Li AL, Mao L. mRNA and small RNA transcriptomes reveal insights into dynamic homoeolog regulation of allopolyploid heterosis in nascent hexaploid wheat. Plant Cell. 2014;26:1878–900.
Kurihara Y, Watanabe Y. Arabidopsis Micro-RNA biogenesis through dicer-like 1 protein functions. PNAS. 2004;34:12753–8.
Brodersen P, Sakvarelidzeachard L, Bruunrasmussen M, Dunoyer P, Yamamoto YY, Sieburth L, Voinnet O. Widespread translational inhibition by plant miRNAs and siRNAs. Science. 2008;320:1185–90.
Unver T, Budak H. Conserved microRNAs and their targets in model grass species Brachypodium distachyon. Planta. 2009;230:659–69.
Kumar R. Role of microRNAs in biotic and abiotic stress responses in crop plants. Appl Biochem Biotech. 2014;174:93–115.
Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell. 2004;116:281–97.
Jin HL. Endogenous small RNAs and antibacterial immunity in plants. FEBS Lett. 2008;582:2679–84.
Fahlgren N, Howell MD, Kasschau KD, Chapman EJ, Sullivan CM, Cumbie JS, et al. High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes. PLoS One. 2007;e219:2.
Song C, Chen W, Zhang C, Korir NK, Yu H, Ma Z, et al. Deep sequencing discovery of novel and conserved microRNAs in trifoliate orange ( Citrus trifoliata). BMC Genomics. 2010;11:431.
Ge AJ, Shangguan LF, Zhang X, Dong QH, Han J, Liu H, et al. Deep sequencing discovery of novel and conserved microRNAs in strawberry (Fragaria×ananassa). Physiol Plantarum. 2013;148:387–96.
Chinnusamy V, Zhu JH, Zhu JK. Cold stress regulation of gene expression in plants. Trend. Plant Sci. 2007;12:444–51.
Thomashow MF. Plant cold acclimation: freezing tolerance genes and regulatory mechanisms. Annu Rev Plant Biol. 1999;50:571–99.
Viswanathan C, Zhu JK. Molecular genetic analysis of cold-regulated gene transcription. Philos T R Soc B. 2002;357:877–86.
Shi YT, Ding YL, Yang SH. Cold signal transduction and its interplay with phytohormones during cold acclimation. Plant Cell Physiol. 2015;56:7–15.
Solanke AU, Sharma AK. Signal transduction during cold stress in plants. Physiol Mol Biol Pla. 2008;14:69–79.
Zhou X, Wang G, Sutoh K, Zhu JK, Zhang W. Identification of cold-inducible microRNAs in plants by transcriptome analysis. BBA - Gene Regul Mech. 1779;2008:780–8.
Zhang JY, YY X, Huan Q, Chong K. Deep sequencing of Brachypodium small RNAs at the global genome level identifies microRNAs involved in cold stress response. BMC Genomics. 2009;10:449.
Thiebaut F, Rojas CA, Almeida KL, Grativol C, Domiciano CC, Lamb CRC, et al. Regulation of miR319 during cold stress in sugarcane. Plant Cell Environ. 2012;35:502–12.
Yang CH, Li DY, Mao DH, Liu X, Ji CJ, Li XB, et al. Overexpression of microRNA319 impacts leaf morphogenesis and leads to enhanced cold tolerance in rice (Oryza sativa L). Plant Cell Environ. 2013;36:2207–18.
Cui N, Sun XL, Sun MZ, Jia BW, Duanmu HZ, Lv DK, et al. Overexpression of OsmiR156k leads to reduced tolerance to cold stress in rice ( Oryza Sativa). Mol Breeding. 2015;35:1–11.
Song JB, Gao S, Wang Y, Li BW, Zhang YL, Yang ZM. miR394 and its target gene LCR are involved in cold stress response in Arabidopsis. Plant Gene. 2016;5:56–64.
Que YX, LP X, QB W, Liu YF, Ling H, Liu YH, et al. Genome sequencing of Sporisorium scitamineum provides insights into the pathogenic mechanisms of sugarcane smut. BMC Genomics. 2014;16:1–20.
Li YR, Yang LT. Sugarcane agriculture and sugar industry in China. Sugar Tech. 2015;17:1–8.
