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 4751

Special Issue Editors


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Guest Editor
Department of Animal Science, Universidade Federal dos Vales do Jequitinhonha e Mucuri (UFVJM), Diamantina, MG, Brazil
Interests: animal breeding; omics; gene networks
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Guest Editor
Department of Animal Science, Universidade Federal dos Vales do Jequitinhonha e Mucuri (UFVJM), Diamantina, MG, Brazil
Interests: animal breeding; genomics; poultry genetics

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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

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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

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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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Published Papers (6 papers)

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Research

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18 pages, 3197 KB  
Article
Weight Gain and Tenderness in Nelore Cattle: Genetic Association and a Potential Pleiotropic Role of Transcription Factors and Genes
by Elora R. P. de S. Borges, Lucio F. M. Mota, Lucas L. Verardo, Lucia G. de Albuquerque, Marcela R. Duarte, Geovana C. Santos, Alice S. Pereira, Lorena M. P. de Carvalho, Lilia S. Carvalho, Emily A. R. Almeida and Ana F. B. Magalhães
Animals 2025, 15(19), 2874; https://doi.org/10.3390/ani15192874 - 30 Sep 2025
Abstract
The inclusion of meat quality traits in breeding programs is a promising strategy to improve beef by selecting animals based on both growth and meat quality. This study aimed to estimate genetic parameters for average daily gain (ADG) and Warner–Bratzler shear force (WBSF), [...] Read more.
The inclusion of meat quality traits in breeding programs is a promising strategy to improve beef by selecting animals based on both growth and meat quality. This study aimed to estimate genetic parameters for average daily gain (ADG) and Warner–Bratzler shear force (WBSF), as well as to perform genome-wide association studies (GWAS) to identify genomic regions and transcription factor (TF) binding sites associated with both traits in Nelore cattle. Genetic parameters were estimated using a bi-trait Bayesian model, and GWAS identified key SNPs explaining over 1% of variance in genomic estimated breeding values. Candidate genes near these SNPs were annotated, TF binding sites predicted, and gene–TF networks constructed. Genetic estimates indicated moderate heritability for ADG, low heritability for WBSF, and a small negative genetic correlation between traits. Genomic regions contained 116 and 151 candidate genes for ADG and WBSF, respectively, with 35 shared between traits. Functional analyses highlighted MYBPC1 and PENK for WBSF, and GHRS and NPY for ADG. TF analysis identified 25 TFs, with 3 key ones highlighted. Gene–TF networks revealed candidates including CAPN1 and LTBP3 for WBSF, and CARM1 and GH1 for ADG. Shared candidate genes identified in the combined network provide valuable insights into the genetic architecture of growth and tenderness in Nelore cattle. Full article
(This article belongs to the Special Issue Livestock Omics)
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14 pages, 1306 KB  
Article
Comparative Analyses of Gene and Protein Expressions and the Lipid Contents in Intramuscular and Subcutaneous Fat Tissues in Fattening Steers
by Kaixi Ji, Ming Yang, Ziying Tan, Hongbo Zhao and Xianglun Zhang
Animals 2025, 15(18), 2733; https://doi.org/10.3390/ani15182733 - 19 Sep 2025
Viewed by 179
Abstract
In this study, we aimed to characterize intramuscular fat (IMF) tissue in fattening steers through a comparison with subcutaneous fat (SCF) tissue. The IMF of the longissimus thoracis et lumborum and the SCF of the back fat from three fattening steers (mean body [...] Read more.
