Tissue-specific transcriptome analysis provides insights into hormone signaling and phenylpropanoid biosynthesis pathway regulations during tomato fruit developmental stages

Late fruit development is crucial for crop production in tomatoes. Although the roles of regulatory signals such as hormones during early fruit development have been studied, the tissue-specific distribution and the sequential initiation of these regulatory signals in late development and ripening stages still need to be explored. In the present study, the transcriptome analysis coupled with physiological studies was used to determine the tissue-specific alternation of genetic variants contributing fruit repining. Gene expression changes in four different stages of the ripening fruits were compared, and a total of 6,277; 4,366; 3,299; and 1,544 genes were differentially expressed at four developmental stages between pulp and seed. Differentially expressed genes (DEGs) were enriched significantly with plant hormone signal transduction and phenylpropanoid biosynthesis in four developmental stages, suggesting specific metabolic events during fruit ripening. The results of the present study provide a foundation for further characterization of hormone signal transduction and phenylpropanoid biosynthesis in tomatoes.