Transcriptome profiles revealed molecular mechanisms of alternating temperatures in breaking the epicotyl morphophysiological dormancy of Polygonatum sibiricum seeds

BACKGROUND: To adapt seasonal climate changes under natural environments, Polygonatum sibiricum seeds have a long period of epicotyl morphophysiological dormancy, which limits their wide-utilization in the large-scale plant progeny propagation. It has been proven that the controlled consecutive warm and cold temperature treatments can effectively break and shorten this seed dormancy status to promote its successful underdeveloped embryo growth, radicle emergence and shoot emergence. To uncover the molecular basis of seed dormancy release and seedling establishment, a SMRT full-length sequencing analysis and an Illumina sequencing-based comparison of P. sibiricum seed transcriptomes were combined to investigate transcriptional changes during warm and cold stratifications. RESULTS: A total of 87,251 unigenes, including 46,255 complete sequences, were obtained and 77,148 unigenes (88.42%) were annotated. Gene expression analyses at four stratification stages identified a total of 27,059 DEGs in six pairwise comparisons and revealed that more differentially expressed genes were altered at the Corm stage than at the other stages, especially Str_S and Eme. The expression of 475 hormone metabolism genes and 510 hormone signaling genes was modulated during P. sibiricum seed dormancy release and seedling emergence. One thousand eighteen transcription factors and five hundred nineteen transcription regulators were detected differentially expressed during stratification and germination especially at Corm and Str_S stages. Of 1246 seed dormancy/germination known DEGs, 378, 790, and 199 DEGs were associated with P. sibiricum MD release (Corm vs Seed), epicotyl dormancy release (Str_S vs Corm), and the seedling establishment after the MPD release (Eme vs Str_S). CONCLUSIONS: A comparison with dormancy- and germination-related genes in Arabidopsis thaliana seeds revealed that genes related to multiple plant hormones, chromatin modifiers and remodelers, DNA methylation, mRNA degradation, endosperm weakening, and cell wall structures coordinately mediate P. sibiricum seed germination, epicotyl dormancy release, and seedling establishment. These results provided the first insights into molecular regulation of P. sibiricum seed epicotyl morphophysiological dormancy release and seedling emergence. They may form the foundation of future studies regarding gene interaction and the specific roles of individual tissues (endosperm, newly-formed corm) in P. sibiricum bulk seed dormancy. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-021-03147-7.