Analysis of the potential involvement of lncRNAs in embryogenic competence of Solanum betaceum Cav. (tamarillo) calli

Somatic embryogenesis (SE) is a process by which somatic cells reprogram, acquire totipotency and embark on embryo formation. Although SE is a valuable tool for micropropagation in many crops, it presents specific challenges in woody species due to some bottlenecks, such as loss of embryogenic competence during subcultures and the often-low somatic embryo conversion into plantlets. Hence, great interest exists in exploring the regulatory networks involved on SE. As transcription modulators, long non-coding RNAs (lncRNAs) have been found essential in a wide range of biological processes. This work aimed to identify lncRNAs related to the embryogenic competence in Solanum betaceum Cav. (tamarillo). Nanopore® long-read sequencing was conducted in cell lines with distinct cell fates and, based on their coding potential, 60 transcripts were selected as lncRNA candidates. Similar expression patterns were found among embryogenic cell lines (EC) and cells that lost their embryogenic potential (herein long-term callus, LTC), whereas non-EC (NEC) showed differentially expressed lncRNAs. Whereas lncRNAs upregulated in EC and LTC were predicted to target embryogenesis-related genes, such as AGAMOUS-like 15 and WUSCHEL-related HOMEOBOX 2, lncRNAs upregulated in NEC were predicted to target mainly genes involved in carbohydrate metabolism, cell wall formation, auxin and ethylene signalling pathways. Altogether, these results show the involvement of lncRNA in the process of somatic embryogenesis in S. betaceum, indicating that EC present a pattern of lncRNA expression that suggests its action on genes that directly modulate the morphogenic response in vitro, while in NEC the modulation through this type of RNAs seems to be predominantly reflected in genes more related to cellular physiology. LncRNAs upregulated in EC/LTC were predicted to target embryogenesis-related genes, while lncRNAs upregulated in NEC were predicted to target genes involved in auxin and ethylene signalling and carbohydrate metabolism.