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Animals
Special Issues
Livestock Omics
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Livestock Omics

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

Deadline for manuscript submissions: 31 October 2025 | Viewed by 1293

Special Issue Editors

Dr. Lucas Lima Verardo

E-Mail Website
Guest Editor
Department of Animal Science, Universidade Federal dos Vales do Jequitinhonha e Mucuri (UFVJM), Diamantina, MG, Brazil
Interests: animal breeding; omics; gene networks
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Ana Magalhães

E-Mail Website
Guest Editor
Department of Animal Science, Universidade Federal dos Vales do Jequitinhonha e Mucuri (UFVJM), Diamantina, MG, Brazil
Interests: animal breeding; genomics; poultry genetics
Prof. Dr. Nuno Carolino

E-Mail Website
Guest Editor
1. National Institute of Agricultural and Veterinary Research, Vale de Santarém, Portugal
2. Vasco da Gama University School, Coimbra, Portugal
Interests: animal breeding and conservation
Dr. Gabriel Machado Dallago

E-Mail Website
Guest Editor
Department of Animal Science, Faculty of Agricultural and Food Sciences, University of Manitoba, Winnipeg, MB, Canada
Interests: precision livestock farming; machine learning; automated phenotyping

Special Issue Information

Dear Colleagues,

A large volume of data has been produced from livestock “omics” studies aiming to implement and improve animal production. Additionally, the “omics” approach can be holistically applied to enhance animal breeding methods and provide a better understanding of the genetic architecture of different species. We are pleased to invite you to share your latest findings on livestock genetics based on omics approaches.

This Special Issue aims to publish studies focused on all production animals involving omics. Original research articles and reviews are welcome. Research areas may include, but are not limited to, the following: genomics, transcriptomics, proteomics, nutrigenomics, epigenetics, metagenomics, metabolomics, and phenomics (including the development of automated systems for phenotyping).

We look forward to receiving your contributions.

Dr. Lucas Lima Verardo
Prof. Dr. Ana Magalhães
Prof. Dr. Nuno Carolino
Dr. Gabriel Machado Dallago
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 100 words) can be sent to the Editorial Office for announcement on this website.

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

  • animal production
  • sustainability
  • animal welfare
  • animal breeding
  • animal genetics
  • precision livestock farming

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  • External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
  • e-Book format: Special Issues with more than 10 articles can be published as dedicated e-books, ensuring wide and rapid dissemination.

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

Published Papers (3 papers)

