Multi-Omics Integration Analysis Revealed the Seed Germination Mechanism of Pecan

As a multi-functional tree species integrating fruit, wood and garden appreciation, pecan has broad development prospects and market demand. The research on the seed germination mechanism of pecan can provide a basis for solving the obstacle of intensification caused by low seed germination rate. The process of seed germination is closely related to proteins, metabolites and microorganisms. In this study, four stages of seed germination of hickory pecan were selected to study the proteome, metabolome and microbiome. To further elucidate the functional significance of the differentially expressed proteins (DEPs) identified during pecan seed germination, we conducted pairwise comparisons across the four germination stages and performed GO annotation and KEGG enrichment analysis. The GO annotation results revealed that the proteins were predominantly involved in catalytic activities, highlighting their role in biochemical transformations. Additionally, these proteins participated in plant hormone signaling and molecular transduction mechanisms, suggesting their involvement in regulating germination-related processes. The KEGG enrichment analysis provided insights into the specific biological pathways enriched by the DEPs. Notably, aflatoxin biosynthesis emerged as the pathway with the highest concentration of differentially up-regulated proteins. On the other hand, anthocyanin biosynthesis was identified as the pathway with the highest concentration of differentially down-regulated proteins. They all involved in secondary metabolism and biosynthesis. In addition, we analyzed the composition of bacterial and fungal communities of hickory pecan seeds at different germination stages at phylum, class, order, family and genus levels, and integrated the study with proteomics, through the correlation heat maps of bacteria and fungi with proteins, respectively. Malate synthase, isocitrate lyase family and cupin were preliminarily related to the microbial community composition of hickory pecan. In conclusion, the in-depth analysis and study of differential proteome is helpful to reveal the molecular mechanism of seed germination of pecan, which has strong theoretical and practical significance.