Production of common beans is constrained by pathogens that include bacteria, fungi, phytoplasms, LY294002 and viruses. Anthracnose (Colletotrichum lindemuthianum), rust (Uromyces appendiculatus) and ascochyta (Phoma

exigua) are considered the most important fungal diseases of this crop worldwide, with an angular leaf spot (Phaeoisariopsis griseola) important in tropical countries [7]. Genetic resistance is the most widely used management strategy for these pathogens [8]. Many major resistance (R) genes have been evaluated by linkage analysis, and many of these genes have been molecularly tagged in common bean, but mostly with older types of markers such as sequence characterized amplified region (SCAR) markers [9] and [10] rather than a SCH772984 nmr newer type marker such as with SSR or single nucleotide polymorphism (SNP) markers, which are more reliable and polymorphic owing to their codominant and multi or bi-allelic nature, respectively [4]. Currently, there is wide interest in the use of resistance-gene homologues (RGHs) for identification of R-genes. This strategy is based on the

design of degenerate primers from highly conserved sequence motifs characteristic of the nucleotide binding site (NBS) domain and has been applied in many crops [10], [11] and [12]. The principle of RGH cloning is simple: if there is a PCR amplicon from RGH related degenerate primers with the desired size, it could be part of a resistance gene. RGH genes are also known as resistance-gene analogs (RGAs) [12], and sometimes as resistance-gene candidates (RGCs) [13], [14] and [15]. Compared to the other domains

common to R-genes, such as LRR repeats or Toll–interleukin receptor (TIR) domains, the NBS domain is associated almost exclusively with disease resistance [15]. After RGHs are identified, a subsequent step consists of their genetic mapping. This operation is difficult because of the high similarity among certain parts of RGH sequences. For this reason, finding Phospholipase D1 specific markers near the RGH genes can be a better approach to genetic mapping of these genes. A commonly used approach is to develop RGH-SSR based on SSR markers that are physically associated with RGH genes on bacterial artificial chromosome (BAC) clones. RGH-SSR genes are often found in BAC sequencing projects but can also be found in the BAC end sequences (BES) of clones containing RGH genes. In this study, we identified individual BAC clones with single or multiple RGH genes by a hybridization-based approach and found SSRs in the BES sequences of these or adjacent BAC clones. The RGH-SSRs thus identified were then located on a genetic map of common bean. To date, a high number of mapping populations have been developed [16], by means of which many R-genes or loci that respond and provide resistance to diseases or biotic stresses have been identified [9].