Expression analysis of miRNAs and their putative target genes confirm a preponderant role of transcription factors in the early response of oil palm plants to salinity stress

Abstract

Background Several mechanisms regulating gene expression contribute to restore and reestablish cellular homeostasis so that plants can adapt and survive in adverse situations. MicroRNAs (miRNAs) play roles important in the transcriptional and post-transcriptional regulation of gene expression, emerging as a regulatory molecule key in the responses to plant stress, such as cold, heat, drought, and salt. This work is a comprehensive and large-scale miRNA analysis performed to characterize the miRNA population present in oil palm (Elaeis guineensis Jacq.) exposed to a high level of salt stress, to identify miRNA-putative target genes in the oil palm genome, and to perform an in silico comparison of the expression profile of the miRNAs and their putative target genes. Results A group of 79 miRNAs was found in oil palm, been 52 known miRNAs and 27 new ones. The known miRNAs found belonged to 28 families. Those miRNAs led to 229 distinct miRNA-putative target genes identified in the genome of oil palm. miRNAs and putative target genes differentially expressed under salinity stress were then selected for functional annotation analysis. The regulation of transcription, DNA-templated, and the oxidation-reduction process were the biological processes with the highest number of hits to the putative target genes, while protein binding and DNA binding were the molecular functions with the highest number of hits. Finally, the nucleus was the cellular component with the highest number of hits. The functional annotation of the putative target genes differentially expressed under salinity stress showed several ones coding for transcription factors which have already proven able to result in tolerance to salinity stress by overexpression or knockout in other plant species. Conclusions Our findings provide new insights into the early response of young oil palm plants to salinity stress and confirm an expected preponderant role of transcription factors - such as NF-YA3, HOX32, and GRF1 - in this response. Besides, it points out potential salt-responsive miRNAs and miRNA-putative target genes that one can utilize to develop oil palm plants tolerant to salinity stress.

Insights from a Multi-Omics Integration (MOI) Study in Oil Palm (Elaeis guineensis Jacq.) Response to Abiotic Stresses: Part One—Salinity

“…Previously, in addition to showing that young oil palm submitted to a high concentration of NaCl reduces the rates of CO 2 assimilation, stomatal conductance to water vapor, and transpiration, our group also confirmed a preponderant role of transcription factors in the early response of oil palm plants to salinity stress [6,15]. Data from ionomics, phenomics, and transcriptomics (mRNA and miRNA) were employed to show that.…”

“…Leaves harvested from control and stressed plants were immediately immersed in liquid nitrogen and stored at −80 • C until RNA extraction; three plants for treatments. Details regarding total RNA extraction and quality analysis, library preparation, and sequencing are in [15,19]. RNA-Seq raw sequence data are in the Sequence Read Archive (SRA) database of the National Center for Biotechnology Information (NCBI) under BioProject number PRJNA573093.…”

“…All the transcriptomics analysis was performed with OmicsBox platform-version 2.0.36 [49], as previously described by [15,17]. The oil palm genome [19,20]-downloaded from NCBI (BioProject PRJNA268357; BioSample SAMN02981535) in September 2021-was the reference genome for RNA-Seq data alignment.…”

“…Then, Ref. [15] confirmed a preponderant role of transcription factors in the early response of oil palm plants to salinity stress, and [16] identified the pathways and the metabolites most affected by drought stress.…”

“…The first challenge is understanding the morphophysiological, biochemical, and molecular responses of oil palm to these two abiotic stresses. In doing so, our group has studied the response of young oil palm plants from different angles, applying different omics platforms, alone or in combination [6,15,16]. Vieira and colleagues showed that young oil palm submitted to a high concentration of NaCl reduces the rates of CO 2 assimilation, stomatal conductance to water vapor, and transpiration [6].…”