Histology, physiology, and transcriptomic and metabolomic profiling reveal the developmental dynamics of annual shoots in tree peonies (Paeonia suffruticosa Andr.)

Abstract

The development of tree peony annual shoots is characterized by “withering”, which is related to whether there are bud points in the leaf axillaries of annual shoots. However, the mechanism of “withering” in tree peony is still unclear. In this study, Paeonia ostii ‘Fengdan’ and P. suffruticosa ‘Luoyanghong’ were used to investigate dynamic changes of annual shoots through anatomy, physiology, transcriptome, and metabolome. The results demonstrated that the developmental dynamics of annual shoots of the two cultivars were comparable. The withering degree of P. suffruticosa ‘Luoyanghong’ was higher than that of P. ostii ‘Fengdan’, and their upper internodes of annual flowering shoots had a lower degree of lignin deposition, cellulose, C/N ratio, showing no obvious sclerenchyma, than the bottom ones and the whole internodes of vegetative shoot, which resulted in the “withering” of upper internodes. A total of 36 phytohormone metabolites were detected, of which 33 and 31 were detected in P. ostii ‘Fengdan’ and P. suffruticosa ‘Luoyanghong’, respectively. In addition, 302 and 240 differentially expressed genes related to lignin biosynthesis, carbon and nitrogen metabolism, plant hormone signal transduction, and zeatin biosynthesis were screened from the two cultivars. Furtherly, 36 structural genes and 40 transcription factors associated with the development of annual shoots were highly co-expressed, and eight hub genes involved in this developmental process were identified. Consequently, this study explained the developmental dynamic on the varied annual shoots through multi-omics, providing a theoretical foundation for germplasm innovation and the mechanized harvesting of tree peony annual shoots.

Acknowledgements

We thank Mr. Zhuxin Wei, Luoyang Zongheng Horticulture Co., LTD., for his help in collecting tree peony materials. We are also grateful to Mrs. Fengqin Dong and Xiuping Xu from Plant Science Facility of Institute of Botany, Chinese Academy of Sciences for providing semi-thin sectioning and scanning electron microscopy technical assistance, respectively. This work was supported by the Strategic Priority Research Program of Chinese Academy of Sciences (grant XDA23080601).

Author contributions

Z.L., B.W. and N.T. designed the experiments. N.T. conducted the experiments and wrote the manuscript. N.T. and L.P. performed data analyses. L.P. and Q.S. revised the manuscript. All the authors read and approved the final manuscript.

Data availability

The data underlying this article are available in the article and in its online supplementary material.

Conflict of interest statement

The authors declare that they have no conflict of interest.

References

[1] Hong DY . Peonies of the World: Taxonomy and Phytogeography. London: Royal Botanic Gardens, Kew; 2010

[2] Yang Y, Sun M, Li S et al. Germplasm resources and genetic breeding of Paeonia: a systematic review . Hortic Res. 2020; 7: 107

[3] Li YC . Study on the Oil Tree Peony in China. Beijing: China Forestry Publishing House; 2019

[4] Zou LM, Liu W, Zhang Z et al. Gene body demethylation increases expression and is associated with self-pruning during grape genome duplication. Hortic Res. 2020; 7: 84

[5] McGarry RC, Ayre BG . Cotton architecture: examining the roles of SINGLE FLOWER TRUSS and SELF-PRUNING in regulating growth habits of a woody perennial crop . Curr Opin Plant Biol. 2021; 59: 101968

[6] Zhang JZ, Zhao K, Ai XY et al. Involvements of PCD and changes in gene expression profile during self-pruning of spring shoots in sweet orange (Citrus sinensis). BMC Genomics. 2014; 15: 892

[7] Wang KL, Zhang Y, Zhang HM et al. MicroRNAs play important roles in regulating rapid growth of the Phyllostachys edulis culm internode . New Phytol. 2021; 231: 2215-30

[8] Wang Y, Chantreau M, Sibout R et al. Plant cell wall lignification and monolignol metabolism. Front Plant Sci. 2013; 4: 220

[9] Rogers LA, Campbell MM . The genetic control of lignin deposition during plant growth and development. New Phytol. 2004; 164: 17-30

