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.
Highlights
Quinoa (Chenopodium quinoa Willd.) is an ancient crop native to South America that is receiving attention worldwide due to its high nutritional value [1]and content in health-promoting compounds [2]
Implementing a model based on read counts and using the cut-off value of two-fold change and an false discovery rate (FDR) p-value
Implementing a model based on read counts and using the cut-off value of two-fold change and 7 of 22 an FDR p-value
Summary
Quinoa (Chenopodium quinoa Willd.) is an ancient crop native to South America (around LakeTiticaca in Bolivia and Peru) that is receiving attention worldwide due to its high nutritional value [1]and content in health-promoting compounds [2]. Quinoa (Chenopodium quinoa Willd.) is an ancient crop native to South America Titicaca in Bolivia and Peru) that is receiving attention worldwide due to its high nutritional value [1]. In 2013, the United Nations Food and Agriculture Organization (FAO) recognized quinoa as a key crop for food security and sustainability under a scenario of global change [5,6]. Interest in the crop is still growing, mainly due to increasing water scarcity and soil salinization on a global scale. The production of quinoa in Chile is low as compared to top quinoa-producing countries, namely Peru and Bolivia. This is in part due to less competitiveness in crop management and market
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