The EpiDiverse Plant Epigenome-Wide Association Studies (EWAS) Pipeline

被引：7

作者：

Can, Sultan Nilay ^{[1
]}

Nunn, Adam ^{[2
,3
]}

Galanti, Dario ^{[4
]}

Langenberger, David ^{[2
]}

Becker, Claude ^{[5
,6
]}

Volmer, Katharina ^{[7
]}

Heer, Katrin ^{[8
,9
]}

Opgenoorth, Lars ^{[10
]}

Fernandez-Pozo, Noe ^{[1
]}

Rensing, Stefan A. ^{[1
,10
,11
]}

机构：

[1] Univ Marburg, Dept Biol, Plant Cell Biol, D-35043 Marburg, Germany

[2] ecSeq Bioinformat GmbH, D-04103 Leipzig, Germany

[3] Univ Leipzig, Dept Comp Sci, Bioinformat Grp, D-04107 Leipzig, Germany

[4] Univ Tubingen, Inst Evolut & Ecol, Plant Evolutionary Ecol, Morgenstelle 5, D-72076 Tubingen, Germany

[5] Austrian Acad Sci, Gregor Mendel Inst Mol Plant Biol GMI, Vienna BioCtr VBC, Dr Bohr Gasse 3, A-1030 Vienna, Austria

[6] Ludwig Maximilians Univ Munchen, Fac Biol, Genet, D-82152 Martinsried, Germany

[7] Nordwestdeutsch Forstliche Versuchsanstalt NWF FV, Dept Forest Genet Resources, D-37079 Gottingen, Germany

[8] Univ Marburg, Dept Biol, Conservat Biol, D-35043 Marburg, Germany

[9] Univ Marburg, Dept Biol, Plant Ecol & Geobot, D-35043 Marburg, Germany

[10] Univ Freiburg, Ctr Biol Signaling Studies BIOSS, D-79104 Freiburg, Germany

[11] Univ Marburg, SYNMIKRO Ctr Synthet Microbiol, D-35043 Marburg, Germany

来源：

EPIGENOMES | 2021年 / 5卷 / 02期

基金：

欧盟地平线“2020”;

关键词：

EWAS; GWAS; plant epigenetics; DNA methylation; non-model species; pipeline; DIFFERENTIALLY METHYLATED REGIONS; DNA METHYLATION; NORWAY SPRUCE; EPIGENETIC MUTATION; R PACKAGE; GENOME; STRESS; ARABIDOPSIS; PATTERNS; INHERITANCE;

D O I：

10.3390/epigenomes5020012

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

Bisulfite sequencing is a widely used technique for determining DNA methylation and its relationship with epigenetics, genetics, and environmental parameters. Various techniques were implemented for epigenome-wide association studies (EWAS) to reveal meaningful associations; however, there are only very few plant studies available to date. Here, we developed the EpiDiverse EWAS pipeline and tested it using two plant datasets, from P. abies (Norway spruce) and Q. lobata (valley oak). Hence, we present an EWAS implementation tested for non-model plant species and describe its use.

引用

页数：20

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