Transcriptome analysis reveals the role of temperature in seed germination of Idesia polycarpa Maxim through the integration of phytohormones and sugar metabolism

The germination of Idesia polycarpa Maxim seeds plays a critical role in successfully cultivating this dioecious species. In order to reveal the mechanisms regulating the germination of I. polycarpa seeds under variable temperature environments, a comparative analysis of the phenotype information and genetic changes before and after germination of the seeds was conducted. Using the paraffin section method, morphological and structural changes were observed at three developmental stages—seed coat cracking (CK), emergence (SE), and radicle elongation (RE). The study also evaluated the relationship between morphological structure variation and the dynamics of endogenous hormones. In addition, three sets of transcriptome data were obtained using high-throughput sequencing technology and analyzed to screen for differential gene function during seed germination. The study found that most seeds effectively released from dormancy after treatment at 5 ℃ for 60 days and the highest germination rate at the variable temperature (15 ℃/25 ℃ for 12 h) environment. The gene ontology (GO) revealed that 26,578 differentially expressed genes (DEGs) were annotated into 52 subclasses under three major classifications: biological processes, molecular functions, and cellular components. KEGG functional classification revealed that 1,764 DEGs were present at different stages of seed germination. I. polycarpa seed germination is achieved by up-regulation of genes related to phenylpropane biosynthesis, phytohormone signaling, flavonoid biosynthesis, photosynthesis, starch and sucrose metabolism, and down-regulation of genes related to ribosomes. Analysis of differential genes at different stages of seed germination in I. polycarpa revealed that 34 differential genes were closely related to seed embryo growth and development, cell wall structure, and endosperm weakening. The RT-qPCR was used to verify the reliability and accuracy of six genes closely related to the seed germination of I. polycarpa. The results indicate that multiple phytohormones, starch, and sugar metabolism coordinately mediate seed germination in I. polycarpa. Further research is required to investigate the potential roles of certain genes in the seed germination of this species.