Identification of aluminum-responsive microRNAs in Medicago truncatula by genome-wide high-throughput sequencing

• Published in: Planta 2012-02, Vol.235 (2), p.375-386
• Main Authors: Chen, Lei, Wang, Tianzuo, Zhao, Mingui, Tian, Qiuying, Zhang, Wen-Hao
• Format: Article
• Language: English
• Subjects: Acidic soils; Agriculture; Alfalfa; Aluminum; Aluminum - metabolism; Aluminum Compounds - pharmacology; Auxins; Biological and medical sciences; Biomedical and Life Sciences; Chlorides - pharmacology; Ecology; Forestry; Fundamental and applied biological sciences. Psychology; Gene Expression Regulation, Plant; Gene Library; Genome, Plant; High-Throughput Nucleotide Sequencing - methods; Libraries; Life Sciences; Medicago truncatula - drug effects; Medicago truncatula - genetics; Medicago truncatula - growth & development; Medicago truncatula - metabolism; MicroRNA; MicroRNAs - classification; MicroRNAs - genetics; MicroRNAs - metabolism; Nucleic Acid Conformation; Original Article; Plant cells; Plant growth; Plant roots; Plant Roots - drug effects; Plant Roots - genetics; Plant Roots - growth & development; Plant Roots - metabolism; Plant Sciences; Plants; Reverse Transcriptase Polymerase Chain Reaction; RNA; RNA Precursors - genetics; RNA Precursors - metabolism; RNA, Plant - genetics; RNA, Plant - isolation & purification; RNA, Plant - metabolism; Root growth; Sequencing; Small interfering RNA
• ISSN: 0032-0935; 1432-2048
• DOI: 10.1007/s00425-011-1514-9

MicroRNAs (miRNAs) play important roles in response of plants to biotic and abiotic stresses. Aluminum (Al) toxicity is a major factor limiting plant growth in acidic soils. However, there has been limited report on the involvement of miRNAs in response of plants to toxic Al³⁺. To identify Al³⁺-responsive miRNAs at wholegenome level, high-throughput sequencing technology was used to sequence libraries constructed from root apices of the model legume plant Medicago truncatula treated with and without Al³⁺. High-throughput sequencing of the control and two Al³⁺-treated libraries led to generation of 17.1, 14.1 and 17.4 M primary reads, respectively. We identified 326 known miRNAs and 21 new miRNAs. Among the miRNAs, expression of 23 miRNAs was responsive to Al³⁺, and the majority of Al³⁺-responsive mRNAs was down-regulated. We further classified the Al³⁺-responsive miRNAs into three groups based on their expression patterns: rapid-responsive, late-responsive and sustained-responsive miRNAs. The majority of Al³⁺-responsive miRNAs belonged to the 'rapid-responsive' category, i.e. they were responsive to short-term, but not long-term Al³⁺ treatment. The Al³⁺-responsive miRNAs were also verified by quantitative real-time PCR. The potential targets of the 21 new miRNAs were predicted to be involved in diverse cellular processes in plants, and their potential roles in Al³⁺-induced inhibition of root growth were discussed. These findings provide valuable information for functional characterization of miRNAs in Al³⁺ toxicity and tolerance.