Red-light-responsive metabolome reveals the crucial role of phytochrome A- and B-dependent secondary metabolism in Arabidopsis seed germination

Phytochrome A (phyA) and phyB are red and far-red photoreceptors that play essential roles in modulating seed germination. Despite extensive research on the roles of hormones and light signaling, the metabolic characteristics of phytochromes during red-light-mediated seed germination remain largely unknown. Using high-throughput non-targeted metabolomics, this study profiled Arabidopsis seeds including the wild-type (Col-0), single mutants (phyA-211 and phyB-9), the double mutant phyAB, and the pifq quadruple mutant during red-light-induced germination, and identified a total of 164 metabolites linked to primary and secondary metabolism. Comparative analysis of the metabolome revealed that the levels of flavonols including quercetin, kaempferol, and relevant glycosides were increased in phyA-211, decreased in Col-0 and phyB-9, and exhibited less change in phyAB, demonstrating that phyA and phyB antagonistically regulate flavonoid biosynthesis. Flavonoid biosynthesis was up-regulated in pifq under red light. Exogenous quercetin and kaempferol treatment modestly inhibited Col-0 and pifq seed germination. Taken together, these results reveal the comprehensive metabolic networks, highlight flavonoid metabolism under red light, and elucidate the synergistic and antagonistic roles of phyA and phyB in regulating seed metabolism. This study provides novel insight into the functional mechanisms of flavonoid metabolism and light signaling in plant development.