Bastet A, Zafirov D, Giovinazzo N, Guyon-Debast A, Nogué F, Robaglia C, Gallois JL (2019) Mimicking natural polymorphism in eIF4E by CRISPR-Cas9 base editing is associated with resistance to potyviruses. Plant Biotechnol J 17(9):1736–1750. https://doi.org/10.1111/pbi.13096

CAS  Article  PubMed  PubMed Central  Google Scholar 

Bechtold N, Pelletier G (1998) In planta Agrobacterium-mediated transformation of adult Arabidopsis thaliana plants by vacuum infiltration Methods Mol. Biol 82:259–266

CAS  Google Scholar 

Beji S, Fontaine V, Devaux R, Thomas M, Negro SS, Bahrman N, Siol M, Aubert G, Burstin J, Hilbert JL, Delbreil B, Lejeune-Hénaut I (2020) Genome-wide association study identifies favorable SNP alleles and candidate genes for frost tolerance in pea. BMC Genomics 21(1):536. https://doi.org/10.1186/s12864-020-06928-w

CAS  Article  PubMed  PubMed Central  Google Scholar 

Butel N, Yu A, Le Masson I, Borges F, Elmayan T, Taochy C, Gursanscky NR, Cao J, Bi S, Sawyer A, Caroll BJ, Vaucheret H (2021) Contrasting epigenetic control of transgenes and endogenous genes promotes post-transcriptional transgene silencing in Arabidopsis. Nat Commun 12(1):2787. https://doi.org/10.1038/s41467-021-22995-3

CAS  Article  PubMed  PubMed Central  Google Scholar 

Charrier B, Champion A, Henry Y, Kreis M (2002) Expression profiling of the whole Arabidopsis shaggy-like kinase multigene family by real-time reverse transcriptase-polymerase chain reaction. Plant Physiol 130(2):577–90. https://doi.org/10.1104/pp.009175

CAS  Article  PubMed  PubMed Central  Google Scholar 

Fürtauer L, Weiszmann J, Weckwerth W, Nägele T (2019) Dynamics of plant metabolism during cold acclimation. Int J Mol Sci 20:5411. https://doi.org/10.3390/ijms20215411

CAS  Article  PubMed Central  Google Scholar 

Géry C, Zuther E, Schulz E, Legoupi J, Chauveau A, McKhann H, Hincha DK, Téoulé E (2011) Natural variation in the freezing tolerance of Arabidopsis thaliana: effects of RNAi-induced CBF depletion and QTL localisation vary among accessions. Plant Sci 180:12–23. https://doi.org/10.1016/j.plantsci.2010.07.010

Hanada K, Zou C, Lehti-Shiu MD, Shinozaki K, Shiu SH (2008) Importance of lineage-specific expansion of plant tandem duplicates in the adaptive response to environmental stimuli. Plant Physiology 148:993–1003. https://doi.org/10.1104/pp.108.122457

CAS  Article  PubMed  PubMed Central  Google Scholar 

Hua J (2016) Defining roles of tandemly arrayed CBF genes in freezing tolerance with new genome editing tools. New Phytol 212:301–302. https://doi.org/10.1111/nph.14183

Article  PubMed  Google Scholar 

Jia Y, Ding Y, Shi Y, Zhang X, Gong Z, Yang S (2016) The cbfs triple mutants reveal the essential functions of CBFs in cold acclimation and allow the definition of CBF regulons in Arabidopsis. New Phytol 212:345–353. https://doi.org/10.1111/nph.14088

CAS  Article  PubMed  Google Scholar 

Kindgren P, Ard R, Ivanov M, Marquardt S (2018) Transcriptional read-through of the long non-coding RNA SVALKA governs plant cold acclimation. Nat Commun 9:4561. https://doi.org/10.1038/s41467-018-07010-6

CAS  Article  PubMed  PubMed Central  Google Scholar 

Lethi-Shiu MD, Zou C, Hanada K, Shiu SH (2009) Evolutionary history and stress regulation of plant receptor-like kinase/pelle genes. Plant Physiology 150:12–26. https://doi.org/10.1104/pp.108.134353

