Abstract
Cold acclimation is crucial for the overwintering process of plants. Cold deacclimation is also important for plant survival in winter, which results in loss of freezing tolerance and initiation of growth. MicroRNAs (miRNAs) play crucial roles in regulating various physiological activities including cold response in plants. However, there is no study on miRNAs and their target genes in response to cold deacclimation in a cold-tolerant crop – barley (Hordeum vulgare L.). Here, we performed high-throughput sequencing of miRNAs of leaves during the cold deacclimation process using two barley cultivars with contrasting cold tolerance (Nure, tolerant and Tremois, sensitive). We found a total of 36 known and 267 novel miRNAs, including 12 known and 112 novel ones that are differentially expressed during cold deacclimation. The number of detected differentially expressed miRNAs was larger in Nure than that in Tremois, and the expression profile of miRNAs was dramatically different between Nure and Tremois. Moreover, we identified 13 known and 97 novel miRNAs, which have putative target genes during cold deacclimation. The putative targets of the novel miRNAs included genes encoding C-repeat binding factor (CBF) transcription factors, phytohormones, antioxidant, osmopretectant and flower development. Our results suggest that barley miRNAs respond quickly to cold deacclimation, and the larger number of miRNAs differentially expressed in the cold tolerant cv. Nure indicating that miRNAs might play an important role in the process of deacclimation. It sets a solid foundation for future studies and breeding programs on low temperature tolerance in barley.
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Data availability
The data are deposited in the National Center for Biotechnology Information Sequence Read Archive, www.ncbi.nlm.nih.gov (Accession Nos. SRR6831270 and SRR6831273).
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Acknowledgements
We thank Dr. Luigi Cattivelli (CRA Agricultural Research Council) for providing seeds of Nure and Tremois.
Funding
This study was supported by the National Key R&D Program of China (2018YFD1000706 and 2018YFD1000700), the Natural Science Foundation of China (31471480), the Natural Science Foundation of Zhejiang Province (LY18C130009), the Science and Technology Project of Hangzhou (20180432B04).
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Supplementary file1 (XLSX 11 kb) Supplementary file 1: Table S1. Summary of miRNA sequences from three different stages of barley cold deacclimation.
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Supplementary file2 (XLSX 65 kb) Supplementary file 2: Table S2. Summary of miRNAs identified in barley leaves during cold deacclimation.
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Supplementary file3 (XLSX 11 kb) Supplementary file 3: Table S3. Differentially expressed miRNAs in two barley genotypes during cold deacclimation treatment.
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Supplementary file4 (DOCX 45 kb) Supplementary file 4: Fig. S1. Validation expression patterns of two miRNAs identifed in Nure and Tremois after cold deacclimation for 1 day (1d), 3 days (3d), and 6 days (6d) by qRT-PCR.
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Supplementary file7 (DOCX 130 kb) Supplementary file 7: Fig. S2. Cluster analysis of miRNA fold change of Nure and Tremois after cold deacclimation treatment for one day (1d), three days (3d), and six days (6d). Expression profiles of differentially expressed miRNAs during deacclimation can be divided into six clusters (A to F).
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Supplementary file8 (XLSX 15 kb) Supplementary file 8: Table S6. Annotation of miRNAs and target genes in the hypothetically integrated schematic diagram of the mechanisms involved in cold deacclimation in Nure and Tremois.
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Supplementary file9 (DOCX 14 kb) Supplementary file 9: Table S7. Primers designed for stem-loop qRT-PCR analysis of miRNAs.
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Chen, F., He, J., Jin, G. et al. Identification of novel microRNAs for cold deacclimation in barley. Plant Growth Regul 92, 389–400 (2020). https://doi.org/10.1007/s10725-020-00646-9
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DOI: https://doi.org/10.1007/s10725-020-00646-9