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Domestic Animal Genetics, Genomics, and Molecular Breeding
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Domestic Animal Genetics, Genomics, and Molecular Breeding

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (30 March 2026) | Viewed by 1508

Special Issue Editor

Dr. Ke Wang

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Guest Editor
Zhanjiang Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524013, China
Interests: functional genomics; product quality; reproduction; molecular breeding; genomic selection; domestic animals; genetic improvement

Special Issue Information

Dear Colleagues,

Against the backdrop of a rapidly expanding global population and sustained economic growth in developing regions, the demand for animal-derived products continues to intensify. To address this challenge, a sustainable and efficient expansion of livestock production is essential. Advances in genetics, genomics, and molecular breeding are critical to improving key traits such as productivity, disease resistance, environmental adaptability, and animal welfare. At the same time, there is growing consumer emphasis on quality, safety, and ethical husbandry practices, driving the need for innovative breeding strategies that align with these values.

This Special Issue, titled "Domestic Animal Genetics, Genomics, and Molecular Breeding", aims to gather high-quality research and review articles that explore the application of modern genetic and genomic tools in the enhancement of domestic animals. We welcome contributions that focus on genome-wide association studies (GWAS), genomic selection, gene editing, functional genomics, molecular marker, and other molecular approaches aimed at optimizing animal production, health, reproduction, and overall resilience.

We look forward to receiving your valuable research and insights to help advance this important field.

Dr. Ke Wang
Guest Editor

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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • genomic selection
  • molecular breeding
  • domestic animals
  • functional genomics
  • genetic improvement
  • product quality
  • reproduction

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Further information on MDPI's Special Issue policies can be found here.

Published Papers (2 papers)

