Abstract
Key message
By studying three cv. Malbec clones cultivated in two vineyards with contrasting environmental conditions, we demonstrated that DNA methylation has an important role in the phenotypic plasticity and that epigenetic modulation is clone-dependent.
Abstract
Clonal selection and vegetative propagation determine low genetic variability in grapevine cultivars, although it is common to observe diverse phenotypes. Environmental signals may induce epigenetic changes altering gene expression and phenotype. The range of phenotypes that a genotype expresses in different environments is known as phenotypic plasticity. DNA methylation is the most studied epigenetic mechanism, but only few works evaluated this novel source of variability in grapevines. In the present study, we analyzed the effects on phenotypic traits and epigenome of three Vitis vinifera cv. Malbec clones cultivated in two contrasting vineyards of Mendoza, Argentina. Anonymous genome regions were analyzed using methylation-sensitive amplified polymorphism (MSAP) markers. Clone-dependent phenotypic and epigenetic variability between vineyards were found. The clone that presented the clearer MSAP differentiation between vineyards was selected and analyzed through reduced representation bisulfite sequencing. Twenty-nine differentially methylated regions between vineyards were identified and associated to genes and/or promoters. We discuss about a group of genes related to hormones homeostasis and sensing that could provide a hint of the epigenetic role in the determination of the different phenotypes observed between vineyards and conclude that DNA methylation has an important role in the phenotypic plasticity and that epigenetic modulation is clone-dependent.
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Acknowledgements
We are grateful to Ricardo Masuelli and Rubén Bottini (IBAM, CONICET-UNCuyo) for their valuable contribution in the study design. We thank Andrea Puebla and Pablo Alfredo Vera (IABIMO, INTA-CONICET) for the RRBS library construction and Fernando Buscema and Catena Institute of Wine (Bodegas Catena Zapata) for their contribution with the plant material and for sharing meteorological data.
Funding
AV and VNI are fellows of the Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). This work was supported by Universidad Nacional de Cuyo (SECTyP-A043 and SIIP 06/A706), Agencia Nacional de Promoción Científica y Tecnológica (PICT-201-110 and PICT-2015-1532) and CONICET (PUE-2016 CONICET-IBAM).
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AV: data curation, methodology, formal analysis, writing, review and editing. VNI: data curation, methodology, formal analysis. RA: Sample collection, methodology, climate analysis. DZ: RRBS data curation, methodology, formal analysis. SA: Funding acquisition, RRBS analysis design, result analysis. SGT: RRBS analysis design, virus analysis. CFM: project conception and administration, funding acquisition, methodology, result analysis, supervision and writing. FJB: project conception and administration, funding acquisition, methodology, result analysis, supervision and writing.
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Varela, A., Ibañez, V.N., Alonso, R. et al. Vineyard environments influence Malbec grapevine phenotypic traits and DNA methylation patterns in a clone-dependent way. Plant Cell Rep 40, 111–125 (2021). https://doi.org/10.1007/s00299-020-02617-w
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DOI: https://doi.org/10.1007/s00299-020-02617-w