Our previous studies have shown that inbreeding adversely affects plant resistance to herbivores in horsenettle (Solanum carolinense). Here, we use tomato microarrays to assess changes in gene expression levels in response to breeding and herbivory. Two rhizome cuttings were regrown from each of two inbred and two outbred plants from each five families. One ramet served as the control and one ramet was subjected to 6-8 hours of herbivory by one third instar Manduca sexta larva and then leaf samples were harvested for microarray analysis. The resulting data were analyzed using PVCA, a modified PCA analysis that employs partial regression, to assess the relative contributions of each factor (Family, Breeding, Treatment) and their 2-way interactions on gene expression and Monte Carlo simulations were used to examine significance of the expression patterns.
We found that > 80% of the total variance in gene expression across the 40 microarrays was explained by the three main effects and two interactions (all of which are significant, p < 0.05). Genes that were up or down regulated significantly (log fold change >2) were compared to UniPROT for a determination of their function, and then categorized into defense, housekeeping, or growth gene ontologies (GOs). Of the 595 differentially expressed, annotated genes, 320 (54%) were categorized as growth-related genes, 234 (39%) were classified under housekeeping GOs, and 41 (7%) were categorized as defense-related genes. All GOs have more genes upregulated by herbivore damage than downregulated. Across all families, outbred plants had similar expression profiles in terms of GO categories and the direction of expression. In contrast, gene expression among inbred plants was much more variable in terms of both the direction of expression and GO categories. This finding suggests that inbred plants may lack some ability to regulate their responses to herbivory and may be upregulating growth and housekeeping genes that are not directly associated with an appropriate damage response and downregulating some defense related genes that are associated with an appropriate damage response.