The high numbers of duplications in non-TIR genes may be explained by our results. In the four hybridization assays where only TIR probes were evaluated, mostly unique positive clones were identified. For example, for TSA HDAC filters 1 and 3 all of the positive clones were unique sequences. However, in assays 5 to 10, performed with non-TIR probes, only 22% of the positive clones were unique sequences. The frequent hybridization of non-TIR probes to the BAC clones of the G19833 library suggests

that the RGH sequences arose before the divergence between monocotyledonous and dicotyledonous plants and have an older evolutionary history [35] and [39]. In contrast, TIR domain sequences have hardly been identified in monocots but have evolved substantially in dicotyledonous plants [40]. Some probes hybridized with more than one BAC clone in the G19833 common bean genomic library. This result was expected, because this BAC library had a genome coverage of 12 × haploid genome equivalents. In addition, duplicated genes or closely related paralogous sequences could account for the redundancy in hybridization. Also, it must be remembered that the probes were designed from sequences

related to RGH genes, which represent a large and diverse Ibrutinib research buy gene family with many copies distributed throughout the genome [41]. If a higher number of gene duplication second events have occurred in non-TIR sequences, then this could be the reason for finding more redundant sequences of this type in common bean. The third major objective and achievement of this work was to develop and genetically map RGH-SSR sequences. This was achieved by identifying RGH-positive BAC clones or adjacent contigged BACs that were associated with SSRs in their BAC ends. The major point of this exercise was the physical linkage of the

BES-SSR to the RGH sequence either as a primary hit in very close proximity within the length of a given BAC, or as a secondary hit within the length of a contig of BACs. The proportion of SSR in BES in regions near RGH genes (35.6%) appears to be higher than in previous estimates using the overall collection by Córdoba et al. [18] and [19]. The high frequency of SSRs in regions with RGH sequences may be a characteristic of genomic regions with RGH clusters. David et al. [38] observed that RGH clusters were interspersed with non-RGH genes, so that these EST providing regions may also be rich in SSRs [20] and [21]. It was also interesting that the proportion of hybridizing BACs falling in singleton BACs rather than contigs showing the difficulty of assembling regions with RGH sequences, owing to their characteristic presence in tandem repeats and their similar sequence domains [42] and [43].