Transcriptome Analysis Identifies Genes Involved in the Somatic Embryogenesis of Eucalyptus

Abstract

Background: Eucalyptus, a highly diverse genus of the Myrtaceae family, is the most widely planted hardwood due to its increasing importance for fiber and energy in the word. Somatic embryogenesis is one method to provide large-scale commercial use for the vegetative propagation of Eucalyptus and dedifferentiation is a key step for plant cells to become meristematic. However, little is known about the molecular changes during the SE of Eucalyptus on transcriptional level.Results: We compared the transcriptome profiles of the differentiated and dedifferentiated tissues of two Eucalyptus cultivars – E. camaldulensis (high embryogenetic potential) and E. grandis x urophylla (low embryogenetic potential). In total, we identified 18,777 to 20,240 genes in all samples. Compared to the differentiated tissues, we identified 9,229 and 8,989 differentially expressed genes (DEGs) in the dedifferentiated tissues of E. camaldulensis and E. grandis x urophylla, respectively. Comparison of DEGs showed that they shared 2,687 up-regulated and 2,581 down-regulated genes. Next, we found 2,003 up-regulated and 1,958 down-regulated genes specifically identified in E. camaldulensis, including 6 somatic embryogenesis receptor kinase, 17 ethylene, 12 auxin, 83 ribosomal protein, 28 zinc finger protein, 10 heat shock protein, 9 histone and 98 transcription factor genes. Genes from other families like ABA, arabinogalactan protein and late embryogenesis abundant protein were also found to be specifically dysregulated in E. camaldulensis. Further, we identified 48,447 variants (SNPs and small indels) specific to E. camaldulensis, including 13,434 exonic variants from 4,723 genes (e.g., annexin, GN, ARF and AP2-like ethylene-responsive transcription factor). qRT-PCR was used to confirm the gene expression patterns in both E. camaldulensis and E. grandis x urophylla. Conclusions: This is the first time to study the somatic embryogenesis of Eucalyptus using transcriptome sequencing. Our results will improve our understanding of the molecular mechanisms of somatic embryogenesis and dedifferentiation in Eucalyptus. Our results provide a valuable resource for future studies in the field of Eucalyptus and will benefit the Eucalyptus breeding program.

Changes and transcriptome regulation of endogenous hormones during somatic embryogenesis in Ormosia henryi Prain

“…Similar results were also found in SE development for G. hirsutum ( Cheng, 2016 ). As an ABA receptor protein, PYL was downregulated in dedifferentiated tissues of eucalyptus ( Xiao et al., 2020 ). Jie (2016) reported that PYL was significantly upregulated during SE for G. hirsutum , which was consistent with the results of this study.…”