Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
5.2
2.7
Journals
Animals
Special Issues
Transcriptomics in Livestock: Unveiling Genetic Insights for Enhanced Productivity and...
share announcement

Transcriptomics in Livestock: Unveiling Genetic Insights for Enhanced Productivity and Health

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

Deadline for manuscript submissions: 31 December 2025 | Viewed by 3255

Special Issue Editors

Dr. Jun-Mo Kim

E-Mail Website
Guest Editor
Animal Functional Genomics and Bioinformatics Lab., Department of Animal Science and Technology, Chung-Ang University, Anseong, Gyeonggi-do, Korea
Interests: quantitative genetics; functional genomics; system biology; bioinformatics
Special Issues, Collections and Topics in MDPI journals
Dr. Byeonghwi Lim

E-Mail Website
Guest Editor
Animal Functional Genomics and Bioinformatics Lab., Department of Animal Science and Technology, Chung-Ang University, Anseong, Gyeonggi-do, Republic of Korea
Interests: immunogenomics; transcriptomics
Dr. Seung-Hoon Lee

E-Mail Website
Guest Editor
Animal Functional Genomics and Bioinformatics Lab., Department of Animal Science and Technology, Chung-Ang University, Anseong, Gyeonggi-do, Republic of Korea
Interests: animal genetics

Special Issue Information

Dear Colleagues,

Transcriptomics, the study of RNA transcripts, has revolutionized our understanding of genetic expression in livestock. By mapping out the complex web of gene activity, researchers can identify key genetic factors that influence productivity and health in farm animals. This field is crucial as it provides insights into improving livestock traits such as growth rates, disease resistance, and overall well-being, which are essential for sustainable agriculture and food security. The following Special Issue aims to bring together cutting-edge research and comprehensive reviews that advance our understanding of transcriptomics in livestock. The focus is on uncovering genetic insights that can be directly applied to enhance productivity and health in various livestock species. By providing a platform for the latest findings, we hope to foster collaborations and drive innovations in livestock genomics. In this Special Issue, original research articles and reviews are welcome. Research areas may include (but are not limited to) the following:

  • Gene expression profiling in different livestock species;
  • The identification of biomarkers for disease resistance and health;
  • Transcriptomic responses to environmental stressors;
  • Comparative transcriptomics across breeds;
  • Functional genomics and gene regulation;
  • The integration of transcriptomics with other 'omics' technologies;
  • The applications of transcriptomics in breeding programs.

We look forward to receiving your contributions.

Dr. Jun-Mo Kim
Dr. Byeonghwi Lim
Dr. Seung-Hoon Lee
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

  • transcriptomics
  • RNA-seq
  • gene expression
  • functional genomics
  • gene regulation
  • genomic technologies
  • livestock
  • health
  • productivity

Benefits of Publishing in a Special Issue

  • Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
  • Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
  • Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
  • External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
  • Reprint: MDPI Books provides the opportunity to republish successful Special Issues in book format, both online and in print.

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

Published Papers (4 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

19 pages, 6789 KiB  
Article
Metabolic Plasticity and Transcriptomic Reprogramming Orchestrate Hypoxia Adaptation in Yak
by Ci Huang, Yilie Liao, Wei Peng, Hai Xiang, Hui Wang, Jieqiong Ma, Zhixin Chai, Zhijuan Wu, Binglin Yue, Xin Cai, Jincheng Zhong and Jikun Wang
Animals 2025, 15(14), 2084; https://doi.org/10.3390/ani15142084 - 15 Jul 2025
Viewed by 138
Abstract
The yak (Bos grunniens) has exceptional hypoxia resilience, making it an ideal model for studying high-altitude adaptation. Here, we investigated the effects of oxygen concentration on yak cardiac fibroblast proliferation and the underlying molecular regulatory pathways using RNA sequencing (RNA-seq) and [...] Read more.
The yak (Bos grunniens) has exceptional hypoxia resilience, making it an ideal model for studying high-altitude adaptation. Here, we investigated the effects of oxygen concentration on yak cardiac fibroblast proliferation and the underlying molecular regulatory pathways using RNA sequencing (RNA-seq) and metabolic analyses. Decreased oxygen levels significantly inhibited cardiac fibroblast proliferation and activity. Intriguingly, while the mitochondrial DNA (mtDNA) content remained stable, we observed coordinated upregulation of mtDNA-encoded oxidative phosphorylation components. Live-cell metabolic assessment further demonstrated that hypoxia led to mitochondrial respiratory inhibition and enhanced glycolysis. RNA-seq analysis identified key hypoxia adaptation genes, including glycolysis regulators (e.g., HK2, TPI1), and hypoxia-inducible factor 1-alpha (HIF-1α), with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses highlighting their involvement in metabolic regulation. The protein–protein interaction network identified three consensus hub genes across five topological algorithms (CCNA2, PLK1, and TP53) that may be involved in hypoxia adaptation. These findings highlight the importance of metabolic reprogramming underlying yak adaptation to hypoxia, providing valuable molecular insights into the mechanisms underlying high-altitude survival. Full article
(This article belongs to the Special Issue Transcriptomics in Livestock: Unveiling Genetic Insights for Enhanced Productivity and Health)
►▼ Show Figures

