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.
Background Soil salinity is a problem in more than 100 countries across all continents. It is one of the abiotic stress that threatens agriculture the most, negatively affecting crops and reducing productivity. Transcriptomics is a technology applied to characterize the transcriptome in a cell, tissue, or organism at a given time via RNA-Seq, also known as full-transcriptome shotgun sequencing. This technology allows the identification of most genes expressed at a particular stage, and different isoforms are separated and transcript expression levels measured. Once determined by this technology, the expression profile of a gene must undergo validation by another, such as quantitative real-time PCR (qRT-PCR). This study aimed to select, annotate, and validate stress-inducible genes—and their promoters—differentially expressed in the leaves of oil palm (Elaeis guineensis) plants under saline stress. Results The transcriptome analysis led to the selection of 14 genes that underwent structural and functional annotation, besides having their expression validated using the qRT-PCR technique. When compared, the RNA-Seq and qRT-PCR profiles of those genes resulted in some inconsistencies. The structural and functional annotation analysis of proteins coded by the selected genes showed that some of them are orthologs of genes reported as conferring resistance to salinity in other species. There were those coding for proteins related to the transport of salt into and out of cells, transcriptional regulatory activity, and opening and closing of stomata. The annotation analysis performed on the promoter sequence revealed 22 distinct types of cis-acting elements, and 14 of them are known to be involved in abiotic stress. Conclusion This study has helped validate the process of an accurate selection of genes responsive to salt stress with a specific and predefined expression profile and their promoter sequence. Its results also can be used in molecular-genetics-assisted breeding programs. In addition, using the identified genes is a window of opportunity for strategies trying to relieve the damages arising from the salt stress in many glycophyte crops with economic importance.
Setaria viridis (L.) P. Beauv. is a species proposed to be used as model plant in reverse genetics studies for the validation of gene function. Soil salinity is a recurring problem present in more than a 100 countries worldwide, and approximately 20% of the agricultural land in the world has saline and/or sodium soils. Saline stress affects all the main processes of the plant, such as germination, growth, and, consequently, the yield. The present study aimed at determining the tolerance levels of S. viridisA10.1 to saline stress and identify its potential as a model plant to validate salt-tolerance candidate genes/alleles as well as promoter sequences from salt-responsive genes. In an initial experiment, the seeds of the plant were sown on a germination medium containing an increasing concentration of NaCl (0, 30, 60, 90, 120, or 150 mM), and maintained there during the initial growth stage; and, in another experiment, the plants at the vegetative growth stage were submitted to increasing doses of NaCl (0.0, 0.2, 0.4, 0.6, 0.8, and 1.0g per 100g of the substrate). The germination rate was found to be affected a little by the salinity, while the seedlings development was impaired right after germination. Plant in the vegetative growth stage experienced a reduction in the evapotranspiration rates and pigment levels, along with an impairment in the system of capture and use of light, and a decrease in the leaf gas exchange rates, resulting in less accumulation of dry and fresh plant biomass proportional to the salt dose used. Plants started to die within a week at doses ≥19.4 dS/m. In conclusion, A10.1 is a glycophyte plant with some level of salt-tolerance and might be used as a model plant to validate salt-tolerance candidate genes/alleles, as well as promoters salt-responsive genes, depending on the right combination of plant age and level of stress. As seed germination is affected only little by salt stress at NaCl doses of about 15 dS/m or less, A10.1 might not be used to validate genes/alleles with a putative role regarding this trait.
The objective of this work was to evaluate different traits of four corn (Zea mays) genotypes with contrasting responses to drought and to determine the main traits associated to such responses. The experiment was carried out in a greenhouse. The plants were grown in pots subjected to full irrigation. Drought was imposed to plants at 54 days after sowing and kept constant for 12 consecutive days; however, a group of plants remained under full irrigation. Traits related to leaf gas exchange, photochemical apparatus, growth, and yield were assessed, and data were subjected to hierarchical agglomerative clustering and principal component analysis. DKB 390 distinguishes from the other genotypes for growth and yield traits, while 2B-707 and DKB 390 discriminate from 'BRS 1030' and 'BRS 1010' for physiological traits. Ear length, kernel number per ear, above-ground dry matter, shoot dry matter, and plant height are the most important growth and yield traits to discriminate genotype-dependent drought tolerance. Among the physiological traits, the most important are: chlorophyll content, absorptivity, leaf temperature, maximum fluorescence in the dark-adapted state, minimum fluorescence in the dark-adapted state, water-use efficiency, and intercellular CO2 concentration.
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