Extent and side effects of wild introgressions in cultivated tomato

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Introgression of wild alleles into cultivated tomato has been a common practice in breeding programs over the last century that has improved important traits like pathogen resistance or fruit quality. As a result, most if not all modern tomato varieties contain introgressions from a variety of wild tomato species. While the genes and functions that motivated each of the introgressions are well described, little known is known about the exact size of these introgressions, the number of genes included in them, or the existence of additional unexpected wild segments scattered throughout the genome due to incomplete backcrossing schemes. These features became evident in the only cultivated tomato reference genome sequence available, where four introgressions could be detected and one of them does not contain any known beneficial gene. Due to their large spans, introgressions from wild species can have significant unexpected consequences different from those intended when the introgressions were originally designed. Documented negative effects include suppression of recombination due to genomic rearrangements in the introgressed region or pleiotropic effects due to unfavorable genes dragged along the beneficial alleles included in the introgression.Here we propose to utilize published whole-genome information of more than 600 tomato accessions encompassing 13 different species to establish the first comprehensive catalog of wild introgressions in more than 400 tomato cultivars. To do this, we propose to first construct a tomato reference genome assembly from a cultivar that does not contain any introgressions. This new high-quality reference genome will greatly simplify the identification of non-cultivated fragments and enable the generation of a comprehensive catalog of wild introgressions in cultivated tomato based on the re-sequencing data mentioned above. The resulting catalog will allow us to select five additional cultivars displaying the most common introgressions segregating in modern tomatoes. The selected accessions will be then used to generate assemblies of their introgressions, thus greatly expanding our knowledge on the gene pool that makes modern tomatoes. Finally, we will combine novel techniques with classic genetic approaches to study the effect of the most common introgressions on the suppression of meiotic recombination and modification of transcriptional landscape of the accessions that carry them. The results of this project will not only generate major resources for future research in tomato, but will also serve as direct guidance to improve tomato cultivars by precision breeding of introgressions. Our consortium combines two groups with complementary strength including long lasting expertise in tomato genetics and evolution with experiences in high-throughput genomic data analysis and genome assembly.