- -

Grafting vigour is associated with DNA de-methylation in eggplant

RiuNet: Repositorio Institucional de la Universidad Politécnica de Valencia

Compartir/Enviar a

Citas

Estadísticas

  • Estadisticas de Uso

Grafting vigour is associated with DNA de-methylation in eggplant

Mostrar el registro sencillo del ítem

Ficheros en el ítem

dc.contributor.author Cerruti, Elisa es_ES
dc.contributor.author Gisbert Domenech, Maria Carmen es_ES
dc.contributor.author Drost, Hajk-Georg es_ES
dc.contributor.author Valentino, Danila es_ES
dc.contributor.author Portis, Ezio es_ES
dc.contributor.author Barchi, Lorenzo es_ES
dc.contributor.author Prohens Tomás, Jaime es_ES
dc.contributor.author Lanteri, Sergio es_ES
dc.contributor.author Comino, Cinzia es_ES
dc.contributor.author Catoni, Marco es_ES
dc.date.accessioned 2022-10-05T18:03:18Z
dc.date.available 2022-10-05T18:03:18Z
dc.date.issued 2021-12 es_ES
dc.identifier.uri http://hdl.handle.net/10251/187092
dc.description.abstract [EN] In horticulture, grafting is a popular technique used to combine positive traits from two different plants. This is achieved by joining the plant top part (scion) onto a rootstock which contains the stem and roots. Rootstocks can provide resistance to stress and increase plant production, but despite their wide use, the biological mechanisms driving rootstock-induced alterations of the scion phenotype remain largely unknown. Given that epigenetics plays a relevant role during distance signalling in plants, we studied the genome-wide DNA methylation changes induced in eggplant (Solanum melongena) scion using two interspecific rootstocks to increase vigour. We found that vigour was associated with a change in scion gene expression and a genome-wide hypomethylation in the CHH context. Interestingly, this hypomethylation correlated with the downregulation of younger and potentially more active long terminal repeat retrotransposable elements (LTR-TEs), suggesting that graft-induced epigenetic modifications are associated with both physiological and molecular phenotypes in grafted plants. Our results indicate that the enhanced vigour induced by heterografting in eggplant is associated with epigenetic modifications, as also observed in some heterotic hybrids. es_ES
dc.description.sponsorship Part of the computations described in this paper was performed using the University of Birmingham's Compute and Storage for Life Sciences (CaStLeS) service. We are grateful to Dr. J. Paszkowski (Sainsbury Laboratory, Cambridge, UK) and all the members of his research group for the support and fruitful scientific discussions during the experimental work, Dr. J. Griffiths (Sainsbury Laboratory, Cambridge, UK) and K. Jeynes-Cupper (University of Birmingham, Birmingham, UK) for the critical reading of the manuscript; R. Schina (FMI, Basel, Switzerland) for helping in the first stages of eggplant development and for software assistance and the Max Planck Society for the support to H.G.D. es_ES
dc.language Inglés es_ES
dc.publisher Springer Nature es_ES
dc.relation.ispartof Horticulture Research es_ES
dc.rights Reconocimiento (by) es_ES
dc.subject.classification GENETICA es_ES
dc.title Grafting vigour is associated with DNA de-methylation in eggplant es_ES
dc.type Artículo es_ES
dc.identifier.doi 10.1038/s41438-021-00660-6 es_ES
dc.rights.accessRights Abierto es_ES
dc.contributor.affiliation Universitat Politècnica de València. Departamento de Biotecnología - Departament de Biotecnologia es_ES
dc.description.bibliographicCitation Cerruti, E.; Gisbert Domenech, MC.; Drost, H.; Valentino, D.; Portis, E.; Barchi, L.; Prohens Tomás, J.... (2021). Grafting vigour is associated with DNA de-methylation in eggplant. Horticulture Research. 8(1):1-10. https://doi.org/10.1038/s41438-021-00660-6 es_ES
dc.description.accrualMethod S es_ES
dc.relation.publisherversion https://doi.org/10.1038/s41438-021-00660-6 es_ES
dc.description.upvformatpinicio 1 es_ES
dc.description.upvformatpfin 10 es_ES
dc.type.version info:eu-repo/semantics/publishedVersion es_ES
dc.description.volume 8 es_ES
dc.description.issue 1 es_ES
dc.identifier.eissn 2052-7276 es_ES
dc.identifier.pmid 34719687 es_ES
dc.identifier.pmcid PMC8558322 es_ES
dc.relation.pasarela S\461420 es_ES
dc.contributor.funder Max Planck Society es_ES
