Transcriptome Analysis of Onobrychis viciifolia During Seed Germination Reveals GA3-Inducible Genes Associated with Phenylpropanoid and Hormone Pathways

Sainfoin (<i>Onobrychis viciifolia</i>) is a type of leguminous plant with high feeding value. It contains a high concentration of tannins at all growth stages, which can precipitate soluble proteins and form a large number of persistent foams in the rumen, so that ruminant livestock will not develop dilatation disease during green feeding and grazing. The germination rate of <i>O. viciifolia</i> seeds is very low under natural conditions. The preliminary experiment showed that 600 mg/L GA₃ treatment significantly improved the germination rate and seed vitality of sainfoin seeds. In comparison to CK, GA₃ significantly decreased the relative content of endogenous inhibitors, with the most notable reduction observed in 4-nitroso-N-phenyl-benzenamine. Therefore, we selected the dry seed stage (GZ), imbibition stage (XZ), split stage (LK), and radicle emergence stage (MF) of four different germination stages treated with GA₃ for transcriptome analysis. RNA-seq identified 1392, 2534 and 4284 differentially expressed genes (DEGs) in GZ vs. XZ, XZ vs. LK, and LK vs. MF, respectively. During seed germination, DEGs are mainly enriched in hormone signaling and phenylalanine biosynthesis pathways, and up-down-regulation of these DEGs may alter hormone and secondary metabolite levels to promote germination. The results of weighted gene co-expression network construction (WGCNA) also indicate that plant hormone signal transduction and phenylpropanoid biosynthesis play a dominant role in GA₃-induced seed germination. In conclusion, the combined analysis of transcriptomic and physiological indicators provided new insights into seed germination and a theoretical basis for further study of candidate genes.