Transcriptome analysis and differential gene expression profiling of two contrasting quinoa genotypes in response to salt stress

Abstract

Background Soil salinity is one of the major abiotic stress factors that affect crop growth and yield, which seriously restricts the sustainable development of agriculture. Quinoa is considered as one of the most promising crops in the future for its high nutrition value and strong adaptability to extreme weather and soil conditions. However, the molecular mechanisms underlying the adaptive response to salinity stress of quinoa remain poorly understood. To identify candidate genes related to salt tolerance, we performed reference-guided assembly and compared the gene expression in roots treated with 300 mM NaCl for 0, 0.5, 2, and 24 h of two contrasting quinoa genotypes differing in salt tolerance. Results The salt-tolerant (ST) genotype displayed higher seed germination rate and plant survival rate, and stronger seedling growth potential as well than the salt-sensitive (SS) genotype under salt stress. An average of 38,510,203 high-quality clean reads were generated. Significant Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified to deeper understand the differential response. Transcriptome analysis indicated that salt-responsive genes in quinoa were mainly related to biosynthesis of secondary metabolites, alpha-Linolenic acid metabolism, plant hormone signal transduction, and metabolic pathways. Moreover, several pathways were significantly enriched amongst the differentially expressed genes (DEGs) in ST genotypes, such as phenylpropanoid biosynthesis, plant-pathogen interaction, isoquinoline alkaloid biosynthesis, and tyrosine metabolism. One hundred seventeen DEGs were common to various stages of both genotypes, identified as core salt-responsive genes, including some transcription factor members, like MYB, WRKY and NAC, and some plant hormone signal transduction related genes, like PYL, PP2C and TIFY10A, which play an important role in the adaptation to salt conditions of this species. The expression patterns of 21 DEGs were detected by quantitative real-time PCR (qRT-PCR) and confirmed the reliability of the RNA-Seq results. Conclusions We identified candidate genes involved in salt tolerance in quinoa, as well as some DEGs exclusively expressed in ST genotype. The DEGs common to both genotypes under salt stress may be the key genes for quinoa to adapt to salinity environment. These candidate genes regulate salt tolerance primarily by participating in reactive oxygen species (ROS) scavenging system, protein kinases biosynthesis, plant hormone signal transduction and other important biological processes. These findings provide theoretical basis for further understanding the regulation mechanism underlying salt tolerance network of quinoa, as well establish foundation for improving its tolerance to salinity in future breeding programs.

Genome-Wide Transcriptomic and Proteomic Exploration of Molecular Regulations in Quinoa Responses to Ethylene and Salt Stress

“…Seeds of a highland ecotype quinoa, 'NL-6 , were obtained from Dr. Feng Li of BellaGen (Jinan, China). In this research, 4-week-old quinoa seedlings of 'NL-6 treated with water, 300 mM NaCl, and 300 mM NaCl with 100 µM ACC for 0, 3, 6, 9, 12, 24, and 36 h, respectively [21,30,33]. The solutions were directly irrigated to the seedling roots until soil was fully saturated, and then the excess solutions were poured out.…”

“…The negative regulator PP2Cs in ABA signaling were proved to confer resistance to salt stress [20]. Several PP2Cs were found significantly up-regulated under salt stress in quinoa [21]. Ethylene also functions in plant responses to salt stress.…”

“…High-throughput genomic transcriptomic analysis provides a way to excavate molecular mechanisms of salt responses in quinoa in the genomic scale [10,21,30,31]. The genome sequence of a quinoa inbred line with an estimated 967 Mb size was fully sequenced in 2017, which provided a reference genome for later transcriptomic analysis [32].…”

“…Salt-induced genes were also identified in quinoa treated with 300 mM NaCl for 1 h and 5 d [30]. The differentially expressed genes (DEGs) compared between a salt-tolerant genotype and salt-sensitive genotype were analyzed after treatment with 300 mM NaCl for 0, 0.5, 2, and 24 h in the roots of quinoa seedlings [21]. Considering the importance of the stress-regulated proteins, detection of the differentially expressed changes in protein levels of quinoa is more valuable and practical.…”

Transcriptome-based analysis of salt-related genes during the sprout stage of common bean (Phaseolus vulgaris) under salt stress conditions

“…Moreover, 13 genes responsive to salinity during the germination stage were revealed by a genome-wide association analysis and the RNA sequencing of 196 upland cotton genotypes [57]. Furthermore, 21 DEGs were detected by an RNA-seq investigation of salt-tolerant and salt-sensitive genotypes exposed to highly saline conditions [58]. In the present study, R (salt-tolerant) and N (salt-sensitive) common bean varieties were compared to identify salt-related genes.…”