Breast cancer (BC) is closely linked to coronary heart disease (CHD), yet the genetic causal relationship and common driving mechanism between the two have not been fully elucidated. The purpose of this study is to infer the causal relationship between BC and CHD at the genetic level and identify the cross-omic molecular characteristics of them through the integrated analysis of multiple genomics. Firstly, large-scale Genome Wide Association Study (GWAS) data were used for bidirectional Mendelian randomization (MR) analysis. Secondly, multi-center transcriptome data were integrated and combined with differential expression analysis (DEGs) and weighted gene co-expression network analysis (WGCNA) to screen for key comorbidity genes. Univariate, Least Absolute Shrinkage and Selection Operator (LASSO), and multivariate Cox regression analyses were used to construct a prognostic model. The Benjamin Hochberg method was used for False Discovery Rate (FDR) correction. Finally, molecular pathways were explored through Gene Set Enrichment Analysis (GSEA), and key genes were validated using quantitative real-time polymerase chain reaction (qRT-PCR) in independent clinical samples. MR analysis revealed a significant positive correlation between BC and CHD in Asian populations (OR = 1.095, 95
Defensins are key innate immune proteins exhibiting pleiotropic functions such as antibacterial activity, antiviral activity, anti-inflammatory activity, immunomodulatory functions, and roles in reproduction. Genomic information inadequately explains the whole gamut of the landscape of β-defensin in Bubalus bubalis and Ovis aries genomes. This study investigates the sequence evaluation and evolutionary relationships of β-defensin with 131 complete sequences in buffalo, sheep, and human. Sequence and domain-based analyses revealed diverse patterns of disulfide bridges and multiple signature patterns, including N- and O-glycosylation sites, N-myristoylation sites, and protein kinase C phosphorylation sites, indicating extensive post-translational regulation involved in various antimicrobial activities, signaling pathways, and reproduction. Phyre2-based 3D structural modeling, followed by PyMOL visualization, revealed β-strands stabilized by cysteine disulfide bonds and a short N-terminal α-helix. Variation analysis of β-defensin sequences identified unique allelic variants with several conserved amino acid positions. All sequences shared the characteristic six conserved cysteine residues, along with conserved glycine (G) in the GXC motif and glutamic acid (E), which contribute to structural stability and proper protein folding. We report sixteen amino acid sites depicting 9 distinct types of mutations within the cysteine residues, with most frequent substitutions of C→S (5/16) and C→P (3/16) amino acids. Phylogenetic and domain-based analyses across humans, sheep, and buffalo revealed eight major clusters, of which cluster I was found to be most diverse (36/131). Altogether, we provide a comprehensive analysis of β-defensin protein sequences revealing conserved features, functional motifs, and evolutionary relationships underpinning the functional role of β-defensins.
TAPBP is a key chaperone of the peptide-loading complex that facilitates peptide loading onto major histocompatibility complex class I (MHC I) molecules. This study characterized TAPBP alleles in Korean Native Chickens (KNCs), identified novel variants, and evaluated allelic associations with BF2. Thirty-six samples representing six KNC lines were genotyped using LEI0258 and the MHC-B SNP panel, and individuals homozygous at both markers were classified into 16 groups. The same samples were subjected to Sanger sequencing of TAPBP exons 3-8. Sequences were assembled and aligned against MHC-B reference alleles of the TAPBP gene and the Red Junglefowl reference. Additional comparisons with “tapasin allele” datasets enabled the identification of novel variants. Six novel nucleotide variants were detected across exons 3-6, including one nonsynonymous substitution in exon 4 (D251H). This residue corresponds to position Q265 in human TAPBP and lies adjacent to residues involved in MHC I interaction, suggesting potential functional relevance. Furthermore, TAPBP exhibited high haplotype diversity (Hd = 0.93) and moderate nucleotide diversity (π = 0.00892), with exon 5 showing the highest diversity (π = 0.01). B9 was the most frequent allele at the nucleotide level, whereas B6/B24 predominated at the amino acid level. Comparison with BF2 data revealed allele-dependent pairing patterns: BF2-B9 consistently matched TAPBP-B9, whereas BF2-B6 was associated with distinct TAPBP nucleotide variants, indicating allelic diversification. Homozygosity at LEI0258 and the SNP panel corresponded with TAPBP homozygosity, supporting marker-based prediction. These findings highlight potential BF2-TAPBP associations and provide a foundation for understanding variation in MHC I peptide loading.
