A 54-kDa polypeptide identified by 2D-PAGE and bulked segregant analysis underlies differences for pH values in tomato fruit

Fruit pH is an important quality attribute in tomato and it is defined during ripening. The aims of this work were to detect pericarp polypeptides associated with pH in an interspecific tomato BC₁ generation by 1D-PAGE and to identify those differentially expressed polypeptides by comparing 2D-PAGE protein profiles from bulked segregant analysis (BSA). Polypeptide patterns were resolved by 1D-PAGE in a BC₁ population obtained by crossing the cv. ‘Caimanta’ of Solanum lycopersicum (recurrent parental genotype) and the accession LA722 of S. pimpinellifolium (donor parental genotype). Putative QTL for fruit quality were detected by single point analysis. The presence of a 54-kDa band at the mature green stage (MG) carried by the wild genotype decreased the mean value of the pH trait. A BSA combined with 2D-PAGE was applied to the extreme phenotypes for pH in the BC₁ segregating population. Four differentially expressed spots were detected when the polypeptide patterns of the bulks were compared. The spots had the expected molecular mass (around 54-kDa), and they were present in the lower-pH bulk and absent in the higher-pH one. The spots were identified by MS MALDI-TOF and two of them showed homology with the ATP synthase CF₁ alpha subunit of S. lycopersicum. These results indicate that the association between the polypeptide marker and a fruit quantitative trait detected by 1D-PAGE not only would indicate genetic linkage but also could be directly related with the gene underlying the quantitative trait.