High temperature germinated pecan seeds by transcriptome and metabolome analysis

Abstract

The pecan tree is a globally recognized fruit-bearing tree of significant economic value. This paper focused on the dynamic changes that occur during the germination stages of pecan seeds. To investigate alterations in transcription and metabolism during the germination process, this paper employed UPLC–MS/MS technology to evaluate the shifts in the metabolite composition of pecan seeds during four different germination processes. This paper unveiled a total of 1426 metabolites, encompassing various categories such as flavonoids, phenolic acids, amino acid derivatives, lipids, and alkaloids. Furthermore, the exploration of the transcriptome through GO and KEGG enrichment analyses revealed a common pathway across all control groups—the “phytohormone signal transduction” pathway. This finding underscores the pivotal role of phytohormones in regulating diverse stages of pecan seed germination. In addition, the investigation into the interplay between differentially expressed genes and metabolites highlighted two key plant hormones, ABA and GA3, as essential drivers of seed germination. Within the ABA synthesis pathway, we observed elevated expression of NCED during the S1 stage, leading us to speculate that NCED is a key enzyme in ABA synthesis. Conversely, GA3ox and GGPPS displayed heightened expression during the S2 and S4 stages, respectively, signifying their critical roles in the GA3 synthesis pathway. To validate our findings, we performed qRT-PCR analysis on nine key genes. In conclusion, this study integrated metabolomics and transcriptomics techniques, furnishing a vital foundational framework for unraveling the intricate molecular mechanisms governing metabolite accumulation in pecan seeds at various stages of germination.