Arzani, A., Ashraf, M., 2016. Smart engineering of genetic resources for enhanced salinity tolerance in crop plants. CRC. Crit. Rev. Plant Sci. 35, 146–189.
Bent, A., 2006. Arabidopsis thaliana floral dip transformation method. Agrobacterium Protoc. 87–104.
Bieniawska, Z., Espinoza, C., Schlereth, A., Sulpice, R., Hincha, D.K., Hannah, M.A., 2008. Disruption of the Arabidopsis circadian clock is responsible for extensive variation in the cold-responsive transcriptome. Plant Physiol. 147, 263–279.
Calixto, C.P.G., Guo, W., James, A.B., Tzioutziou, N.A., Entizne, J.C., Panter, P.E., Knight, H., Nimmo, H.G., Zhang, R., Brown, J.W.S., 2018. Rapid and dynamic alternative splicing impacts the Arabidopsis cold response transcriptome. Plant Cell 30, 1424–1444.
Chen, C., Ridzon, D.A., Broomer, A.J., Zhou, Z., Lee, D.H., Nguyen, J.T., Barbisin, M., Xu, N.L., Mahuvakar, V.R., Andersen, M.R., Lao, K.Q., Livak, K.J., Guegler, K.J., 2005. Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res. 33, e179.
Chen, Y., Jiang, J., Song, A., Chen, S., Shan, H., Luo, H., Gu, C., Sun, J., Zhu, L., Fang, W., Chen, F., 2013. Ambient temperature enhanced freezing tolerance of Chrysanthemum dichrum CdICE1Arabidopsis via miR398. BMC Biol. 11, 121.
Chinnusamy, V., Ohta, M., Kanrar, S., Lee, B.-H., Hong, X., Agarwal, M., Zhu, J.-K., 2003. ICE1: a regulator of cold-induced transcriptome and freezing tolerance in Arabidopsis. Genes Dev. 17, 1043–1054.
Chinnusamy, V., Schumaker, K., Zhu, J.-K., 2004. Molecular genetic perspectives on cross-talk and specificity in abiotic stress signalling in plants. J. Exp. Bot. 55, 225–236.
Chinnusamy, V., Zhu, J., Zhu, J.-K., 2007. Cold stress regulation of gene expression in plants. Trends Plant Sci. 12, 444–451.
Clough, S.J., Bent, A.F., 1998. Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J. 16, 735–743.
Dean, J.D., Goodwin, P.H., Hsiang, T., 2002. Comparison of relative RT-PCR and northern blot analyses to measure expression of β-1, 3-glucanase in Nicotiana benthamiana infected with Colltotrichum destructivum. Plant Mol. Biol. Report. 20, 347–356.
Dellaporta, S.L., Wood, J., Hicks, J.B., 1983. A plant DNA minipreparation: Version II. Plant Mol. Biol. Report. 1, 19–21.
Ding, Y., Li, H., Zhang, X., Xie, Q., Gong, Z., Yang, S., 2015. OST1 kinase modulates freezing tolerance by enhancing ICE1 stability in Arabidopsis. Dev. Cell 32, 278–289.
Dong, C.-H., Pei, H., 2014. Over-expression of miR397 improves plant tolerance to cold stress in Arabidopsis thaliana. J. Plant Biol. 57, 209–217.
Drake, T., Keating, M., Summers, R., Yochikawa, A., Pitman, T., Dodd, A.N., 2016. The cultivation of Arabidopsis for experimental research using commercially available peat-based and peat-free growing media. PLoS One 11, e0153625.
Egert, A., Keller, F., Peters, S., 2013. Abiotic stress-induced accumulation of raffinose in Arabidopsis leaves is mediated by a single raffinose synthase (RS5, At5g40390). BMC Plant Biol. 13, 218.
Gallegos, J., 2018. Alternative splicing plays a major role in plant response to cold temperatures.
Gao, P., Bai, X., Yang, L., Lv, D., Pan, X., Li, Y., Cai, H., Ji, W., Chen, Q., Zhu, Y., 2010. Osa-MIR393: A salinity- and alkaline stress-related microRNA gene. Mol. Biol. Rep. 38, 237–242.
