Extending the Genotype in Brachypodium by Including DNA Methylation Reveals a Joint Contribution with Genetics on Adaptive Traits.

G3 : Genes - Genomes - Genetics
Steven R EichtenJustin O Borevitz

Abstract

Epigenomic changes have been considered a potential missing link underlying phenotypic variation in quantitative traits but is potentially confounded with the underlying DNA sequence variation. Although the concept of epigenetic inheritance has been discussed in depth, there have been few studies attempting to directly dissect the amount of epigenomic variation within inbred natural populations while also accounting for genetic diversity. By using known genetic relationships between Brachypodium lines, multiple sets of nearly identical accession families were selected for phenotypic studies and DNA methylome profiling to investigate the dual role of (epi)genetics under simulated natural seasonal climate conditions. Despite reduced genetic diversity, appreciable phenotypic variation was still observable in the measured traits (height, leaf width and length, tiller count, flowering time, ear count) between as well as within the inbred accessions. However, with reduced genetic diversity there was diminished variation in DNA methylation within families. Mixed-effects linear modeling revealed large genetic differences between families and a minor contribution of DNA methylation variation on phenotypic variation in select traits. Tak...Continue Reading

References

Jun 21, 2007·PLoS Biology·Matthew W VaughnRobert A Martienssen
Oct 24, 2008·Journal of Dairy Science·P M VanRaden
Oct 9, 2009·Nature·Teri A ManolioPeter M Visscher
Feb 12, 2010·Nature·UNKNOWN International Brachypodium Initiative
Apr 16, 2011·Bioinformatics·Felix Krueger, Simon R Andrews
Jan 10, 2012·Proceedings of the National Academy of Sciences of the United States of America·Or ZukEric S Lander
Mar 8, 2013·Nature·Robert J SchmitzJoseph R Ecker
Aug 8, 2013·The Plant Cell·Steven R EichtenNathan M Springer
Feb 8, 2014·Science·Sandra CortijoFrank Johannes
Mar 22, 2014·Current Opinion in Plant Biology·Tim B BrownJustin O Borevitz
May 30, 2014·Plant Physiology·Steven R EichtenNathan M Springer
Jul 29, 2015·Human Genomics·Marco TrerotolaSaverio Alberti
Sep 10, 2015·Nature·Meilina Ong-AbdullahRobert A Martienssen
Feb 22, 2017·Nature Methods·Jared T SimpsonWinston Timp
Jun 1, 1992·Evolution; International Journal of Organic Evolution·Mark D Rausher
Jul 4, 2017·Nature Reviews. Genetics·Nathan M Springer, Robert J Schmitz
Nov 15, 2017·Methods in Molecular Biology·Philip KelleherDouwe van Sinderen
Aug 11, 2018·Genome Research·Laura-Jayne GardinerAnthony Hall
Oct 27, 2018·Nature Communications·Marc W SchmidUeli Grossniklaus

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Citations

Oct 15, 2020·International Journal of Molecular Sciences·Vasily V AshapkinBoris F Vanyushin

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Datasets Mentioned

BETA
PRJNA349755

Methods Mentioned

BETA
Assay
Methyl-Seq

Software Mentioned

R package “
Bismark
bowtie1
Trim Galore
SolarCalc
HOME
R ”
Asreml

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