Abstract
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 (Ne) 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.
Introduction
Xenotransplantation—the transplantation of cells, tissues, or organs between species—has emerged as a leading solution for the global shortage of human donor organs. Among possible donor species, pigs are considered the most promising because of their anatomical and physiological similarities to humans, rapid reproductive cycles, and amenability to precise genetic modifications. 1 These attributes have allowed sustained survival in preclinical primate models and enabled the world’s first clinical pig-to-human transplantation using extensively gene-edited donors. 2
A major immunological barrier to pig-to-human transplantation is hyperacute rejection (HAR) caused by human antibodies targeting the alpha-Gal epitope produced by the enzyme alpha-1,3-galactosyltransferase (GGTA1). 3 GGTA1-knock-out (GTKO) pigs successfully eliminate this xenoantigen and show significantly reduced early immune rejection.4,5 Historically, GTKO has been critical in preventing HAR. However, with this primary immunological hurdle being addressed, delayed xenograft rejection has emerged as a major barrier to long-term graft survival. Since then, xenotransplantation models have incorporated additional gene knock-outs, such as CMAH and B4GALNT2, and transgenes encoding human complement and coagulation regulators to prolong graft survival. 6
The XENO pig line used in this study was established by recloning postmortem ear fibroblasts from a GTKO Chicago miniature pig, 7 followed by a single cross with Landrace (LR) pigs. It was subsequently maintained for at least 11 generations of inbreeding. Morphometric analysis of the XENO lineage confirmed predictable scaling of kidney and heart dimensions relative to body weight, validating its anatomical suitability for transplantation research. 8 In parallel, the Massachusetts General Hospital (MGH) miniature swine, developed through selective inbreeding to fix swine leukocyte antigen (SLA) haplotypes, which are commonly used in preclinical xenotransplantation studies, was included as a reference model because of its well-characterized immunogenetic background. 9
Because each new edit is introduced into a limited founder population, maintaining genomic integrity is critical, because a narrow founder base might reduce the effective population size and exacerbate genetic drift over generations. According to Korea’s national guidelines 10 on xenotransplantation products, source pigs must be managed under closed-herd conditions with a traceable pedigree and regular genomic monitoring to prevent transgene segregation and control inbreeding. Although the genetic background of MGH pigs has been well documented, the long-term genomic stability of XENO colonies has not yet been characterized in direct comparison with other donor sources.
In the present study, we assessed the population genomic structure of GTKO-based XENO pigs (generations 7–11) relative to that of MGH, purebred LR, and Yorkshire × Landrace (Y × L) crossbred pigs. Using 67,283 genome-wide single nucleotide polymorphisms (SNPs), we performed principal component analysis (PCA), linkage disequilibrium decay profiling, estimation of effective population size (Ne), phylogenetic reconstruction, and ancestry inference via ADMIXTURE. This analysis aimed to evaluate whether the XENO line maintained genetic uniformity while remaining distinct from other reference donor populations relevant to xenotransplantation.
Materials and methods
Ethics approval
The protocols and standard operating procedures for the treatment of the pigs used in this study were reviewed and approved by the Institutional Animal Care and Use Committee of the National Institute of Animal Science, Rural Development Administration of Korea (approval number: NIAS2024-0029). All methods were performed in accordance with the relevant guidelines and regulations of the committee. This study was conducted in accordance with ARRIVE 2.0 guidelines for transparent reporting of animal research.
