DOMESTICATION AND INTENSIVE BREEDING HAS MADE TOMATO (SOLANUM LYCOPERSICUM) ONE OF THE WORLD MOST IMPORTANT AGRICULTURAL CROPS. TRAITS SUCH AS FRUIT SIZE, PLANT HABIT AND EASE OF GERMINATION, MAKE MODERN CULTIVARS PARTICULARLY AMENABLE TO COMMERCIAL CULTIVATION AND DISTINGUISH DOMESTICATED CULTIVATED TOMATO FROM ITS WILD RELATIVES. SINCE DOMESTICATION HAS RESULTED IN LIMITED GENETIC DIVERSITY WITHIN THE CULTIVATED GERMPLASM, UTILIZING WILD SPECIES IS A COMMON FEATURE OF MODERN BREEDING PROGRAMS. THE WILD RELATIVES OF TOMATO REPRESENT A RICH SOURCE OF PHENOTYPIC VARIATION, INCLUDING VALUABLE METABOLIC DIVERSITY, WITH GREAT POTENTIAL TO IMPROVE CULTIVATED VARIETIES. HOWEVER, THE MOLECULAR BASIS FOR PHENOTYPIC DIFFERENCES BETWEEN CULTIVATED AND WILD SPECIES OF TOMATO IS STILL LARGELY UNKNOWN AND FINDING THE GENES THAT INFLUENCE TRAITS SUCH AS FRUIT SHAPE, SIZE AND METABOLITE CONTENT, IS OFTEN LENGTHY AND TECHNICALLY CHALLENGING. INTERESTINGLY, MANY SUCH GENES CAUSE PHENOTYPIC DIFFERENCES AS A RESULT OF CHANGES IN GENE REGULATION RATHER THAN CHANGES IN PROTEIN FUNCTION. ONE METHOD TO IDENTIFY SUCH GENES IS TO COMPARE GENE EXPRESSION BETWEEN SPECIES. HOWEVER, SIMPLE COMPARISONS CANNOT DISTINGUISH GENES DIFFERENTIALLY REGULATED BY INDIRECT FACTORS SUCH AS DIFFERENCES IN GROWTH HABIT, PLANT ANATOMY OR CELLULAR ENVIRONMENT AS OPPOSED TO TRUE REGULATORY VARIANTS.THIS PROJECTS APPLIES A NEW APPROACH BASED ON THE ANALYSIS OF HYBRIDS OF WILD AND CULTIVATED TOMATO SPECIES TO IDENTIFY CANDIDATE GENES AFFECTING PHENOTYPIC VARIATION, PARTICULARLY TRAITS RELATED TO FRUIT QUALITY. BY SIMULTANEOUSLY ANALYZING THE EXPRESSION OF WILD AND CULTIVATED ALLELES IN A HYBRID PLANT, IT IS POSSIBLE TO ELIMINATE BACKGROUND EFFECTS ON GENE EXPRESSION AND UNCOVER GENES SHOWING CIS-REGULATION (E.G. CHANGES IN EXPRESSION DUE TO PROMOTER VARIATION) WHICH CONSTITUTE INTERESTING TARGETS FOR CROP IMPROVEMENT. WE WILL APPLY THIS APPROACH TO HYBRIDS OF A RANGE OF CULTIVATED TOMATO SPECIES AND TOMATO WILDSPECIES AT DIFFERENT DEVELOPMENTAL STAGES, AND ANALYZE DISTINCT FRUIT TISSUES, TO GENERATE A COMPREHENSIVE DATASET OF CIS-REGULATED GENES AND A LIST OF VERIFIED HIGH PRIORITY CANDIDATE GENES TO IMPROVE FRUIT QUALITY. TOMATO IS AN ECONOMICALLY IMPORTANT VEGETABLE CROP WORLDWIDE AND AN IMPORTANT SOURCE OF NUTRIENTS BENEFICIAL TO HUMAN HEALTH. DEVELOPING TOMATO VARIETIES THAT ACHIEVE OPTIMAL FRUIT YIELD WHILE MAINTAINING FRUIT QUALITY (FLAVOR, AROMA, HEALTH-RELATED METABOLITES) IS OF HIGH ECONOMIC IMPORTANCE BUT PRESENTS COMPLEX CHALLENGES. BY GENERATING A DATASET OF CANDIDATE GENES CONTROLLING PHENOTYPIC VARIATION, THIS RESEARCH WILL PROVIDE NEW TOOLS FOR DESIGNING STRATEGIES TO ENHANCE VALUED FRUIT TRAITS. IN ADDITION, THIS STUDY WILL OFFER INSIGHTS INTO THE REGULATORY EVENTS THAT ACCOMPANIED TOMATO DOMESTICATION.