Identification and analysis of differentially expressed genes in Solanum lines in response to challenge with a Ralstonia solanacearum phylotype I strain

Identification of differentially expressed genes is a direct approach to understand the molecular basis of physiological processes. In this study, the GeneFishing™ PCR technique was used to identify genes which were differentially expressed in two Solanum lycopersicum lines, the resistant Lycopersicon cerasiforme and a susceptible cultivar known as Quatre carrées, after inoculation with a phylotype I strain of Ralstonia solanacearum. With twenty annealing control primers (ACPs), nineteen differentially expressed genes (DEGs) were identified, 17 of which were from the L. cerasiforme line and 2 from the Quatre carrées cultivar. Six DEGs (DEG1, DEG5, DEG8, DEG12, DEG15 and DEG18) were chosen for further studies based on the blast results. Primers were designed for the six DEGs and quantitative real-time PCR was carried out to confirm the differential expression. Expression of the six DEGs was also tested in Solanum commersonii, the Solanum tuberosum cultivar, Spunta and the S. lycopersicum lines MST 32/1, CRA 66 and Hawaii 7996. Level of expression was closely related to the phenotype of the plants, in terms of susceptibility and resistance to the pathogen. The resistant lines L. cerasiforme, S. commersonii, CRA 66 and Hawaii 7996 always had higher levels of gene expression than the moderately resistant MST 32/1 cultivar and the susceptible Quatre carrées and Spunta cultivars.