Animals
The GTKO-based XENO pig line used in this study originated from a miniature pig referred to in Korea as the Chicago pig, also known as the Minnesota mini pig11 –13 by the National Swine Resource and Research Center in the United States. This breed was imported into Korea and genetically modified via somatic cell nuclear transfer to knock out GGTA1, thereby producing a single male GTKO founder (F0). 7 F0 males were subsequently mated with five LR females to generate the F1 generation. Closed breeding was maintained exclusively within the offspring population; F1 intercrosses produced F2, and subsequent generations were generated by breeding only within the population without introducing any external pig genetic material. Using this strategy, a genetically closed population was established and maintained as a closed herd through generation 11, resulting in what we define as the XENO pig line. For genetic comparisons over time, the XENO animals used in this study were divided into two subgroups: XENO_G1 (generations 7–9) and XENO_G2 (generations 10–11). For comparative purposes, three additional pig groups were included in the study: (1) MGH pigs, a closed population developed in the United States for xenotransplantation research; (2) LR pigs; and (3) Y × L pigs (Table 1). All XENO and MGH pigs were reared in individual pens (2.2 m × 3.6 m) within a controlled animal facility at the National Institute of Animal Science. For the LR and Y × L groups, blood samples were collected directly from the commercial farms for subsequent genetic analysis.
Summary of pig populations used for genetic diversity analysis.
LR: Landrace; MGH: Massachusetts General Hospital miniature pig; XENO_G1: XENO generations 7–9; XENO_G2: XENO generations 10–11; Y × L: Yorkshire × Landrace cross; GTKO: GGTA1-knock-out
Phenotypic growth comparison between XENO and MGH pigs
Body weight, shoulder height, body length, and heart girth were recorded every fourth Friday from birth to 18 months of age in both XENO and MGH miniature pigs. The sample sizes for each sex and time point are shown in Supplemental material Table 1 online. Body weight was measured using a calibrated electronic scale, whereas shoulder height and body length were assessed using a height stick and flexible measuring tape. All pigs were weaned at four weeks of age and reared under identical conditions at the National Institute of Animal Science, receiving a commercial grower diet (800 g/day from weaning onward) and ad libitum access to water. Health and welfare were monitored daily by trained animal-care staff and veterinarians. The monitoring program included observation of clinical signs of illness (e.g. respiratory distress and diarrhea), appetite, skin/coat condition, and mobility. Any deviation from normal behavior or physical health resulted in immediate veterinary intervention. For each trait, sex-specific trajectories (mean ± SEM) were plotted, and group differences across time points were analyzed using repeated-measures analysis of variance (ANOVA) (GraphPad Prism 5, La Jolla, California, USA).
DNA extraction and SNP genotyping
Whole blood (5 ml) was collected into K2-EDTA tubes and stored on ice until DNA extraction. Blood samples were analyzed within 24 h of collection. Blood samples from the LR and Y × L groups were purchased from nearby commercial pig farms and transported on ice. All the samples were processed within 4 h of collection. Cells were lysed overnight at 65°C in lysis buffer with gentle agitation, and genomic DNA was purified using a KingFisher Flex workstation (Thermo Fisher Scientific, Waltham, Massachusetts, USA). DNA concentration and purity (A260/A280) were verified with a µQuant™ plate reader (BioTek Instruments, Winooski, Vermont, USA); samples with A260/A280 = 1.8-2.0 and >20 ng µl−1 were stored at −20°C for downstream use. Genome-wide genotyping was performed using an Illumina Porcine 80 K BeadChip. Briefly, 200 ng DNA per sample was processed using an Infinium HD Ultra assay on an iScan system (Illumina, San Diego, California, USA). Genotypes were called in GenomeStudio v.2.0 and exported as PLINK PED/MAP files.
SNP quality control
PLINK v.1.9 14 was used to exclude SNPs with a call-rate <95%, minor-allele frequency <0.05, or Hardy–Weinberg equilibrium P < 1 × 10−6 within each breed. Samples with a call-rate <95% or excess heterozygosity (>±3 SD) were removed. After quality control, 67,283 high-quality SNPs from 139 pigs (XENO = 51, MGH = 47, LR = 20, Y × L, 21) were retained for analysis.
