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. 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. 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.

中文翻译：

---

两种盐胁迫的藜麦基因型的转录组分析和差异基因表达谱

土壤盐分是影响作物生长和产量的主要非生物胁迫因素之一，严重制约了农业的可持续发展。藜麦因其高营养价值和对极端天气和土壤条件的强适应性，被认为是未来最有前景的作物之一。但是，对藜麦盐分胁迫适应性反应的分子机制仍然知之甚少。为了鉴定与耐盐性相关的候选基因，我们进行了参考引导的组装，并比较了在300 mM NaCl处理的0、0.5、2和24 h两种耐盐性不同的藜麦基因型的根中的基因表达。耐盐（ST）基因型显示出更高的种子发芽率和植物存活率，在盐胁迫下，幼苗生长潜力也比盐敏感（SS）基因型强。平均产生了38,510,203个高质量的干净读取。确定了重要的基因本体论（GO）术语和《京都议定书》的基因与基因组百科全书（KEGG）途径，以更深入地了解差异反应。转录组分析表明，藜麦中的盐反应基因主要与次生代谢产物的生物合成，α-亚麻酸代谢，植物激素信号转导和代谢途径有关。此外，ST基因型中的差异表达基因（DEGs）之间显着丰富了几种途径，例如苯丙烷类生物合成，植物-病原体相互作用，异喹啉生物碱生物合成和酪氨酸代谢。两种基因型的不同阶段共有一百一十七个DEG，它们被确定为核心盐反应基因，包括一些转录因子成员，例如MYB，WRKY和NAC，以及一些植物激素信号转导相关基因，例如PYL，PP2C和TIFY10A，在适应该物种的盐条件中起重要作用。通过实时定量PCR（qRT-PCR）检测了21个DEG的表达模式，并证实了RNA-Seq结果的可靠性。我们鉴定了与藜麦耐盐性有关的候选基因，以及一些仅以ST基因型表达的DEG。盐胁迫下两种基因型共有的DEGs可能是藜麦适应盐分环境的关键基因。这些候选基因主要通过参与活性氧（ROS）清除系统，蛋白激酶的生物合成，植物激素信号转导和其他重要的生物学过程来调节盐耐受性。这些发现为进一步理解藜麦耐盐性网络的调控机制提供了理论依据，并为提高其对未来盐渍化方案的耐盐性奠定了基础。