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Article

Genome-Wide Variation in DNA Methylation Predicts Variation in Leaf Traits in an Ecosystem-Foundational Oak Species

1
Department of Ecology and Evolutionary Biology, Charles E. Young Drive, University of California, Los Angeles, CA 90095-1438, USA
2
UCLA La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095-1496, USA
3
USDA-Forest Service Pacific Southwest Research Station, 1731 Research Park Dr., Davis, CA 95618, USA
4
Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095-1496, USA
*
Author to whom correspondence should be addressed.
Academic Editors: Mary Ashley and Janet R. Backs
Forests 2021, 12(5), 569; https://doi.org/10.3390/f12050569
Received: 26 March 2021 / Revised: 28 April 2021 / Accepted: 29 April 2021 / Published: 1 May 2021
(This article belongs to the Special Issue Quercus Genetics: Insights into the Past, Present, and Future of Oaks)
Epigenetic modifications such as DNA methylation are a potential mechanism for trees to respond to changing environments. However, it remains controversial the extent to which DNA methylation impacts ecologically important traits that influence fitness. In this study, we used reduced-representation bisulfite sequencing to associate genomic and epigenomic variation with seven phenotypic traits related to growth, leaf function, and disease susceptibility in 160 valley oak (Quercus lobata) saplings planted across two common gardens in California. We found that DNA methylation was associated with a significant fraction of phenotypic variance in plant height, leaf lobedness, powdery mildew infection, and trichome density. Two of the seven traits were significantly associated with DNA methylation in the CG context, three traits were significantly associated with CHG methylation, and two traits were significantly associated with CHH methylation. Notably, controlling for genomic variation in SNPs generally reduced the amount of trait variation explained by DNA methylation. Our results suggest that DNA methylation may serve as a useful biomarker to predict phenotypic variation in trees, though it remains unclear the degree to which DNA methylation is a causal mechanism driving phenotypic variation in forest tree species. View Full-Text
Keywords: phenotype; DNA methylation; Quercus; single nucleotide polymorphisms; functional traits; leaf traits; bisulfite sequencing phenotype; DNA methylation; Quercus; single nucleotide polymorphisms; functional traits; leaf traits; bisulfite sequencing
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MDPI and ACS Style

Browne, L.; MacDonald, B.; Fitz-Gibbon, S.; Wright, J.W.; Sork, V.L. Genome-Wide Variation in DNA Methylation Predicts Variation in Leaf Traits in an Ecosystem-Foundational Oak Species. Forests 2021, 12, 569. https://doi.org/10.3390/f12050569

AMA Style

Browne L, MacDonald B, Fitz-Gibbon S, Wright JW, Sork VL. Genome-Wide Variation in DNA Methylation Predicts Variation in Leaf Traits in an Ecosystem-Foundational Oak Species. Forests. 2021; 12(5):569. https://doi.org/10.3390/f12050569

Chicago/Turabian Style

Browne, Luke, Brandon MacDonald, Sorel Fitz-Gibbon, Jessica W. Wright, and Victoria L. Sork. 2021. "Genome-Wide Variation in DNA Methylation Predicts Variation in Leaf Traits in an Ecosystem-Foundational Oak Species" Forests 12, no. 5: 569. https://doi.org/10.3390/f12050569

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