The early response of oil palm (Elaeis guineensis Jacq.) plants to water deprivation: Expression analysis of miRNAs and their putative target genes, and similarities with the response to salinity stress

Abstract

Oil palm (Elaeis guineensis Jacq.) is a oilseed crop of great economic importance drastically affected by abiotic stresses. MicroRNAs (miRNAs) play crucial roles in transcription and post-transcription regulation of gene expression, being essential molecules in the response of plants to abiotic stress. To better understand the molecular mechanisms behind the response of young oil palm plants to drought stress, this study reports on the prediction and characterization of miRNAs and their putative target genes in the apical leaf of plants subjected to 14 days of water deprivation. Then, the data from this study were compared to the data from a similar study that focused on salinity stress. Both, the drought-and salt-responsive miRNAs and their putative target genes underwent correlation analysis to identify similarities and dissimilarities among them. Among the 81 identified miRNAs, 29 are specific for oil palm, including two (egu-miR28ds and egu-miR29ds) new ones – described for the first time. As for the expression profile, 62 miRNAs were significantly differentially expressed under drought stress, being five up-regulated (miR396e, miR159b, miR529b, egu-miR19sds, and egu-miR29ds) and 57 down-regulated. Transcription factors, such as MYBs, HOXs, and NF-Ys, were predicted as putative miRNA-target genes in oil palm under water deprivation; making them the most predominant group of such genes. Finally, the correlation analysis study revealed a group of putative target genes with similar behavior under salt and drought stresses. Those genes that are upregulated by these two abiotic stresses encode lncRNAs and proteins linked to stress tolerance, stress memory, modulation of ROS signaling, and defense response regulation to abiotic and biotic stresses. In summary, this study provides molecular evidence for the possible involvement of miRNAs in the drought stress response in oil palm. Besides, it shows that, at the molecular level, there are many similarities in the response of young oil palm plants to these two abiotic stresses.

The Role of Noncoding RNAs in the Response of Oil Palm Plants to Abiotic Stresses

“…We did find 81 miRNAs-52 known ones and 29 new ones (Figure 2)-and 139 differentially expressed putative miRNA-target genes [15,64]. In Salgado et al [15], miR166, miR169, miR319, miR396, miR529, and egu-miR24sds showed altered expression profiles in young oil palm plants subjected to salt stress, both targeting TF, indicating a miRNA-dependent posttransitional regulation during the plant's response to the environment.…”

“…Our research group reported prospecting and characterizing miRNAs in oil palm plants under salinity stress (Table 1) [15]. That was the first step in a study prospecting and characterizing miRNAs in oil palm plants under salinity [64] or drought stress and looking for insights on commonalities-miRNAs and putative miRNA-target genes-on the molecular response of young oil palm plants to these two abiotic stresses.…”

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

“…Plant response to water deprivation shows several similarities with the first phase of salinity stress, the osmotic effect [ 8 , 9 , 10 ]. The current study is a step further in a study in our lab that applies different omics platforms to characterize the morphophysiological and molecular responses of young oil palms to two abiotic stresses—salinity and drought [ 17 , 20 , 21 , 22 , 23 ].…”

“…The present study, and the one by Bittencourt et al [ 17 ], used transcriptome datasets from the apical leaf of young oil palm plants already showing extensive necrosis [ 20 , 23 ]. The reason stachyose synthase gene in E. guineensis increased approximately 32-fold under drought but decreased by almost 100% under saline stress, and considering that the transcriptome profiles used came from leaves with extensive necrosis, this is a question that needs further study to be answered.…”

“…For the omics (transcriptomics, metabolomics, and proteomics) analysis described in the present study, we collected the apical leaves from control and stressed plants 14 days after imposing the treatments (DAT). See Rodrigues-Neto et al [ 21 ] and Salgado et al [ 23 ] for additional details regarding growth conditions, experimental design, drought stress, and the morphophysiological response of the oil palm plants.…”