Abstract
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.
Highlights
IntroductionSalinity is often seen as a problem for the agricultural sector, prompting actions aimed at prevention or remediation in the affected areas; in the scope of biosaline agriculture, this problem is seen as an opportunity for the production of food, fibers, and bioenergy, as well as for the recovery of degraded areas and the use of marginal ones (Joshi et al, 2020; Tıpırdamaz et al, 2020; Duarte & Caçador, 2021)
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
Five out of these seven salt-responsive genes code for proteins with studies showing that their overexpression increased the tolerance to salinity stress in several plant species (Kwon et al, 2007; Yu et al, 2007; Brotman et al, 2012; Guo et al, 2013; Zou et al, 2013; Gangadhar et al, 2016; Czolpinska & Rurek, 2018; Waseem et al, 2019; Qiu et al, 2020). Three of these five genes showed an expression value lower than 100, and two higher than 100 at 12 days after the stress onset (DAT) (Table 3). These results put these five genes as candidate genes for future studies aiming at the generation of oil palm plants tolerant to salt stress, via a constitutive overexpression strategy
Summary
Salinity is often seen as a problem for the agricultural sector, prompting actions aimed at prevention or remediation in the affected areas; in the scope of biosaline agriculture, this problem is seen as an opportunity for the production of food, fibers, and bioenergy, as well as for the recovery of degraded areas and the use of marginal ones (Joshi et al, 2020; Tıpırdamaz et al, 2020; Duarte & Caçador, 2021) In this context, cultivation systems for saline environments are developed, using the ability of some plants to grow under saline conditions in combination with the use of saline soils and water resources, and better soil and water management (Ventura et al, 2015; Duarte & Caçador, 2021). Due to the technological advances and cost reduction achieved with the RNA-seq technique, we have witnessed an explosion in the amount of transcriptome data generated and made public (Lowe et al, 2017)
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