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Combined small RNA and degradome sequencing to identify miRNAs and their targets in response to drought in foxtail millet.

ABSTRACT: Foxtail millet (Setaria italica) is a diploid C4 panicoid species. Because of its prominent drought resistance, small genome size, self-pollination, and short life cycle, foxtail millet has become an ideal model system for studying drought tolerance of crops. MicroRNAs (miRNAs) are endogenous, small RNAs that play important regulatory roles in the development and stress response in plants.In this study, we applied Illumina sequencing to systematically investigate the drought-responsive miRNAs derived from S. italica inbred An04-4783 seedlings grown under control and drought conditions. Degradome sequencing was applied to confirm the targets of these miRNAs at a global level. A total of 81 known miRNAs belonging to 28 families were identified, among which 14 miRNAs were upregulated and four were downregulated in response to drought. In addition, 72 potential novel miRNAs were identified, three of which were differentially expressed under drought conditions. Degradome sequencing analysis showed that 56 and 26 genes were identified as targets of known and novel miRNAs, respectively.Our analysis revealed post-transcriptional remodeling of cell development, transcription factors, ABA signaling, and cellar homeostasis in S.italica in response to drought. This preliminary characterization provided useful information for further studies on the regulatory networks of drought-responsive miRNAs in foxtail millet.

SUBMITTER: Wang Y

PROVIDER: S-EPMC4828802 | biostudies-literature | 2016 Apr

REPOSITORIES: biostudies-literature

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Combined small RNA and degradome sequencing to identify miRNAs and their targets in response to drought in foxtail millet.

Wang Yongqiang Y Li Lin L Tang Sha S Liu Jianguang J Zhang Hanshuang H Zhi Hui H Jia Guanqing G Diao Xianmin X

BMC genetics 20160412

<h4>Background</h4>Foxtail millet (Setaria italica) is a diploid C4 panicoid species. Because of its prominent drought resistance, small genome size, self-pollination, and short life cycle, foxtail millet has become an ideal model system for studying drought tolerance of crops. MicroRNAs (miRNAs) are endogenous, small RNAs that play important regulatory roles in the development and stress response in plants.<h4>Results</h4>In this study, we applied Illumina sequencing to systematically investiga ...[more]

PMID: 27068810

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Project description:BackgroundFoxtail millet (Setaria italica L. P. Beauv) has been considered as a tractable model crop in recent years due to its short growing cycle, lower amount of repetitive DNA, inbreeding nature, small diploid genome, and outstanding abiotic stress-tolerance characteristics. With modern agriculture facing various adversities, it's urgent to dissect the mechanisms of how foxtail millet responds and adapts to drought and stress on the proteomic-level.ResultsIn this research, a total of 2474 differentially expressed proteins were identified by quantitative proteomic analysis after subjecting foxtail millet seedlings to drought conditions. 321 of these 2474 proteins exhibited significant expression changes, including 252 up-regulated proteins and 69 down-regulated proteins. The resulting proteins could then be divided into different categories, such as stress and defense responses, photosynthesis, carbon metabolism, ROS scavenging, protein synthesis, etc., according to Gene Ontology annotation. Proteins implicated in fatty acid and amino acid metabolism, polyamine biosynthesis, hormone metabolism, and cell wall modifications were also identified. These obtained differential proteins and their possible biological functions under drought stress all suggested that various physiological and metabolic processes might function cooperatively to configure a new dynamic homeostasis in organisms. The expression patterns of five drought-responsive proteins were further validated using western blot analysis. The qRT-PCR was also carried out to analyze the transcription levels of 21 differentially expressed proteins. The results showed large inconsistency in the variation between proteins and the corresponding mRNAs, which showed once again that post-transcriptional modification performs crucial roles in regulating gene expression.ConclusionThe results offered a valuable inventory of proteins that may be involved in drought response and adaption, and provided a regulatory network of different metabolic pathways under stress stimulation. This study will illuminate the stress tolerance mechanisms of foxtail millet, and shed some light on crop germplasm breeding and innovation.

Project description:BACKGROUND: In plants, microRNAs (miRNAs) are endogenous ~22 nt RNAs that play important regulatory roles in many aspects of plant biology, including metabolism, hormone response, epigenetic control of transposable elements, and stress response. Extensive studies of miRNAs have been performed in model plants such as rice and Arabidopsis thaliana. In maize, most miRNAs and their target genes were analyzed and identified by clearly different treatments, such as response to low nitrate, salt and drought stress. However, little is known about miRNAs involved in maize ear development. The objective of this study is to identify conserved and novel miRNAs and their target genes by combined small RNA and degradome sequencing at four inflorescence developmental stages. RESULTS: We used deep-sequencing, miRNA microarray assays and computational methods to identify, profile, and describe conserved and non-conserved miRNAs at four ear developmental stages, which resulted in identification of 22 conserved and 21-maize-specific miRNA families together with their corresponding miRNA*. Comparison of miRNA expression in these developmental stages revealed 18 differentially expressed miRNA families. Finally, a total of 141 genes (251 transcripts) targeted by 102 small RNAs including 98 miRNAs and 4 ta-siRNAs were identified by genomic-scale high-throughput sequencing of miRNA cleaved mRNAs. Moreover, the differentially expressed miRNAs-mediated pathways that regulate the development of ears were discussed. CONCLUSIONS: This study confirmed 22 conserved miRNA families and discovered 26 novel miRNAs in maize. Moreover, we identified 141 target genes of known and new miRNAs and ta-siRNAs. Of these, 72 genes (117 transcripts) targeted by 62 differentially expressed miRNAs may attribute to the development of maize ears. Identification and characterization of these important classes of regulatory genes in maize may improve our understanding of molecular mechanisms controlling ear development.

Dataset Information

Combined small RNA and degradome sequencing to identify miRNAs and their targets in response to drought in foxtail millet.

Publications

Combined small RNA and degradome sequencing to identify miRNAs and their targets in response to drought in foxtail millet.

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