In this study, we aimed to characterize intramuscular fat (IMF) tissue in fattening steers through a comparison with subcutaneous fat (SCF) tissue. The IMF of the longissimus thoracis et lumborum and the SCF of the back fat from three fattening steers (mean body weight of 703.50 ± 11.45 kg) were collected, and the muscle tissue, connective tissue, and fascia were carefully removed. Gene and protein expressions and the lipid contents were assessed via transcriptomic, proteomic, and lipidomic analyses, respectively. Subsequently, tissue-specific factors were identified using integrated analysis. The results revealed that the expressions of sarcoplasmic/endoplasmic reticulum Ca2+ transporting 2 (ATP2A2), enolase 3 (ENO3), fructose-bisphosphatase 2 (FBP2), myosin heavy chain 7 (MYH7), myosin light chain 3 (MYL3), myosin light chain kinase (MYLK), glycogen phosphorylase (PYGM), troponin C1 (TNNC1), and tropomyosin 2 (TPM2) significantly increased in IMF at both the mRNA and protein levels, whereas those of fatty acid-binding protein 4 (FABP4), stearoyl-CoA desaturase (SCD), and apolipoprotein E (APOE) were reduced. The abundances of both phosphatidylinositol (PI) (18:1/20:4) and phosphatidylcholine (PC) (15:0/18:2) were positively correlated with APOE. Conversely, that of PI (18:1/20:4) was negatively correlated with ENO3 and PYGM, whereas PC (15:0/18:2) was negatively correlated with TNNC1 and MYLK. In conclusion, we identified calcium signaling and glycolysis as key IMF-regulating pathways. ATP2A2, ENO3, FBP2, MYH7, MYL3, MYLK, PYGM, TNNC1, TPM2, and LPE 18:0 were negatively associated with IMF deposition, whereas FABP4, SCD, APOE, PI (18:1/20:4), and PC (15:0/18:2) were positively associated with it. These findings offer underlying IMF-related targets to promote IMF deposition in cattle. Full article
(This article belongs to the Special Issue Livestock Omics)
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16 pages, 2767 KB  
Article
Screening of Protein Related to Wool Development and Fineness in Gansu Alpine Fine-Wool Sheep
by Zhaohua He, Liming Tian, Guan Wang, Fangfang Zhao, Pengfei Zhao, Shuhong Zhang, Shaobin Li and Guangli Yang
Animals 2025, 15(17), 2578; https://doi.org/10.3390/ani15172578 - 2 Sep 2025
Viewed by 507
Abstract
Fiber fineness is a critical determinant of wool quality and is of great significance in enhancing the overall quality of wool. The aim of this research was to pinpoint the key proteins that participate in the regulation of wool fineness. To achieve this, [...] Read more.
Fiber fineness is a critical determinant of wool quality and is of great significance in enhancing the overall quality of wool. The aim of this research was to pinpoint the key proteins that participate in the regulation of wool fineness. To achieve this, we utilized Astral—DIA proteomics technology to examine the disparities in proteins, pathways, and GO terms among the wool tissues of Gansu alpine fine-wool sheep with varying mean fiber diameters (MFD). The experiment was divided into two groups: coarse (group C, MFD = 22.36 ± 0.75 μm, n = 4) and fine (group F, MFD = 16.89 ± 0.36 μm, n = 4). The results indicated that 67 differentially expressed proteins (DEPs) were identified from the wool tissues of Gansu alpine fine-wool sheep in groups C and F. Functional enrichment analysis demonstrated that several key differential proteins, including MGST3, KRT26, KRT72, KRT74, KRT71, etc., were mainly enriched in multiple functional pathways. These pathways included glutathione metabolism, oxidative phosphorylation, the degradation of valine, leucine, and isoleucine, intermediate filaments, serine protease activity, and cysteine protease activity (p < 0.05). Furthermore, protein–protein interaction (PPI) network analysis suggested that type II keratin and type I keratin (such as CTSF, PSAP, TMEM106B, LYPD3, KRT71, KRT72), along with glutathione metabolism (MGST3, W5QDB7), are closely related to hair follicle development and the regulation of wool fineness. In summary, this study enriches the existing sheep proteinome database and offers novel perspectives on the regulatory mechanisms of wool fineness. Full article
(This article belongs to the Special Issue Livestock Omics)
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21 pages, 4618 KB  
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
Cited by 2 | Viewed by 672
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 KB  
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 727
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 KB  
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
Cited by 1 | Viewed by 1459
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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