[10] Zhao Q . Lignification: flexibility, biosynthesis and regulation. Trends Plant Sci. 2016; 21: 713-21

[11] Huang JL, Gu M, Lai Z et al. Functional analysis of the Arabidopsis PAL gene family in plant growth, development, and response to environmental stress . Plant Physiol. 2010; 153: 1526-38

[12] Schilmiller AL, Stout J, Weng JK et al. Mutations in the cinnamate 4-hydroxylase gene impact metabolism, growth and development in Arabidopsis. Plant J. 2009; 60: 771-82

[13] Franke R, McMichael CM, Meyer K et al. Modified lignin in tobacco and poplar plants over-expressing the Arabidopsis gene encoding ferulate 5-hydroxylase . Plant J. 2000; 22: 223-34

[14] Atanassova R, Favet N, Martz F et al. Altered lignin composition in transgenic tobacco expressing O-methyltransferase sequences in sense and antisense orientation . Plant J. 1995; 8: 465-77

[15] Meyermans H, Morreel K, Lapierre C et al. Modifications in lignin and accumulation of phenolic glucosides in poplar xylem upon down-regulation of caffeoyl-coenzyme a O-methyltransferase, an enzyme involved in lignin biosynthesis . J Biol Chem. 2000; 275: 36899-909

[16] Higuchi T, Ito T, Umezawa T et al. Red-brown color of lignified tissues of transgenic plants with antisense CAD gene: wine-red lignin from coniferyl aldehyde . J Biotechnol. 1994; 37: 151-8

[17] Weyers JDB, Paterson NW . Plant hormones and the control of physiological processes. New Phytol. 2001; 152: 375-407

[18] Wang J, Yan DW, Yuan TT et al. A gain-of-function mutation in IAA8 alters Arabidopsis floral organ development by change of jasmonic acid level . Plant Mol Biol. 2013; 82: 71-83

[19] Ellis CM, Nagpal P, Young JC et al. AUXIN RESPONSE FACTOR1 and AUXIN RESPONSE FACTOR2 regulate senescence and floral organ abscission in Arabidopsis thaliana. Development. 2005; 132: 4563-74

[20] Ren H, Gray WM . SAUR proteins as effectors of hormonal and environmental signals in plant growth. Mol Plant. 2015; 8: 1153-64

[21] Khan S, Stone JM . Arabidopsis thaliana GH3.9 influences primary root growth . Planta. 2007; 226: 21-34

[22] Xu CZ, Shen Y, He F et al. Auxin-mediated aux/IAA-ARF-HB signaling cascade regulates secondary xylem development in Populus. New Phytol. 2019; 222: 752-67

[23] Claeys H, De Bodt S, Inzé D . Gibberellins and DELLAs: central nodes in growth regulatory networks. Trends Plant Sci. 2014; 19: 231-9

[24] Yamaguchi S . Gibberellin metabolism and its regulation. Annu Rev Plant Biol. 2008; 59: 225-51

[25] Daviere JM, Achard P . Gibberellin signaling in plants. Development. 2013; 140: 1147-51

[26] Singh V, Sergeeva L, Ligterink W et al. Gibberellin promotes sweetpotato root vascular lignification and reduces storage-root formation. Front Plant Sci. 2019; 10: 1320

[27] Cortleven A, Leuendorf JE, Frank M et al. Cytokinin action in response to abiotic and biotic stress in plants. Plant Cell Environ. 2019; 42: 998-1018

[28] Liu H, Zhang H, Dong YX et al. DNA METHYLTRANSFERASE1-mediated shoot regeneration is regulated by cytokinin-induced cell cycle in Arabidopsis. New Phytol. 2018; 217: 219-32

[29] Schaller GE, Bishopp A, Kieber JJ . The yin-yang of hormones: cytokinin and auxin interactions in plant development. Plant Cell. 2015; 27: 44-63

[30] Wen XX, Sun L, Chen Y et al. Rice dwarf and low tillering 10 (OsDLT10) regulates tiller number by monitoring auxin homeostasis . Plant Sci. 2020; 297: 110502

