Genes highly overexpressed in salt-stressed Young oil palm (Elaeis guineensis) plants

Abstract

RNA-seq is a technique based on the large-scale sequencing of transcript-derived cDNAs using next-generation sequencing platforms mostly used today to characterize an organism’s transcriptome. The analysis of RNA-seq data allows for identifying genes differentially expressed in a given condition, such as salt stress. This study aimed to search and characterize genes from the African oil palm (Elaeis guineensis Jacq.) highly up-regulated during salt stress, with a long-term goal of gene promoter prospection and validation. The apical leaves from the control (electrical conductivity of ~2 dS m-1) and salt-stressed (~40 dS m-1) young oil palm plants, collected at 5 and 12 days after the beginning of the stress, were subjected to extraction of total RNA, with three plants (replicates) per treatment. The complete genome ofE. guineensis, available at the National Center for Biotechnology Information, was used as the reference genome - BioProject PRJNA192219. The differential expression analysis led to the selection for further characterization of seven genes, which had increased expressions of 37-84 times under salt stress. The strategy used in this study enabled the selection of seven salt-responsive genes highly up-regulated during salt stress, and some of them coded for proteins already reported as responsible for salinity tolerance in other plant species through over-expression or knockout.

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

“…In the case of oil palm, Refs. [6,18,19] reported the development of salinization protocols, which are necessary to study the response of E. guineensis to this abiotic stress in the search for some intraspecific trait variability. Such protocols are also needed to select tolerant oil palm genotypes developed via genetic engineering or genome editing strategies.…”

“…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. The pairwise differential expression analysis between experimental conditions (Stressed Plants-12 DAT X Control-12 DAT) was performed through edgeR software version 3.28.0 [50], applying a simple design and an exact statistical test without the use of a filter for low counts genes.…”

Structural and functional analysis of stress-inducible genes and their promoters selected from young oil palm (Elaeis guineensis) under salt stress

“…The current study is another step in our work on characterizing the morphophysiological and molecular responses of oil palm plants to salinity stress [ 47 – 50 ]. Besides developing a salinization protocol successful in generating different levels of stress by gradients of electrical conductivity and water potential [ 47 ], the studies that followed up led to the identification of salt-responsive miRNAs and their putative target genes [ 48 ], as well as mapping the main pathways affected by this abiotic stress [ 49 ].…”

“…For the present study, we collected the apical leaves from three stressed plants (2.0 g NaCl, or ~ 40 dS m − 1 of electrical conductivity) at 05 and 12 days after the stress onset (DAT), together with the apical leaves from three control plants at 12 days (0.0 g NaCl, or ~ 2 dS m − 1 ), immediately frozen in liquid nitrogen and stored at − 80 °C until RNA-Seq. More details about the plant material, growth conditions, saline stress conditions, and the experimental design used in the study that generated this database were previously reported [ 47 – 50 ].…”