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Abstract
Tomato flavor is a critical factor influencing consumer preferences and is largely determined by volatile organic compounds. However, breeding programs have traditionally overlooked flavor due to its genetic complexity, environmental influence, expensive phenotyping, and limited knowledge of the underlying genetics. Identifying additional loci and genes associated with flavor improvement could enhance our understanding of the genetic mechanisms controlling fruit flavor and provide novel breeding tools. This dissertation catalogues genetic diversity in a well-characterized collection of fully wild Solanum pimpinellifolium, semi-domesticated Solanum lycopersicum var. cerasiforme, ancestral Solanum lycopersicum var. lycopersicum landraces from South and Central America and a subset of cultivated accessions. The focus is on exploring how genetic diversity underlies the regulation of flavor volatiles in red-fruited tomatoes. This is achieved through a range of techniques, including genotyping-by-sequencing, QTL mapping, genome-wide association studies (GWAS), structural variant analysis, and haplotype analysis. Using a biparental mapping population, this study identified a locus on chromosome 2 strongly associated with fruit methyl salicylate levels and harboring a subclade of tomato methyl esterases, SlMES1-4, responsible for converting methyl salicylate to salicylic acid in ripe tomato fruit. This locus contains four tandemly duplicated Methylesterase (MES) genes and genome sequence investigations at the locus identified nine distinct haplotypes. Functional and non-functional haplotypes for MES were identified, and the study showed a strong interaction between the MES and Non-Smoky Glucosyl Transferase1 loci. The combination of non-functional haplotypes for these two important loci resulted in high methyl salicylate levels in ripe fruits. Furthermore, the thesis investigates the genetic basis of 68 fruit volatiles across seven major biochemical pathways to extend the understanding of their regulation. GWAS and biparental QTL mapping together identified several strong QTLs, including both novel and previously identified, affecting the metabolism and regulation of flavor volatiles. Overall, this study provides valuable insights into the complex genetic architecture of tomato flavor volatiles and offers resources for targeted flavor breeding in tomato and other fruit crops. Further investigation of the mapped novel loci could help identify the underlying genes and improve our understanding of the flavor volatile biosynthesis.