Gil, K.-E., Park, C.-M., 2019. Thermal adaptation and plasticity of the plant circadian clock. New Phytol. 221, 1215–1229.
Gilchrist, E., Haughn, G., 2010. Reverse genetics techniques: engineering loss and gain of gene function in plants. Brief. Funct. Genomics 9, 103–110.
Goni, R., García, P., Foissac, S., 2009. The qPCR data statistical analysis. Integromics White Pap. 1, 1–9.
Gorpenchenko, T.Y., Veremeichik, G.N., Shkryl, Y.N., Yugay, Y.A., Grigorchuk, V.P., Bulgakov, D. V, Rusapetova, T. V, Vereshchagina, Y. V, Mironova, A.A., Subbotin, E.P., 2023. Suppression of the HOS1 Gene Affects the Level of ROS Depending on Light and Cold. Life 13, 524.
Karimi, M., Ghazanfari, F., Fadaei, A., Ahmadi, L., Shiran, B., Rabei, M., Fallahi, H., 2016. The Small-RNA Profiles of Almond (Prunus dulcis Mill.) Reproductive Tissues in Response to Cold Stress. PLoS One 11, e0156519–e0156519.
Kis, A., Tholt, G., Ivanics, M., Várallyay, É., Jenes, B., Havelda, Z., 2016. Polycistronic artificial miRNA-mediated resistance to Wheat dwarf virus in barley is highly efficient at low temperature. Mol. Plant Pathol. 17, 427–437.
Kosová, K., Vítámvás, P., Urban, M.O., Klíma, M., Roy, A., Prášil, I.T., 2015. Biological Networks Underlying Abiotic Stress Tolerance in Temperate Crops--A Proteomic Perspective. Int. J. Mol. Sci. 16, 20913–20942.
Kozera, B., Rapacz, M., 2013. Reference genes in real-time PCR. J. Appl. Genet. 54, 391–406.
Lee, H., Xiong, L., Gong, Z., Ishitani, M., Stevenson, B., Zhu, J.K., 2001. The Arabidopsis HOS1 gene negatively regulates cold signal transduction and encodes a RING finger protein that displays cold-regulated nucleo--cytoplasmic partitioning. Genes Dev. 15, 912–924.
Liu, Q., Chen, Y.-Q., 2010. A new mechanism in plant engineering: the potential roles of microRNAs in molecular breeding for crop improvement. Biotechnol. Adv. 28, 301–307.
MacGregor, D.R., Gould, P., Foreman, J., Griffiths, J., Bird, S., Page, R., Stewart, K., Steel, G., Young, J., Paszkiewicz, K., Millar, A.J., Halliday, K.J., Hall, A.J., Penfield, S., 2013. HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENES1 Is Required for Circadian Periodicity through the Promotion of Nucleo-Cytoplasmic mRNA Export in Arabidopsis . Plant Cell 25, 4391–4404.
Meng, X., Muszynski, M.G., Danilevskaya, O.N., 2011. The FT-like ZCN8 Gene Functions as a Floral Activator and Is Involved in Photoperiod Sensitivity in Maize. Plant Cell 23, 942–960.
Miura, K., Furumoto, T., 2013. Cold signaling and cold response in plants. Int. J. Mol. Sci. 14, 5312–5337.
Ossowski, S., Schwab, R., Weigel, D., 2008. Gene silencing in plants using artificial microRNAs and other small RNAs. Plant J. 53, 674–690.
Pieczynski, M., Marczewski, W., Hennig, J., Dolata, J., Bielewicz, D., Piontek, P., Wyrzykowska, A., Krusiewicz, D., Strzelczyk-Zyta, D., Konopka-Postupolska, D., Krzeslowska, M., Jarmolowski, A., Szweykowska-Kulinska, Z., 2013. Down-regulation of CBP80 gene expression as a strategy to engineer a drought-tolerant potato. Plant Biotechnol. J. 11, 459–469.
Robison, J.D., Yamasaki, Y., Randall, S.K., 2019. The Ethylene Signaling Pathway Negatively Impacts CBF/DREB-Regulated Cold Response in Soybean (Glycine max) . Front. Plant Sci. .
