Analysis of wild-species introgressions in tomato inbreds uncovers ancestral origins

Decades of intensive tomato breeding using wild germplasm has resulted in genomes of domesticated accessions (Solanum lycopersicum) to be intertwined with introgressions from their wild relatives. Here we present the first whole genome sequences of two tomato inbreds Gh13 and BTI87, both carrying a begomovirus resistance gene, Ty3, introgressed from a wild tomato species. Introgressions of different sizes on chromosome 6 of Gh13 and BTI87, both corresponding to the Ty3 region, were identified as from a source close to S. chilense. Other introgressions were identified throughout the genomes of the inbred lines, showing major differences in the breeding history of the two lines. Interestingly, large introgressions from the close tomato relative S. pimpinellifolium were identified in both lines, whereas some of the predicted introgressions were attributed to introgressions in the reference ‘Heinz 1706’ genome. NGS technology can be used for rapid and efficient analyses of tomato germplasm with interesting phenotypes. Comparative analysis of genomes among cultivated tomatoes and wild species that contribute genetic variation can help identify desirable genes, such as those that confer disease resistance. The methods developed in this work can be used to discover introgressions to elucidate the history of tomato breeding, to develop molecular markers for phenotypic selection, to fine map and discover candidate genes for important phenotypes, and to identify novel variation for the improvement of tomato. These methods can easily be applied to other crops.