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Animals
Special Issues
Genetic Basis of Complex Traits and Breeding Innovation in Pigs
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Genetic Basis of Complex Traits and Breeding Innovation in Pigs

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

Deadline for manuscript submissions: 30 October 2026 | Viewed by 1150

Editors

Dr. Zitao Chen

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Guest Editor
Department of Animal Breeding and Genetics, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
Interests: functional genomics; molecular breeding; statistic genomics
Dr. Jinyan Teng

E-Mail Website
Guest Editor
Department of Animal Breeding and Genetics, College of Animal Sciences, South China Agricultural University, Guangzhou 510642, China
Interests: statistical genetics; molecular QTL mapping; animal breeding
Dr. Zhiting Xu

E-Mail Website
Guest Editor
Department of Animal Science, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
Interests: population genetics; animal breeding; meta-GWAS

Special Issue Information

Dear Colleagues,

The successful release of resources like PigGTEx has catalyzed a new era in porcine genomics. Large-scale genetic analyses have begun to unravel the architecture of over 200 complex traits, and initiatives such as the PigBiobank platform are providing invaluable datasets for the research community. While these advances have mapped numerous quantitative trait loci and identified potential candidate genes, some challenges remain. The genetic basis for certain traits may still be limited by sample size or breed diversity, and a number of economically and biologically important characteristics await comprehensive investigation. A key frontier lies in innovatively leveraging these vast biological priors to develop new models and methods for prediction and selection. Furthermore, the rapid evolution of sequencing technologies is continuously revealing new molecular traits (e.g., isoform and methylation). Integrating these multi-omics layers is crucial for pinpointing key causal genes and variants. This Special Issue aims to compile cutting-edge research that addresses these gaps and opportunities from dissecting the genetic mechanisms of complex traits to pioneering novel analytical and genomic strategies that directly empower the next generation of precision breeding in pigs.

Dr. Zitao Chen
Dr. Jinyan Teng
Dr. Zhiting Xu
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 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

  • pig genotype-tissue expression
  • pig breeding
  • genomic selection
  • molecular QTL mapping
  • gene expression
  • GWAS
  • TWAS
  • colocalization
  • mendelian randomization

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Published Papers (1 paper)

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Research

19 pages, 4324 KB  
Article
Fine-Mapping-Based Variant Prioritization and Genomic Prediction Enhance Genetic Analyses of Teat Traits in Pigs
by Dongbin Yao, Cai-Xia Yang, Bing Deng, Pan Wang, Shuaipeng He, Zhi-Qiang Du and Zuhong Liu
Animals 2026, 16(12), 1855; https://doi.org/10.3390/ani16121855 - 16 Jun 2026
Viewed by 435
Abstract
Identifying causal genetic variants and candidate genes underlying complex traits remains a central challenge in animal breeding and genetics. Genome-wide association studies (GWAS) are widely used for this purpose. However, their reliance on marginal variant effects and sensitivity to linkage disequilibrium (LD) can [...] Read more.
Identifying causal genetic variants and candidate genes underlying complex traits remains a central challenge in animal breeding and genetics. Genome-wide association studies (GWAS) are widely used for this purpose. However, their reliance on marginal variant effects and sensitivity to linkage disequilibrium (LD) can lead to redundant and less accurate identification of variants or genes of biological relevance. Here, we propose SNP prioritization (GWAS-based and fine-mapping-based) strategies within a unified framework, designed to improve the selection of more informative variants and candidate genes by explicitly modeling LD structure and genetic architectures of three pig teat-related traits (total teat number, teat symmetry, and teat adequacy). While GWAS prioritization favored variants with strong marginal effects, fine-mapping substantially improved joint explanatory performance and prediction accuracy. For total teat number, the best-performing fine-mapping-derived SNP subset achieved a mean PCC of 0.6599 across 10-fold cross-validation, compared with 0.3755 for GWAS-based prioritization. Similarly, for teat adequacy, the highest mean AUC increased from 0.7012 (GWAS) to 0.8547 (fine-mapping). Moreover, fine-mapping-derived SNP sets identified more coherent and trait-specific biological pathways and functionally relevant candidate genes. Taken together, our findings demonstrate that fine-mapping provides a more accurate and biologically meaningful framework for SNP and candidate gene prioritization, supporting its integration into genetic analysis and breeding applications. Full article
(This article belongs to the Special Issue Genetic Basis of Complex Traits and Breeding Innovation in Pigs)
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