Saha, P., Sade, N., Arzani, A., Wilhelmi, M. del M.R., Coe, K.M., Li, B., Blumwald, E., 2016. Effects of abiotic stress on physiological plasticity and water use of Setaria viridis (L.). Plant Sci. 251, 128–138.
Schwab, R., Ossowski, S., Riester, M., Warthmann, N., Weigel, D., 2006. Highly specific gene silencing by artificial microRNAs in Arabidopsis. Plant Cell 18, 1121–1133.
Schwab, R., Ossowski, S., Warthmann, N., Weigel, D., 2010. Directed gene silencing with artificial microRNAs. Methods Mol. Biol. 592, 71–88.
Seo, P.J., Park, M.-J., Lim, M.-H., Kim, S.-G., Lee, M., Baldwin, I.T., Park, C.-M., 2012. A self-regulatory circuit of CIRCADIAN CLOCK-ASSOCIATED1 underlies the circadian clock regulation of temperature responses in Arabidopsis. Plant Cell 24, 2427–2442.
Shi, Y., Ding, Y., Yang, S., 2015. Cold signal transduction and its interplay with phytohormones during cold acclimation. Plant Cell Physiol. 56, 7–15.
Siritunga, D., Sayre, R.T., 2003. Generation of cyanogen-free transgenic cassava. Planta 217, 367–373.
Sun, X., Fan, G., Su, L., Wang, W., Liang, Z., Li, S., Xin, H., 2015. Identification of cold-inducible microRNAs in grapevine. Front. Plant Sci. 6, 595.
Varkonyi-Gasic, E., Wu, R., Wood, M., Walton, E.F., Hellens, R.P., 2007. Protocol: a highly sensitive RT-PCR method for detection and quantification of microRNAs. Plant Methods 3, 12.
von Born, P., Bernardo-Faura, M., Rubio-Somoza, I., 2018. An artificial miRNA system reveals that relative contribution of translational inhibition to miRNA-mediated regulation depends on environmental and developmental factors in Arabidopsis thaliana. PLoS One 13, e0192984.
Wagaba, H., Patil, B.L., Mukasa, S., Alicai, T., Fauquet, C.M., Taylor, N.J., 2016. Artificial microRNA-derived resistance to Cassava brown streak disease. J. Virol. Methods 231, 38–43.
Xia, Z., Zhao, Z., Jiao, Z., Xu, T., Wu, Y., Zhou, T., Fan, Z., 2018. Virus-Derived Small Interfering RNAs Affect the Accumulations of Viral and Host Transcripts in Maize. Viruses 10, 664.
Yeoh, C.C., Balcerowicz, M., Laurie, R., Macknight, R., Putterill, J., 2011. Developing a method for customized induction of flowering. BMC Biotechnol. 11, 36.
Zhang, Y., Zhu, X., Chen, X., Song, C., Zou, Z., Wang, Y., Wang, M., Fang, W., Li, X., 2014. Identification and characterization of cold-responsive microRNAs in tea plant (Camellia sinensis) and their targets using high-throughput sequencing and degradome analysis. BMC Plant Biol. 14, 271.
Zhao, Q., Xiang, X., Liu, D., Yang, A., Wang, Y., 2018. Tobacco Transcription Factor NtbHLH123 Confers Tolerance to Cold Stress by Regulating the NtCBF Pathway and Reactive Oxygen Species Homeostasis. Front. Plant Sci. 9, 381.
Zhou, M., Chen, H., Wei, D., Ma, H., Lin, J., 2017. Arabidopsis CBF3 and DELLAs positively regulate each other in response to low temperature. Sci. Rep. 7, 39819.
Zuker, M., 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31, 3406–3415.
Zuo, Z.-F., Kang, H.-G., Park, M.-Y., Jeong, H., Sun, H.-J., Yang, D.-H., Lee, Y.-E., Song, P.-S., Lee, H.-Y., 2019. Overexpression of ICE1, a Regulator of Cold-Induced Transcriptome, Confers Cold Tolerance to Transgenic Zoysia japonica. J. Plant Biol. 62, 137–146.