Temporal transcriptomics reveal the molecular mechanism of dormancy and germination regulated by temperature in Paris polyphylla seed

The mature seed of Paris polyphylla var. chinensis (PPC) is morphophysiologically dormant and develops differently under warm and cold temperatures. To elucidate the molecular mechanisms underlying temperature-dependent regulation of PPC seed dormancy and germination, we investigated the dynamic changes in PPC seed transcript levels under warm and cold temperature stratification (WS and CS, respectively) by time-resolved RNA sequencing, focusing on genes related to hormone metabolism and signaling and cell wall remodeling (CWRM) and encoding transcription factors/regulators (TFs/TRs). A total of 48 765 and 47 836 differentially expressed genes (DEGs) were associated with WS and CS, respectively; of these, 17 581 and 16 652 DEGs, respectively, were unique and 5 386 were common to both temperature stratifications across 9 analyzed growth stages. The expression of hormone metabolism and signaling, TF/TR, and CWRM genes was closely associated with temperature. More genes related to gibberellin (GA), cytokinin, auxin, and brassinosteroid biosynthetic were upregulated in WS as compared to CS seeds, while genes related to dormancy release and germination were downregulated in WS seeds. However, only GA and abscisic acid levels were altered in PPC seeds breaking morphophysiological dormancy (MPD). Overall, 37 TF and 5 TR families were upregulated whereas 24 TF and 16 TR families were downregulated in WS as compared to CS seeds. Most CWRM families were highly expressed under WS as compared to CS, suggesting that they promote endosperm weakening and embryo growth of WS seeds and facilitate MPD release and germination. A coexpression analysis revealed positive correlations between TFs/TRs and DEGs involved in hormone metabolism and signaling and CWRM. These results provided a basis for investigating the interaction between the endosperm and underdeveloped embryo in the regulation of PPC seed germination and seedling emergence.