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Open AccessArticle

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

Departamento de Agricultura del Desierto, Facultad de Recursos Naturales, Universidad Arturo Prat, Campus Huayquique, Av. Arturo Prat S/N, Iquique 1100000, Chile
Departamento de Producción Agrícola, Laboratorio de Genómica Funcional y Bioinformática, Universidad de Chile, Av. Santa Rosa 11315, Santiago 8820808, Chile
Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Via Irnerio 42, 40126 Bologna, Italy
Authors to whom correspondence should be addressed.
These authors have equally contributed to this paper.
Genes 2019, 10(12), 1042;
Received: 28 October 2019 / Revised: 26 November 2019 / Accepted: 7 December 2019 / Published: 16 December 2019
(This article belongs to the Special Issue Abiotic Stress in Plants: Current Challenges and Perspectives)
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. View Full-Text
Keywords: ethylene-related genes; gene expression; halotolerant crop; salinity; transcriptome ethylene-related genes; gene expression; halotolerant crop; salinity; transcriptome
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Ruiz, K.B.; Maldonado, J.; Biondi, S.; Silva, H. RNA-seq Analysis of Salt-Stressed Versus Non Salt-Stressed Transcriptomes of Chenopodium quinoa Landrace R49. Genes 2019, 10, 1042.

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