气候变化领域集成服务门户(CCPortal): Patterns of DNA methylation changes in elite Eucalyptus clones across contrasting environments

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DOI	10.1016/j.foreco.2020.118319
	Patterns of DNA methylation changes in elite Eucalyptus clones across contrasting environments
	Jacinto Pereira W.; de Castro Rodrigues Pappas M.; Camargo Campoe O.; Stape J.L.; Grattapaglia D.; Joannis Pappas Jr G.
发表日期	2020
ISSN	0378-1127
卷号	474
英文摘要	Phenotypic plasticity refers to the ability of a single genotype to express distinct phenotypes in response to the environment, a crucial feature for sessile organisms like forest trees, especially in a scenario of global climate change. Several studies show that epigenetic regulation plays an important role in this plastic adaptation response, driving the search for associations between natural epigenetic variation with environmental cues and phenotypic traits based on patterns of cytosine methylation. Clonally propagated trees across variable sites offer a robust system to control for the confounding effect of the background genetic variation among genotypes, allowing the analysis of epigenetic modifications in response to variable environments. In this study we investigated the overall patterns of epigenetic changes by the analysis of the genome-wide DNA methylation status based on high throughput MS-DArT-seq (Methyl Sensitive DArT-seq sequencing) of reduced genome complexity representations. We compared patterns of DNA methylation of biological replicates of leaf and xylem tissue samples of four commercially planted elite Eucalyptus grandis × Eucalyptus urophylla clones and one Eucalyptus urophylla in two contrasting sites in Brazil, and the association of these methylation patterns with the environments and growth traits. DNA sequence reads were mapped against the Eucalyptus grandis reference genome, counting and annotating differentially methylated sites. A total of 90,378 MS-DArT-seq sites were identified, the majority (~70%) located in genes and 10% in transposable elements. The distribution of methylation sites showed extensive variation between the five genotypes and the environments. Sets of methylation sites exclusive to each location were identified for each clone but no consistently shared epigenetic marks for all five clones were found across environments. Multiple correspondence analysis suggests a significant contribution of the genetic background on the distribution of methylation changes. We used a gene-environment association analysis to search for association of methylation patterns with growth traits. A total of 445 methylation sites across all 11 Eucalyptus chromosomes were found significantly associated with one or more of the three measured traits (total height, estimated volume and breast high diameter). The absence of clustered differentially methylated sites is consistent with the fact that complex growth traits are governed by a large number of loci of small effect across the entire genome suggesting that this same pattern will likely hold for what regards epigenetic marks. © 2020 Elsevier B.V.
英文关键词	Epigenetics; MS-DArT-seq; Phenotypic plasticity; TECHS
语种	英语
scopus关键词	Alkylation; Climate change; Cloning; DNA; Environmental regulations; Forestry; Gene encoding; Association analysis; Epigenetic modification; Epigenetic regulation; Global climate changes; Multiple correspondence analysis; Phenotypic plasticity; Transposable elements; Variable environment; Methylation; adaptation; complexity; correspondence analysis; DNA; environmental response; evergreen tree; genetic variation; genome; global change; methylation; phenotypic plasticity; sampling; xylem; Alkylation; Environmental Regulations; Eucalyptus Grandis; Forestry; Methylation; Nucleic Acids; Patterns; Sites; Brazil; Eucalyptus; Eucalyptus grandis; Eucalyptus urophylla
来源期刊	Forest Ecology and Management
文献类型	期刊论文
条目标识符	http://gcip.llas.ac.cn/handle/2XKMVOVA/155112
作者单位	Department of Cell Biology, University of Brasília, Brasília, DF, Brazil; Embrapa Genetic Resources and Biotechnology, Brasília, DF, Brazil; Department of Forest Sciences, Federal University of Lavras – UFLA, Lavras, MG 37.200-000, Brazil; Department of Forest Science, São Paulo State University – UNESP, Botucatu, SP 18600, Brazil; Department of Forestry and Environmental Resources – Suzano, Itapetininga-SP, Brazil; Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
推荐引用方式 GB/T 7714	Jacinto Pereira W.,de Castro Rodrigues Pappas M.,Camargo Campoe O.,et al. Patterns of DNA methylation changes in elite Eucalyptus clones across contrasting environments[J],2020,474.
APA	Jacinto Pereira W.,de Castro Rodrigues Pappas M.,Camargo Campoe O.,Stape J.L.,Grattapaglia D.,&Joannis Pappas Jr G..(2020).Patterns of DNA methylation changes in elite Eucalyptus clones across contrasting environments.Forest Ecology and Management,474.
MLA	Jacinto Pereira W.,et al."Patterns of DNA methylation changes in elite Eucalyptus clones across contrasting environments".Forest Ecology and Management 474(2020).