New Updates in the Area of Pig Genomics and Genetics

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: 15 September 2026 | Viewed by 1295

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Department of Animal Molecular Biology, National Research Institute of Animal Production, 32-083 Balice, Poland
Interests: pig; chicken; horse genomics; transcriptomics and epigenomics
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Special Issue Information

Dear Colleagues,

Over the past three years, research into pig molecular genetics and genomics has advanced rapidly due to the widespread application of high-throughput sequencing technologies and integrative multi-omics approaches. Whole-genome sequencing, genome-wide association studies (GWAS), and high-density SNP arrays have enabled the identification of numerous candidate genes and genomic regions associated with economically important traits, including growth rate, feed efficiency, carcass composition, meat quality, fat deposition, and reproductive performance, which have significantly improved the accuracy and efficiency of genomic selection in modern pig breeding programs.

A major breakthrough in recent years has been the development and application of genome-editing technologies, particularly CRISPR/Cas9 and its derivatives, such as base editing and prime editing. These tools allow precise and efficient modification of the pig genome and are increasingly used for functional validation of candidate genes, improvement of disease resistance, and generation of pigs with desirable production traits. In parallel, genome editing has expanded the role of pigs as valuable biomedical models for human diseases.

Recent studies increasingly focus on functional genomics and regulatory mechanisms, including transcriptomics, epigenomics, and the analysis of non-coding RNAs such as lncRNAs and miRNAs. Integrating genomic, transcriptomic, and epigenetic data has improved understanding of complex regulatory networks underlying adipogenesis, muscle development, immune response, and environmental adaptation. Publicly available resources and databases integrating multi-omics data across tissues and breeds further support comparative and functional analyses.

In summary, this Special Issue will present how the progress in pig molecular genetics and genomics reflects a shift toward integrative, systems-level approaches combining genomic selection, functional genomics, and genome editing. These advances provide a strong foundation for sustainable pig breeding, improved animal health and welfare, and expanded applications of pigs in translational and biomedical research.

Dr. Katarzyna Piórkowska
Guest Editor

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Keywords

  • pig breeding
  • pig molecular genetics
  • genome-editing technologies
  • CRISPR/Cas9
  • functional genomics
  • transcriptomics
  • epigenomics
  • non-coding RNAs

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Published Papers (2 papers)

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Research

17 pages, 2315 KB  
Article
Tracing of Porcine lncRNA MALAT1 Shaped by Tissue Localisation and Adipogenesis
by Katarzyna Piórkowska, Ewa Ocłoń, Ksenia Wróblewska, Karolina Zygmunt, Piotr Pawlicki and Laura Pardyak
Genes 2026, 17(8), 888; https://doi.org/10.3390/genes17080888 - 29 Jul 2026
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Abstract
Background: The long non-coding RNA MALAT1 is known to regulate various cellular processes; however, its role in porcine adipose tissue remains largely unexplored. Methods: In this study, we examined MALAT1 in pigs differing in fat-deposition traits by combining promoter sequencing, in silico analysis [...] Read more.
Background: The long non-coding RNA MALAT1 is known to regulate various cellular processes; however, its role in porcine adipose tissue remains largely unexplored. Methods: In this study, we examined MALAT1 in pigs differing in fat-deposition traits by combining promoter sequencing, in silico analysis of transcription factor binding site analysis, expression profiling, and in vitro adipogenesis assays. Results: We identified three novel polymorphisms in the MALAT1 promoter regions. Several SNPs were predicted to alter binding sites for transcription factors related to metabolism and immunity, such as NFAT5, NFATC1, and BCL6B. One variant, rs329590882, differed significantly in frequency between breeds and may influence MALAT1 regulation. During adipocyte differentiation, expression of the MALAT1 isoform ENSSSCT00000080860 increased as adipogenesis progressed. Notably, this isoform was more highly expressed in lean-type Pietrain pigs than in the fatty Złotnicka Spotted (ZS) breed, suggesting that its function may not be directly related to fat accumulation. Additionally, we identified novel exon–exon junctions in MALAT1, including a junction associated with the ENSSSCT00000077869 isoform. Conclusions: These findings provide new insights into the potential role of MALAT1 in porcine adipose tissue development and immunometabolic regulation and highlight the need for improved annotation of porcine lncRNAs. Full article
(This article belongs to the Special Issue New Updates in the Area of Pig Genomics and Genetics)
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14 pages, 2406 KB  
Article
Dynamic Histone Modification Patterns in Key Transcription Factor Genes During Porcine Adipogenesis
by Mehmet Onur Aksoy, Jakub Wozniak, Monika Stachowiak and Izabela Szczerbal
Genes 2026, 17(5), 521; https://doi.org/10.3390/genes17050521 - 28 Apr 2026
Viewed by 591
Abstract
Background: Adipogenesis is governed by a complex interplay between transcriptional regulation and epigenetic remodeling. While many transcriptional pathways have been well characterized, less is known about how chromatin-level regulation shapes the timing of gene expression, particularly in large animal models such as pigs. [...] Read more.
Background: Adipogenesis is governed by a complex interplay between transcriptional regulation and epigenetic remodeling. While many transcriptional pathways have been well characterized, less is known about how chromatin-level regulation shapes the timing of gene expression, particularly in large animal models such as pigs. In this study, we investigated histone modification patterns associated with four key adipogenic transcription factor genes—PPARG, GATA2, CEBPA, and CEBPB—in porcine mesenchymal stem cells (MSCs) undergoing adipogenic differentiation. Methods: Using RT-qPCR and ChIP-qPCR, we profiled gene transcription levels and epigenetic marks, including promoter- and exon-specific enrichment of the activating histone marks H3K9ac and H4K8ac, as well as the repressive mark H4K20me3, across six time points (day 0, 2, 4, 6, 8, and 10). Results: Although PPARG and GATA2 are located in close proximity on porcine chromosome 13, they exhibited distinct histone modification profiles. PPARG showed progressive promoter acetylation (H4K8ac) accompanied by transcriptional activation, whereas GATA2 displayed decreased exon acetylation (H3K9ac) associated with declining expression. In contrast, the H4K20me3 profile was similar for both genes, suggesting no direct association with their transcriptional activity. Interestingly, CEBPA (chromosome 6) and CEBPB (chromosome 17) exhibited temporally distinct histone modification patterns consistent with their roles in intermediate and early stages of adipogenic differentiation, respectively. Increased enrichment of the H3K9ac mark preceded the rise in transcript levels of the analyzed genes. Promoter regions showed higher enrichment of H4K8ac compared with exonic regions. A higher level of H4K20me3 was also observed for CEBPA and CEBPB than for PPARG and GATA2, which appeared to be more related to chromosomal localization than to direct transcriptional regulation. Conclusions: Together, these results reveal complex interactions between transcriptional dynamics and selected histone modifications that depend on both the gene analyzed and the stage of adipocyte differentiation. This study provides new insights into the epigenetic regulation of porcine adipogenesis and highlights chromatin context as an additional layer influencing transcriptional control. Full article
(This article belongs to the Special Issue New Updates in the Area of Pig Genomics and Genetics)
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