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Identification of Drought-Responsive MicroRNAs from Roots and Leaves of Alfalfa by High-Throughput Sequencing

Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
Author to whom correspondence should be addressed.
These authors contributed equally to this work.
Academic Editor: Bin Yu
Genes 2017, 8(4), 119;
Received: 12 January 2017 / Revised: 5 April 2017 / Accepted: 6 April 2017 / Published: 13 April 2017
(This article belongs to the Section Plant Genetics and Genomics)
PDF [2207 KB, uploaded 13 April 2017]


Alfalfa, an important forage legume, is an ideal crop for sustainable agriculture and a potential crop for bioenergy resources. Drought, one of the most common environmental stresses, substantially affects plant growth, development, and productivity. MicroRNAs (miRNAs) are newly discovered gene expression regulators that have been linked to several plant stress responses. To elucidate the role of miRNAs in drought stress regulation of alfalfa, a high-throughput sequencing approach was used to analyze 12 small RNA libraries comprising of four samples, each with three biological replicates. From the 12 libraries, we identified 348 known miRNAs belonging to 80 miRNA families, and 281 novel miRNAs, using Mireap software. Eighteen known miRNAs in roots and 12 known miRNAs in leaves were screened as drought-responsive miRNAs. With the exception of miR319d and miR157a which were upregulated under drought stress, the expression pattern of drought-responsive miRNAs was different between roots and leaves in alfalfa. This is the first study that has identified miR3512, miR3630, miR5213, miR5294, miR5368 and miR6173 as drought-responsive miRNAs. Target transcripts of drought-responsive miRNAs were computationally predicted. All 447 target genes for the known miRNAs were predicted using an online tool. This study provides a significant insight on understanding drought-responsive mechanisms of alfalfa. View Full-Text
Keywords: alfalfa; drought; microRNA; small RNA; differential expression alfalfa; drought; microRNA; small RNA; differential expression

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Li, Y.; Wan, L.; Bi, S.; Wan, X.; Li, Z.; Cao, J.; Tong, Z.; Xu, H.; He, F.; Li, X. Identification of Drought-Responsive MicroRNAs from Roots and Leaves of Alfalfa by High-Throughput Sequencing. Genes 2017, 8, 119.

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