Population-genetic analyses
The SNP data were subjected to multiple population genetic analyses. PCA was conducted by generating eigenvectors in PLINK and visualizing them in R v.4.2.2, 15 with breeds color-coded to inspect clustering. To evaluate linkage disequilibrium and estimate historical Ne, pairwise r2 was computed in PLINK, and mean r2 values were plotted against physical distance in 5-kb bins to generate linkage disequilibrium-decay curves. Historical Ne was estimated using the Tenesa method implemented in SNeP v.1.1. 16 Pairwise Nei’s genetic distances were calculated using the R package StAMPP, 17 and neighbor-joining trees were constructed using the ape package and annotated by breed. To infer ancestral composition, a model-based approach using ADMIXTURE v.1.3, 18 a model-based clustering algorithm that estimates individual ancestry proportions based on multilocus genotype data, was run for K = 2–6 with fivefold cross-validation. K with the lowest cross-validation error was deemed optimal, and the ancestry proportions were plotted as stacked bars in R v.4.2.2. 15
Results
No significant differences in growth trajectories between XENO and MGH
Body weight, shoulder height, body length, and heart girth were monitored in both male and female pigs monthly for 18 months (Figure 1). Repeated-measures ANOVA detected no significant effects of line or line × sex interactions on any growth trait over the 18-month monitoring period (all p > 0.05). Although the mean values for XENO pigs were slightly lower at some time points, the overall trajectories of the XENO and MGH pigs were similar under identical management conditions.

Longitudinal growth trajectories of XENO and Massachusetts General Hospital (MGH) pigs. Mean ± SEM monthly measurements of ((a) and (e)) body weight (kilograms), ((b) and (f)) shoulder height (centimeters), ((c) and (g)) body length (centimeters), and ((d) and (h)) heart girth (centimeters) for male (top row; (a) to (d)) and female (bottom row; (e) to (h)) pigs monitored from 1 to 18 months. Repeated-measures analysis of variance detected no significant effect of line or line × sex interaction for any trait at any time point (all p > 0.05).
XENO forms a distinct genetic cluster
Genome-wide SNP-based PCA revealed three clearly separated clusters (Figure 2(a)): XENO_G1 + _G2, LR + Y × L, and MGH, with PC1 and PC2 explaining 41.8% and 32.9% of total variance, respectively. Population-level neighbor-joining trees (Figure 2(b)) and Nei’s pairwise distance heat-map (Figure 2(c)) mirrored the PCA, placing XENO_G1 and XENO_G2 in a single clade distinct from commercial LR and Y × L, and far removed from MGH. Individual-level phylogeny (Figure 2(d)) showed minor intermixing between XENO_G1 and XENO_G2, which was consistent with their closed-herd breeding history. PCA and phylogenetic metrics consistently positioned XENO as a unique cluster clearly separated from LR, Y × L, and MGH.

Population genetic structure of XENO and reference pig groups. (a) Principal component analysis of genome-wide single nucleotide polymorphism data; percentages indicate the variance explained by PC1 and PC2. (b) Neighbor-joining tree based on pairwise Nei’s genetic distance (Nei’s D) among five groups. (c) Heat map of pairwise Nei’s D (darker colors indicate greater genetic distance). (d) Individual-level neighbor-joining tree illustrating genetic relationships within and between groups. (e) Chromosome-wide heat map of linkage disequilibrium (r2), illustrating extended linkage disequilibrium blocks in XENO relative to the MGH pig line.
Closed breeding elevates linkage disequilibrium and reduces effective population size
A chromosome-wide linkage disequilibrium heat-map (Figure 2(e)) highlighted markedly longer linkage disequilibrium blocks in the XENO than in the MGH. The linkage disequilibrium-decay curves (Figure 3) confirmed this pattern: LR and Y × L exhibited rapid decay with r2 < 0.5 by ~20 kb, whereas XENO_G1, XENO_G2, and MGH retained strong linkage disequilibrium (initial r2 > 0.8) up to ~50 kb. XENO_G2 decayed the slowest, indicating increased homozygosity over generations. Ne estimates derived from linkage disequilibrium (Figure 4) were ~1.5-fold higher for LR and Y × L than for XENO and MGH; within the latter, XENO_G2 showed a further ~10% reduction relative to XENO_G1. Eleven generations of closed breeding in XENO had extended linkage disequilibrium blocks and halved Ne relative to commercial breeds.

