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Identification of drought-responsive microRNAs in tomato using high-throughput sequencing

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Abstract

Drought is a major abiotic stress affecting crop productivity and quality. As a class of noncoding RNA, microRNA (miRNA) plays important roles in plant growth, development, and stress response. However, their response and roles in tomato drought stress is largely unknown. Here, by using high-throughput sequencing, we compared the miRNA profiles before and after drought treatment in two tomato genotypes: M82, a drought-sensitive cultivated tomato (Solanum lycopersicum), and IL2-5, a drought-tolerant introgression line derived from M82 and the tomato wild species S. pennellii (LA0716). A total of 108 conserved and 208 novel miRNAs were identified, among them, 32 and 68 were significantly changed in expression after stress. Further, 1936 putative target genes were predicted for those differentially-expressed miRNAs. Gene ontology and pathway analysis showed that many of the target genes were involved in stress resistance, such as genes in GO terms including response to stress, defense response, response to stimulus, phosphorylation, and signal transduction. Our results suggested that miRNAs play an essential role in the drought response of tomato. This work will help to further characterize specific miRNAs functioning in drought tolerance.

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Abbreviations

miRNA:

microRNA

nt:

Nucleotide

qRT-PCR:

Quantitative real-time PCR

GO:

Gene ontology

KEGG:

Kyoto encyclopedia of genes and genomes

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Funding

This work was supported by the National Natural Science Foundation of China (U1503186, 31572133) and the Applied Basic Research Program (2016020101010092) of Science and Technology Bureau of Wuhan City, Hubei, China.

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Authors

Contributions

Bo Ouyang and Minmin Liu designed the experiments and wrote the manuscript. Minmin Liu and Huiyang Yu analyzed the data. Minmin Liu, Gangjun Zhao, Qiufeng Huang, and Yongen Lu carried out the experiments. All authors read and approved the final manuscript.

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Correspondence to Bo Ouyang.

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The authors declare that they have no conflict of interest.

Electronic supplementary material

Supplementary Table S1

- Conserved miRNAs expressed in the drought-sensitive and -tolerant tomato genotypes. (XLSX 27 kb)

Supplementary Table S2

- Novel miRNAs expressed in drought-sensitive and -tolerant tomato genotypes. (XLSX 37 kb)

Supplementary Table S3

- Target gene prediction results of differentially-expressed miRNAs. (XLSX 456 kb)

Supplementary Table S4

- Enriched GO terms of drought-responsive miRNA targets in tomato. (XLSX 90 kb)

Supplementary Table S5

- KEGG pathway terms of drought-responsive miRNA targets in tomato. (XLSX 15 kb)

Supplementary Table S6

- The primers of miRNAs and target genes used for qRT-PCR verification. (XLSX 9 kb)

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Liu, M., Yu, H., Zhao, G. et al. Identification of drought-responsive microRNAs in tomato using high-throughput sequencing. Funct Integr Genomics 18, 67–78 (2018). https://doi.org/10.1007/s10142-017-0575-7

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  • DOI: https://doi.org/10.1007/s10142-017-0575-7

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