Small RNA populations reflect the complex dialogue established between heterograft partners in grapevine

Abstract

Grafting is an ancient method that has been intensively used for the clonal propagation of vegetables and woody trees. Despite its importance in agriculture the physiological and molecular mechanisms underlying phenotypic changes of plants following grafting are still poorly understood. In the present study, we analyse the populations of small RNAs in homo and heterografts and take advantage of the sequence differences in the genomes of heterograft partners to analyse the possible exchange of small RNAs. We demonstrate that the type of grafting per se dramatically influences the small RNA populations independently of genotypes but also show genotype specific effects. In addition, we demonstrate that bilateral exchanges of small RNAs, mainly short interfering RNAs, may occur in heterograft with the preferential transfer of small RNAs from the scion to the rootstock. Altogether, the results suggest that small RNAs may have an important role in the phenotype modifications observed in heterografts.

References

[1] Mudge K, Janick J, Scofield S, Goldschmidt EE . A History of Grafting . Horticultural Reviews. 2009; 35: 437-493.

[2] Wang J, Jiang L, Wu R . Plant grafting: how genetic exchange promotes vascular reconnection. New Phytol. 2017; 214: 56-65.

[3] Powell KS . Grape phylloxera: an overview. In: Root Feeders: An Ecosystem Perspective.CAB International: Wallingford, 2008, 96-114.

[4] Ollat N, Peccoux A, Papura D et al. Rootstocks as a component of adaptation to environment. In: Grapevine in a Changing Environment: A Molecular and Ecophysiological Perspective , Wiley. 2016; 1: 68-108.

[5] Baron D, Esteves Amaro AC, Pina A, Ferreira G . An overview of grafting re-establishment in woody fruit species. Sci Hortic. 2019; 243: 84-91.

[6] Gaion LA, Carvalho RF . Long-distance signaling: what grafting has revealed? J Plant Growth Regul. 2018; 37: 694-704.

[7] Lu X, Liu W, Wang T et al. Systemic long-distance signaling and communication between rootstock and Scion in grafted vegetables. Front Plant Sci. 2020; 11: 460.

[8] Dunoyer P, Melnyk C, Molnar A, Slotkin RK . Plant mobile small RNAs. Cold Spring Harb Perspect Biol. 2013; 5: a017897.

[9] Singh A, Gautam V, Singh S et al. Plant small RNAs: advancement in the understanding of biogenesis and role in plant development. Planta. 2018; 248: 545-58.

[10] Kamthan A, Chaudhuri A, Kamthan M, Datta A . Small RNAs in plants: recent development and application for crop improvement. Front Plant Sci. 2015; 6: 208.

[11] Borges F, Martienssen RA . The expanding world of small RNAs in plants. Nat Rev Mol Cell Biol. 2015; 16: 727-41.

[12] Berger MMJ, Gallusci P, Teyssier E. Chapter Seven - Roles of Epigenetic Mechanisms in Grafting and Possible Applications. In: Mirouze M, Bucher E, Gallusci P, eds. vol. 88, Advances in Botanical Research.Academic Press, 2018; 88: 203-46.

[13] Melnyk CW, Molnar A, Baulcombe DC . Intercellular and systemic movement of RNA silencing signals. EMBO J. 2011; 30: 3553-63.

[14] Pagliarani C, Gambino G . Small RNA mobility: spread of RNA silencing effectors and its effect on developmental processes and stress adaptation in plants. Int J Mol Sci. 2019; 20: 4306.

[15] Maizel A, Markmann K, Timmermans M, Wachter A . To move or not to move: roles and specificity of plant RNA mobility. Curr Opin Plant Biol. 2020; 57: 52-60.

[16] Dunoyer P, Himber C, Ruiz-Ferrer V et al. Intra- and intercellular RNA interference in Arabidopsis thaliana requires components of the microRNA and heterochromatic silencing pathways. Nat Genet. 2007; 39: 848-56.

[17] Molnar A, Melnyk CW, Bassett A et al. Small silencing RNAs in plants are mobile and direct epigenetic modification in recipient cells. Science. 2010; 328: 872-5.

[18] Buhtz A, Springer F, Chappell L et al. Identification and characterization of small RNAs from the phloem of Brassica napus. Plant J. 2008; 53: 739-49.

[19] Yoo BC, Kragler F, Varkonyi-Gasic E et al. A systemic small RNA signaling system in plants. Plant Cell. 2004; 16: 1979-2000.

[20] Ruiz-Medrano R, Xoconostle-Cázares B, Lucas WJ . Phloem long-distance transport of CmNACP mRNA: implications for supracellular regulation in plants. Development. 1999; 126: 4405-19.

[21] Bai S, Kasai A, Yamada K et al. A mobile signal transported over a long distance induces systemic transcriptional gene silencing in a grafted partner. J Exp Bot. 2011; 62: 4561-70.

[22] Zhao D, Zhong GY, Song GQ . Transfer of endogenous small RNAs between branches of scions and rootstocks in grafted sweet cherry trees. PLoS One. 2020; 15: e0236376.

[23] Pagliarani C, Vitali M, Ferrero M et al. The accumulation of miRNAs differentially modulated by drought stress is affected by grafting in grapevine. Plant Physiol. 2017; 173: 2180-95.

[24] Paim Pinto DL, Brancadoro L, Santo SD et al . The influence of genotype and environment on small RNA profiles in grapevine berry. Front Plant Sci. 2016; 7: 1459.