Figure 1

17 pages, 4402 KiB  
Article
Integrated mRNA and miRNA Analysis Reveals Layer-Specific Mechanisms of Antler Yield Variation in Sika Deer
by Derui Zhao, Zhen Zhang, Qianghui Wang and Heping Li
Animals 2025, 15(13), 1964; https://doi.org/10.3390/ani15131964 - 4 Jul 2025
Viewed by 293
Abstract
Antlers exhibit exceptionally rapid growth, representing a rare biological phenomenon among mammals. In addition to their scientific significance, antlers are widely used in traditional medicine, and their yield directly impacts the economic efficiency of the deer farming industry. However, antler yield varies substantially [...] Read more.
Antlers exhibit exceptionally rapid growth, representing a rare biological phenomenon among mammals. In addition to their scientific significance, antlers are widely used in traditional medicine, and their yield directly impacts the economic efficiency of the deer farming industry. However, antler yield varies substantially among individuals, and the molecular mechanisms underlying this variation remain poorly understood. This study aimed to elucidate the transcriptomic and post-transcriptional mechanisms underlying antler yield variation by comparing gene and miRNA expression profiles across four distinct antler tissue layers—dermis (D), reserve mesenchyme (RM), pre-cartilage (PC), and cartilage (C)—in sika deer with different yields. RNA-seq and miRNA-seq were performed, followed by differential expression, GO and KEGG pathway enrichment, and miRNA–mRNA co-expression network analyses. Our results reveal layer-specific expression patterns and key regulatory genes and miRNAs associated with proliferation, chondrogenesis, angiogenesis, and mineralization. In particular, genes such as FBP2, TPT1, TFRC, ZEB1, and PHOSPHO1 were upregulated in high-yield deer across specific tissue layers, while NFATC2 was downregulated in these high-yield deer. Additionally, miRNAs such as miR-140, miR-296-3p, and let-7e exhibited layer-specific expression patterns linked to growth and differentiation. Our miRNA–mRNA regulatory network analysis highlighted significant interactions, particularly miR-296-3p–PHOSPHO1 and miR-296-3p–FBP2, as key regulators of antler growth. Enrichment of PI3K-Akt and TGF-β signaling pathways further suggests their involvement in promoting chondrogenesis and ossification. These findings provide novel insights into the molecular basis of antler growth and yield, which may inform future strategies for selective breeding in deer farming. Full article
(This article belongs to the Special Issue Transcriptomics in Livestock: Unveiling Genetic Insights for Enhanced Productivity and Health)
►▼ Show Figures

