Epigenetics

Methylome sequencing reveals potential epigenetic effects in the development of White Striping in broiler chickens

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Abstract

White Striping (WS), a high frequency breast myopathy (12%), characterized by white striations parallel to broiler muscle fibers, negatively affects meat quality and consumer acceptance, leading to great economic losses. Genome-wide association and transcriptomic studies have identified candidate genes associated with WS. However, the epigenetic mechanisms underlying WS development remain unexplored. Therefore, this study aimed to identify differentially methylated regions (DMRs) between normal and WS-affected chickens. For this, 8 well characterized samples from the Pectoralis major muscle of 35-day-old broilers from a Brazilian paternal line developed by Embrapa Swine and Poultry National Research Center were used: four mild WS-affected (muscle fibers of variable size and rounded with hyaline degeneration and lipidosis) and four normal samples (with no evidence of WS or other myopathy). DNA was extracted with the DNeasy Blood and Tissue Kit (Qiagen) and libraries to perform whole-genome bisulfite sequencing (WGBS) were prepared with the EZ DNA Methylation-Lightning (Zymo Research) and Nextera (Illumina) kits, which were sequenced on an Illumina NovaSeq X (paired-end, 150 bp). Sequences underwent quality control with TrimGalore and mapping with Bismark using chicken reference genome (GRCg7b, Ensembl 112). CpG sites were identified using MethylDackel and grouped in regions of 1,000 bp, and the DMRs were identified with methylKit package in R (meth diff ≥ 15% and q-value <0.01). DMRs were annotated to genomic features using Genomation package in R, and differentially methylated genes (DMGs) were retrieved using biomaRt. Gene ontology and enriched pathways were identified with clusterProfiler package in R, using the MSigDB and the KEGG databases. The methylome profile of 20.6 million CpG sites was accessed and further grouped into 495,826 regions across the chicken genome. Out of these regions, 1,049 were identified as DMRs between normal and WS-affected chickens, with 648 hyper and 401 hypomethylated in the WS-affected broilers. Most DMRs were located in genic regions, mainly in introns (known to encompass regulatory elements), suggesting that DNA methylation may influence gene expression in cis, contributing to the development of WS. The DMRs were annotated to genes, resulting in the identification of 452 DMGs between normal and WS-affected chickens. Despite the sample size used, gene ontology analysis and pathways enrichment revealed that these DMGs were enriched in 153 biological processes and 8 pathways (p < 0.05) involved with calcium and muscle contraction, which are processes already related to the manifestation of myopathies in chickens. Therefore, DMGs participating in these processes or pathways could have modified their expression and, consequently, altered the functioning of calcium pathways and regulation of muscle contraction, favoring the appearance of WS. Overall, these results highlight the complexity of WS and suggest that DNA methylation plays a regulatory role in its pathogenesis.

Keywords: 2026

How to Cite:

Padilha, S., Martins, R., Ibelli, A., Cantão, M., Peixoto, J., Pértille, F., Moreira, G., Coutinho, L., Dias, L. & Ledur, M., (2026) “Methylome sequencing reveals potential epigenetic effects in the development of White Striping in broiler chickens”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2283940. doi: https://doi.org/10.31274/wcgalp.23540

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