title: Genome-Wide Architecture of Disease Resistance Genes in Lettuce.
abstract: Genome-wide motif searches identified 1134 genes in the lettuce reference genome of cv. Salinas that are potentially involved in pathogen recognition, of which 385 were predicted to encode nucleotide binding-leucine rich repeat receptor (NLR) proteins. Using a maximum-likelihood approach, we grouped the NLRs into 25 multigene families and 17 singletons. Forty-one percent of these NLR-encoding genes belong to three families, the largest being RGC16 with 62 genes in cv. Salinas. The majority of NLR-encoding genes are located in five major resistance clusters (MRCs) on chromosomes 1, 2, 3, 4, and 8 and cosegregate with multiple disease resistance phenotypes. Most MRCs contain primarily members of a single NLR gene family but a few are more complex. MRC2 spans 73 Mb and contains 61 NLRs of six different gene families that cosegregate with nine disease resistance phenotypes. MRC3, which is 25 Mb, contains 22 RGC21 genes and colocates with Dm13. A library of 33 transgenic RNA interference tester stocks was generated for functional analysis of NLR-encoding genes that cosegregated with disease resistance phenotypes in each of the MRCs. Members of four NLR-encoding families, RGC1, RGC2, RGC21, and RGC12 were shown to be required for 16 disease resistance phenotypes in lettuce. The general composition of MRCs is conserved across different genotypes; however, the specific repertoire of NLR-encoding genes varied particularly of the rapidly evolving Type I genes. These tester stocks are valuable resources for future analyses of additional resistance phenotypes.
authors.affiliation: Genome Center and Department of Plant Sciences, University of California, Davis, California 95616.
authors.forename: Marilena
authors.initials: M
authors.lastname: Christopoulou
authors.affiliation: Genome Center and Department of Plant Sciences, University of California, Davis, California 95616.
authors.forename: Sebastian Reyes-Chin
authors.initials: SR
authors.lastname: Wo
authors.affiliation: Genome Center and Department of Plant Sciences, University of California, Davis, California 95616.
authors.forename: Alex
authors.initials: A
authors.lastname: Kozik
authors.affiliation: Genome Center and Department of Plant Sciences, University of California, Davis, California 95616.
authors.forename: Leah K
authors.initials: LK
authors.lastname: McHale
authors.affiliation: Genome Center and Department of Plant Sciences, University of California, Davis, California 95616.
authors.forename: Maria-Jose
authors.initials: MJ
authors.lastname: Truco
authors.affiliation: Genome Center and Department of Plant Sciences, University of California, Davis, California 95616.
authors.forename: Tadeusz
authors.initials: T
authors.lastname: Wroblewski
authors.affiliation: Genome Center and Department of Plant Sciences, University of California, Davis, California 95616 rwmichelmore@ucdavis.edu.
authors.forename: Richard W
authors.initials: RW
authors.lastname: Michelmore
mesh_terms: D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D060467:Disease Resistance / Q000235:genetics*; D020868:Gene Silencing; D017343:Genes, Plant; D056426:Genetic Loci; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D023281:Genomics; D005838:Genotype; D054884:Host-Pathogen Interactions / Q000235:genetics; D018545:Lactuca / Q000145:classification / Q000235:genetics*; D005810:Multigene Family; D010641:Phenotype; D010802:Phylogeny; D010935:Plant Diseases / Q000235:genetics*; D034622:RNA Interference; D034741:RNA, Small Interfering / Q000235:genetics
chemical_list: D034741:RNA, Small Interfering
keywords: Bremia lactucae; NB-LRR; gene silencing; lettuce downy mildew; reverse genetics