Analysis of the Alfalfa Root Transcriptome in Response to Salinity Stress

Abstract

Salinity is one of the major abiotic factors affecting alfalfa productivity. Identifying genes that control this complex trait will provide critical insights for alfalfa breeding programs. To date, no studies have been published on a deep sequencing-based profiling of the alfalfa transcriptome in response to salinity stress. Observations gathered through research on reference genomes may not always be applicable to alfalfa. In this work, Illumina RNA-sequencing was performed in two alfalfa genotypes contrasting in salt tolerance, in order to estimate a broad spectrum of genes affected by salt stress. A total of 367,619,586 short reads were generated from cDNA libraries originated from roots of both lines. More than 60,000 tentative consensus sequences (TCs) were obtained and, among them, 74.5% had a significant similarity to proteins in the NCBI database. Mining of simple sequence repeats (SSRs) from all TCs revealed 6,496 SSRs belonging to 3,183 annotated unigenes. Bioinformatics analysis showed that the expression of 1,165 genes, including 86 transcription factors (TFs), was significantly altered under salt stress. About 40% of differentially expressed genes were assigned to known gene ontology (GO) categories using Arabidopsis GO. A random check of differentially expressed genes by quantitative real-time PCR confirmed the bioinformatic analysis of the RNA-seq data. A number of salt-responsive genes in both tested genotypes were identified and assigned to functional classes, and gene candidates with roles in the adaptation to salinity were proposed. Alfalfa-specific data on salt-responsive genes obtained in this work will be useful in understanding the molecular mechanisms of salinity tolerance in alfalfa.

Salt stress alters DNA methylation levels in alfalfa (Medicago spp)

“…The alteration of DNA methylation levels at the HpaI site in response to the salinity treatments varied among the landraces (Figure 3). This result is in agreement with the widely accepted view that closely related species may possess some methylome flexibility, and consequently gene expression diversity (Postnikova et al, 2013). For example, rice cultivars with different salinity-tolerance capacities exhibit different DNA methylation patterns in response to salinity stress (Ferreira et al, 2015;Garg et al, 2015;Wang et al, 2015b).…”

De Novo Transcriptome Characterization, Gene Expression Profiling and Ionic Responses of Nitraria sibirica Pall. under Salt Stress

“…Hundreds of plant species have been experimentally investigated for their salt tolerance to understand the molecular aspects of vegetative salt tolerance in halophytes and glycophytes, including barley, soybean, paddy, cotton, and alfalfa [15][16][17][18][19]. Many genes of these plants are induced that either directly protect the plant from salt stress or regulate the expression of other target genes upon exposure to salt stress [18].…”

De novo transcriptome analysis of tobacco seedlings and identification of the early response gene network under low-potassium stress

“…Now, the next-generation sequencing method RNA-seq can provide a large amount of expressed sequence tags and transcript expression information between samples (Vanverk et al, 2013). This technique has been applied in studies of plant responses to various abiotic stressors (Postnikova et al, 2013;Zeng et al, 2014).…”