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Research

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21 pages, 4618 KiB  
Article
Heat Stress Influences Immunity Through DUSP1 and HSPA5 Mediated Antigen Presentation in Chickens
by Xiaomeng Wang, Xiaohuan Chao, Wenwu Zhang, Xiquan Zhang, Jiongwen Wu, Chutian Ye, Xuerong Ma, Zhexia Fan, Manqing Liu, Cheng Fang and Qingbin Luo
Animals 2025, 15(8), 1141; https://doi.org/10.3390/ani15081141 - 16 Apr 2025
Viewed by 249
Abstract
The objective of this study was to elucidate the immune system response to heat stress in chickens. In this study, mRNA-seq was conducted on the spleen and bursa of experimental chickens, six differentially expressed genes associated with immunity were present in the spleen [...] Read more.
The objective of this study was to elucidate the immune system response to heat stress in chickens. In this study, mRNA-seq was conducted on the spleen and bursa of experimental chickens, six differentially expressed genes associated with immunity were present in the spleen following immunization. Following exposure to heat stress, 15 differentially expressed genes related to immune and heat shock proteins were identified. Furthermore, the expression levels of DUSP1 and HSPA5 were significantly lower in the non-stressed group. With regard to the mechanism, overexpression of DUSP1 or HSPA5 resulted in no significant difference in MHC-I, MHC-II, and CD80 mRNA expression. However, following stimulation with LPS, mRNA expression of MHC-II, CD80, CD86, CD1C, IL1B, and TLR4 was significantly increased. Furthermore, the enhancement was observed to occur at an earlier stage than when LPS was stimulated alone, thereby facilitating the recognition of LPS by HD11. Following the inhibition of DUSP1 or HSPA5 and the stimulation of LPS, no significant alterations were detected. However, CD1C expression was notably diminished. In conclusion, DUSP1 and HSPA5 have been demonstrated to play important roles in immunity to heat stress by affecting antigen presentation. The present study provides a theoretical basis for the regulation mechanism of disease resistance in poultry. Full article
(This article belongs to the Special Issue Livestock Omics)
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18 pages, 3231 KiB  
Article
Transcriptomics Reveals the Differences in mRNA Expression Patterns in Yak Uterus of Follicular, Luteal, and Pregnant Phases
by Shaohui Beng, Daoliang Lan, Yueyue Li, Deping Li, Yuehuan Zhang, Zelang Ma, Jianbo Zhu, Shunyang Liu, Kechao Chen, Jian Li, Peng Wang and Wei Fu
Animals 2025, 15(6), 837; https://doi.org/10.3390/ani15060837 - 14 Mar 2025
Viewed by 439
Abstract
The yak, an important livestock mostly living in the Qinghai–Tibet Plateau region, has attracted massive attention due to its reproductive specificity. However, the molecular mechanism regulating yak uterine functions remains to be explored. This study utilized transcriptomics to identify differentially expressed genes (DEGs) [...] Read more.
The yak, an important livestock mostly living in the Qinghai–Tibet Plateau region, has attracted massive attention due to its reproductive specificity. However, the molecular mechanism regulating yak uterine functions remains to be explored. This study utilized transcriptomics to identify differentially expressed genes (DEGs) in yaks across uteruses undergoing the follicular phase (UFP) (n = 3/group), luteal phase (ULP) (n = 3/group), and pregnant phase (UPP) (n = 3/group), aiming to depict and compare their transcriptomic characteristics. For the UFP and ULP groups, 495 DEGs were identified, including 329 upregulated and 166 downregulated DEGs in group ULP compared to UFP. Advanced analysis indicated that these DEGs between UFP and ULP were primary participants in GO items, such as adhesion, cell differentiation, and development, and were significantly enriched in KEGG signaling pathways like arachidonic acid metabolism, retinol metabolism, and cAMP signaling pathways. For the UFP and UPP groups, 353 DEGs were obtained, comprising 198 upregulated and 155 downregulated DEGs in group UPP compared to UFP. Advanced analysis showed that these DEGs between UFP and UPP were mainly related to GO items such as adhesion, binding, and the extracellular region, and were prominently enriched in KEGG signaling pathways like ECM-receptor interaction, the relaxing signaling pathway, and focal adhesion. For the groups ULP and UPP, 1303 DEGs were identified, encompassing 709 upregulated and 594 downregulated DEGs in group UPP compared to ULP. Advanced analysis indicated that these DEGs between ULP and UPP were associated with GO items such as multicellular organismal processes, cell differentiation, and the extracellular region, and mainly gathered in KEGG signaling pathways like signal transduction, cell differentiation, metabolism, and autophagy. These results provide valuable insights into the key biomarkers observable via dynamic changes in the yak uterus and offer a theoretical basis for further studies on yak reproductive mechanisms and improving production performance. Full article
(This article belongs to the Special Issue Livestock Omics)
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Review

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21 pages, 591 KiB  
Review
Application of Omics in Donkey Meat Research: A Review
by Qifei Zhu, Yongdong Peng, Xiaotong Liu, Wenting Chen, Mingyang Geng, Jincheng Na, Muhammad Zahoor Khan and Changfa Wang
Animals 2025, 15(7), 991; https://doi.org/10.3390/ani15070991 - 29 Mar 2025
Viewed by 277
Abstract
This review comprehensively examines the molecular basis of donkey meat characteristics and growth-associated genes, integrating findings from multiple omics approaches. This study examines the nutritional profile of donkey meat, which is rich in protein, essential amino acids, and unsaturated fatty acids. Through a [...] Read more.
This review comprehensively examines the molecular basis of donkey meat characteristics and growth-associated genes, integrating findings from multiple omics approaches. This study examines the nutritional profile of donkey meat, which is rich in protein, essential amino acids, and unsaturated fatty acids. Through a systematic literature search across Web of Science, Google Scholar, PubMed, and Scopus databases (2000–2024), we collected and analyzed data from 400 research articles using predefined inclusion criteria focused on nutritional composition, omics approaches, and meat quality parameters in donkey populations. The study also evaluates various factors affecting meat quality, including breed differences, age, feeding management, and storage conditions. Advanced genomic and transcriptomic analyses have revealed numerous candidate genes, such as ACTN3, BMP7, NR6A1, Wnt7a, HOXC8, LCORL, TPM2, and TPM3, associated with growth traits and meat quality characteristics, providing valuable insights for genetic improvement programs. Furthermore, the review discusses various authentication methods for ensuring donkey meat quality and preventing adulteration, highlighting the integration of traditional and modern analytical approaches. Full article
(This article belongs to the Special Issue Livestock Omics)
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