Genetics and Genomics of Lettuce-Pathogen Interactions

The genome of Lactuca sativa cv. Salinas has been sequenced. High quality Illumina reads providing 72x coverage were assembled into 13,352 scaffolds over 2 kb covering 2.5 Gb (representing ~90% of the genome) with a N50 of 461 kb. The assembly was validated using over 11,000 loci from an ultra-dense, transcript-based genetic map. Genotyping by sequencing of RILS from the core L. sativa x L. serriola mapping population is being used to assemble many scaffolds into chromosomal linkage groups. Approximately 45,000 genes were annotated using manual and automated pipelines including over 350 NB-LRR encoding genes. Comparative studies of the complete L. sativa and L. serriola genomes are ongoing. Ultimately, this will lead to understanding of the genome architecture of transcribed sequences and the organization and evolution of gene families, with particular emphasis on disease resistance genes.  Resequencing of multiple genotypes of Lactuca spp. and B. lactucae and RNAseq of compatible and incompatible interactions are progress to identify genes involved in this disease. Over 750 candidate genes potentially involved in disease resistance have been mapped relative to 52 phenotypes for 11 different diseases. The majority of these disease resistance phenotypes co-segregate with clusters of NB-LRR encoding genes.  A subset are being analyzed using RNAi; transgenic RNAi tester stocks for over 33 candidates have been evaluated so far and we have identified seven sequences that can trigger silencing of 15 different resistance phenotypes. We are pyramiding multiple disease resistance genes to generate different lettuce lines with increased durability of resistance.