Transcriptome sequencing and analysis during seed growth and development in tomato

Seed development is a complex process that includes the changes in seed size and the accumulation of various nutrients, and the process is regulated by many genes. Tomato is an important vegetable crop with extremely high nutritional value. Previous studies on tomato have focused mainly on fruit development and ripening, while few studies on the molecular mechanism of tomato seed development have been reported. In this study, we first compared the morphology of five stages of tomato seed development and measured the physiological changes of each stage. RNA-Seq showed that numerous differentially expressed genes (DEGs) were involved in seed development, including transcription factors (TFs), hormone biosynthesis and signal transduction, and starch biosynthesis-related genes. Of these genes, 54 DEGs were identified as the key candidate genes for tomato seed size by homologous query of known seed size-related genes in different plants. On this basis, 20 DEGs related to seed development were validated by quantitative real-time polymerase chain reaction (qRT-PCR), and the results showed high consistency with the RNA-Seq results. Finally, the yeast two-hybrid results showed that SlMBP3 interacts with three transcription factors, which may play important roles in tomato seed development. In short, our results analyzed in depth the gene expression profile of hormone-, transcription factor- and starch-related genes involved in tomato seed development. This study not only provides abundant genomic resources for seed development but also provides many references for future research on seed development and insights into the dynamics of gene regulation underlying seed development in tomato.