dc.description.references Gautier, A. T. et al. Merging genotypes: graft union formation and scion–rootstock interactions. J. Exp. Bot. 70, 747–755 (2019). es_ES
dc.description.references Goldschmidt, E. E. Plant grafting: new mechanisms, evolutionary implications. Front. Plant Sci. 5, 727 (2014). es_ES
dc.description.references Colla, G., Pérez-Alfocea, F. & Schwarz, D. Vegetable Grafting: Principles and Practices (CABI, 2017). es_ES
dc.description.references Kumar, P., Rouphael, Y., Cardarelli, M. & Colla, G. Vegetable grafting as a tool to improve drought resistance and water use efficiency. Front. Plant Sci. 8, 1130. (2017). es_ES
dc.description.references Warschefsky, E. J. et al. Rootstocks: diversity, domestication, and impacts on shoot phenotypes. Trends Plant Sci. 21, 418–437 (2016). es_ES
dc.description.references Bai, S., Kasai, A., Yamada, K., Li, T. & Harada, T. A mobile signal transported over a long distance induces systemic transcriptional gene silencing in a grafted partner. J. Exp. Bot. 62, 4561–4570 (2011). es_ES
dc.description.references Lewsey, M. G. et al. Mobile small RNAs regulate genome-wide DNA methylation. Proc. Natl Acad. Sci. USA 113, E801–E810 (2016). es_ES
dc.description.references Melnyk, C. W., Molnar, A. & Baulcombe, D. C. Intercellular and systemic movement of RNA silencing signals. EMBO J. 30, 3553–3563 (2011). es_ES
dc.description.references Molnar, A. et al. Small silencing RNAs in plants are mobile and direct epigenetic modification in recipient cells. Science 328, 872–875 (2010). es_ES
dc.description.references Thieme, C. J. et al. Endogenous Arabidopsis messenger RNAs transported to distant tissues. Nat. Plants 1, 15025 (2015). es_ES
dc.description.references Zhang, H., Lang, Z. & Zhu, J.-K. Dynamics and function of DNA methylation in plants. Nat. Rev. Mol. Cell Biol. 19, 489 (2018). es_ES
dc.description.references Lee, J.-M. & Oda, M. in Horticultural Reviews (ed. Janic, J.) Ch. 2 (John Wiley & Sons, Ltd, 2010). es_ES
dc.description.references Gisbert, C., Prohens, J., Raigón, M. D., Stommel, J. R. & Nuez, F. Eggplant relatives as sources of variation for developing new rootstocks: effects of grafting on eggplant yield and fruit apparent quality and composition. Sci. Hortic. 128, 14–22 (2011). es_ES
dc.description.references Schwarz, D., Rouphael, Y., Colla, G. & Venema, J. H. Grafting as a tool to improve tolerance of vegetables to abiotic stresses: thermal stress, water stress and organic pollutants. Sci. Hortic. 127, 162–171 (2010). es_ES
dc.description.references Bogoescu, M. I. R. V. & Doltu, M. Effect of grafting eggplant (Solanum melongena L.) on its selected useful characters. Bull. Univ. Agric. Sci. Vet. Med. Cluj.-Napoca Hortic. 72, 318–326 (2015). es_ES
dc.description.references Miceli, A., Sabatino, L., Moncada, A., Vetrano, F. & D’Anna, F. Nursery and field evaluation of eggplant grafted onto unrooted cuttings of Solanum torvum Sw. Sci. Hortic. 178, 203–210 (2014). es_ES
dc.description.references Wu, R. et al. Inter-species grafting caused extensive and heritable alterations of DNA methylation in Solanaceae plants. PLoS ONE 8, e61995 (2013). es_ES
dc.description.references Melnyk, C. W. in Plant Hormones: Methods and Protocols (eds. Kleine-Vehn, J. & Sauer, M.) Ch. 2 (Springer, 2017). es_ES
dc.description.references Wang, P. et al. Factors influencing gene family size variation among related species in a plant family, Solanaceae. Genome Biol. Evol. 10, 2596–2613 (2018). es_ES
dc.description.references Zhong, S. et al. Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening. Nat. Biotechnol. 31, 154–159 (2013). es_ES
dc.description.references Moglia, A. et al. Identification of DNA methyltransferases and demethylases in Solanum melongena L., and their transcription dynamics during fruit development and after salt and drought stresses. PLoS ONE 14, e0223581 (2019). es_ES
dc.description.references Ge, S. X., Jung, D. & Yao, R. ShinyGO: a graphical gene-set enrichment tool for animals and plants. Bioinformatics 36, 2628–2629 (2020). es_ES
dc.description.references Saeki, N. et al. Molecular and cellular characteristics of hybrid vigour in a commercial hybrid of Chinese cabbage. BMC Plant Biol. 16, 45 (2016). es_ES
dc.description.references Yang, M. et al. Genomic architecture of biomass heterosis in Arabidopsis. Proc. Natl Acad. Sci. USA 114, 8101–8106 (2017). es_ES