[31] Takatsuka H, Umeda M . ABA inhibits root cell elongation through repressing the cytokinin signaling. Plant Signal Behav. 2019; 14: e1578632

[32] Du L, Xu F, Fang J et al. Endosperm sugar accumulation caused by mutation of PHS8/ISA1 leads to pre-harvest sprouting in rice . Plant J. 2018; 95: 545-56

[33] Olds CL, Glennon EKK, Luckhart S . Abscisic acid: new perspectives on an ancient universal stress signaling molecule. Microbes Infect. 2018; 20: 484-92

[34] Swarup R, Parry G, Graham N et al. Auxin cross-talk: integration of signalling pathways to control plant development. Plant Mol Biol. 2002; 49: 411-26

[35] Nanda AK, Melnyk CW . The role of plant hormones during grafting. J Plant Res. 2018; 131: 49-58

[36] Fichtner F, Dissanayake IM, Lacombe B et al. Sugar and nitrate sensing: a multi-billion-year story. Trends Plant Sci. 2021; 26: 352-74

[37] Li QQ et al. Research progress of source-sink relationship and its underlying regulation mechanisms. Jiangsu Agric Sci. 2020; 48: 50-6

[38] Luo K et al. Effects of exogenous plant growth regulators on carbon-nitrogen metabolism and flower-pod abscission of relay strip intercropping soybean. Acta Agron Sin. 2021; 47: 752-60

[39] Chikov V, Bakirova G . Relationship between carbon and nitrogen metabolisms in photosynthesis. The role of photooxidation processes. Photosynthetica. 1999; 37: 519-27

[40] Krapp A, Traong HN . Regulation of C/N interaction in model plant species. J Crop Improv. 2006; 15: 127-73

[41] Wiedemuth K, Müller J, Kahlau A et al. Successive maturation and senescence of individual leaves during barley whole plant ontogeny reveals temporal and spatial regulation of photosynthetic function in conjunction with C and N metabolism. J Plant Physiol. 2005; 162: 1226-36

[42] Martin T, Oswald O, Graham IA . Arabidopsis seedling growth, storage lipid mobilization, and photosynthetic gene expression are regulated by carbon:nitrogen availability . Plant Physiol. 2002; 128: 472-81

[43] Chen DQ, Wang SW, Xiong BL et al. Carbon/nitrogen imbalance associated with drought-induced leaf senescence in Sorghum bicolor. PLoS One. 2015; 10: e0137026

[44] Aoyama S, Huarancca Reyes T, Guglielminetti L et al. Ubiquitin ligase ATL31 functions in leaf senescence in response to the balance between atmospheric CO₂ and nitrogen availability in Arabidopsis. Plant Cell Physiol. 2014; 55: 293-305

[45] Vanholme R, De Meester B, Ralph J et al. Lignin biosynthesis and its integration into metabolism. Curr Opin Biotechnol. 2019; 56: 230-9

[46] Gamuyao R, Nagai K, Ayano M et al. Hormone distribution and transcriptome profiles in bamboo shoots provide insights on bamboo stem emergence and growth. Plant Cell Physiol. 2017; 58: 702-16

[47] Cui K, He CY, Zhang JG et al. Characteristics of temporal and spatial tissue development during the rapidly growing stage of Moso bamboo culms. For Res. 2012; 25: 425-31

[48] Ishimaru K, Togawa E, Ookawa T et al. New target for rice lodging resistance and its effect in a typhoon. Planta. 2008; 227: 601-9

[49] Kashiwagi T, Madoka Y, Hirotsu N et al. Locus prl5 improves lodging resistance of rice by delaying senescence and increasing carbohydrate reaccumulation . Plant Physiol Biochem. 2006; 44: 152-7

[50] Verbancic J, Lunn JE, Stitt M et al. Carbon supply and the regulation of cell wall synthesis. Mol Plant. 2018; 11: 75-94

[51] Novaes E, Kirst M, Chiang V et al. Lignin and biomass: a negative correlation for wood formation and lignin content in trees. Plant Physiol. 2010; 154: 555-61

