Journal of Animal Breeding and Genomics (J Anim Breed Genom)
Indexed in KCI
OPEN ACCESS, PEER REVIEWED
pISSN 1226-5543
eISSN 2586-4297
Technical Protocol

DNA methylation profiling using whole-genome bisulfite sequencing data

Dayeon Kang1,2,†, Seongmin Kim1,2,†, Sung-Lim Lee3, Jaemin Kim1,2,*

1Division of Applied Life Science (BK21), Gyeongsang National University, Jinju 52828, Republic of Korea
2Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea
3College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea

†These authors contributed equally to this work.

Correspondence to Jaemin Kim, E-mail: jmkim85@gnu.ac.kr

Volume 10, Number 2, Pages 33–42, June 2026.
Journal of Animal Breeding and Genomics 2026, 10(2), 33–42. https://doi.org/10.12972/jabng.2026.10.2.1
Received on June 02, 2026, Revised on June 16, 2026, Accepted on June 19, 2026, Published on June 30, 2026.
Copyright © 2026 Korean Society of Animal Breeding and Genetics.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0).

ABSTRACT

Whole-genome bisulfite sequencing (WGBS) enables DNA methylation profiling across the genome at single base resolution, but bisulfite-converted reads require specialized processing to generate reliable methylation information. This technical protocol integrates established bioinformatic tools into a reproducible workflow for converting raw WGBS data into CpG-level methylation profiles and differentially methylated region (DMR) calls. The workflow operates on CpG methylation values ordered by genomic coordinates to generate de novo DMRs. We illustrate the workflow using whole blood-derived WGBS data from Beagle dogs, showing how candidate DMRs are filtered, summarized by direction, and consolidated into a final DMR set. By linking raw data processing to regional methylation interpretation, the protocol offers a reproducible framework for downstream genomic annotation and functional analysis.
KEYWORDS

Whole-genome bisulfite sequencing (WGBS), DNA methylation, Differentially methylated region (DMR)

INTRODUCTION

under publication

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