Proteomic pattern-based identification of molecular phenotypes from Arabidopsis thaliana ecotypes

Ecotypes are geographic variants of plants. Using two-dimensional gel electrophoresis, we performed a comparative analysis of intra-species proteome variation in Arabidopsis ecotypes. The effect of single gene mutations on parental ecotype proteome patterns was also examined. Three Arabidopsis ecotypes, Col-0, Ler-0 and Ws-0, were compared to identify characteristic proteome patterns. From the protein expression profile of whole seedling protein extracts, 13 differentially expressed group of proteins were distinguished by self-organizing map clustering analysis. Proteins in each cluster were identified by peptide mass fingerprinting. These isolated clusters were used as a molecular phenotype for comparison of Col-0, Ler-0, and Ws-0 with genetically close or distant ecotypes, as well as several single locus mutants. Comparison of protein patterns with other ecotypes showed that the genetic diversity of the ecotypes was reflected in quantitative differences in the protein expression patterns. Single locus mutations usually did not alter the parental protein pattern significantly, although a few mutations did cause a dramatic change relative to the parental pattern.