Solanum lycopersicum Transcriptome or Gene expression

Tomato is a model and economically important crop plant with little information available about gene expression in roots. Currently, there have only been only a few studies that examined hormonal responses in tomato roots and none not at a at a genome-wide level. In this study we examined a the transcriptome atlas of tomato root regions (root tip, lateral roots, and whole roots) and the transcriptional regulation of each root region in response to the plant hormones cytokinin and auxin using Illumina RNA sequencing. More than 165 million 1x54 base pair reads were mapped onto the Solanum lycopersicum reference genome and differential expression (DE) patterns in each root region in response to each hormone were assessed. Many novel cytokinin and auxin induced and repressed genes were identified as significantly DE differentially expressed and the expression levels of several were confirmed by qPCR. A number of these regulated genes represent tomato orthologs of cytokinin or auxin regulated genes identified in other species including: CKXs, type-A RRs, Aux/IAAs, and ARFs. Additionally, our data confirms some of the hormone regulation studies for recently examined genes in tomato such as: SlIAAs and SlGH3s. Moreover, genes expressed abundantly in each root region were identified which provide a spatial distribution of many classes of genes, including plant defense, secondary metabolite production, and general metabolism across the root. Overall this study presents the first global expression patterns of hormone regulated transcripts in tomato roots which should will be functionally relevant for future studies directed towards tomato root growth and development.