A liquid capture SNP panel enables standardized genetic monitoring and validates breeding histories in laboratory miniature pigs

Miniature pigs, particularly Chinese indigenous breeds such as Wuzhishan (WZS) and Bama, are important biomedical models. However, the genetic management of these colonies is often fragmented across breeding facilities, leading to undocumented genetic drift and inconsistencies in germplasm quality. A reproducible SNP-based tool for colony-level genetic monitoring and provenance evaluation is therefore needed. We developed a targeted genotyping system based on multiplex liquid capture sequencing. Candidate SNPs were identified from whole-genome resequencing data of 20 WZS and 20 Bama pigs. After screening and panel optimization, 207 SNPs were retained for genotyping. The panel was evaluated in 154 individuals from eight pig populations across six breeding facilities, including closed colonies, inbred lines, and a New Zealand White (NZW) outgroup. Genetic diversity, population structure, linkage disequilibrium (LD), runs of homozygosity (ROH), and individual identification parameters were analyzed to assess colony-level genetic patterns. The 207-SNP panel distinguished the major breed backgrounds and captured facility-associated population structure. It separated the WZS-1 foundation stock from the WZS-2/WZS-3 inbred lineages and differentiated Bama populations maintained in independent facilities. The NZW population from Unit 6 formed a distinct cluster separate from the Chinese miniature pig populations. Genetic diversity, LD, and ROH analyses were broadly consistent with known colony management histories. WZS-1 and BAMA-1 showed relatively high heterozygosity and faster LD decay, whereas the inbred lines showed reduced heterozygosity, higher ROH burden, and lower LD-based Ne estimates. Although ascertainment bias was observed in the NZW outgroup, the panel retained strong individual discrimination power, with cumulative Probability of Identity (PI) values ranging from 6.3 × 10⁻⁷⁵ in WZS-1 to 8.8 × 10⁻²⁰ in BANNA-2. Across all populations, PI values were below the stringent reference benchmark of 1 × 10⁻⁹ used in this study. This 207-SNP liquid capture panel provides a practical and reproducible tool for routine genetic monitoring and colony-level authentication of laboratory miniature pigs. The panel is particularly useful for evaluating genetic diversity, facility-associated population structure, and breeding-history consistency in populations represented in this study. However, LD- and Ne-related estimates derived from this targeted low-density panel should be interpreted mainly as relative comparisons, and broader application to weakly differentiated or external populations will require further validation.