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At least 10 Dm genes conferring resistance to the Oomycete downy mildew fungus Bremia lactucae, map to the major resistance cluster in lettuce. We investigated the structure of this cluster in the lettuce cultivar Diana that contains Dm3. A deletion break point map of the chromosomal region flanking Dm3 was saturated with a variety of molecular markers. Several of these markers are components of a family of resistance gene candidates (RGC2) that encode a nucleotide binding site and a leucine-rich repeat region. These motifs are characteristic of plant disease resistance genes. Bacterial artificial chromosome (BAC) clones were identified using duplicated restriction fragment length polymorphism markers from the region, including the nucleotide binding site-encoding region of RGC2. Twenty-two distinct members of the RGC2 family were characterized from the bacterial artificial chromosomes; at least two additional family members exist. The RGC2 family is highly divergent; the nucleotide identity was as low as 53% between the most distantly related copies. These RGC2 genes span at least 3.5 Mb. Eighteen members were mapped on the deletion break point map. A comparison between the phylogenetic and physical relationships of these sequences demonstrated that closely related copies are physically separated from one another and indicated that complex rearrangements have shaped this region. Analysis of low-copy genomic sequences detected no genes in addition to RGC2 in the Dm3 region, other than sequences related to retrotransposons and transposable elements. The related but divergent family of RGC2 genes may act as a resource for the generation of new resistance phenotypes through infrequent recombination or unequal crossing over.

Deletion break point map with positions of RGC2-containing BACs. The mutants have been ordered according to their left break points. Genomic regions present in each mutant were inferred by the presence of the markers. Positions of RGC2 BAC groups (Table 2) are given below the map. Markers in bold are present on the BACs indicated below by the connecting dotted line. Markers in normal typeface mapped to the region but were not detected on a BAC. The positions of markers that could not be located precisely are shown as a bar. Individual bands of multicopy markers are denoted by a colon and the letter or number designating the individual band. Identical duplicated markers, which were detected by their presence on nonoverlapping BACs, are noted by a dagger. The order could not be determined when several groups of BACs mapped within the same break points.