Small Non-Coding RNAs at the Crossroads of Regulatory Pathways Controlling Somatic Embryogenesis in Seed Plants

Abstract

Small non-coding RNAs (sncRNAs) are molecules with important regulatory functions during development and environmental responses across all groups of terrestrial plants. In seed plants, the development of a mature embryo from the zygote follows a synchronized cell division sequence, and growth and differentiation events regulated by highly regulated gene expression. However, given the distinct features of the initial stages of embryogenesis in gymnosperms and angiosperms, it is relevant to investigate to what extent such differences emerge from differential regulation mediated by sncRNAs. Within these, the microRNAs (miRNAs) are the best characterized class, and while many miRNAs are conserved and significantly represented across angiosperms and other seed plants during embryogenesis, some miRNA families are specific to some plant lineages. Being a model to study zygotic embryogenesis and a relevant biotechnological tool, we systematized the current knowledge on the presence and characterization of miRNAs in somatic embryogenesis (SE) of seed plants, pinpointing the miRNAs that have been reported to be associated with SE in angiosperm and gymnosperm species. We start by conducting an overview of sncRNA expression profiles in the embryonic tissues of seed plants. We then highlight the miRNAs described as being involved in the different stages of the SE process, from its induction to the full maturation of the somatic embryos, adding references to zygotic embryogenesis when relevant, as a contribution towards a better understanding of miRNA-mediated regulation of SE.

Weighted Gene Correlation Network Analysis (WGCNA) of Arabidopsis Somatic Embryogenesis (SE) and Identification of Key Gene Modules to Uncover SE-Associated Hub Genes

“…Further, it is reported that miRNAs (e.g., miR156, miR159, miR162, miR164, miR166, miR167, miR169, miR168, miR171, miR319, miR393, and miR396) play an important role in SE [87][88][89][90][91]. Consistent with previous studies, several TFs targeted by miRNAs were recovered from the SE-related GCN.…”

Regulatory non-coding RNAs: Emerging roles during plant cell reprogramming and in vitro regeneration

“…Despite being reported as key regulators in plant SE ( Chen et al., 2018 ; López-Ruiz et al., 2019a ; Siddiqui et al., 2019 ; Alves et al., 2021 ), the ncRNAs’ involvement in plant cell plasticity is still far from being fully understood. Nevertheless, the increasing evidence of the importance of the ncRNAs-mediated regulation in cell pluripotency and regeneration ability brings to light important questions to discuss, such as: (1) To what extent do ncRNAs impact plant regeneration processes?…”

miR160 Interacts in vivo With Pinus pinaster AUXIN RESPONSE FACTOR 18 Target Site and Negatively Regulates Its Expression During Conifer Somatic Embryo Development

“…In addition, miRNAs control of transcription factors and phytohormone metabolic pathways is key during different steps of the SE process (reviewed in Siddiqui et al, 2019 ). As in Arabidopsis , other angiosperms like Oryza sativa , Zea mays , Gossypium hirsutum , Solanum lycopersicum , and Dimocarpus longan , show differential expression of miRNAs at several developmental stages of SE (reviewed by Alves et al, 2021 ). In gymnosperms, on the other hand, not many miRNA studies are reported.…”