Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population

• Published in: Genome research Vol. 23; no. 10; pp. 1663 - 1674
• Main Authors: Schmitz, Robert J, He, Yupeng, Valdés-López, Oswaldo, Khan, Saad M, Joshi, Trupti, Urich, Mark A, Nery, Joseph R, Diers, Brian, Xu, Dong, Stacey, Gary, Ecker, Joseph R
• Format: Journal Article
• Language: English
• Published: United States Cold Spring Harbor Laboratory Press 01-10-2013
• Subjects: Arabidopsis - genetics; Arabidopsis - metabolism; BASIC BIOLOGICAL SCIENCES; Biochemistry & Molecular Biology; Biotechnology & Applied Microbiology; Bisulfite; Cell Division; Chromosome Mapping; Cytosine - metabolism; DNA Methylation; DNA Transposable Elements; DNA, Plant - genetics; DNA, Plant - metabolism; DNA, Recombinant; Epigenesis, Genetic; Epigenomics; Gene Expression Regulation, Plant; Genes, Plant; Genetic Variation; Genetics & Heredity; Genome, Plant; Genotype; Glycine max - genetics; Glycine max - metabolism; Inbreeding; Polymorphism, Single Nucleotide; Quantitative Trait Loci; Sequence Analysis
• ISSN: 1088-9051; 1549-5469
• DOI: 10.1101/gr.152538.112

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.