Understanding the Molecular Basis of Phytonutrient Composition Differences in Organic Tomatoes Via Quantitative Transcriptome Analysis - Tomato (Solanum lycopersicum)

In a previous study, it was shown that tomatoes fertilized with organic nitrogen sources had higher phytonutrient content than those fertilized with conventional nitrogen sources. In particular, lycopene, ascorbate, soluble solids, and antioxidant contents were found to be higher in ripe fruit tissue from plants fertilized with organic nitrogen.  We employed a transcriptomic approach testing the hypothesis that the genomic response of a tomato genotype differs when fertilized with organic vs. conventional nitrogen. Fruit and leaf samples from the plants grown in the previous study were used to generate quantitative transcriptome data. Alignment of the transcriptome data to the tomato genome revealed that the quantity and amplitude of genetic expression differs according to the specific treatment, thereby implying the two soil management regimes elicit differential genomic responses from a single genotype. Transcriptome data analysis revealed a high degree of variation between the different treatments. Relative gene expression ratios were calculated and compared between the treatments. 3,034 of the 109,262 leaf tissue and 2,324 of 97,738 fruit tissue sequences were significantly over or under expressed between the organic and conventional treatments. BLAST and Gene Ontology analysis was performed and the annotated sequences underwent enzyme mapping to identify associated biochemical pathways. The analysis revealed metabolic pathway genes associated with phytonutrients, such as ascorbate and lycopene, were preferentially upregulated in the organic treatment. This observation leads to the hypothesis that different varieties of tomato will show differential genetic responses leading to the identity of genotypes amenable to production under organic practices.