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Genetic Diversity, Innovative Utilization and Microbiome Profile of Local Pig Breeds: Second Edition

A special issue of Animals (ISSN 2076-2615). This special issue belongs to the section "Pigs".

Deadline for manuscript submissions: closed (31 March 2026) | Viewed by 898

Special Issue Editors


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Guest Editor
Department of Veterinary Sciences, University of Messina, Via Palatucci, 98168 Messina, ME, Italy
Interests: animal breeding; genetic improvement; genomic selection; conservation; biodiversity; gene regulation; breed traceability; coat color
Special Issues, Collections and Topics in MDPI journals
College of Animal Science and Technology, Yangzhou University, Yangzhou, China
Interests: pigs; mobilome; retrotransposon insertion polymorphism; marker development; genome selection; gene regulation; bioinformatics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The role of livestock is, above all, to provide sufficient food that is protein-rich, safe, and healthy with high nutritional and organoleptic values for humans. In recent years, there has been growing awareness of the importance of adaptive traits in local breeds, forming a reservoir of valuable genetic variation with the potential for more sustainable added-value oriented pork production, emphasizing their historical and cultural value. In the past, the development of livestock production was mainly based on the formation of local breeds well-adapted to specific conditions and rearing practices. However, in the second half of the twentieth century, the lower economic performance of these breeds when raised under intensive production conditions resulted in a significant reduction in local pig breed populations; these were replaced by modern, highly productive pig breeds adapted to farm conditions and constraints.

The higher economic value of typical production compared to conventional commercial products and the growing consumer preference towards high-quality food could support plans for livestock biodiversity conservation.

Dr. Enrico D’Alessandro
Dr. Cai Chen
Guest Editors

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Keywords

  • pigs
  • local breeds
  • genetic improvement
  • genomics selection
  • QTL
  • pig production
  • meat quality
  • traceability
  • typical product
  • conservation
  • biodiversity
  • food safety
  • microbiome

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Published Papers (1 paper)

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Research

13 pages, 1239 KB  
Article
Genetic Diversity Evaluation of Shanghai Local Pig Breeds Using Liquid-Phase Chip Technology
by Mengqian Cao, Jun Gao, Shushan Zhang, Weilong Tu, Lingwei Sun, Jiehuan Xu, Mengqian He, Jianjun Dai, Caifeng Wu and Defu Zhang
Animals 2026, 16(3), 479; https://doi.org/10.3390/ani16030479 - 3 Feb 2026
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Abstract
This study developed a 60K single-nucleotide polymorphism (SNP) liquid-phase chip (‘Shenxin I’) based on genotyping by target sequencing (GBTS) technology. The chip was used to genotype 1451 individuals spanning five conserved local pig breeds: Fengjing (FJ), Meishan (MMS), Pudong White (PD), Shaowutou (SW), [...] Read more.
This study developed a 60K single-nucleotide polymorphism (SNP) liquid-phase chip (‘Shenxin I’) based on genotyping by target sequencing (GBTS) technology. The chip was used to genotype 1451 individuals spanning five conserved local pig breeds: Fengjing (FJ), Meishan (MMS), Pudong White (PD), Shaowutou (SW), and Shanghai White (SHW), and newborn purebred Meishan offspring (MMS_New). The study assessed the genetic diversity, population structure, and genomic breed composition (GBC) of these breeds. The GBC analysis provided insights into genomic introgression within admixed individuals. Results indicate that PD and FJ breeds exhibited the higher fraction of the genome covered by runs of homozygosity (FROH) and slower linkage disequilibrium (LD) decay rate, suggesting higher genetic inbreeding level in these two breeds. The study conducted genetic distance of identity-by-state (IBS) analysis and molecular pedigree construction for the MMS population. Subsequently, purebred mating was implemented by selecting boars from different pedigrees to mate with sows and excluding individuals with high inbreeding coefficients from the breeding program. This resulted in a significant reduction in the overall inbreeding level of the born progeny and an increase in genetic diversity compared to the original population. Consequently, the study concludes that utilizing liquid-phase chip technology for genotyping, constructing molecular pedigrees, and optimizing mating combinations in small populations of locally conserved pig breeds contributes to enhancing the conservation effectiveness. Full article
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