Integration of mRNA and miRNA Analysis Reveals the Molecular Mechanism Underlying Salt and Alkali Stress Tolerance in Tobacco

Abstract

Salinity is one of the most severe forms of abiotic stress and affects crop yields worldwide. Plants respond to salinity stress via a sophisticated mechanism at the physiological, transcriptional and metabolic levels. However, the molecular regulatory networks involved in salt and alkali tolerance have not yet been elucidated. We developed an RNA-seq technique to perform mRNA and small RNA (sRNA) sequencing of plants under salt (NaCl) and alkali (NaHCO3) stress in tobacco. Overall, 8064 differentially expressed genes (DEGs) and 33 differentially expressed microRNAs (DE miRNAs) were identified in response to salt and alkali stress. A total of 1578 overlapping DEGs, which exhibit the same expression patterns and are involved in ion channel, aquaporin (AQP) and antioxidant activities, were identified. Furthermore, genes involved in several biological processes, such as “photosynthesis” and “starch and sucrose metabolism,” were specifically enriched under NaHCO3 treatment. We also identified 15 and 22 miRNAs that were differentially expressed in response to NaCl and NaHCO3, respectively. Analysis of inverse correlations between miRNAs and target mRNAs revealed 26 mRNA-miRNA interactions under NaCl treatment and 139 mRNA-miRNA interactions under NaHCO3 treatment. This study provides new insights into the molecular mechanisms underlying the response of tobacco to salinity stress.

MicroRNAs: Potential Targets for Developing Stress-Tolerant Crops

“…Nitrogen starvation [149] miR156, miR164, miR167, miR168, miR528, miR820, miR821, miR1318 Low-nitrogen stress [150] multiple miRNAs Abiotic stress [151] osa-miR414, osa-miR164e, osa-miR408 Salt stress [152] Soybean (Glycine max) multiple miRNAs Water deficit [153] Sugarcane (Saccharum L.) multiple miRNAs Water-deficit stress [154] multiple miRNAs Low temperature stress [155] multiple miRNAs Waterlogging condition [156] multiple miRNAs Drought stress [157] multiple miRNAs Drought stress [158] Sweet Potato (Ipomoea batatas) multiple miRNAs Drought and CO 2 stress [159] multiple miRNAs Salt stress [160] Switchgrass (Panicum virgatum) multiple miRNAs Drought and heat stress [161] multiple miRNAs Salt stress [162] Tobacco (Nicotiana tabacum) multiple miRNAs Salt and alkali stress [163] Tomato (Solanum lycopersicum) multiple miRNAs Drought and heat stress [164] multiple miRNAs Drought stress [165] Turnip (Brassica rapa) miR166h-3p-1, miR398b-3p, miR398b-3p-1, miR408d, miR156a-5p, miR396h, miR845a-1, miR166u, Bra-novel-miR3153-5p and Bra-novel-miR3172-5p…”

Combined transcriptomic and metabolomic analyses uncover rearranged gene expression and metabolite metabolism in tobacco during cold acclimation

“…The concentration and quality of the RNA samples were determined using a Nanodrop 2000 instrument (Thermo, Waltham, USA) and an Agilent 2100 bioanalyzer (Agilent, Palo Alto, USA). RNA-seq libraries were constructed using an Illumina TruSeq RNA Sample Prep Kit (Illumina, San Diego, USA) according to the manufacturer's protocol and were sequenced on the Illumina HiSeq X ten platform (Illumina, San Diego, USA) 63 . After removing the adapters and low-quality sequence reads from the raw reads by Trimmomatic 64 , the clean reads were mapped to the tobacco genome (ftp://ftp.solgenomics.net/genomes/ Nicotiana_tabacum/) using HISAT2 65 .…”

Comparative transcriptome analysis of NaCl and KCl stress response in Malus hupehensis Rehd. Provide insight into the regulation involved in Na+ and K+ homeostasis

“…Therefore, strategies to improve the salt tolerance of M. hupehensis, a widely used apple rootstock in China, should be explored. However, the studies on the physiological and molecular mechanisms of plants' response to salt stress focus on model plants, such as Arabidopsis, rice, and tobacco [4][5][6]. The defense response mechanism of M. hupehensis to salt stress remains unclear.…”