Transcriptome and small RNA analysis reveal potential miRNA-mediated interactions involved in somatic embryogenesis of Taxodium hybrid 'zhongshanshan'.

Key message: Antioxidant-related miRNA-mRNA pairs play crucial roles in modulating the dominant embryo formation in Taxodium hybrid 'zhongshanshan'. SE (somatic embryogenesis) has been instrumental in the successful breeding of Taxodium hybrid 'zhongshanshan', a valuable timber tree species of great ecological importance. However, the underlying molecular mechanisms remain largely unknown. By examining the transcriptome and small RNA throughout the entire SE process, we observed notable differences in gene expression and miRNA profiles. DEGs (differentially expressed genes) associated with phenylpropanoid biosynthesis, glutathione metabolism, starch and sucrose metabolism, and pentose and glucuronate interconversions played pivotal roles in dominant embryo formation and cotyledonary embryo maturation. The physiological measurements showed that the contents of organic compounds were higher in embryogenic callus and cotyledonary embryo stage. Endogenous GSH (glutathione) and GSSG (oxidized glutathione disulfide) contents reached the peak values in the dominant embryo stage. Additionally, a total of 271 mature miRNAs were detected, with 244 being previously identified and 27 being novel plant miRNAs. Among these, 71 DE miRNAs (differentially expressed miRNAs) were screened out during the transition from embryogenic callus to cotyledon embryo stage of SE, which suggested that miRNAs played important roles in somatic embryo development. By predicting target genes for these DE miRNAs and conducting correlation analysis with DEGs, several key miRNA-mRNA pairs were identified, which mainly regulated the dominant embryo formation in Taxodium hybrid 'zhongshanshan'. Furthermore, the exogenous addition of 0.3 g·L^-1 GSH effectively improved SE efficiency. Taken together, this study provided valuable information in the SE of Taxodium hybrid 'zhongshanshan', thereby facilitating its breeding programs.