Zhang BQ, Yang LT, Li YR. Physiological and biochemical characteristics related to cold resistance in sugarcane. Sugar Tech. 2015;17:49–58.
Ebrahim MK, Zingsheim O, El-Shourbagy MN, Moore PH, Komor E. Growth and sugar storage in sugarcane grown at temperatures below and above optimum. J Plant Physiol. 1998;153:593–602.
Yang YT, Zhang X, Chen Y, Guo JL, Ling H, Gao SW, et al. Selection of reference genes for normalization of microRNA expression by RT-qPCR in sugarcane buds under cold stress. Front Plant Sci. 2016;7:1–10.
Medina J, Catalá R, Salinas J. The CBFs: three Arabidopsis transcription factors to cold acclimate. Plant Sci. 2011;1:3–11.
Zhao CZ, Lang ZB, Zhu JK. Cold responsive gene transcription becomes more complex. Trends Plant Sci. 2015;8:466–8.
Yang YT, ZW F, YC S, Zhang X, Li G, Guo JL, et al. A cytosolic glucose-6-phosphate dehydrogenase gene, ScG6PDH, plays a positive role in response to various abiotic stresses in sugarcane. Sci Rep. 2014;4:70–90.
Yang RR, Zeng YL, Yi XY, Zhao LJ, Zhang YF. Small RNA deep sequencing reveals the important role of microRNAs in the halophyte Halostachys caspica. Plant Biotech J. 2015;13:395–408.
YB L, Yang LT, Qi YP, Li Y, Li Z, Chen YB, et al. Identification of boron-deficiency-responsive microRNAs in Citrus sinensis roots by Illumina sequencing. BMC Plant Biol. 2014;14:1–16.
Allen E, Xie Z, Gustafson AM, Carrington JC. microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell. 2005;121:207–21.
Schwab R, Palatnik JF, Riester M, Schommer C, Schmid M, Weigel D. Specific effects of microRNAs on the plant transcriptome. Dev Cell. 2005;8:517–27.
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, et al. Eppig, gene ontology: tool for the unification of biology. Nat Genet. 2000;25:25–9.
Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, et al. KEGG for linking genomes to life and the environment. Nucleic Acids Res. 2008;36:480–4.
Schmittgen TD, Livak KJ. Analyzing real-time PCR data by the comparative C(T) method. Nat Protoc. 2008;3:1101–8.
Du SC, Hwang IS, Hwang BK. Requirement of the cytosolic interaction between pathogenesis-related protein10 and leucine-rich repeat protein1 for cell death and defense signaling in pepper. Plant Cell. 2012;24:1675–90.
Gou JY, Felippes FF, Liu CJ, Weigel D, Wang JW. Negative regulation of anthocyanin biosynthesis in Arabidopsis by a miR156-targeted SPL transcription factor. Plant Cell. 2011;23:1512–22.
Liu HH, Tian X, Li YJ, CA W, Zheng CC. Microarray-based analysis of stress-regulated microRNAs in Arabidopsis thaliana. RNA. 2008;14:836–43.
Ding D, Zhang LF, Wang H, Liu ZJ, Zhang ZX, Zheng YL. Differential expression of miRNAs in response to salt stress in maize roots. Ann Bot. 2009;103:29–38.
Kasuga M, Miura S, Shinozak K, Yamaguchi-Shinozaki K. A Combination of the Arabidopsis DREB1A gene and stress-inducible rd29A promoter improved drought- and low-temperature stress tolerance in tobacco by gene transfer. Plant Cell Physiol. 2004;45:346–50.
Wang W, Vinocur B, Altman A. Plant responses to drought, salinity and extreme temperatures: towards genetic engineering for stress tolerance. Planta. 2003;218:1–14.
Khraiwesh B, Zhu JK, Zhu JH. Role of miRNAs and siRNAs in biotic and abiotic stress responses of plants. BBA - Gene Regul Mec. 1819;2012:137–48.
Zhang BH. MicroRNA: a new target for improving plant tolerance to abiotic stress. J Exp Bot. 2015;66:1740–61.
Zhang XN, Li X, Liu JH. Identification of conserved and novel cold-responsive microRNAs in trifoliate orange (Poncirus trifoliata (L.) Raf.) using high-throughput sequencing. Plant Mol Biol Rep. 2013;32:328–41.
