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

Schmitz, Robert J.; He, Yupeng; Valdes-Lopez, Oswaldo; Khan, Saad M.; Joshi, Trupti; Urich, Mark A.; Nery, Joseph R.; Diers, Brian; Xu, Dong; Stacey, Gary; Ecker, Joseph R.

doi:10.1101/gr.152538.112

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

Journal Article · Wed Jun 05 00:00:00 EDT 2013 · Genome Research

DOI:https://doi.org/10.1101/gr.152538.112· OSTI ID:1625624

Schmitz, Robert J. ^[1]; He, Yupeng ^[2]; Valdes-Lopez, Oswaldo ^[3]; Khan, Saad M. ^[4]; Joshi, Trupti ^[5]; Urich, Mark A. ^[6]; Nery, Joseph R. ^[6]; Diers, Brian ^[7]; Xu, Dong ^[5]; Stacey, Gary ^[8]; Ecker, Joseph R. ^[9]

Salk Institute for Biological Studies, La Jolla, CA (United States). Plant Biology Lab.; Salk Institute for Biological Studies, La Jolla, CA (United States). Genomic Analysis Lab.
Salk Institute for Biological Studies, La Jolla, CA (United States). Genomic Analysis Lab.; Univ. of California, San Diego, CA (United States). Bioinformatics Program
Univ. of Missouri, Columbia, MO (United States). Christopher S. Bond Life Sciences Center
Univ. of Missouri, Columbia, MO (United States). Christopher S. Bond Life Sciences Center; Univ. of Missouri, Columbia, MO (United States). Informatics Inst.
Univ. of Missouri, Columbia, MO (United States). Christopher S. Bond Life Sciences Center; Univ. of Missouri, Columbia, MO (United States). Informatics Inst.; Univ. of Missouri, Columbia, MO (United States). Dept. of Computer Science ; Univ. of Missouri, Columbia, MO (United States). National Center for Soybean Biotechnology
Salk Institute for Biological Studies, La Jolla, CA (United States). Genomic Analysis Lab.
Univ. of Illinois at Urbana-Champaign, IL (United States). Dept. of Crop Sciences
Univ. of Missouri, Columbia, MO (United States). Christopher S. Bond Life Sciences Center; Univ. of Missouri, Columbia, MO (United States). National Center for Soybean Biotechnology; Univ. of Missouri, Columbia, MO (United States). Divisions of Plant Science and Biochemistry
Salk Institute for Biological Studies, La Jolla, CA (United States). Plant Biology Lab.; Salk Institute for Biological Studies, La Jolla, CA (United States). Genomic Analysis Lab.; Salk Institute for Biological Studies, La Jolla, CA (United States). Howard Hughes Medical Inst.

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.

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Research Organization:: Univ. of Missouri, Columbia, MO (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: FG02-02ER15309

OSTI ID:: 1625624

Journal Information:: Genome Research, Vol. 23, Issue 10; ISSN 1088-9051

Publisher:: Cold Spring Harbor Laboratory PressCopyright Statement

Country of Publication:: United States

Language:: English

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