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Deciphering the Molecular Architecture of Complex Traits in Livestock and...
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Deciphering the Molecular Architecture of Complex Traits in Livestock and Poultry via Integrative Multi-Omics

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

Deadline for manuscript submissions: 15 September 2026 | Viewed by 1961

Editor

Dr. Xubin Lu

E-Mail Website
Guest Editor
College of Animal Science and Technology, Yangzhou University, Yangzhou, China
Interests: animal quantitative genetics and statistical genomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The complex traits of livestock and poultry, including growth, reproduction, health, product quality and environmental adaptation, are governed by intricate genetic structures and multi-level molecular regulatory mechanisms. Recent advances in high-throughput omics technologies have enabled the generation of large-scale datasets spanning genomics, transcriptomics, epigenomics, proteomics, metabolomics and microbiomics, offering unprecedented opportunities for systematically investigating the biological foundations of these traits.

This Special Issue aims to dissect complex traits in livestock and poultry through integrated multi-omics analysis, with a particular emphasis on combining multiple omics layers with phenotypic data using quantitative genetics, statistical genomics, systems biology and advanced computational methods. We welcome original research papers and reviews covering topics such as functional gene identification, regulatory network construction, prioritization of disease-causing variants and genotype–phenotype associations across different livestock and poultry species. This Special Issue combines methodological innovation with applied research to enhance our understanding of the molecular mechanisms underlying complex traits and to facilitate the effective translation of multi-omics findings into animal breeding, management and genetic improvement programs.

Dr. Xubin Lu
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-anonymized 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 breeding
  • complex traits
  • livestock and poultry
  • multi-omics
  • genomics

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Published Papers (2 papers)

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Research

24 pages, 53003 KB  
Article
Integrative Transcriptomic and Metabolomic Analysis Reveal Mechanisms Underlying Differential Fecundity in Yangtze River Delta White Goat
by Jiahao Sun, Wenjun Tang, Rahmani Mohammad Malyar and Fangxiong Shi
Animals 2026, 16(13), 2034; https://doi.org/10.3390/ani16132034 - 2 Jul 2026
Viewed by 594
Abstract
Differential fecundity in goats is a complex trait governed by coordinated molecular regulation across reproductive and endocrine tissues. In this study, we performed integrated metabolomic profiling of follicular fluid, serum, thyroid tissue, and uterine luminal fluid together with transcriptomic sequencing of follicular, thyroid, [...] Read more.
Differential fecundity in goats is a complex trait governed by coordinated molecular regulation across reproductive and endocrine tissues. In this study, we performed integrated metabolomic profiling of follicular fluid, serum, thyroid tissue, and uterine luminal fluid together with transcriptomic sequencing of follicular, thyroid, and uterine horn tissues from high-fecundity (HF) and low-fecundity (LF) Yangtze River Delta White goats. In addition, weighted gene co-expression network analysis (WGCNA) was conducted to elucidate the molecular mechanisms underlying differential litter size. High-fecundity goats exhibited enhanced follicular steroidogenesis, superior corpus luteum function, and more stable hypothalamic–pituitary–thyroid (HPT) axis activity, accompanied by increased uterine gland density and greater myometrial thickness. Metabolomic profiling identified 6640 metabolites displaying tissue-specific differential abundance patterns. Pathway enrichment analysis highlighted steroid hormone biosynthesis and energy metabolism in follicular fluid, PPAR signaling and tyrosine metabolism in thyroid tissue, and glycerophospholipid and one-carbon metabolism in uterine luminal fluid as major pathways associated with fecundity. Transcriptomic analysis identified 1596 differentially expressed genes (DEGs), including 20 genes shared across all examined tissues, constituting a systemic molecular signature associated with fecundity. WGCNA further revealed three functional tissue axes associated with follicular development (ELOVL4, INHA, NR5A2), thyroid endocrine regulation (GRHL2, NAPRT), and uterine receptivity (RSPO1, AGTR2, PTGER3). Low-fecundity-associated modules were predominantly concentrated in follicular and thyroid tissues, whereas the high-fecundity-specific module was mainly enriched in uterine horn. These findings provide a multi-tissue molecular framework underlying differential fecundity in goats and identify candidate hub genes and metabolites that may serve as candidate biomarkers for fecundity assessment and selective breeding programs. Full article
(This article belongs to the Special Issue Deciphering the Molecular Architecture of Complex Traits in Livestock and Poultry via Integrative Multi-Omics)
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18 pages, 8213 KB  
Article
Integrated Transcriptomic and Metabolomic Analysis Deciphers the Molecular and Metabolic Mechanisms Underlying Growth Rate Divergence in Dezhou Donkeys
by Xinhao Zhang, Haijing Li, Xiangnan Zhou, Xianggang Cao, Manna Dou, Changfa Wang and Wenqiang Li
Animals 2026, 16(8), 1271; https://doi.org/10.3390/ani16081271 - 21 Apr 2026
Viewed by 986
Abstract
Dezhou donkey is a premium indigenous Chinese livestock breed with high economic value for meat, hide and medicinal uses, and growth rate is a core trait determining farming profitability. However, the molecular and metabolic mechanisms underlying divergent growth rates in this breed have [...] Read more.
Dezhou donkey is a premium indigenous Chinese livestock breed with high economic value for meat, hide and medicinal uses, and growth rate is a core trait determining farming profitability. However, the molecular and metabolic mechanisms underlying divergent growth rates in this breed have not been fully characterized, with no integrated transcriptomic and metabolomic studies reported. Here, 12 age-matched healthy male Dezhou donkeys were assigned to faster-growing (n = 6) and slower-growing (n = 6) groups by average daily gain, followed by plasma transcriptome sequencing and untargeted LC-MS/MS metabolomics. We identified 480 differentially expressed genes, with the slower-growing group enriching in immune/inflammatory/apoptotic pathways, and the faster-growing group in energy metabolism and transmembrane transport. Lipids and lipid-like molecules represented the largest proportion (44.9%) of the differential metabolites; the slower-growing group was enriched in lipid peroxidation and pro-inflammatory mediators, while the faster-growing group was enriched in unsaturated fatty acids and antioxidants. Integrated analysis revealed core pathways (cAMP signaling, arachidonic acid/unsaturated fatty acid biosynthesis) and key candidate genes/metabolites. Our findings clarify that excessive lipid peroxidation and inflammatory imbalance restrict growth, while efficient energy metabolism promotes faster growth, providing theoretical support for genetic improvement and precision nutrition of Dezhou donkeys. Full article
(This article belongs to the Special Issue Deciphering the Molecular Architecture of Complex Traits in Livestock and Poultry via Integrative Multi-Omics)
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