Proteomic Dynamics of Taxus chinensis var. mairei Seeds During Natural Stratification

Taxus chinensis var. mairei is valued for paclitaxel but suffers from poor regeneration and wild resource scarcity. To elucidate seed dormancy mechanisms and support large-scale cultivation, seeds were stratified under natural conditions for 9 months and subjected to physiological and proteomic analyses. During stratification, ABA increased significantly from 0 to 3 months, showed a slight non-significant decrease from 3 to 6 months, and then increased significantly to reach its highest level at 9 months; GA3 increased significantly from 0 to 3 months and remained stable thereafter. IAA rose to a peak at 6 months and then declined. Concurrently, soluble protein peaked then declined, free amino acids showed the opposite trend, and soluble sugar, starch, and fat content continuously decreased; peroxidase (POD) activity increased then decreased, while acid phosphatase (ACP) activity decreased then increased. TMT-based quantitative proteomics identified 3047 differentially expressed proteins (DEPs were defined as protein with fold change >1.2 or <0.83 and p < 0.05) and Benjamini–Hochberg adjusted p < 0.05. GO annotation indicated enrichment in metabolic and catalytic processes, with more DEPs detected in late versus early stages. KEGG pathway analysis implicated DEPs in endoplasmic reticulum protein processing, fatty acid metabolism, carbohydrate metabolism, peroxisome pathways, and hormone signal transduction, with candidate proteins including calreticulin, protein disulfide isomerase, ACCase, acyl-CoA oxidase, phosphofructokinase, glyceraldehyde-3-phosphate dehydrogenase, catalase, PYR/PYL, and SRK2; these candidates require future functional validation. Collectively, these findings provide insights into the physiological and proteomic changes during natural stratification that are associated with progressive dormancy alleviation in T. chinensis var. mairei seeds.