We combined cDNA amplified fragment length polymorphism (cDNA-AFLP) with bulked segregant analysis (BSA) to detect genes that control tomato (Lycopersicon esculentum) bacterial wilt infected with Ralstonia solanacearum, resistance in F 2 population derived from a cross between a bacterial wilt-resistant variety, T51A, and a bacterial wilt-susceptible variety, T9230. In cDNA-AFLP analysis among bulked-resistant F 2 (B R ) pool, bulked-susceptible F 2 (B S ) pool, bulked-resistant T51A (B A ) pool and bulked-susceptible T9230 (B B ) pool, 34 differentially expressed transcript-derived fragments (DE-TDFs) that were present in only B R and B A pools were detected. Analysis of differential DE-TDF expression in individual resistant F 2 resulted in the isolation of a caffeoyl CoA 3-Omethyltransferase (CCoAOMT) gene not previously described from tomato and which showed similarity to an CCoAOMT gene from tobacco and potato plants. This CCoAOMT gene may play a role in innate generalized response to pathogen infection as it was downregulated in susceptible tomato following infection with the bacterium. CCoAOMT gene plays an essential role in the synthesis of guaiacyl lignin units and supply substrates for the synthesis of syringyl lignin units.
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