PsmiR159b-PsMYB65 module functions in the resumption of bud growth after endodormancy by affecting the cell cycle in tree peony

Abstract

Bud endodormancy in perennial plants is a sophisticated system that adapts to seasonal climatic changes. Growth-promoting signals such as low temperature and gibberellins (GAs) are crucial for facilitating budbreak following endodormancy release (EDR). However, the regulatory mechanisms underlying GA-mediated budbreak in tree peony (Paeonia suffruticosa) remain unclear. In tree peony, the expression of PsmiR159b among three differentially expressed miR159 members was inhibited with the prolonged chilling, and overexpression of PsMIR159b delayed budbreak, whereas silencing PsmiR159b promoted budbreak after dormancy. PsMYB65, a downstream transcription factor in the GA pathway, was induced by prolonged chilling and exogenous GA₃ treatments. PsMYB65 was identified as a target of PsmiR159b, and promoted budbreak in tree peony. RNA-seq of PsMYB65-slienced buds revealed significant enrichment in the GO terms regulation of ‘cell cycle’ and ‘DNA replication’ among differentially expressed genes. Yeast one-hybrid and electrophoretic mobility shift assays demonstrated that PsMYB65 directly bound to the promoter of the type-D cyclin gene PsCYCD3;1. Dual-luciferase reporter assay indicated that PsMYB65 positively regulate PsCYCD3;1 expression, suggesting that miR159b-PsMYB65 module contributes to budbreak by influencing the cell cycle. Our findings revealed that the PsmiR159b-PsMYB65 module functioned in budbreak after dormancy by regulating cell proliferation, providing valuable insights into the endodormancy release regulation mechanism.

Acknowledgements

This work was supported by grants from National Natural Science Foundation of China (32271941, 31972452, 32371938), the Agricultural Seed Engineering Project of Shandong Province (2020LZGC011-1-4). The funding bodies had no role in the design of the study, the collection, analysis, and interpretation of data, or in writing the manuscript. We would like to thank Editage (www.editage.cn) for English language editing.

Author contributions

TZ, XW, and YY: Writing-original draft, Validation, Methodology, Investigation, Formal analysis, Data curation. SZ and CL: Writing-original draft, Formal analysis, Investigation, Data curation. YZ: Writing-review & editing, Validation, Methodology, Conceptualization. SG: Writing-review & editing, Supervision, Project administration, Conceptualization.

Data availability

The RNA-seq data have been deposited National Center for Biotechnology Information (NCBI) under accession number PRJNA813336. Sequence data used in this article can be found in the Arabidopsis Genome TAIR database or GenBank database under the following accession numbers: PsCYCD1;1 (OP142277), PsCYCD3;1 (OP142273), PsCYCD3;2 (OP142275), PsCYCD3;3 (OP142274), PsCYCD6;1 (OP142276), AtCYCD3 (AT4G34160), PtCYCD3;2 (CAN88857), AtCYCD3;3 (AT3G50070), AtCYCD3;2 (AT5G67260), PtCYCD6;1 (CAN88865), AtCYCD1;1 (AT1G70210), AtCYCD4;1 (AT5G65420), AtCYCD7;1 (AT5G02110), AtCYCD2;1 (AT2G22490), AtMYB97 (AT4G26930), AtMYB120 (AT5G55020), AtMYB101 (AT2G32460), PsMYB65 (MT211968), AtMYB65 (AT3G11440), AtMYB33 (AT5G06100), AtMYB104 (AT2G26950), AtMYB81 (AT2G26960).

Conflict of interest statement

The authors declare no competing interests.

Supplementary data

Supplementary data is available at Horticulture Research online.

References

[1] Busov VB. Plant development: dual roles of poplar SVL in vegetative bud dormancy. Curr Biol. 2019; 29:R68-70

[2] Yang Q, Gao Y, Wu X. et al. Bud endodormancy in deciduous fruit trees: advances and prospects. Hortic Res. 2021; 8:139

[3] Maurya JP, Bhalerao RP. Photoperiod- and temperature-mediated control of growth cessation and dormancy in trees: a molecular perspective. Ann Bot. 2017; 120:351-60

[4] Singh RK, Svystun T, AlDahmash B. et al. Photoperiod- and temperature-mediated control of phenology in trees - a molecular perspective. New Phytol. 2017; 213:511-24

[5] Böhlenius H, Huang T, Charbonnel-Campaa L. et al. CO/FT regulatory module controls timing of flowering and seasonal growth cessation in trees. Science. 2006; 312:1040-3

[6] Ruttink T, Arend M, Morreel K. et al. A molecular timetable for apical bud formation and dormancy induction in poplar. Plant Cell. 2007; 19:2370-90

[7] Tylewicz S, Tsuji H, Miskolczi P. et al. Dual role of tree florigen activation complex component FD in photoperiodic growth control and adaptive response pathways. Proc Natl Acad Sci USA. 2015; 112:3140-5