[25] Albacete A, Martínez-Andújar C, Martínez-Pérez A et al. Unravelling rootstock×scion interactions to improve food security. J Exp Bot. 2015; 66: 2211-26.

[26] Maré C, Mica E, Cattivelli L . Molecular advances in rootstock-scion interaction in grapevine. in I International Symposium on Grapevine Roots 1136 155-160 actahort.org, 2014.

[27] Cookson SJ, Ollat N . Grafting with rootstocks induces extensive transcriptional re-programming in the shoot apical meristem of grapevine. BMC Plant Biol. 2013; 13: 147.

[28] Chitarra W, Perrone I, Avanzato CG et al. Grapevine grafting: Scion transcript profiling and defense-related metabolites induced by rootstocks. Front Plant Sci. 2017; 8: 654.

[29] Yang Y, Mao L, Jittayasothorn Y et al. Messenger RNA exchange between scions and rootstocks in grafted grapevines. BMC Plant Biol. 2015; 15: 251.

[30] Cookson SJ, Moreno MJC, Hevin C et al. Graft union formation in grapevine induces transcriptional changes related to cell wall modification, wounding, hormone signalling, and secondary metabolism. J Exp Bot. 2013; 64: 2997-3008.

[31] Cochetel N, Escudié F, Cookson SJ et al. Root transcriptomic responses of grafted grapevines to heterogeneous nitrogen availability depend on rootstock genotype. J Exp Bot. 2017; 68: 4339-55.

[32] Schmieder R, Edwards R . Quality control and preprocessing of metagenomic datasets. Bioinformatics. 2011; 27: 863-4.

[33] Jansen RK, Kaittanis C, Saski C et al. Phylogenetic analyses of Vitis (Vitaceae) based on complete chloroplast genome sequences: effects of taxon sampling and phylogenetic methods on resolving relationships among rosids. BMC Evol Biol. 2006; 6: 32.

[34] Langmead B, Trapnell C, Pop M, Salzberg SL . Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009; 10: R25.

[35] Kalvari I, Argasinska J, Quinones-Olvera N et al. Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families. Nucleic Acids Res. 2018; 46: D335-42.

[36] Axtell MJ . ShortStack: comprehensive annotation and quantification of small RNA genes. RNA. 2013; 19: 740-51.

[37] Meyers BC, Axtell MJ, Bartel B et al. Criteria for annotation of plant MicroRNAs. Plant Cell. 2008; 20: 3186-90.

[38] Girollet N, Rubio B, Lopez-Roques C et al. De novo phased assembly of the Vitis riparia grape genome. Sci Data. 2019; 6: 127.

[39] Minio A, Massonnet M, Figueroa-Balderas R et al. Iso-Seq allows genome-independent transcriptome profiling of grape berry development. G3 (Bethesda). 2019; 9: 755-67.

[40] Quinlan AR . BEDTools: the Swiss-Army tool for genome feature analysis. Curr Protoc Bioinformatics. 2014; 47: 11.12.1-34.

[41] Alexa A, Rahnenführer J, Lengauer T . Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics. 2006; 22: 1600-7.

[42] Kobayashi S, Goto-Yamamoto N, Hirochika H . Retrotransposon-induced mutations in grape skin color. Science. 2004; 304: 982.

[43] Kasschau KD, Fahlgren N, Chapman EJ et al. Genome-wide profiling and analysis of Arabidopsis siRNAs. PLoS Biol. 2007; 5: e57.

[44] Assunção M, Santos C, Brazão J et al. Understanding the molecular mechanisms underlying graft success in grapevine. BMC Plant Biol. 2019; 19: 396.

[45] Li S, Wang X, Xu W et al. Unidirectional movement of small RNAs from shoots to roots in interspecific heterografts. Nature Plants. 2021; 7: 50-9.

[46] Sun X, Fan G, Su L et al. Identification of cold-inducible microRNAs in grapevine. Front Plant Sci. 2015; 6: 595.

[47] Pantaleo V, Vitali M, Boccacci P et al. Novel functional microRNAs from virus-free and infected Vitis vinifera plants under water stress. Sci Rep. 2016; 6: 20167.

[48] Lewsey MG, Hardcastle TJ, Melnyk CW et al. Mobile small RNAs regulate genome-wide DNA methylation. Proc Natl Acad Sci U S A. 2016; 113: E801-10.

[49] Sarkies P, Miska EA . Small RNAs break out: the molecular cell biology of mobile small RNAs. Nat Rev Mol Cell Biol. 2014; 15: 525-35.

[50] de Felippes FF, Waterhouse PM . The whys and wherefores of transitivity in plants. Front Plant Sci. 2020; 11: 579376.

[51] Molnar A, Melnyk C, Baulcombe DC . Silencing signals in plants: a long journey for small RNAs. Genome Biol. 2011; 12: 215.

[52] Berger MMJ, Gallusci P, Teyssier E . Roles of epigenetic mechanisms in grafting and possible applications. Adv Bot Res. 2018; 88: 203-46.

[53] Uthup TK, Karumamkandathil R, Ravindran M, Saha T . Heterografting induced DNA methylation polymorphisms in Hevea brasiliensis. Planta. 2018; 248: 579-89.

[54] Neves DM, da Hora Almeida, Santana-Vieira DDS et al. Recurrent water deficit causes epigenetic and hormonal changes in citrus plants. Sci Rep. 2017; 7: 13684.

[55] Huang Y, Xu Y, Jiang X et al. Genome of a citrus rootstock and global DNA demethylation caused by heterografting. Hortic Res. 2021; 8: 69.