allele within a segregating BC6F2 population of 84 individuals. This result suggests that OA141100 and Up 2 are tightly linked. Andean and Mesoamerican bean germ plasm, with and without the Up 2 allele, were assayed for the presence of OA141100. Apparently, the marker is of Andean origin because all Andean lines, with or without the Up 2 allele, contained the marker, and the marker was absent in all Mesoamerican germ plasm except the lines to which Up-2 had been purposely transferred. These results suggest that OA141100 will be most useful for pyramiding Up 2 with other rust resistance genes into germ plasm of Mesoamerican origin where the marker does not traditionally exist. The use of bulked DNA samples may have concentrated resources toward the identification of RAPDs that were tightly linked to the target locus. Marker-based selection may provide an alternative to the time-consuming testcrosses required to pyramid bean rust resistance genes that exhibit epistasis.

Rust in bean (Phaseolus vulgaris L.), caused byUromyces appendiculatus (Pers.) Unger var.appendiculatus [ =U. phaseoli (Reben) Wint.], is a major disease problem and production constraint in many parts of the world. The predominant form of genetic control of the pathogen is a series of major genes which necessitate the development of efficient selection strategies. Our objective was focused on the identification of RAPD (random amplified polymorphic DNA) markers linked to a major bean rust resistance gene block enabling marker-based selection and facilitating resistance gene pyramiding into susceptible bean germplasm. Using pooled DNA samples of genotyped individuals from two segregating populations, we identified two RAPD markers linked to the gene block of interest. One such RAPD, OF10970 (generated by a 5'-GGAAGCTTGG-3' decamer), was found to be closely linked (2.15±1.50 centi Morgans) in coupling with the resistance gene block. The other identified RAPD, OI19460 (generated by a 5'-AATGCGGGAG-3' decamer), was shown to be more tightly linked (also in coupling) than OF10970 as no recombinants were detected among 97 BC6F2 segregating individuals in the mapping population. Analysis of a collection of resistant and susceptible cultivars and experimental lines, of both Mesoamerican and Andean origin, revealed that: (1) recombination between OF10970 and the gene block has occurred as evidenced by the presence of the DNA fragment in several susceptible genotypes, (2) recombination between OI19460 and the gene block has also occurred indicating that the marker is not located within the gene block itself, and (3) marker-facilitated selection using these RAPD markers, and another previously identified, will enable gene pyramiding in Andean germplasm and certain Mesoamerican bean races in which the resistance gene block does not traditionally exist. Observations of variable recombination among Mesoamerican bean races suggested suppression of recombination between introgressed segments and divergent recurrent backgrounds.

The Guatemalan black bean (Phaseolus vulgaris L.) plant introduction (PI) 181996 is resistant to all known US races of the bean rust fungus Uromyces appendiculatus (Pers. ex Pers.) Unger var. appendiculatus [syn. U. phaseoli (Reben) Wint.]. We report on two random amplified polymorphic DNA (RAPD) markers OAC20490 tightly linked (no recombinants) in coupling phase and OAE19890 linked in repulsion phase (at 6.2±2.8 cM) to PI 181996 rust resistance. These RAPDs, generated by single decamer primers in the polymerase chain reaction, were identified in near-isogenic bulks of non-segregating resistant and susceptible BC4F2 (NX-040*4/PI 181996) lines. Linkage of the RAPD markers was confirmed by screening 19 BC4F2 and 57 BC4F3 individuals segregating for PI 181996 resistance. Utility of the RAPDs OAC20490 and OAE19890 was investigated in a diverse group of common bean cultivars and lines. All cultivars into which the PI 181996 resistance was introgressed had the RAPD OAC20490. A RAPD similar in size to OAC20490, observed in some susceptible common bean lines, was confirmed by Southern blotting to be homologous to the RAPD OAC20490. Use of the RAPDs OAC20490 and OAE19890 in marker-assisted selection (MAS) is proposed. The coupling-phase RAPD is most useful for MAS of resistant BCnF1individuals during traditional backcross breeding. The repulsion-phase RAPD has greatest utility in MAS of homozygous-resistant individuals in F2 or later-segregating generations.

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.