Methylation in the CHH context allows to predict recombination in rice

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dc.creatorPeñuela, Mauricio
dc.creatorGallo-Franco, Jenny Johana
dc.creatorFinke, Jorge
dc.creatorRocha, Camilo
dc.creatorGkanogiannis, Anestis
dc.creatorGhneim-Herrera, Thaura
dc.creatorLorieux, Mathias
dc.date2022-10-19
dc.date2023-02-16T11:18:12Z
dc.date2023-02-16T11:18:12Z
dc.date.accessioned2026-06-27T13:33:14Z
dc.descriptionDNA methylation is the most studied epigenetic trait. It is considered a key factor in regulating plant development and physiology, and has been associated with the regulation of several genomic features, including transposon silencing, regulation of gene expression, and recombination rates. Nonetheless, understanding the relation between DNA methylation and recombination rates remains a challenge. This work explores the association between recombination rates and DNA methylation for two commercial rice varieties. The results show negative correlations between recombination rates and methylated cytosine counts for all contexts tested at the same time, and for CG and CHG contexts independently. In contrast, a positive correlation between recombination rates and methylated cytosine count is reported in CHH contexts. Similar behavior is observed when considering only methylated cytosines within genes, transposons, and retrotransposons. Moreover, it is shown that the centromere region strongly affects the relationship between recombination rates and methylation. Finally, machine learning regression models are applied to predict recombination using the count of methylated cytosines in the CHH context as the entrance feature. These findings shed light on the understanding of the recombination landscape of rice and represent a reference framework for future studies in rice breeding, genetics, and epigenetics.
dc.formatapplication/pdf
dc.identifierhttps://hdl.handle.net/10568/128722
dc.identifier.urihttp://hdl.handle.net/123456789/63019
dc.languageen
dc.publisherMDPI
dc.rightsOpen Access
dc.sourcePeñuela, M.; Gallo-Franco, J.J.; Finke, J.; Rocha, C.; Gkanogiannis, A.; Ghneim-Herrera, T.; Lorieux, M. (2022) Methylation in the CHH context allows to predict recombination in rice. International Journal of Molecular Sciences 23(20):12505 14 p. ISSN: 1661-6596
dc.subjectmethylation
dc.subjectepigenetics
dc.subjectmachine learning
dc.subjectmodelling
dc.subjectmetilación
dc.subjectepigenético
dc.subjectaprendizaje automático
dc.titleMethylation in the CHH context allows to predict recombination in rice
dc.typeJournal Article

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