Jia L, Zhang DY, Qi XW, Ma B, Xiang ZH, He NJ. Identification of the conserved and novel miRNAs in mulberry by high-throughput sequencing. PLoS One. 2014;9:e104409.
Borges F, Martienssen RA. The expanding world of small RNAs in plants. Nat Rev Mol Cell Bio. 2015;12:727.
Xie F, Jr CNS, Taki FA, He Q, Liu H, Zhang B. High-throughput deep sequencing shows that microRNAs play important roles in switchgrass responses to drought and salinity stress. Plant Biotech J. 2014;12:354–66.
XB X, Yin LL, Ying QC, Song HM, Xue DW, Lai TF, et al. High-throughput sequencing and degradome analysis identify miRNAs and their targets involved in fruit senescence of Fragaria ananassa. PLoS One. 2013;8:e70959.
Li QW, Long FY, Tai W. Deep sequencing on genome-wide scale reveals the unique composition and expression patterns of microRNAs in developing pollen of Oryza sativa. Genome Biol. 2011;12:1–16.
Glazińska P, Wojciechowski W, Wilmowicz E, Zienkiewicz A, Frankowski K, Kopcewicz J. The involvement of InMIR167 in the regulation of expression of its target gene InARF8, and their participation in the vegetative and generative development of Ipomoea nil plants. J Plant Physiol. 2013;171:225–34.
Chen ZH, Bao ML, Sun YZ, Yang YJ, Xu XH, Wang JH, et al. Regulation of auxin response by miR393-targeted transport inhibitor response protein 1 is involved in normal development in Arabidopsis. Plant Mol Biol. 2011;77:619–29.
Koc I, Filiz E, Tombuloglu H. Assessment of miRNA expression profile and differential expression pattern of target genes in cold-tolerant and cold-sensitive tomato cultivars. Biotechnol Biotech E. 2015;29:851–60.
Sunkar R, Zhu JK. Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell. 2004;16:2001–19.
Tang ZH, Zhang LP, CG X, Yuan SH, Zhang FT, Zheng YL, et al. Uncovering small RNA-mediated responses to cold stress in a wheat thermosensitive genic male-sterile line by deep sequencing. Plant Physiol. 2012;159:721–38.
Ma C, Burd S, Lers A. miR408 is involved in abiotic stress responses in Arabidopsis. Plant J. 2015;84:167–87.
Yu N, Niu QW, Ng KH, Chua NH. The role of miR156/SPLs modules in Arabidopsis lateral root development. Plant J. 2015;83:673–85.
Yu S, Galvão VC, Zhang YC, Horrer D, Zhang TQ, Hao YH, et al. Gibberellin regulates the Arabidopsis floral transition through miR156-targeted SQUAMOSA PROMOTER BINDING–LIKE transcription factors. Plant Cell. 2012;24:3320–32.
Cui LG, Shan JX, Shi M, Gao JP, Lin HX. The miR156-SPL9-DFR pathway coordinates the relationship between development and abiotic stress tolerance in plants. Plant J. 2014;80:1108–17.
Ni ZY, Hu Z, Jiang QY, Zhang H. GmNFYA3, a target gene of miR169, is a positive regulator of plant tolerance to drought stress. Plant Mol Biol. 2013;82:113–29.
Song QX, Liu YF, XY H, Zhang WK, Ma B, Chen SY, et al. Identification of miRNAs and their target genes in developing soybean seeds by deep sequencing. BMC Plant Biol. 2011;11:1–16.
Singh KB, Foley RC, Oñate-Sánchez L. Transcription factors in plant defense and stress responses. Curr Opin Plant Biol. 2002;5:430–6.
Wang M, Wang QL, Zhang BH. Response of miRNAs and their targets to salt and drought stresses in cotton (Gossypium hirsutum L). Gene. 2013;530:26–32.
Kong Y, Elling AA, Chen B, Deng X. Differential expression of microRNAs in maize inbred and hybrid lines during salt and drought stress. Am J Plant Sci. 2010;1:69–76.
Chalker-Scott L. Environmental significance of anthocyanins in plant stress responses. Photochem Photobiol. 1999;70:1–9.
Oh JE, Kim YH, Kim JH, Kwon YR, Lee HJ. Enhanced level of anthocyanin leads to increased salt tolerance in Arabidopsis PAP1-D plants upon sucrose treatment. J Korean Soc Appl Bi. 2011;54:79–88.