Integrated multi-omics approach to reveal the molecular networks underlying the seed germination of Polygonatum cyrtonema

Abstract

Abstract Background Polygonatum cyrtonema (P. cyrtonema), a famous traditional medicinal resource for over two thousand years in China, is in high demand with the vigorous development of the health industry. The rhizome propagation could easily lead to germplasm degradation, severe pests, diseases, etc., and thus, the seed propagation method is a superior alternative to artificially cultivating seedlings on a large scale. However, the seeds of P. cyrtonema need at least two years dormancy period under natural circumstances to undergo morphological and physiological maturation, and germination of seeds has not been fully understood. To reveal the mechanisms of hormone crosstalk and metabolic process regulating germination, transcriptomic, proteomic and plant hormonomics analyses of P. cyrtonema seeds in three different germinating stages (the fresh mature seed, named S1, the emergence of radicle, named S2 and the phase between primary rhizome and cotyledon emergence, named S3) were performed. Results Transcriptome analysis revealed that 11,565 differentially expressed genes (DEGs) between S1 and S2, 10,196 between S1 and S3, 7,696 between S2 and S3. Proteome analysis revealed 647 differentially expressed proteins (DEPs) between S1 and S2, 1720 between S1 and S3, and 1475 between S1 and S3. Comprehensive transcriptomic and proteomic analysis indicated that metabolism and plant hormone signal transduction might be the main pathways involved in seed germination of P. cyrtonema. In addition, several proteins, including abscisic acid receptor PYL4 (PYL4) and protein phosphatase 2C (PP2C) bind ABA to form PYL-ABA-PP2C complex, associated with ABA signaling, were down-regulated between S1 and S3. And the sucrose synthase (SUS), involving in the antagonism between ABA and GA, decreased between S1 and S3. While, these proteins such as beta-fructofuranosidase (INV), alpha-xylosidase (α-Xyl), beta-D-xylosidase (β-D-Xyl) and beta-glucosidase (bglX), related to starch and sucrose metabolism, were up-regulated between S1 and S3. Hormone content detection showed that ABA, GAs, IAA, JA and SA decreased significantly, while, the ratio of GAs/ABA increased distinctly from S1 to S3, suggesting that transduction in plant hormones, especially ABA-GA antagonism might regulate seed germination. Conclusion The current study showed a possible schematic and a novel insight to explain the dynamic seed germination mechanism of P. cyrtonema, and emphasized that phytohormone cross-talk, ABA signaling and shydrolysis of starch to glucose might play an important role in regulating seed germination.