Identification of Salt-Stress-Induced Genes from the RNA-Seq Data ofReaumuria trigynaUsing Differential-Display Reverse Transcription PCR

Abstract

Next generation sequencing (NGS) technologies have been used to generate huge amounts of sequencing data from many organisms. However, the correct choice of candidate genes and prevention of false-positive results computed from digital gene expression (DGE) of RNA-seq data are vital when using these genetic resources. We indirectly identified 18 salt-stress-induced Reaumuria trigyna transcripts from the transcriptome sequencing data using differential-display reverse transcription PCR (DDRT-PCR) combined with local BLAST searches. Highly consistent with the DGE results, the quantitative real-time PCR expression patterns of these transcripts showed strong upregulation by salt stress, suggesting that these genes may play important roles in R. trigyna's survival under high-salt environments. The method presented here successfully identified responsive genes from the massive amount of RNA-seq data. Thus, we suggest that DDRT-PCR could be employed to mine NGS data in a wide range of applications in transcriptomic studies. In addition, the genes identified in the present study are promising candidates for further elucidation of the salt tolerance mechanisms in R. trigyna.

Progress in Studying Salt Secretion from the Salt Glands in Recretohalophytes: How Do Plants Secrete Salt?

“…Recently, the application of transriptomics in recretohalo phytes enhances the discovery of candidate genes involved in salt secretion. The transcription profiles of the recretohalophyte R. trigyna indicated that the genes related to ion transport were relevant to the salt secretion function of this species ( Dang et al, 2013 , 2014 ). Similarly, the candidate genes encoding ion transporters were also suggested in Sporobolus virginicus by RNA-seq ( Yamamoto et al, 2015 ).…”

Seed priming with ZNPs reduced expression of salinity tolerance genes in Glycine max L. and improved yield traits

“…Generally, stress results in changes in the cellular program that involve significant transcriptional alterations aimed at increasing the chances of survival (Diédhiou et al, 2008). A study by Dang et al (2014) proved that overexpression of GmPAP3 improved rice salt tolerance by increasing the ROS-scavenging ability and decreasing oxidative damage. Similarly, a possible tolerance role of GmPAP3 under oxidative stress was demonstrated in soybean, indicating that the GmPAP3 gene expression is regulated by salinity, osmotic, and oxidative stresses (Liao et al, 2003;Li et al, 2008b;Soleimani et al, 2017).…”

Adaptation of Recretohalophytes to Salinity

“…The use of transcriptomics in recretohalophytes has helped uncover candidate genes involved in salt secretion. Candidate genes encoding ion transporters have been identified in the recretohalophytes R. trigyna (Dang et al 2013(Dang et al , 2014, Sporobolus virginicus (Yamamoto et al 2015), and L. bicolor (Yuan et al 2016b) via RNA-seq of plants under different NaCl treatments. Proteomics has also accelerated the investigation of salinity-responsive proteins in recretohalophytes.…”