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Research

21 pages, 10193 KB  
Article
Meat Quality Differences Correlated with Rumen Microbiota and Lipid Metabolism in Beef Cattle vs. Castrated Cattle
by Meng Liu, Nan Su, Zhen Ma, Wenzhong Chen, Yuxia Zhang, Xiangmin Yan and Wujun Liu
Int. J. Mol. Sci. 2026, 27(5), 2296; https://doi.org/10.3390/ijms27052296 - 28 Feb 2026
Viewed by 610
Abstract
Intramuscular fat (IMF) significantly influences meat quality, particularly flavor. The gastrointestinal microbiota can regulate lipid metabolism. The relationship between intramuscular fat metabolism, rumen microbiota, and beef quality remains unclear. This study enrolled 22 30-month-old Xinjiang Brown Beef cattle, which were randomly allocated to [...] Read more.
Intramuscular fat (IMF) significantly influences meat quality, particularly flavor. The gastrointestinal microbiota can regulate lipid metabolism. The relationship between intramuscular fat metabolism, rumen microbiota, and beef quality remains unclear. This study enrolled 22 30-month-old Xinjiang Brown Beef cattle, which were randomly allocated to two groups: an intact bull group (n = 15) and a castrated bull group (n = 7). All experimental animals were housed and maintained under consistent feeding and management conditions throughout the entire experimental period. By combining in vivo ultrasonography, slaughter trials, rumen microbiome diversity analysis, and metabolomics techniques, and after adjusting for covariates including intramuscular fat (IMF) content, body weight, and backfat thickness, the present study demonstrated that castration regulates muscle lipid metabolism by reshaping the composition of the rumen microbial community, thereby exerting a cascading effect on key beef quality traits. (1) Production and meat quality: Live weight, carcass weight, eye muscle area, backfat thickness, and intramuscular fat (IMF) content were significantly higher in the YN group than in the GN group (p < 0.01). Conversely, dressing percentage, shear force value, and muscle protein content were significantly lower in the YN group than in the GN group (p < 0.01 or p < 0.05). (2) Rumen microbiota–metabolite correlation: Significant differences existed in microbial composition and community structure between groups (with significant differences in both α and β diversity). Core microbes regulated by castration exhibited distinct co-variation patterns with metabolites: genera such as Anaeroplasma showed significant positive correlations with hydroxy fatty acids, while Sharpea and others showed significant negative correlations with saturated fatty acids. (3) Microbial–metabolite axis and host phenotype correlation: Axes composed of Eubacterium uniforme and others showed significant positive correlations with IMF, while Docosapentaenoic acid (22n-3) exhibited significant negative correlations with IMF. Anaeroplasma and others showed significant positive correlations with oleic acid and others, as well as BFT, while saturated fatty acids showed significant negative correlations with BFT. (4) Covariate validation: After adjusting for covariates including body weight, backfat thickness, and IMF, castration was confirmed to significantly regulate the abundance/content of core genera such as Anaeroplasma, Eubacterium uniforme, as well as key metabolites such as hydroxy fatty acids and docosapentaenoic acid (22n-3) (p < 0.05 after adjustment), making it a core driver regulating rumen microbial composition and muscle lipid metabolism. After adjustment, the regulatory effects of IMF, body weight, and backfat thickness on the aforementioned microorganisms and metabolites were no longer significant (adjusted p > 0.05). Intramuscular fat (IMF), body weight, and backfat thickness are not independent drivers but rather indirect effects resulting from castration-induced physiological state remodeling. This study did not include feeding rate measurements, which represents a limitation. Future research should incorporate this data to further validate the conclusions. This study elucidates the interactive mechanisms between rumen microbiota and their metabolites, identifies the key pathways governing intramuscular fat (IMF) deposition, pinpoints potential regulatory targets for beef quality optimization, and clarifies the intermediate regulatory mechanisms underlying the modulation of meat quality traits by castration. Full article
(This article belongs to the Special Issue Domestic Animal Genetics, Genomics, and Molecular Breeding)
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15 pages, 3267 KB  
Article
Transcriptome Dynamics and Regulatory Networks of Postnatal Muscle Development in Leizhou Black Goats
by Jiancheng Han, Jing Huang, Mengning Xu, Yuelang Zhang, Ke Wang and Hanlin Zhou
Int. J. Mol. Sci. 2026, 27(1), 88; https://doi.org/10.3390/ijms27010088 - 21 Dec 2025
Viewed by 497
Abstract
Postnatal muscle development involves complex transcriptional regulation that remains poorly characterized in goats. This study employed RNA-Seq to profile the Longissimus dorsitranscriptome of Leizhou Black goats across three developmental stages: birth, six months, and two years. We identified dynamic gene expression patterns, widespread [...] Read more.
Postnatal muscle development involves complex transcriptional regulation that remains poorly characterized in goats. This study employed RNA-Seq to profile the Longissimus dorsitranscriptome of Leizhou Black goats across three developmental stages: birth, six months, and two years. We identified dynamic gene expression patterns, widespread alternative splicing events, and stage-specific co-expression networks that collectively orchestrate muscle maturation. A significant transcriptional shift occurred between six months and two years, marked by the downregulation of proliferation-related genes (e.g., RRM2, TOP2A) and the activation of pathways governing muscle contraction and energy metabolism. Functional enrichment analyses highlighted the importance of PI3K-Akt, PPAR, and calcium signaling pathways throughout development. Additionally, 905 novel transcripts were discovered, many enriched in mitochondrial functions, indicating incompleteness in the current goat genome annotation. Weighted gene co-expression network analysis revealed modules correlated with developmental stages, and protein–protein interaction analysis identified hub genes regulating cell cycle progression and muscle function. Key results were validated via qRT-PCR, confirming the temporal expression patterns of genes such as CYP4B1, HACD1, and ACTC1. These findings provide mechanistic insights into the transcriptional reprogramming driving postnatal muscle development and offer valuable genetic resources for improving meat production in goats through molecular breeding. Full article
(This article belongs to the Special Issue Domestic Animal Genetics, Genomics, and Molecular Breeding)
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