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

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.

Automated summary

This study aimed to select, annotate, and validate stress-inducible genes differentially expressed in the leaves of oil palm plants under saline stress. Through transcriptome analysis and validation using qRT-PCR, 14 genes were selected, annotated, and their expression profiles were examined. The analysis revealed that some of these genes are orthologs of salt resistance genes in other species, coding for proteins involved in salt transport, transcriptional regulation, and stomata opening and closing. The study also identified various cis-acting elements in the promoter sequences of these genes, some of which are known to be involved in abiotic stress. The results provide valuable information for gene selection, promoter sequence analysis, and molecular-genetics-assisted breeding programs.