[52] Wang F, Ge S, Xu X et al. Multiomics analysis reveals new insights into the apple fruit quality decline under high nitrogen conditions. J Agric Food Chem. 2021; 69: 5559-72

[53] Nielsen DC, Vigil MF, Benjamin JG . The variable response of dryland corn yield to soil water content at planting. Agric Water Manag. 2009; 96: 330-6

[54] Yu JL et al. Effects of enzymes related to nitrogen reuse on nitrogen redistribution and nitrogen use efficiency in Brassica napus. Agric Technol Sci. 2014; 15: 215-8

[55] Woodward AW, Bartel B . Auxin: regulation, action, and interaction. Ann Bot. 2005; 95: 707-35

[56] Péret B, Swarup K, Ferguson A et al. AUX/LAX genes encode a family of auxin influx transporters that perform distinct functions during Arabidopsis development. Plant Cell. 2012; 24: 2874-85

[57] Sato A, Yamamoto KT . Overexpression of the non-canonical aux/IAA genes causes auxin-related aberrant phenotypes in Arabidopsis. Physiol Plant. 2008; 133: 397-405

[58] Wang RH, Estelle M . Diversity and specificity: auxin perception and signaling through the TIR1/AFB pathway. Curr Opin Plant Biol. 2014; 21: 51-8

[59] Hardtke CS, Berleth T . The Arabidopsis gene MONOPTEROS encodes a transcription factor mediating embryo axis formation and vascular development . EMBO J. 1998; 17: 1405-11

[60] Staswick PE, Serban B, Rowe M et al. Characterization of an Arabidopsis enzyme family that conjugates amino acids to indole-3-acetic acid . Plant Cell. 2005; 17: 616-27

[61] Spartz AK, Lee SH, Wenger JP et al. The SAUR19 subfamily of SMALL AUXIN UP RNA genes promote cell expansion . Plant J. 2012; 70: 978-90

[62] Schmülling T, Schafer S, Romanov G . Cytokinins as regulators of gene expression. Physiol Plant. 1997; 100: 505-19

[63] Jung JH, Kim SG, Seo PJ et al. Molecular mechanisms underlying vascular development. Adv Bot Res. 2008; 48: 1-68

[64] Köllmer I, Novák O, Strnad M et al. Overexpression of the cytosolic cytokinin oxidase/dehydrogenase (CKX7) from Arabidopsis causes specific changes in root growth and xylem differentiation . Plant J. 2014; 78: 359-71

[65] Koornneef M, Bentsink L, Hilhorst H . Seed dormancy and germination. Curr Opin Plant Biol. 2002; 5: 33-6

[66] Uozu S, Tanaka-Ueguchi M, Kitano H et al. Characterization of XET-related genes of rice . Plant Physiol. 2000; 122: 853-60

[67] Zheng YY, Gao ZP, Zhu ZQ . DELLA-PIF modules: old dogs learn new tricks. Trends Plant Sci. 2016; 21: 813-5

[68] Cao ZL . Molecular Mechanisms of Endogenous Hormone Regulation in Stump Sprouting of Hippophae Rhamnoides Subsp. Sinensis. Beijing Forestry University; 2019

[69] Cao FY, Yoshioka K, Desveaux D . The roles of ABA in plant-pathogen interactions. J Plant Res. 2011; 124: 489-99

[70] Yang M, Zhu L, Pan C et al. Transcriptomic analysis of the regulation of rhizome formation in temperate and tropical lotus (Nelumbo nucifera). Sci Rep. 2015; 5: 13059

[71] Yue JY, Wang R, Ma X et al. Full-length transcriptome sequencing provides insights into the evolution of apocarotenoid biosynthesis in Crocus sativus. Comput Struct Biotechnol J. 2020; 18: 774-83

[72] Zhao DQ, Luan Y, Xia X et al. Lignin provides mechanical support to herbaceous peony (Paeonia lactiflora pall.) stems. Hortic Res. 2020; 7: 213

[73] Zhong FR, Huang L, Qi LM et al. Full-length transcriptome analysis of Coptis deltoidea and identification of putative genes involved in benzylisoquinoline alkaloids biosynthesis based on combined sequencing platforms . Plant Mol Biol. 2020; 102: 477-99

