Genome-wide identification and integrative analysis of long non-coding RNAs regulating embryogenic transition during cotton somatic embryogenesis

The low efficiency of somatic cell embryogenesis severely limited genetic transformation and genome modification breeding in cotton, and the underlying molecular mechanism remains largely unknown. Long non-coding RNA (lncRNA) as a kind of novel regulator has attracted increasing attention in research on plant growth and development. The present study investigated roles of lncRNAs in cotton somatic embryogenesis. By integrating full-length Iso-Seq and RNA-Seq, we identified 9761 lncRNAs involved in cotton somatic embryogenesis, of which 2124 were differentially expressed across the nine developmental stages. LncRNA expression profiles showed that different developmental stages were dominated by different lncRNAs during somatic embryogenesis, especially between the non-embryogenic and embryogenic stages. Time-series clustering of differentially expressed lncRNAs and weighted correlation network analysis (WGCNA) identified 15 and 14 co-expression modules respectively, among which several lncRNA sets from three co-expression modules were predicted associated with the key embryogenic transition step during cotton somatic embryogenesis. Functional analysis suggested that hormone signaling and cell cycle pathways may be regulated by these lncRNAs, potentially through directly targeting of related genes and indirectly acting as precursors or target mimics of specific regulatory miRNAs. Moreover, a competing endogenous RNA (ceRNA) regulatory network comprising 13 lncRNAs, 61 mRNAs, and 13 miRNAs during cotton somatic embryogenesis was constructed, and the lncRNA PB.15563.2 – miR169 – NF-YA module was predicted to play an important role in cotton somatic embryogenesis by integrating both cell cycle and hormone signaling regulation. Collectively, our findings highlight the potential significance of lncRNAs in cotton somatic embryogenesis, providing novel insights into the regulatory mechanisms of cotton somatic embryogenesis. The identified regulatory modules offer promising targets for future manipulation of embryogenic competence and warrant further experimental validation.