[8] Karlberg A, Bako L, Bhalerao RP. Short day-mediated cessation of growth requires the downregulation of AINTEGUMENTA-LIKE 1 transcription factor in hybrid aspen. PLoS Genet. 2011; 7:e1002361

[9] Tylewicz S, Petterle A, Marttila S. et al. Photoperiodic control of seasonal growth is mediated by ABA acting on cell-cell communication. Science. 2018; 360:212-5

[10] Zheng C, Halaly T, Acheampong AK. et al. Abscisic acid (ABA) regulates grape bud dormancy, and dormancy release stimuli may act through modification of ABA metabolism. J Exp Bot. 2015; 66:1527-42

[11] Zhang T, Yuan Y, Zhan Y. et al. Metabolomics analysis reveals Embden Meyerhof Parnas pathway activation and flavonoids accumulation during dormancy transition in tree peony. BMC Plant Biol. 2020; 20:1-17

[12] Singh RK, Miskolczi P, Maurya JP. et al. A tree ortholog of SHORT VEGETATIVE PHASE floral repressor mediates photoperiodic control of bud dormancy. Curr Biol. 2019; 29:128-133.e2

[13] Azeez A, Zhao YC, Singh RK. et al. EARLY BUD-BREAK 1 and EARLY BUD-BREAK 3 control resumption of poplar growth after winter dormancy. Nat Commun. 2021; 12:1123

[14] Singh RK, Maurya JP, Azeez A. et al. A genetic network mediating the control of bud break in hybrid aspen. Nat Commun. 2018; 9:4173

[15] Zhang Y, Yuan Y, Liu Z. et al. GA₃ is superior to GA₄ in promoting bud endodormancy release in tree peony (Paeonia suffruticosa) and their potential working mechanism. BMC Plant Biol. 2021; 65:323-32

[16] Zheng C, Kwame Acheampong A, Shi Z. et al. Distinct gibberellin functions during and after grapevine bud dormancy release. J Exp Bot. 2018; 69:1635-48

[17] Liu Q, Wu K, Harberd NP. et al. Green revolution DELLAs: from translational reinitiation to future sustainable agriculture. Mol Plant. 2021; 14:547-9

[18] Gao L, Niu D, Chi T. et al. PsRGL1 negatively regulates chilling- and gibberellin-induced dormancy release by PsF-box1-mediated targeting for proteolytic degradation in tree peony. Hortic Res. 2023; 10:uhad044

[19] Ding Q, Zeng J, He XQ. Deep sequencing on a genome-wide scale reveals diverse stage-specific microRNAs in cambium during dormancy-release induced by chilling in poplar. BMC Plant Biol. 2014; 14:267

[20] Liu J, Guo X, Zhai T. et al. Genome-wide identification and characterization of microRNAs responding to ABA and GA in maize embryos during seed germination. Plant Biol. 2020; 22:949-57

[21] Zhang Y, Wang Y, Gao X. et al. Identification and characterization of microRNAs in tree peony during chilling induced dormancy release by high-throughput sequencing. Sci Rep. 2018; 8:1-14

[22] Zhang Y, Gao L, Wang Y. et al. Dual functions of PsmiR172b-PsTOE3 module in dormancy release and flowering in tree peony (Paeonia suffruticosa). Hortic Res. 2023; 10:uhad033

[23] Yu J, Bennett D, Dardick C. et al. Genome-wide changes of regulatory non-coding RNAs reveal pollen development initiated at ecodormancy in peach. Front Mol Biosci. 2021; 8:612881

[24] Guo C, Xu Y, Shi M. et al. Repression of miR156 by miR159 regulates the timing of the juvenile-to-adult transition in Arabidopsis. Plant Cell. 2017; 29:1293-304

[25] Gocal GFW, Sheldon CC, Gubler F. et al. GAMYB-like genes, flowering, and gibberellin signaling in Arabidopsis. Plant Physiol. 2001; 127:1682-93

[26] Millar AA, Gubler F. The Arabidopsis GAMYB-like genes, MYB33 and MYB65, are microRNA-regulated genes that redundantly facilitate anther development. Plant Cell. 2005; 17:705-21

[27] Ko SS, Li MJ, Ho YC. et al. Rice transcription factor GAMYB modulates bHLH142 and is homeostatically regulated by TDR during anther tapetal and pollen development. J Exp Bot. 2021; 72:4888-903

[28] Gai S, Zhang Y, Liu C. et al. Transcript profiling of Paoenia ostii during artificial chilling induced dormancy release identifies activation of GA pathway and carbohydrate metabolism. PLoS One. 2013; 8:e55297

[29] Huang X, Zhu W, Dai S. et al. The involvement of mitochondrial phosphate transporter in accelerating bud dormancy release during chilling treatment of tree peony (Paeonia suffruticosa). Planta. 2008; 228:545-52

