Whole genome resequencing reveals novel loci associated with bacterial wilt resistance in tomato

Tomato (Solanum lycopersicum) is the most economically important vegetable crop worldwide. Bacterial wilt (BW, caused by Ralstonia solanacearum species complex) is one of the most devastating tomato diseases, especially in the tropics and subtropics. Management of BW using pesticides has limited usefulness and strategies such as crop rotation are difficult due to the persistence of the pathogen in the soil. Thus, host resistance is the most effective disease management strategy. Previous multilocation testing of a mapping population derived from ‘Hawaii 7996’ (H7996) in nine locations revealed the presence of two major genomic regions (Bwr-12 and Bwr-6) and additional QTLs with minor or strain-specific effects conditioning BW resistance. However, molecular markers in these regions do not completely account for resistance in H7996, and other resistance QTLs are likely present. Recent efforts to fine map these regions did not result in the identification of novel resistance genes. To better understand resistance and identify additional genomic regions boosting resistance, we conducted whole genome re-sequencing of 10 diverse resistant and 10 diverse susceptible tomato breeding lines and cultivars, including H7996. We identified 7,644,342 and 4,357,576 polymorphisms between the reference genome and the resistant and susceptible panel, respectively. However, only 112 SNPs and 582 indels were consistently present between the resistant and susceptible groups. Forty of the 694 polymorphisms were located in or near a gene with high homology to previously identified resistance genes and were considered candidates for validation in segregating populations. The research identified novel genes that could be associated with resistance to BW and provides a basis for future work in this area.