Epigenetics

Epigenetic landscape differences in Aseel and Layer chicken breeds

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Abstract

While genomic variation is commonly regarded as the primary driver of phenotypic variation, transcriptional changes influenced by epigenetic modifications also significantly impact phenotypic expression. Epigenetic marks, specifically 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC), are key regulators of gene expression, with 5mC typically linked to gene silencing and 5hmC associated with gene activation and DNA demethylation processes. This study explores the epigenetic landscapes of Aseel and Layer parent cocks to identify breed-specific differential methylation regions (DMRs) that may inform genomic selection and adaptation strategies. Blood samples were pooled from 10 individuals per breed and sequenced using the Promethion flow cell from Oxford Nanopore Technologies (ONT). This technique directly identified single-base methylation status, and quality control and mapping statistics were calculated for the chicken genome. Global methylation statistics were derived using MethylArtist v1.3.1. To ascertain methylation status across the genome, gene features (exons, introns, promoters [2 kb downstream of the transcription termination site], and 3′ and 5′ UTRs) were extracted from the GCA_000002315.5 GTF file. The Modkit 'DMR pair' tool was used to identify significant DMRs for 5mC and 5hmC, which were then mapped to genomic features using ChIPseeker. Significant DMRs were defined by a corrected p-value < 0.05, a DMR score > 20, and a fold-change > 2. DMR scores were computed using a hidden Markov model and Bayesian framework. Interestingly, DNA modification was highly noticed in intronic region and 3'UTR, compared to other genomic features. Similarly, differentially methylated region was also noticed in introns of various gene. The PAX7 and NRTN genes were hypomethylated and KIAA1671, HDAC4, MIR6557, NCAM1, and CPSF6 are hypermethylated in both forms were as NFIA, EPB41, PTK7 were hypermethylated 5mC and hypomethylated 5hmC.Overall, 5mC and 5hmC levels were 54.44% and 4.07% in Aseel, and 53.70% and 4.17% in Layer chickens, respectively. DNA modification was notably more abundant in intronic regions and 3′ UTRs compared to other genomic features

Keywords: 2026

How to Cite:

Peters, S., Muthusamy, M., Akinsola, O., Thiruvenkadan, A., Rekaya, R. & Aggrey, S., (2026) “Epigenetic landscape differences in Aseel and Layer chicken breeds”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2287281. doi: https://doi.org/10.31274/wcgalp.24255

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