Figure 1

18 pages, 7293 KiB  
Article
Comparative Transcriptomic Analysis Between High- and Low-Growth-Rate Meat-Type Rabbits Reveals Key Pathways Associated with Muscle Development
by Chao Yang, Lingxi Zhu, Li Tang, Xiangyu Zhang, Min Lei, Xiaohong Xie, Cuixia Zhang, Dingsheng Yuan, Congyan Li and Ming Zhang
Animals 2025, 15(11), 1585; https://doi.org/10.3390/ani15111585 - 29 May 2025
Viewed by 500
Abstract
Rabbit meat constitutes a high-protein, low-fat nutritional resource demonstrating rising consumption, particularly within the Asia-Pacific region. Consequently, muscle growth and developmental pattern in meat rabbits represent critical economic considerations. To elucidate the primary signaling pathways governing muscle development, we first performed comparative body [...] Read more.
Rabbit meat constitutes a high-protein, low-fat nutritional resource demonstrating rising consumption, particularly within the Asia-Pacific region. Consequently, muscle growth and developmental pattern in meat rabbits represent critical economic considerations. To elucidate the primary signaling pathways governing muscle development, we first performed comparative body weight analyses between two rabbit breeds exhibiting divergent growth rates: the fast-growing Checkered Giant (Ju) and slow-growing Sichuan Ma rabbit. Subsequent, post-natal qualities of thigh and longissimus dorsi muscle fiber were quantified across three developmental phases (28, 56, and 84 days post-natal). The results showed the body weight of Ju rabbit was significantly higher than that of Ma rabbit beyond 3 weeks post-natal (p < 0.05), while Ma rabbit exhibited larger muscle fiber areas in both tissues at 56 days (p < 0.05). The transcriptome analysis showed that 284 and 305 differentially expressed genes (DEGs) (|log2FC| > 1, padj < 0.05) were identified in thigh muscle and longissimus dorsi muscle, respectively. GO (Gene Ontology) analysis of DEGs indicated DEGs in the thigh muscle were enriched in these terms related to biological processes of muscle cell migration and smooth muscle cell migration, cellular components of sarcomere, myofibril, and actin filament bundle, while DEGs in longissimus dorsi muscle were enriched in these terms associated with biological processes of muscle cell migration, smooth muscle cell migration and muscle structure development, cellular component of actin cytoskeleton, contractile fiber, myofibril, myosin complex and molecular function of actin filament binding. Integrated GO, KEGG and PPI analyses of co-expressive DEGs implicated the HIF-1 signaling pathway and Glycolysis/Gluconeogenesis in muscular development. Different expression of energy metabolism hub-genes might be the primary reason for interbreed muscle developmental disparities. Full article
(This article belongs to the Special Issue Transcriptomics in Livestock: Unveiling Genetic Insights for Enhanced Productivity and Health)
►▼ Show Figures

Figure 1

16 pages, 769 KiB  
Article
Expression of Genes Related to Meat Productivity, Metabolic and Morphological Significance of Broiler Chickens with the Use of Nutritional Phytochemicals
by Marina I. Selionova, Vladimir I. Trukhachev, Artem Yu. Zagarin, Egor I. Kulikov, Dmitry M. Dmitrenko, Vera N. Martynova, Arina K. Kravchenko and Vladimir G. Vertiprakhov
Animals 2024, 14(20), 2958; https://doi.org/10.3390/ani14202958 - 14 Oct 2024
Cited by 2 | Viewed by 1719
Abstract
The study aimed to analyze gene expression linked to skeletal muscle growth and lipid metabolism in broiler chickens fed with plant extracts. Five groups of chickens were formed: four experimental groups and one control group. The diets of the experimental groups were supplemented [...] Read more.
The study aimed to analyze gene expression linked to skeletal muscle growth and lipid metabolism in broiler chickens fed with plant extracts. Five groups of chickens were formed: four experimental groups and one control group. The diets of the experimental groups were supplemented with different plant extracts: chicory, St. John’s wort, maral root, and creeping thyme, whereas the control group received feed without phytobiotic compounds. Weekly weighings were conducted (n = 36). The chickens were slaughtered at day 26 for tissue sampling of four birds from each group. Gene expression (MYOG, MSTN, FASN) related to muscle growth and fatty acid synthesis was analyzed using the β-actin ACTB gene as a reference. Blood samples were taken at day 35 for biochemical analysis and anatomical dissection was performed. The study revealed that using plant extracts from chicory, thyme, and maral root increased MYOG gene activity by 4.21, 7.45, and 8.93 times, respectively. T. serpyllum extract boosted the MSTN gene by 10.93 times, impacting muscle growth regulation. FASN gene expression for fatty acid synthesis increased significantly by 18.22–184.12 times with plant extracts. The best results regarding meat productivity of chickens were obtained when using R. carthamoides extract. The results of the study will serve as a basis for further development of a phytocomposition designed to increase the meat productivity of broiler chickens in the production of environmentally safe poultry products. Full article
(This article belongs to the Special Issue Transcriptomics in Livestock: Unveiling Genetic Insights for Enhanced Productivity and Health)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-4
Back to TopTop