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 in the world due to its increasing importance for fiber and energy. Somatic embryogenesis (SE) is one large-scale method to provide commercial use of 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 Eucalyptus SE.Results: We compared the transcriptome profiles of the differentiated and dedifferentiated tissues of two Eucalyptus species – E. camaldulensis (high embryogenetic potential) and E. grandis x urophylla (low embryogenetic potential). Initially, 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, and 2,687 up-regulated and 2,581 down-regulated genes shared. Next, we identified 2,003 up-regulated and 1,958 down-regulated genes only 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, 122 cell wall related 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 the dedifferentiation process of 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. It 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.

BREVIPEDICELLUS and ERECTA mediate expression ofAtPRX17in preventing Arabidopsis callus retardation and browning

“…Callus is like the meristematic tissues, which is a self-renewing structure consisting of stem cells and their immediate daughters (Springer and Kohn, 1979; Xiao et al, 2020), but the mechanism on how to maintain this self-renewing structure is unclear. Reactive oxygen species (ROS) play an important role in maintaining plant cell proliferation (Vemoux et al, 2000; Wells et al, 2010).…”

Proteome profiles during early stage of somatic embryogenesis of two Eucalyptus species

“…Previously, our lab published the transcriptome and miRNA profiles of tissue-culture induced callus of two Eucalyptus species-E. camaldulensis (high regeneratively potential) and E. grandis x urophylla (low regenerative ability) [2,28,29]. We found that early stage of SE is important for downstream callus development as it prepares for the acquisition of SE potential of callus via dedifferentiation on transcriptional level [2].…”

“…Since Steward firstly reported the asexual embryogenesis in the cell suspension cultures of carrot in 1958, in vitro SE systems have been established in many plant species [1]. For Eucalyptus -a highly diverse genus of the Myrtaceae family widely planted across the world for its increasing importance for timber and pulp [2,3], Ouyang et al reported the SE from the callus of seedlings for the first time in 1980 [4]. Early SE is the callus induction in which differentiated somatic cells (e.g., seed, leaf, stem) acquire embryogenetic competence with or without a dedifferentiation step [5].…”

Chloroplast activity provides in vitro regeneration capability in contrasting cultivars

“…Many plant species have been examined for the characterisation of genes particularly expressed during somatic embryogenesis, including wheat (Chu et al, 2017), cotton (Zeng et al, 2006; Wu et al, 2009; Cheng et al, 2016; Cao et al, 2017), peanut (Rani et al, 2005), carrot (Aleith and Richter, 1991), grape (Gianazza et al, 1992), alfalfa (Domoki et al, 2006), conifer (John and Gerald, 2007; Yakovlev et al, 2016), papaya (Jamaluddin et al, 2017), maize (Salvo et al, 2014) and banana (Enríquez-Valencia et al, 2019). These studies have identified genes that are differentially expressed in SE, including SOMATIC EMBRYOGENESIS RECEPTOR KINASE (SERK) (Schmidt et al, 1997), LEAFY COTYLEDON (LEC) (Curaba et al, 2004), ABSCISIC ACID INSENSITIVE3 (ABI3), FUSCA3 (FUS3) (Freitas et al, 2019), BABY BOOM (BBM) (Boutilier et al, 2002; Maulidiya et al, 2020), WUSCHEL (WUS) (Zuo et al, 2002,), AUXIN RESPONSE FACTOR 19 (ARF19) (Xiao et al, 2020), and LATE EMBRYOGENESIS ABUNDANT (LEA) protein (Wickramasuriya and Dunwell, 2015; Jamaluddin et al, 2017). Although RNA-Seq (RNA Sequencing) analyses have been conducted to investigate genome-wide gene expression in response to somatic embryogenesis (SE) in many plants, the expressions of genes involved along with the key factors determining gene changes and regulations in somatic embryo maturation in cereals have not been previously investigated.…”