Comparative transcriptome analysis provides insights into dwarfism in cherry tomato (Solanum lycopersicum var. cerasiforme)

Tomato, which can be eaten as a vegetable or fruit, is one of the most popular and nutritionally important crops around the world. Although most plants of the cherry tomato cultivar ‘Minichal’ have a normal phenotype, some plants have a stunted phenotype with reduced plant height, leaf size, and fruit size, as well as altered leaf and fruit shape. To investigate the molecular mechanisms underlying these differences, we generated RNA-seq libraries from pooled leaf samples of 10 normal (N) and 10 stunted (S) plants. Using the Illumina sequencing platform, we obtained a total of 115.45 million high-quality clean reads assembled into 35,216 genes and 35,216 transcripts. A total of 661 genes were differentially expressed between N and S plants. Of these, 420 differentially expressed genes (DEGs) were up-regulated, and 221 DEGs were down-regulated. The RNA-seq data were validated using quantitative reverse-transcription PCR. Enrichment analysis of DEGs using the Kyoto Encyclopedia of Genes and Genomes (KEGG) showed that the enriched pathways were involved in steroid biosynthesis, homologous recombination, and mismatch repair. Among these, three genes related to steroid biosynthesis, including 3BETAHSD/D2, DIM and DWF5 were down-regulated in S compared to N. Of these, DIM and DWF5 are known to be involved in brassinosteroid biosynthesis. Our results thus provide a useful insight into dwarfism in cherry tomato, and offer a platform for evaluating related species.