miRNome profiling reveals differential miRNAs associated with embryogenic potential in the somatic embryogenesis of Araucaria angustifolia

Abstract

Somatic embryogenesis occurs through complex processes modulated by gene regulatory networks at an appropriate spatiotemporal scale important for cell division and differentiation. Post-transcription regulation mechanisms mediated by miRNAs control the expression of several genes involved in embryogenesis. Transcript and proteomics studies in embryogenic cultures from Araucaria angustifolia, an endangered native Brazilian conifer with ecological and economic importance, have indicated a role for post-transcriptional regulation in this process. One example is the differential abundance of ARGONAUTE between two contrasting embryogenic cell lines. Here, we profiled the miRNA expression pattern in two cell lines of A. angustifolia with distinct embryogenic potential using small RNA sequencing technology. We identified 165 mature miRNAs, of which 143 were novel and 22 were conserved plant miRNAs. Seven miRNA conserved families were identified: miR156, miR169, miR394, miR482, miR536, miR1030, and miR1314. Most miRNAs were differentially expressed during the transition from proliferation to the maturation stage of somatic embryogenesis, suggesting that miRNAs play more important roles in the early somatic embryo development. A total of 98 potential target genes were found for 89 miRNAs, involved in post-transcriptional processes, transporters, defense response, sugar regulation, stress, ABA controlling and signaling, cell-to-cell communication, maintaining suspensor cell identity, brassinosteroids signaling, and cell division. Negative correlations of expression patterns between miRNAs and their targets were detected for miR1030-PRL1, miR1314-ADR1-Like, and Aang34-LRR modules, when analyzed by RT-qPCR. Taken together, our findings provide new insights into the regulatory roles of miRNAs and their target genes in the somatic embryogenesis of Brazilian pine.