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5.2
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Animals
Special Issues
Epigenetic Signatures in Domestic Animals
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Epigenetic Signatures in Domestic Animals

A special issue of Animals (ISSN 2076-2615). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: 31 May 2026 | Viewed by 1728

Special Issue Editors

Dr. Deyin Zhang

E-Mail Website
Guest Editor
College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China
Interests: economic trait; functional genomics; molecular breeding; multi-omics; genomics and epigenomics
Prof. Dr. Weimin Wang

E-Mail Website
Guest Editor
College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China
Interests: microbiome; phenomes; agronomic traits; genome selection
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue focuses on the cutting-edge exploration of epigenetic signatures in domestic animals. Epigenetic marks—such as DNA methylation, histone modifications, and non-coding RNAs—play pivotal roles in regulating phenotypic traits critical to livestock production (e.g., growth, meat quality, and reproductive efficiency) and animal health (e.g., disease resistance and stress adaptation). We welcome original research articles, reviews, and perspectives that feature the latest advancements in epigenetic analysis techniques, novel findings regarding the functional roles of epigenetic signatures, and their implications for domestic animal breeding, health, welfare, and adaptive responses to environmental shifts.

Topics of interest include, but are not limited to, the following:

  • Identification and characterization of epigenetic signatures associated with important traits in domestic animals.
  • Epigenetic regulation of key phenotypic traits and dynamic changes in epigenetic marks across domestic animal life stages.
  • Functional epigenomics approaches to elucidate the molecular mechanisms linking epigenetic signatures to trait variation in domestic animals.
  • Integration of epigenomics with multi-omics data to decode the epigenetic-genetic interplay in shaping complex traits of domestic animals.

We encourage researchers from diverse disciplines—including epigenetics, genomics, animal science, veterinary medicine, agricultural biology, and molecular biology—to contribute their expertise and insights to this Special Issue. By bringing together cutting-edge research on epigenetic signatures in domestic animals, we aim to foster interdisciplinary collaboration, facilitate knowledge exchange, and accelerate the translation of epigenetic findings into innovative strategies for enhancing sustainable domestic animal production and animal welfare globally.

Dr. Deyin Zhang
Prof. Dr. Weimin Wang
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 250 words) can be sent to the Editorial Office for assessment.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Animals is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2400 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • epigenetic signatures
  • domestic animals
  • important traits
  • multi-omics

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Published Papers (3 papers)