CAS  Article  Google Scholar 

Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 25(4):402–8. https://doi.org/10.1006/meth.2001.1262

CAS  Article  PubMed  Google Scholar 

Lopez-Obando M, Hoffmann B, Géry C, Guyon-Debast A, Téoulé E, Rameau C, Bonhomme S, Nogué F (2016) Simple and efficient targeting of multiple genes through CRISPR-Cas9 in Physcomitrella patens. G3 Bethesda 6(11):3647–3653. https://doi.org/10.1534/g3.116.033266

CAS  Article  PubMed  PubMed Central  Google Scholar 

McKhann H, Géry C, Bérard A, Lévêque S, Zuther E, Hincha DK, de Mita S, Brunel D, Téoulé E (2008) Natural variation in CBF gene sequence, gene expression and freezing tolerance in the Versailles core collection of Arabidopsis thaliana. BMC Plant Biol 8:105. https://doi.org/10.1186/1471-2229-8-105

CAS  Article  PubMed  PubMed Central  Google Scholar 

Novillo F, Alonso JM, Ecker JR, Salinas J (2004) CBF2/DREB1C is a negative regulator of CBF1/DREB1B and CBF3/DREB1A expression and plays a central role in stress tolerance in Arabidopsis. Proc Natl Acad Sci USA 101(11):3985–90. https://doi.org/10.1073/pnas.0303029101

CAS  Article  PubMed  PubMed Central  Google Scholar 

Ohno S (1970) Evolution by gene duplication. Springer-Verlag, Berlin

Book  Google Scholar 

Panchy N, Lehti-Shiu M, Shiu SH (2016) Evolution of duplication in plants. Plant Physiology 171:2294–2316. https://doi.org/10.1104/pp.16.00523

CAS  Article  PubMed  PubMed Central  Google Scholar 

Pareek A, Khurana A, Sharma AK, Kumar R (2017) An overview of signaling regulons during cold stress tolerance in plants. Curr Genomics 18:498–511. https://doi.org/10.2174/1389202918666170228141345

CAS  Article  PubMed  PubMed Central  Google Scholar 

Park S, Lee CM, Doherty CJ, Gilmour SJ, Kim Y, Thomashow MF (2015) Regulation of the Arabidopsis CBF regulon by a complex low-temperature regulatory network. Plant J 82(2):193–207. https://doi.org/10.1111/tpj.12796

CAS  Article  PubMed  Google Scholar 

Ritonga FN, Chen S (2020) Physiological and molecular mechanism involved in cold stress tolerance in plants. Plants 9:560. https://doi.org/10.3390/plants9050560

CAS  Article  PubMed Central  Google Scholar 

Rizzon C, Ponger L, Gaut BS (2006) Striking similarities in the genomic distribution of tandemly arrayed genes in Arabidopsis and rice. PLoS Comput Biol 2(9):e115. https://doi.org/10.1371/journal.pcbi.0020115

CAS  Article  PubMed  PubMed Central  Google Scholar 

Thomashow MF (1999) Plant cold acclimation: freezing tolerance genes and regulatory mechanisms. Ann Rev Plant Physiol Plant Mol Biol 50:571–599

CAS  Article  Google Scholar 

Tondelli A, Francia E, Barabaschi D, Pasquariello M, Pecchioni N (2011) Inside the CBF locus in Poaceae. Plant Sci 108:39–45. https://doi.org/10.1016/j.plantsci.2010.08.012

CAS  Article  Google Scholar 

Zhang J (2003) Evolution by gene duplication: an update. Trends Ecol Evol 18:292–298. https://doi.org/10.1016/S0169-5347(03)00033-8

Article  Google Scholar 

Zhao C, Zhang Z, Xie S, Si T, Li Y, Zhu JK (2016) Mutational evidence for the critical role of CBF transcription factors in cold acclimation in Arabidopsis. Plant Physiol 171:2744–2759. https://doi.org/10.1104/pp.16.00533

CAS  Article  PubMed  PubMed Central  Google Scholar