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Genetic Diversity Evaluation of Shanghai Local Pig Breeds Using Liquid-Phase Chip Technology
Mengqian Cao1,2,3, Jun Gao1,2,3,4, Shushan Zhang1,2,3,4
1Institute of Animal Science and Veterinary Medicine, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China.
Animals : an Open Access Journal From MDPI
|February 13, 2026
Summary
A new liquid-phase chip effectively genotypes pig breeds, revealing higher inbreeding in Pudong White and Fengjing breeds. Optimized mating strategies significantly reduced inbreeding and boosted genetic diversity in conserved pig populations.
Area of Science:
- Animal Genetics
- Genomics
- Conservation Biology
Background:
- Conserving local pig breeds is crucial for maintaining genetic diversity.
- Understanding population structure and inbreeding levels is essential for effective conservation strategies.
- Genotyping technologies play a vital role in assessing genetic diversity and managing breeding programs.
Purpose of the Study:
- To develop and apply a novel 60K single-nucleotide polymorphism (SNP) liquid-phase chip for genotyping conserved pig breeds.
- To assess genetic diversity, population structure, and genomic breed composition (GBC) in five local Chinese pig breeds.
- To evaluate the effectiveness of molecular pedigree construction and optimized mating strategies in reducing inbreeding and enhancing genetic diversity.
Main Methods:
- Development of a 60K SNP liquid-phase chip using genotyping by target sequencing (GBTS) technology.
- Genotyping of 1451 individuals from five local pig breeds (Fengjing, Meishan, Pudong White, Shaowutou, Shanghai White) and Meishan offspring.
- Analysis of genetic diversity, population structure, genomic breed composition (GBC), runs of homozygosity (FROH), linkage disequilibrium (LD), genetic distance of identity-by-state (IBS), and molecular pedigree construction.
Main Results:
- The Pudong White and Fengjing breeds showed higher fractions of the genome covered by runs of homozygosity (FROH) and slower linkage disequilibrium (LD) decay, indicating elevated inbreeding.
- Genomic breed composition (GBC) analysis provided insights into genomic introgression within admixed individuals.
- Optimized purebred mating, excluding individuals with high inbreeding coefficients, significantly reduced inbreeding levels and increased genetic diversity in the progeny compared to the original Meishan population.
Conclusions:
- Liquid-phase chip technology is a valuable tool for genotyping and conservation of small, locally conserved pig breeds.
- Molecular pedigree construction and strategic mating are effective in managing inbreeding and enhancing genetic diversity in endangered pig populations.
- The study highlights the importance of integrating advanced genotyping technologies with traditional breeding management for successful livestock conservation efforts.
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