RNA-seq Analysis of Salt-Stressed Versus Non Salt-Stressed Transcriptomes of Chenopodium quinoa Landrace R49

Abstract

Quinoa (Chenopodium quinoa Willd.), a model halophytic crop species, was used to shed light on salt tolerance mechanisms at the transcriptomic level. An RNA-sequencing analysis of genotype R49 at an early vegetative stage was performed by Illumina paired-ends method comparing high salinity and control conditions in a time-course pot experiment. Genome-wide transcriptional salt-induced changes and expression profiling of relevant salt-responsive genes in plants treated or not with 300 mM NaCl were analyzed after 1 h and 5 days. We obtained up to 49 million pairs of short reads with an average length of 101 bp, identifying a total of 2416 differentially expressed genes (DEGs) based on the treatment and time of sampling. In salt-treated vs. control plants, the total number of up-regulated and down-regulated genes was 945 and 1471, respectively. The number of DEGs was higher at 5 days than at 1 h after salt treatment, as reflected in the number of transcription factors, which increased with time. We report a strong transcriptional reprogramming of genes involved in biological processes like oxidation-reduction, response to stress and response to abscisic acid (ABA), and cell wall organization. Transcript analyses by real-time RT- qPCR supported the RNA-seq results and shed light on the contribution of roots and shoots to the overall transcriptional response. In addition, it revealed a time-dependent response in the expression of the analyzed DEGs, including a quick (within 1 h) response for some genes, suggesting a “stress-anticipatory preparedness” in this highly salt-tolerant genotype.

Transcriptomic Analysis of Salt-Stress-Responsive Genes in Barley Roots and Leaves

“…Furthermore, Luo et al [ 19 ] detected more DEGs in roots than in leaves of salt-stress-treated sweet potato with also a greater number of upregulated DEGs than downregulated DEGs (544 up and 392 down) in roots and more downregulated DEGs than upregulated DEGs (75 up and 145 down) in leaves. Even in quinoa and peach, similar trends of DEG distribution between roots and leaves subjected to salt stress were reported [ 33 , 34 ]. The high number of downregulated genes in leaves under high salinity could be attributed to the efficiency in conserving resources and energy under stress conditions by repressing the transcriptional process of genes mainly associated with oxidative activities and cell wall compartment, which could be constitutively active.…”

Genome-Wide Transcriptomic and Proteomic Exploration of Molecular Regulations in Quinoa Responses to Ethylene and 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].…”

Current Understanding of Role of Vesicular Transport in Salt Secretion by Salt Glands in Recretohalophytes

“…Some of the transcriptomes and proteomes of the recretohalophytes were constructed from plant leaves [ 82 , 83 , 84 , 85 , 86 , 87 ], which largely comprise mesophyll and epidermal cells. The salt glands represent only a small part of these tissues, meaning the differential expression of genes in these cells when undergoing salt secretion cannot typically be detected.…”