Metabolome and transcriptome analyses unravel the inhibition of embryo germination by abscisic acid in pear

It is well-known that abscisic acid (ABA) inhibits seed germination, but the mechanism is still unclear. In this study, after removing the seed coats, the seeds treated with 1 ppm ABA to inhibit embryo germination. A total of 715 compounds that were involved in 271 metabolic pathways were identified from a broadly targeted metabolome. Of these compounds, the number of flavonoids is most and accounting for 21%. Moreover, compared to the control embryos, over 80% of the differentially accumulated compounds (DACs) were down-regulated in the ABA-treated embryos, while only 46 compounds were up-regulated. These differentially accumulated compounds were involved in 26 metabolic pathways. Transcriptome analysis showed that 6348 genes were differentially expressed between ABA-treated and control embryos. These differentially expressed genes (DEGs) were enriched into 28 metabolic pathways including photosynthesis. Interestingly, both DEG and DAC analyses had identified the 10 common metabolic pathways, including oxidative phosphorylation, phenylpropanoid biosynthesis, flavonoid biosynthesis, pyrimidine metabolism, ascorbate and aldarate metabolism, galactose metabolism, glycolysis/gluconeogenesis, carbon metabolism, amino sugar and nucleotide sugar metabolism, and valine, leucine and isoleucine degradation. Taken together, ABA represses the expression of the genes involved in photosynthesis and those 10 metabolic pathways to suppress the secondary metabolism of the embryos, resulting in the inhibition of embryo germination.