Mining Alleles In Wild Tomato Species

Much of the genetic variation available for improving yield-related traits of cultivated tomatoes (Solanum lycopersicum) is present in its wild relatives. Commercial varieties, such as the processing tomato accession ‘Heinz’, often have genomic introgressions from various wild species as a result of breeding programs exploiting the ease of outcrossing to wild tomatoes. In contrast, heirloom lines have been perpetuated from lines of S. lycopersicum, and are not expected to have wild introgressions. We have made a step for the detection of introgressions in S. lycopersicum ‘Heinz’ by using variation found amongst the genome sequences of two wild tomato species, a heirloom line, and ‘Heinz’. We used the publicly available genome of the wild tomato, Solanum pimpinellifolium, and sequenced the genomes of Solanum galapagense, a perennial wild tomato species indigenous to the Galapagos Islands, and the genome of the heirloom line, Solanum lycopersicum ‘Yellow Pear’. We performed a survey of genomic discordance to detect putatively introgressed regions and also resolved the placement of S. galapagense on the Solanum phylogenic tree. In addition, this approach has been used to detect the origins of introgressions in an inbred disease-resistant tomato line. The high quality reference tomato genome, and the dropping costs of sequencing, open great opportunities for utilizing genomic tools for investigating allele variation in wild species, and elucidating the origins of introgressions in cultivated lines for improving breeding speed and outcomes.