dc.description.references Barchi, L. et al. A chromosome-anchored eggplant genome sequence reveals key events in Solanaceae evolution. Sci. Rep. 9, 1–13 (2019). es_ES
dc.description.references Drost, H.-G. LTRpred: _de novo_ annotation of intact retrotransposons. J. Open Source Softw. 5, 2170 (2020). es_ES
dc.description.references Blum, A. Heterosis, stress, and the environment: a possible road map towards the general improvement of crop yield. J. Exp. Bot. 64, 4829–4837 (2013). es_ES
dc.description.references Catoni, M. & Cortijo, S. in Advances in Botanical Research Vol. 88 (eds. Mirouze, M., Bucher, E. & Gallusci, P.) Ch. 4 (Academic Press 2018). es_ES
dc.description.references Groszmann, M. et al. Changes in 24-nt siRNA levels in Arabidopsis hybrids suggest an epigenetic contribution to hybrid vigor. Proc. Natl Acad. Sci. USA 108, 2617–2622 (2011). es_ES
dc.description.references Dapp, M. et al. Heterosis and inbreeding depression of epigenetic Arabidopsis hybrids. Nat. Plants 1, 15092 (2015). es_ES
dc.description.references Lauss, K. et al. Parental DNA methylation states are associated with heterosis in epigenetic hybrids. Plant Physiol. 176, 1627–1645 (2018). es_ES
dc.description.references Greaves, I. K. et al. Trans chromosomal methylation in arabidopsis hybrids. Proc. Natl Acad. Sci. USA 109, 3570–3575 (2012). es_ES
dc.description.references Harris, K. D. & Zemach, A. Contiguous and stochastic CHH methylation patterns of plant DRM2 and CMT2 revealed by single-read methylome analysis. Genome Biol. 21, 194 (2020). es_ES
dc.description.references Du, J. et al. Dual binding of chromomethylase domains to H3K9me2-containing nucleosomes directs DNA methylation in plants. Cell 151, 167–180 (2012). es_ES
dc.description.references Saze, H., Scheid, O. M. & Paszkowski, J. Maintenance of CpG methylation is essential for epigenetic inheritance during plant gametogenesis. Nat. Genet. 34, 65–69 (2003). es_ES
dc.description.references Kundariya, H. et al. MSH1-induced heritable enhanced growth vigor through grafting is associated with the RdDM pathway in plants. Nat. Commun. 11, 5343 (2020). es_ES
dc.description.references Wang, Z. & Baulcombe, D. C. Transposon age and non-CG methylation. Nat. Commun. 11, 1–9 (2020). es_ES
dc.description.references Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for illumina sequence data. Bioinformatics https://doi.org/10.1093/bioinformatics/btu170 (2014). es_ES
dc.description.references Krueger, F. & Andrews, S. R. Bismark: a flexible aligner and methylation caller for bisulfite-seq applications. Bioinformatics 27, 1571–1572 (2011). es_ES
dc.description.references Ding, Q.-X., Liu, J. & Gao, L. The complete chloroplast genome of eggplant (Solanum melongena L.). Mitochondrial DNA Part B 1, 843–844 (2016). es_ES
dc.description.references Derrien, T. et al. Fast computation and applications of genome mappability. PLoS ONE 7, e30377 (2012). es_ES
dc.description.references Catoni, M. et al. DNA sequence properties that predict susceptibility to epiallelic switching. EMBO J. 36, 617–628 (2017). es_ES
dc.description.references Catoni, M., Tsang, J. M., Greco, A. P. & Zabet, N. R. DMRcaller: a versatile R/bioconductor package for detection and visualization of differentially methylated regions in CpG and non-CpG contexts. Nucleic Acids Res. 46, e114 (2018). es_ES
dc.description.references Trapnell, C., Pachter, L. & Salzberg, S. L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105–1111 (2009). es_ES
dc.description.references Anders, S., Pyl, P. T. & Huber, W. HTSeq—a Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166–169 (2015). es_ES
dc.description.references Catoni, M. & Zabet, N. R. In Plant Transposable Elements: Methods and Protocols (ed. Cho, J.) 219–238 (Springer, 2021). es_ES
dc.description.references Lawrence, M. et al. Software for computing and annotating genomic ranges. PLoS Comput. Biol. 9, e1003118 (2013). es_ES
dc.description.references Anders, S. & Huber, W. Differential expression analysis for sequence count data. Genome Biol. 11, R106 (2010). es_ES
dc.subject.ods 02.- Poner fin al hambre, conseguir la seguridad alimentaria y una mejor nutrición, y promover la agricultura sostenible es_ES


Este ítem aparece en la(s) siguiente(s) colección(ones)

Mostrar el registro sencillo del ítem