Population-genomic stability of a closed-herd GGTA1-knock-out miniature pig line for xenotransplantation

Genetically engineered pigs are essential donors for xenotransplantation, requiring phenotypic stability and genetic definition. We evaluated the newly established GGTA1-knock-out "XENO" line, maintained as a closed herd for >10 generations, against Massachusetts General Hospital (MGH) miniature swine, commercial Landrace (LR), and Yorkshire × Landrace (Y × L) populations. One hundred and thirty-nine pigs were genotyped using an 80K SNP BeadChip. Morphometric monitoring at 18 months showed no significant differences in body weight, length, height, or heart girth between XENO and MGH pigs (all p > 0.05). Principal component and phylogenetic analyses separated the four groups into distinct genetic clusters, confirming the uniqueness of the XENO line. Chromosome-wide linkage disequilibrium was markedly higher in XENO (initial r² > 0.8; half-decay ≈ 50 kb) than in commercial lines, reflecting intensive inbreeding. Linkage disequilibrium-derived historical effective population size (N_e) in XENO was approximately 1.5-fold lower than in LR/Y × L, but comparable to MGH. ADMIXTURE analysis supported K = 3 ancestral components with <2% introgression into XENO. These findings demonstrate that closed-herd management preserves phenotypic uniformity while establishing a genetically homogeneous, independent donor line. XENO pigs exhibited overlapping growth trajectories with MGH animals, providing a genomically stable resource for preclinical xenotransplantation.