[30] Yan J, Gu Y, Jia X. et al. Effective small RNA destruction by the expression of a short tandem target mimic in Arabidopsis. Plant Cell. 2012; 24:415-27

[31] Wu HJ, Ma YK, Chen T. et al. PsRobot: a web-based plant small RNA meta-analysis toolbox. Nucleic Acids Res. 2012; 40:W22-8

[32] Lescot M, Déhais P, Thijs G. et al. PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res. 2002; 30:325-7

[33] Achard P, Herr A, Baulcombe DC. et al. Modulation of floral development by a gibberellin-regulated microRNA. Development. 2004; 131:3357-65

[34] da Silva EM, Silva GFF, Bidoia DB. et al. microRNA159-targeted SlGAMYB transcription factors are required for fruit set in tomato. Plant J. 2017; 92:95-109

[35] Gao J, Chen H, Yang H. et al. A brassinosteroid responsive miRNA-target module regulates gibberellin biosynthesis and plant development. New Phytol. 2018; 220:488-501

[36] Zheng Z, Wang N, Jalajakumari M. et al. MiR159 represses a constitutive pathogen defense response in tobacco. Plant Physiol. 2020; 182:2182-98

[37] Mathiason K, He D, Grimplet J. et al. Transcript profiling in Vitis riparia during chilling requirement fulfillment reveals coordination of gene expression patterns with optimized bud break. Funct Integr Genomics. 2009; 9:81-96

[38] Dong QK, Hu BB, Zhang C. microRNAs and their roles in plant development. Front Plant Sci. 2022; 13:824240

[39] Azeez A, Miskolczi P, Tylewicz S. et al. A tree ortholog of APETALA1 mediates photoperiodic control of seasonal growth. Curr Biol. 2014; 24:717-24

[40] Hu Z, Shen X, Xiang X. et al. Evolution of MIR159/319 genes in Brassica campestris and their function in pollen development. Plant Mol Biol. 2019; 101:537-50

[41] Wang C, Jogaiah S, Zhang W. et al. Spatio-temporal expression of miRNA159 family members and their GAMYB target gene during the modulation of gibberellin-induced grapevine parthenocarpy. J Exp Bot. 2018; 69:3639-50

[42] Jing WK, Gong FF, Liu GQ. et al. Petal size is controlled by the MYB73/TPL/HDA19-miR159-CKX6 module regulating cytokinin catabolism in Rosa hybrida. Nat Commun. 2023; 14:7106

[43] Wojtania A, Markiewicz M, Waligórski P. Regulation of the bud dormancy development and release in micropropagated rhubarb ’Malinowy’. Int J Mol Sci. 2022; 23:1480

[44] Shimotohno A, Aki SS, Takahashi N. et al. Regulation of the plant cell cycle in response to hormones and the environment. Annu Rev Plant Biol. 2021; 72:273-96

[45] Vandepoele K, Raes J, De Veylder L. et al. Genome-wide analysis of core cell cycle genes in Arabidopsis. Plant Cell. 2002; 14:903-16

[46] Achard P, Gusti A, Cheminant S. et al. Gibberellin signaling controls cell proliferation rate in Arabidopsis. Curr Biol. 2009; 19:1188-93

[47] Xue T, Liu Z, Dai X. et al. Primary root growth in Arabidopsis thaliana is inhibited by the miR159 mediated repression of MYB33, MYB65 and MYB101. Plant Sci. 2017; 262:182-9

[48] Guan C, Xue Y, Jiang P. et al. Overexpression of ptocycd3;3 promotes growth and causes leaf wrinkle and branch appearance in Populus. Int J Mol Sci. 2021; 22:1-21

[49] Zhang Y, Yu D, Liu C. et al. Dynamic of carbohydrate metabolism and the related genes highlights PPP pathway activation during chilling induced bud dormancy release in tree peony (Paeonia suffruticosa). Sci Hortic (Amsterdam). 2018; 242:36-43

[50] Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol. 2016; 33:1870-4

[51] Chen C, Chen H, Zhang Y. et al. TBtools: an integrative toolkit developed for interactive analyses of big biological data. Mol Plant. 2020; 13:1194-202

[52] Liu W, Xie Y, Ma J. et al. IBS: an illustrator for the presentation and visualization of biological sequences. Bioinformatics. 2015; 31:3359-61

[53] Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2^-ΔΔCT method. Methods. 2001; 25:402-8

[54] Jefferson RA, Kavanagh TA, Bevan MW. GUS fusions: beta-glucuronidase as a sensitive and versatile gene fusion marker in higher plants. EMBO J. 1987; 6:3901-7

[55] Chen J, Li Y, Li Y. et al. Auxin response factor 18-histone deacetylase 6 module regulates floral organ identity in rose (Rosa hybrida). Plant Physiol. 2021; 186:1074-87