The Influenza Paradigm for Resistance Gene Deployment in Lettuce

We have been characterizing variation in both lettuce and its pathogens in order to enable informed deployment of resistance genes to provide more durable control.  Over 50 phenotypic resistance genes are known in lettuce, many for resistance to Bremia lactucae the causal agent of downy mildew.  Over 25 phenotypic resistance loci co-localize to three of five major resistance clusters (MRC) on chromosomes 1, 2, and 4. Additional resistance genes are being rapidly mapped using next-gen sequencing of near-isogenic lines and isoforms identified using PacBio sequencing.  The majority of candidate resistance genes that encode nucleotide binding-leucine rich repeat (NLR) proteins genetically co-localize with phenotypic resistance loci. MRC1 and MRC4 each span over 65 Mb containing 104 and 24 NLR encoding genes in the reference genome of cv. Salinas, respectively, as well as ~850 and ~681 genes which are not related to NLRs. Forward and reverse genetic approaches have been applied to dissect MRC1 and MRC4 and identify the causal genes.  In parallel, we have monitored variation in B. lactucae in California since 1982 at the phenotypic and sequence levels.  We have sequenced ~50 isolates of B. lactucae that differ in geographical and temporal origin as well as virulence phenotype.  These data are providing the basis for deploying pyramids of resistance genes.  Different resistance genes are being deployed in different lettuce types in order to fragment the selection pressure on the pathogen population.