Integrated Transcriptomic, Proteomic, and miRNA Profiling Reveals the Regulatory Mechanisms Underlying Pecan Seed Germination

Abstract

Pecan is a well-known nut tree native to the United States and Mexico. It is valued as a high-quality source of dried fruit, oil trees, and wood. Seed germination, beginning with imbibition, comprises a series of coordinated physiological and morphogenetic processes that play a key role in the growth of pecan seedlings. Several factors influence the germination of pecan seeds. To explore the mechanisms underlying pecan seed germination, we performed transcriptomic, proteomic, and microRNA (miRNA) analyses on seeds sampled at four different stages to compare changes in messenger RNA (mRNA), protein, and miRNA. Transcriptomic and proteomic analyses highlight pathways associated with plant hormone signal transduction. miRNA profiling identified both conserved and novel miRNAs, with differential expression indicating regulatory roles in germination. A putative miR396–growth regulating factor (GRF) regulatory module was identified and may participate in pecan seed germination, potentially through its association with plant hormone regulation. This multiomics study provides insights into potential molecular regulatory processes underlying pecan seed germination and offers a theoretical basis for future functional studies, seedling cultivation, and breeding improvement.