CANDIDATE GENE ANALYSIS FOR AGRICULTURALLY IMPORTANT TRAITS IN LETTUCE

¹ Dept. of Vegetable Crops, University of California at Davis, Davis, CA 95616

² Biology Department, University of Massachusetts, Boston, MA 02125

As part of the Compositae Genome Project (CGP, http://compgenomics.ucdavis.edu), candidate genes for agriculturally important traits have been mapped relative to QTL determining these traits, to leverage information being generated on Arabidopsis and other model species. An informative subset of F_7:8 Recombinant Inbred Lines (RILs) has been derived from a cross of the cultivated Lactuca sativa cv. Salinas x wild Lactuca serriola. Candidate sequences for a range of traits were identified from the set of ~19,000 unigenes assembled from over 66,0000 lettuce ESTs. We have initially focused on genes involved in disease resistance, flowering, root development, and seed germination. Sequences that were present in the database from both parents of the mapping population were screened for polymorphisms in silico. Alternatively, potential intron positions were identified by comparison to Arabidopsis sequences and primers designed to amplify across the intron. Various methods are being used to detect and subsequently map these polymorphisms including detection of Single Nucleotide Polymorphisms (SNPs) via heteroduplex analysis using temperature gradient capillary electrophoresis (Spectrumedix, State College, PA). We have also identified a Conserved Orthologous Set of markers in order to establish patterns of macro- and microsynteny with sunflower, tomato and Arabidopsis. Functional analysis of candidate genes is being initiated using RNAi.