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Research

12 pages, 2805 KB  
Article
The Influence of the FGF8 Gene on the Proliferation and Differentiation of Preadipocytes in Sheep
by Wei Han, Huan Zhang, Fengyi Gao, Liming Tian, Zhaohua He, Guan Wang, Shuhong Zhang, Tenggang Di, Menghan Chang, Shaobin Li, Fangfang Zhao and Guangli Yang
Animals 2026, 16(7), 1121; https://doi.org/10.3390/ani16071121 - 7 Apr 2026
Viewed by 318
Abstract
The growth and development of adipose tissue in sheep tails are closely associated with adipocyte proliferation and differentiation. However, the functional role and regulatory mechanisms of the FGF8 gene in sheep preadipocytes remain incompletely understood. In this study, liposome-mediated transfection was employed to [...] Read more.
The growth and development of adipose tissue in sheep tails are closely associated with adipocyte proliferation and differentiation. However, the functional role and regulatory mechanisms of the FGF8 gene in sheep preadipocytes remain incompletely understood. In this study, liposome-mediated transfection was employed to overexpress the FGF8 gene and assess its effects on the proliferation and differentiation of sheep preadipocytes. The results of the Cell Counting Kit-8 (CCK-8) assay indicated that the overexpression of FGF8 promoted preadipocyte viability of preadipocytes. Subsequently, this was verified by RT-qPCR analysis, which showed significant upregulation of proliferation marker genes, including CyclinB (p < 0.001) and Proliferating Cell Nuclear Antigen (PCNA) (p < 0.01), while CyclinD mRNA expression increased compared with the control group, though the increase was not statistically significant. During adipogenic induction, the mRNA expression levels of differentiation markers, such as Peroxisome Proliferator-Activated Receptor Gamma (PPARγ), CCAAT/Enhancer Binding Protein Alpha (C/EBPα), Adipocyte type Fatty Acid Binding Protein 4 (FABP4), and Adiponectin, initially increased and then decreased. The expression of all four markers peaked on day 10 of induction, exceeding levels observed in the control group. In vitro experiments showed that FGF8 affected the proliferation and differentiation of sheep preadipocytes and may be involved in the regulation of tail fat deposition. Full article
(This article belongs to the Special Issue Epigenetic Signatures in Domestic Animals)
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18 pages, 3091 KB  
Article
Multi-Omics Epigenetic Landscape Unveils Regulatory Mechanisms Underlying Heterosis in Sheep Muscle Development
by Jiangbo Cheng, Dan Xu, Huibin Tian, Xiaoxue Zhang, Liming Zhao, Runan Zhang, Jianlin Wang, Jinyu Xiao, Fadi Li, Weimin Wang and Deyin Zhang
Animals 2026, 16(7), 1112; https://doi.org/10.3390/ani16071112 - 4 Apr 2026
Viewed by 347
Abstract
Hybridization effectively enhances breeding efficiency and significantly boosts sheep productivity. However, the epigenetic mechanisms underlying the superior production performance of crossbreds remain largely elusive. In this study, Hu sheep were crossbred with Suffolk rams used as the paternal line. We integrated RNA-seq, ATAC-seq, [...] Read more.
Hybridization effectively enhances breeding efficiency and significantly boosts sheep productivity. However, the epigenetic mechanisms underlying the superior production performance of crossbreds remain largely elusive. In this study, Hu sheep were crossbred with Suffolk rams used as the paternal line. We integrated RNA-seq, ATAC-seq, and CUT&Tag (H3K4me3, H3K4me1, H3K27ac, and H3K27me3) techniques to characterize epigenetic regulatory differences in the longissimus dorsi muscle between Hu sheep (HU) and crossbred progeny (SH). Phenotypic and transcriptomic analyses revealed that SH crossbred sheep exhibited superior growth performance (p < 0.05), and the upregulated genes in the Apelin signaling pathway were significantly correlated with eye muscle area (p < 0.05). Utilizing a Hidden Markov Model, we annotated 15 distinct chromatin states in both HU and SH sheep, systematically characterizing the dynamic epigenomic landscapes across the two breeds. In contrast to SH sheep, the genome of HU sheep exhibited enrichment of repressive chromatin modifications typified by H3K27me3. Strong active enhancers (EnhA) were significantly enriched within upregulated genes in SH. A total of 1862 SH-specific and 691 HU-specific EnhA elements were characterized in this study. Motif analysis revealed that SH-specific EnhA were enriched for myogenic MEF2 family motifs (p < 0.05), which promote muscle and vascular development. By integrating multi-omics data, we constructed a putative regulatory network potentially modulated by SH-specific enhancers, identifying CMKLR1, PPARGC1A, and TLE3 as the core hub genes. Collectively, this study provides a robust data resource, identifying candidate genes and regulatory elements associated with crossbreeding-related muscle phenotypes. Full article
(This article belongs to the Special Issue Epigenetic Signatures in Domestic Animals)
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19 pages, 3704 KB  
Article
Transcriptome-Wide Analysis of N6-Methyladenosine Modification in the Liver of Geese at Different Growth Stages
by Chuan Li, Jintao Wu, Shuibing Liu, Wentao Zhang, Jing Liu, Sanfeng Liu and Biao Chen
Animals 2026, 16(6), 981; https://doi.org/10.3390/ani16060981 - 20 Mar 2026
Viewed by 333
Abstract
N6-methyladenosine (m6A) is a reversible RNA modification that dynamically regulates gene expression by modulating RNA stability, splicing, nuclear export, translation, and maturation—thereby orchestrating organismal development. In birds, including geese, the liver is a multi-functional organ central to metabolic regulation. Studies on [...] Read more.
N6-methyladenosine (m6A) is a reversible RNA modification that dynamically regulates gene expression by modulating RNA stability, splicing, nuclear export, translation, and maturation—thereby orchestrating organismal development. In birds, including geese, the liver is a multi-functional organ central to metabolic regulation. Studies on the dynamic patterns of RNA m6A modifications during healthy liver growth and development remain limited. Here, we performed integrative methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA sequencing (RNA-seq) on liver tissues from geese at three biologically defined stages: post-hatch day 0 (0 week, P), fast growth (10 weeks, F), and sexual maturation (30 weeks, S). The level of m6A modification in total RNA extracted from liver tissues was higher in P than in F samples. Compared with other groups, the S group recorded the lowest m6A modification. In addition, 1641, 668, and 558 m6A peaks were differentially modified in the P, F, and S groups, respectively. The m6A peaks in the liver of the three groups were mainly enriched in the coding sequence and 3′ untranslated region. Moreover, integrated multi-omics analysis (MeRIP-seq and RNA-seq), combined with protein–protein interaction networks analysis, identified CDK1 as a core cell cycle regulator and IGF2BP3—a well-established m6A reader—as a consistently differentially expressed gene across all developmental stages. The m6A-regulated cell cycle, p53 signaling pathway, and pyrimidine metabolism pathway were identified in liver tissue as novel potential targets for controlling geese growth and metabolism. Together, these findings shed light on the dynamic regulation of RNA methylation during distinct growth phases in geese and advance our understanding of epigenetic mechanisms underlying poultry liver development. Full article
(This article belongs to the Special Issue Epigenetic Signatures in Domestic Animals)
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