Genome-wide linkage disequilibrium (LD) decay profiles. Mean pairwise r2 values are plotted against physical distance (kb) for the five pig groups. The rate of LD decay reflects the extent of historical recombination and population structure.

Effective population size (Ne) inferred from linkage disequilibrium. (a) Estimated Ne for each pig group at specific generations ago. The size of the circles corresponds to the estimated Ne value, with error bars representing the 95% confidence interval. (b) Trajectories of estimated Ne over generations ago for each pig group calculated using SNeP. The X-axis indicates generations ago (log scale), and the Y-axis represents the estimated Ne.
Admixture analysis supports three ancestral components
The cross-validation identified K = 3 as the optimal number of ancestral populations (Figure 5(a)). ADMIXTURE bar plots at this K (Figure 5(b)) assigned nearly identical ancestry proportions to XENO_G1 and XENO_G2, while LR and Y × L shared a second ancestry component, and MGH remained almost entirely unique, exhibiting <2% admixture from any other group. Thus, ADMIXTURE assigned XENO a nearly exclusive ancestry profile, confirming minimal introgression and the effectiveness of the closed breeding program.

ADMIXTURE analysis of population structure. (a) Cross-validation error rates for different numbers of ancestral populations (K = 1 to K = 10). The lowest cross-validation error indicates the optimal K. (b) Ancestry proportions for K = 2, K = 3, and K = 4 ancestral populations. Each vertical bar represents an individual pig, and colored segments indicate the proportion of ancestry derived from each inferred ancestral population.
Discussion
Xenotransplantation requires donor pigs that are immunologically compatible with humans and genetically uniform to ensure reproducible preclinical outcomes. Here, we benchmarked the newly established XENO line against the long-standing MGH model, commercial LR and Y × L lines, and literature values for wild boars.
No significant line effect was detected for any growth trait over the 18-month monitoring period (all p > 0.05); the growth trajectories of the XENO and MGH pigs overlapped, indicating similar phenotypic development under identical management conditions.
Principal component, neighbor-joining, and Nei’s distance analyses consistently placed XENO_G1 and XENO_G2 in a single compact clade that was clearly separated from both the LR and Y × L clusters and the MGH lineage. The tight clustering of the two XENO generations showed that 11 generations of closed breeding have stabilized the genome.
These findings fit within the broader domestication landscape: wild boars retain expected heterozygosity (He) values up to 0.80, far above commercial breeds such as Hampshire (He ≈ 0.53).19,20 Commercial Landrace and Yorkshire populations typically show mean r2 values of 0.36–0.39 and Ne below 50, whereas XENO pigs form an even more compact cluster owing to targeted inbreeding for xenotransplantation traits. 21 The chromosome-wide linkage disequilibrium heat-map (Figure 2(e)) and linkage disequilibrium-decay curves (Figure 3) show that XENO retains haplotype correlations over roughly twice the physical distance observed in LR/Y × L. Linkage disequilibrium-derived estimates place Ne for XENO_G2 at ~10% lower than XENO_G1 and roughly half that of commercial reference lines (Figure 4). To further contextualize the genomic tightening observed across generations, we compared historical Ne between XENO_G1 and XENO_G2. Both snapshots and longitudinal representations (Figure 5(a) and (b)) revealed a declining trend, consistent with the progressive loss of recombination due to continued inbreeding. This Ne contraction reinforces the importance of regular genomic surveillance to prevent fixation of deleterious alleles while preserving the desired xenotransplantation traits. Progressive extension of linkage disequilibrium blocks is expected with sibling and parent–offspring matings, which are used to maintain the line.
Elevated linkage disequilibrium simplifies the genome-wide association study within XENO by reducing the marker density required, but increases the risk that deleterious alleles will hitch alongside favorable edits. Therefore, routine genomic surveillance is essential to sustain health and fertility.
