Genome-wide annotation of genes and noncoding RNAs of foxtail millet in response to simulated drought stress by deep sequencing

Abstract

Drought is a major abiotic stress that affects plant growth, production, and survival. Plants have evolved sophisticated and highly complex reactions to drought stress, including large-scale transcriptome reconfiguration. Foxtail millet (Setaria italica) is a member of the Poaceae family. Because of its outstanding tolerance to drought stress foxtail millet has the potential to become a new model organism. To enrich our knowledge of the processes that contribute to drought resistance, we have used a deep sequencing approach to generate a genome-wide transcriptome of foxtail millet after exposure to simulated drought stress. A large number of differentially expressed genes were characterized; in particular, we examined the roles of small interfering RNAs (siRNAs) and long noncoding RNAs (lncRNAs) in response to a water-deficit condition. These RNAs have remained largely unexplored in previous studies of stress-induced transcriptomes. We found that the reduced levels of 24-nt siRNA flanking genes were associated, for the most part, with proximal up-regulated genes, indicating a potential effect of 24-nt siRNAs on drought-regulated gene expression. Several lncRNAs that responded to the simulated drought stress were also identified, and we found that one of them shared sequence conservation and colinearity with its counterpart in sorghum (Sorghum bicolor). Our findings provide new insights into drought-induced changes in the foxtail millet transcriptome.

Genome-Wide Characterization of Maize Small RNA Loci and Their Regulation in the required to maintain repression6-1 (rmr6-1) Mutant and Long-Term Abiotic Stresses

“…Previous studies have found much larger numbers of differentially expressed sRNAs under abiotic stresses in Brachypodium and foxtail millet (Qi et al, 2013). Our experiments detected a much smaller number of stress-modulated sRNA loci.…”

“…Our experiments detected a much smaller number of stress-modulated sRNA loci. This could be due to the different stress protocols: the previous studies applied more severe stress conditions, such as polyethylene glycol-simulated drought conditions (Qi et al, 2013), or measured the stress effects after a much shorter period of treatment Wang et al, 2015). There also may be species-specific differences within the grasses.…”

A Nucleus-Localized Long Non-Coding RNA Enhances Drought and Salt Stress Tolerance

“…By using a deep transcriptome sequencing approach, Qi et al (2013) identified 584 lncRNAs in foxtail millet. Among them, 17 lincRNAs and two NATs are drought responsive.…”

“…Several reports also show that drought or salt stress could alter lncRNA expression in plants. For example,19,664, and 98 drought-responsive lncRNAs were identified in foxtail millet (Setaria italica), maize (Zea mays), and rice, respectively (Qi et al, 2013;Zhang et al, 2014a;Chung et al, 2016). Salt stress and dehydration stress also alter the accumulation of eight and six lncRNAs, respectively, in Arabidopsis (Arabidopsis thaliana; Ben Amor et al, 2009).…”

Initiation of Setaria as a model plant

“…A rapid and high throughput screening for drought tolerance during germination in foxtail millet was developed which used polyethylene glycol (PEG-6000) to generate osmotic stress [15]. Multiple methods of gene expression profiling have been employed to identify genes related to drought tolerance in foxtail millet, and these methods identified hundreds of significant changes in expression that corresponded to genes involved in metabolism, proteolysis, and signaling [16][17][18][19]. However, the detailed genetic mechanisms responsible for variation in drought tolerance among foxtail millet lines remain uncharacterized.…”