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Animals
Special Issues
Advances in Omics to Enhance Livestock Production
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Advances in Omics to Enhance Livestock Production

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 2025 | Viewed by 2421

Special Issue Editors

Dr. Loan Nguyen

E-Mail Website
Guest Editor
Centre for Animal Science, The University of Queensland, Brisbane, Australia
Interests: multi-omics; nanopore sequencing; structural variants; functional regulatory elements; animal biotechnology; gene expression and network; genetics; epigenetics (DNA methylation)
Dr. Harrison Lamb

E-Mail Website1 Website2
Guest Editor
Centre for Animal Science, The University of Queensland, Brisbane, Australia
Interests: nanopore sequencing; structural variation; genomic selection; ag-tech

Special Issue Information

Dear Colleagues,

With the growing human population expected to reach 9.7 billion by 2050, we are facing increasing pressure on global food supply chains. Economic growth in developing countries is further increasing the demand for higher-quality and more diverse food products, including animal-based products. To address this challenge, innovative technologies are essential to help improve livestock productivity and quality. Omics technologies, including genomics, transcriptomics, proteomics, and metabolomics, have been used and continue to show their potential in understanding the genetics and molecular pathways driving economically important traits such as animal growth, fertility and product quality. Additionally, with the help of advancements in bioinformatics and machine learning technologies, the integration of large omics datasets will become more efficient for precise breeding strategies, optimising animal growth rate and meat quality. We kindly invite researchers to contribute their original research papers, reviews, and short communications to this Special Issue.

Dr. Loan Nguyen
Dr. Harrison Lamb
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

  • livestock production
  • omics
  • animal growth
  • product quality
  • fertility
  • machine learning

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

Published Papers (2 papers)

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Research

17 pages, 867 KiB  
Article
Correlated Responses to Selection for Intramuscular Fat on the Gut Microbiome in Rabbits
by Marina Martínez-Álvaro, Agostina Zubiri-Gaitán, Pilar Hernández, Cristina Casto-Rebollo, Noelia Ibáñez-Escriche, Maria Antonia Santacreu, Alejandro Artacho, Vicente Pérez-Brocal and Agustín Blasco
Animals 2024, 14(14), 2078; https://doi.org/10.3390/ani14142078 - 16 Jul 2024
Viewed by 624
Abstract
Intramuscular fat (IMF) content is important for meat production and human health, where the host genetics and its microbiome greatly contribute to its variation. The aim of this study is to describe the consequences of the genetic modification of IMF by selecting the [...] Read more.
Intramuscular fat (IMF) content is important for meat production and human health, where the host genetics and its microbiome greatly contribute to its variation. The aim of this study is to describe the consequences of the genetic modification of IMF by selecting the taxonomic composition of the microbiome, using rabbits from the 10th generation of a divergent selection experiment for IMF (high (H) and low (L) lines differ by 3.8 standard deviations). The selection altered the composition of the gut microbiota. Correlated responses were better distinguished at the genus level (51 genera) than at the phylum level (10 phyla). The H-line was enriched in Hungateiclostridium, Limosilactobacillus, Legionella, Lysinibacillus, Phorphyromonas, Methanosphaera, Desulfovibrio, and Akkermansia, while the L-line was enriched in Escherichia, Methanobrevibacter, Fonticella, Candidatus Amulumruptor, Methanobrevibacter, Exiguobacterium, Flintibacter, and Coprococcus, among other genera with smaller line differences. A microbial biomarker generated from the abundance of four of these genera classified the lines with 78% accuracy in a logit regression. Our results demonstrate different gut microbiome compositions in hosts with divergent IMF genotypes. Furthermore, we provide a microbial biomarker to be used as an indicator of hosts genetically predisposed to accumulate muscle lipids, which opens up the opportunity for research to develop probiotics or microbiome-based breeding strategies targeting IMF. Full article
(This article belongs to the Special Issue Advances in Omics to Enhance Livestock Production)
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15 pages, 4408 KiB  
Article
Whole-Genome Resequencing of Ujimqin Sheep Identifies Genes Associated with Vertebral Number
by Chuanqing Zhou, Yue Zhang, Teng Ma, Dabala Wu, Yanyan Yang, Daqing Wang, Xiunan Li, Shuchun Guo, Siqi Yang, Yongli Song, Yong Zhang, Yongchun Zuo and Guifang Cao
Animals 2024, 14(5), 677; https://doi.org/10.3390/ani14050677 - 21 Feb 2024
Viewed by 1381
Abstract
The number of vertebrae is a crucial economic trait that can significantly impact the carcass length and meat production in animals. However, our understanding of the quantitative trait loci (QTLs) and candidate genes associated with the vertebral number in sheep (Ovis aries [...] Read more.
The number of vertebrae is a crucial economic trait that can significantly impact the carcass length and meat production in animals. However, our understanding of the quantitative trait loci (QTLs) and candidate genes associated with the vertebral number in sheep (Ovis aries) remains limited. To identify these candidate genes and QTLs, we collected 73 Ujimqin sheep with increased numbers of vertebrae (T13L7, T14L6, and T14L7) and 23 sheep with normal numbers of vertebrae (T13L6). Through high-throughput genome resequencing, we obtained a total of 24,130,801 effective single-nucleotide polymorphisms (SNPs). By conducting a selective-sweep analysis, we discovered that the most significantly selective region was located on chromosome 7. Within this region, we identified several genes, including VRTN, SYNDIG1L, LTBP2, and ABCD4, known to regulate the spinal development and morphology. Further, a genome-wide association study (GWAS) performed on sheep with increased and normal vertebral numbers confirmed that ABCD4 is a candidate gene for determining the number of vertebrae in sheep. Additionally, the most significant SNP on chromosome 7 was identified as a candidate QTL. Moreover, we detected two missense mutations in the ABCD4 gene; one of these mutations (Chr7: 89393414, C > T) at position 22 leads to the conversion of arginine (Arg) to glutamine (Gln), which is expected to negatively affect the protein’s function. Notably, a transcriptome expression profile in mouse embryonic development revealed that ABCD4 is highly expressed during the critical period of vertebral formation (4.5–7.5 days). Our study highlights ABCD4 as a potential major gene influencing the number of vertebrae in Ujimqin sheep, with promising prospects for future genome-assisted breeding improvements in sheep. Full article
(This article belongs to the Special Issue Advances in Omics to Enhance Livestock Production)
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