Cross-validation pinpointed K = 3 ancestral components corresponding to XENO, LR, Y × L, and MGH. XENO_G1 and XENO_G2 harbored <2% non-XENO introgression, confirming the effectiveness of the closed breeding program. LR and Y × L exhibited reciprocal introgression consistent with their shared Landrace foundations. ADMIXTURE is a well-established and validated approach for ancestral-component inference in population genetic studies. 22 Using this method, we assessed the population structure of XENO and reference pig lines to examine the ancestral composition and potential genetic stratification across generations.
The extreme linkage disequilibrium and low Ne of XENO parallel those reported for the highly inbred MGH pigs (⩾7 generations of sib-mating; Ne ≈ 1), yet PCA shows that XENO and MGH occupy distinct genetic spaces. 23 This independence offers an alternative donor background that might lead to unforeseen epistatic interactions that limit either line.
These three avenues warrant further investigation. First, digital PCR and long-read sequencing should be used to quantify and, if necessary, delete residual porcine endogenous retroviral copies, as complete CRISPR excision has been proven feasible. 24 Second, full-length characterization of the SLA complex, including potential humanized alleles, will clarify graft rejection kinetics and guide donor-specific immunosuppression. 25 This increased genetic homogeneity is expected to reduce background genetic variation within the population, which might lower inter-individual variability in experimental outcomes. Under appropriate experimental conditions that account for effect size and variance, this reduction in variability has the potential to improve the sensitivity of statistical comparisons and thereby increase statistical power. Consequently, this model could support the principle of reduction by enabling fewer animals to be used in future preclinical xenotransplantation studies.
Conclusion
The XENO line is genetically homogeneous and phenotypically consistent under controlled management conditions. Its distinct genetic background relative to the MGH line provides an additional donor source for preclinical xenotransplantation research.
Supplemental Material
sj-docx-1-lan-10.1177_00236772261432004 – Supplemental material for Population-genomic stability of a closed-herd GGTA1-knock-out miniature pig line for xenotransplantation
Supplemental material, sj-docx-1-lan-10.1177_00236772261432004 for Population-genomic stability of a closed-herd GGTA1-knock-out miniature pig line for xenotransplantation by Won Kil Lee, Sang Eun Kim, Dongwon Seo, Seunghoon Lee, Jin-Gu No, Seokho Kim, Min Hwa Do, Joo Young Lee, Namwoong Hyeong, Hwi-Cheul Lee, Poongyeon Lee and Keon Bong Oh in Laboratory Animals
Footnotes
Author contributions
Won Kil Lee: formal analysis, data interpretation, visualization, and writing of the original draft
Sang Eun Kim: investigation, animal handling, sample collection;
Dongwon Seo: methodology, software, visualization
Sangwon Yoon: methodology, software;
Seunghoon Lee: investigation, animal handling, visualization;
Jin-Gu No: animal measurement, data generation;
Seokho Kim: investigation, sample collection;
Min Hwa Do: genotyping, laboratory support;
Joo Young Lee: animal handling, measurement, data generation;
Namwoong Hyeong: animal handling, measurement, sample collection;
Hwi-Cheul Lee: conceptualization, formal analysis, data interpretation, supervision, project administration, and acquisition;
Poongyeon Lee: conceptualization, data interpretation, supervision, project administration, acquisition;
Keon Bong Oh: conceptualization, supervision, project administration, acquisition, writing—review and editing, and funding acquisition.
All authors read and approved the final manuscript.
Data availability statement
Genotyping data and analysis scripts will be made available in Zenodo under DOI (to be provided upon publication).
Declaration of conflicting interests
The authors declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.
Funding
The authors disclosed receipt of the following financial support for the research, authorship, and/or publication of this article: This research was supported by a grant from the Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health and Welfare, Republic of Korea (grant number: RS-2023-KH135861).
Supplemental material
Supplemental material for this article is available online.
References
Supplementary Material
Please find the following supplemental material available below.
For Open Access articles published under a Creative Commons License, all supplemental material carries the same license as the article it is associated with.
For non-Open Access articles published, all supplemental material carries a non-exclusive license, and permission requests for re-use of supplemental material or any part of supplemental material shall be sent directly to the copyright owner as specified in the copyright notice associated with the article.
