| In order to gain a detailed understanding of the genetic basis of disease resistance in lettuce, candidate resistance genes were mapped relative to resistance phenotypes, resistance candidate genes which cosegregated with phenotypes were analyzed for function, and a genome wide analysis was made for signals of positive selection. Over 700 resistance candidate genes were identified by mining the Compositae EST database (http://cgpdb.ucdavis.edu) and by amplification and sequencing of conserved domains with degenerate oligonucleotides. These included members of 20 nucleotide binding site-leucine rich repeat (NBS-LRR) encoding gene families and genes encoding signal transduction components and defense response proteins. Candidate resistance genes cosegregated with the majority of the 36 resistance phenotypes analyzed. These genes provided candidates for functional analysis by means of RNA interference (RNAi) and sequencing of alleles from susceptible mutants as well as sequences suitable for marker assisted selection of resistance phenotypes. Six NBS-LRR encoding genes were analyzed for their role in determining disease resistance phenotypes at three loci. The downy mildew resistances Dm7 and Dm5/8 were shown to be conferred by a toll interleukin receptor-NBS-LRR and a coiled-coil-NBS-LRR encoding gene, respectively. Over 215,000 sequences were compared within and between five genomes of Lactuca spp. to test for signals of positive selection, a possible result of plant-pathogen co-evolution. This revealed several genes which may be involved in plant-pathogen interactions, domestication and/or weediness traits. This study provided a detailed picture of the genetic architecture of disease resistance in lettuce. Further dissection of disease resistance genes in lettuce will be aided by new sequencing technologies and by massively parallel, high-throughput genotyping. |
