Multiomics strategies for decoding seed dormancy breakdown in Paris polyphylla

BACKGROUND: The disruption of seed dormancy is a complicated process and is controlled by various factors. Among these factors, membrane lipids and plant hormones are two of the most important ones. Paris polyphylla is an important Chinese herbaceous species, and the dormancy trait of its seed limits the cultivation of this herb. RESULTS: In this study, we investigate the global metabolic and transcriptomic profiles of Paris polyphylla during seed dormancy breaking. Widely targeted metabolomics revealed that lysophospholipids (lysoPLs) increased during P. polyphylla seed dormancy breaking. The expression of phospholipase A2 (PLA2), genes correlated to the production of lysoPLs, up-regulated significantly during this process. Abscisic acid (ABA) decreased dramatically during seed dormancy breaking of P. polyphylla. Changes of different GAs varied during P. polyphylla seeds dormancy breaking, 13-OH GAs, such as GA(53) were not detected, and GA(3) decreased significantly, whereas 13-H GAs, such as GA(15), GA(24) and GA(4) increased. The expression of CYP707As was not synchronous with the change of ABA content, and the expression of most UGTs, GA20ox and GA3ox up-regulated during seed dormancy breaking. CONCLUSIONS: These results suggest that PLA2 mediated production of lysoPLs may correlate to the seed dormancy breaking of P. polyphylla. The conversion of ABA to ABA-GE catalysed by UGTs may be the main cause of ABA degradation. Through inhibition the expression of genes related to the synthesis of 13-OH GAs and up-regulation genes related to the synthesis of 13-H GAs, P. polyphylla synthesized more bioactive 13-H GA (GA(4)) to break its seed dormancy. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-023-04262-3.