[74] Rao GD, Zhang JG, Liu XX et al. Identification of putative genes for polyphenol biosynthesis in olive fruits and leaves using full-length transcriptome sequencing. Food Chem. 2019; 300: 125246

[75] Yoon J, Choi H, An G . Roles of lignin biosynthesis and regulatory genes in plant development. J Integr Plant Biol. 2015; 57: 902-12

[76] Li YH, Qian Q, Zhou Y et al. BRITTLE CULM1, which encodes a COBRA-like protein, affects the mechanical properties of rice plants. Plant Cell. 2003; 15: 2020-31

[77] Sewalt V, Ni W, Blount JW et al. Reduced lignin content and altered lignin composition in transgenic tobacco down-regulated in expression of l-phenylalanine ammonia-lyase or cinnamate-4-hydrixylase. Plant Physiol. 1997; 115: 41-50

[78] Zhao Q, Dixon RA . Transcriptional networks for lignin biosynthesis: more complex than we thought? Trends Plant Sci. 2011; 16: 227-33

[79] Gallego-Giraldo L, Posé S, Pattathil S et al. Elicitors and defense gene induction in plants with altered lignin compositions. New Phytol. 2018; 219: 1235-51

[80] Shafrin F, Ferdous AS, Sarkar SK et al. Modification of monolignol biosynthetic pathway in jute: different gene, different consequence. Sci Rep. 2017; 7: 39984

[81] Shan LL, Li X, Wang P et al. Characterization of cDNAs associated with lignification and their expression profiles in loquat fruit with different lignin accumulation. Planta. 2008; 227: 1243-54

[82] Rao XL, Dixon RA . Current models for transcriptional regulation of secondary cell wall biosynthesis in grasses. Front Plant Sci. 2018; 9: 399

[83] Zhang J, Tuskan GA, Tschaplinski TJ et al. Transcriptional and post-transcriptional regulation of lignin biosynthesis pathway genes in Populus. Front Plant Sci. 2020; 11: 652

[84] Jin HL, Cominelli E, Bailey P et al. Transcriptional repression by AtMYB4 controls production of UV-protecting sunscreens in Arabidopsis. EMBO J. 2000; 19: 6150-61

[85] Tian QY, Wang X, Li C et al. Functional characterization of the poplar R2R3-MYB transcription factor PtoMYB216 involved in the regulation of lignin biosynthesis during wood formation. PLoS One. 2013; 8: e76369

[86] Zhong RQ, Richardson EA, Ye ZH . The MYB46 transcription factor is a direct target of SND1 and regulates secondary wall biosynthesis in Arabidopsis. Plant Cell. 2007; 19: 2776-92

[87] Wang HZ, Avci U, Nakashima J et al. Mutation of WRKY transcription factors initiates pith secondary wall formation and increases stem biomass in dicotyledonous plants. Proc Natl Acad Sci U S A. 2010; 107: 22338-43

[88] Zhu XB, Zhang GF, Chen P . Research progress in the transcriptional regulation of secondary cell wall thickening. Plant Physiol J. 2017; 53: 1598-608

[89] Tong NN, Peng LP, Liu ZA et al. Comparative transcriptomic analysis of genes involved in stem lignin biosynthesis in woody and herbaceous Paeonia species . Physiol Plant. 2021; 173: 961-77

[90] Foster CE, Martin TM, Pauly M . Comprehensive compositional analysis of plant cell walls (lignocellulosic biomass) part I: lignin. J Vis Exp. 2010; 37: 1745

[91] Foster CE, Martin TM, Pauly M . Comprehensive compositional analysis of plant cell walls (lignocellulosic biomass) part II: carbohydrates. J Vis Exp. 2010; 37: 1837

[92] Li WZ, Godzik A . Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics. 2006; 22: 1658-9

[93] Dobin A, Davis CA, Schlesinger F et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013; 29: 15-21

[94] Trapnell C, Williams BA, Pertea G et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010; 28: 511-5

[95] Anders S, Huber W . Differential expression analysis for sequence count data. Genome Biol. 2010; 11: R106

[96] 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