title: Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population.
abstract: Cytosine DNA methylation is one avenue for passing information through cell divisions. Here, we present epigenomic analyses of soybean recombinant inbred lines (RILs) and their parents. Identification of differentially methylated regions (DMRs) revealed that DMRs mostly cosegregated with the genotype from which they were derived, but examples of the uncoupling of genotype and epigenotype were identified. Linkage mapping of methylation states assessed from whole-genome bisulfite sequencing of 83 RILs uncovered widespread evidence for local methylQTL. This epigenomics approach provides a comprehensive study of the patterns and heritability of methylation variants in a complex genetic population over multiple generations, paving the way for understanding how methylation variants contribute to phenotypic variation.
authors.affiliation: Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA;
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Schmitz
authors.forename: Yupeng
authors.initials: Y
authors.lastname: He
authors.forename: Oswaldo
authors.initials: O
authors.lastname: Valdés-López
authors.forename: Saad M
authors.initials: SM
authors.lastname: Khan
authors.forename: Trupti
authors.initials: T
authors.lastname: Joshi
authors.forename: Mark A
authors.initials: MA
authors.lastname: Urich
authors.forename: Joseph R
authors.initials: JR
authors.lastname: Nery
authors.forename: Brian
authors.initials: B
authors.lastname: Diers
authors.forename: Dong
authors.initials: D
authors.lastname: Xu
authors.forename: Gary
authors.initials: G
authors.lastname: Stacey
authors.forename: Joseph R
authors.initials: JR
authors.lastname: Ecker
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism; D002455:Cell Division; D002874:Chromosome Mapping; D003596:Cytosine / Q000378:metabolism*; D019175:DNA Methylation; D004251:DNA Transposable Elements; D018744:DNA, Plant / Q000235:genetics / Q000378:metabolism*; D004274:DNA, Recombinant; D044127:Epigenesis, Genetic; D057890:Epigenomics; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D014644:Genetic Variation; D018745:Genome, Plant; D005838:Genotype; D007178:Inbreeding; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D017421:Sequence Analysis; D013025:Glycine max / Q000235:genetics* / Q000378:metabolism
chemical_list: D004251:DNA Transposable Elements; D018744:DNA, Plant; D004274:DNA, Recombinant; D003596:Cytosine