Understanding how environmental heterogeneity drives spatially varying selection is key to deciphering adaptive evolution. The Major Histocompatibility Complex (MHC) provides an ideal model to study this process. We investigated the MHC class II DQA gene across seven subspecies of wild argali sheep (Ovis ammon) in China. High-throughput sequencing of 98 individuals revealed high diversity (25 alleles), with balancing selection maintaining allelic richness and trans-species polymorphism indicating long-term balancing selection. Molecular evolutionary analyses uncovered heterogeneous positive selection on antigen-binding sites among subspecies (ω = 1.181-3.000), mirroring variable pathogen-driven pressures. Mantel tests detected no significant isolation-by-distance or isolation-by-environment. However, Spearman correlations identified significant associations between specific alleles (e.g., Ovam-DQA*08) and climatic variables, as well as between allele frequencies and MaxEnt-predicted suitability. Redundancy analysis showed that temperature and precipitation explained 54.7
The major histocompatibility complex (MHC) plays a central role in vertebrate adaptive immunity by encoding receptors that recognize pathogen-derived antigens. Migratory shorebirds, such as the Hudsonian Godwit (Limosa haemastica), encounter diverse pathogen landscapes across a wide range of habitats along their migratory routes. Therefore, migratory birds are expected to maintain a robust and effective immune system that minimizes the effects of infection without compromising their migration performance. We examined the genetic diversity of MHC class I exon 3 and MHC class IIB exon 2 across the species range. A total of 57 MHC-I and 13 MHC-IIB alleles were identified, with high polymorphisms observed in the peptide-binding regions (PBR). Signatures of positive selection were more pronounced in PBR sites from MHC-I than from MHC-IIB, suggesting stronger selective pressure from intracellular pathogens. In contrast, the relatively low allelic diversity and weaker selection signatures of MHC-IIB may reflect reduced exposure to extracellular pathogens. Despite broad geographic sampling, no evidence of an adaptive population structure was detected, indicating limited local adaptation and the likely influence of gene flow or neutral processes. Phylogenetic analyses revealed that some L. haemastica alleles clustered with those from closely related Scolopacidae species. These findings highlight the importance of pathogen-mediated selection in shaping MHC variation, providing valuable insights into the variability of a key group of adaptive immune genes in exceptional avian migratory species facing growing environmental pressure.
Pemphigus vulgaris (PV) is a rare autoimmune blistering disease mediated by pathogenic autoantibodies. Although both HLA and non-HLA loci contribute to disease susceptibility, their combined roles in immune regulation remain incompletely understood. This study investigated the joint contribution of HLA-DRB1 and FCGR2B variants to PV susceptibility within an integrative immunogenetic framework. Genotype data from 286 individuals (200 controls and 86 PV patients) were analyzed using bias-reduced association models, two-locus genotype combination analyses, and cumulative genetic risk modeling. Gene-gene relationships were explored through epistasis testing, while functional relevance was examined using biological annotation approaches. HLA-DRB1*04:02 and *14:01 were significantly associated with increased PV risk, whereas *11:01 and *16:01 demonstrated protective effects after multiple testing correction (q < 0.05). The FCGR2B c.671T > C (I232T) variant showed a modest effect in single-locus analyses but did not remain statistically significant after correction for multiple testing. Several two-locus genotype combinations involving FCGR2B and HLA-DRB1 were enriched among patients; however, interaction analyses supported an additive immunogenetic architecture rather than epistasis. Genetic risk modeling demonstrated improved discrimination with weighted scores, and explainable machine-learning analysis identified HLA-DRB1 as the dominant predictor, with FCGR2B contributing a secondary modulatory signal. These findings delineate an additive immunogenetic framework underlying PV susceptibility, emphasizing the central role of HLA-DRB1. Although FCGR2B did not retain independent statistical significance after multiple-testing correction, the results suggest a potential modulatory contribution within the broader immunogenetic architecture of PV.
The humoral immune response relies on a diverse antibody repertoire, which is expanded through processes such as somatic hypermutation, class-switch recombination and gene conversion. These processes are primarily mediated by activation-induced cytidine deaminase (AID). Gene conversion generates diversity in immunoglobulin heavy and light chains (IGHVs) in species such as chickens and rabbits, though it has not been widely studied. Since 80% of the equine IGHV repertoire originates from only three functional gene segments, we examined gene conversion events in horses to assess their role in antibody diversification. Using a modified version of BrepConvert, which optimized analysis time, we identified gene conversion events in 6.9% of immunoglobulin sequences. The results showed a local preference, with most events occurring at the beginning of framework region 1 (FR1) and within complementarity-determining region 2 (CDR2). Pseudogenes IGHV4-35, IGHV4-53, and IGHV4-38 were utilized most frequently, while functional genes IGHV4-21, IGHV4-22, and IGHV4-29 exhibited the highest event frequencies. Interestingly, while most mismatched regions were only three nucleotides long, 91% of these events are flanked by specific sequences (six nucleotides at the 5' end and one nucleotide at the 3' end). Furthermore, functional pseudogene pairs often share identical leader regions of 5-26 nucleotides, suggesting expanded events. We also identified a potential association between these events and local non-B DNA conformations, as well as with the zinc finger protein ZNF691, which supports the involvement of DNA-binding factors. Together, these findings demonstrate that gene conversion significantly contributes to equine antibody diversity by targeting specific IGHV regions.
Major histocompatibility complex class II beta (MHC-class IIB) genes are highly polymorphic and play important roles in immune function, making them valuable DNA markers for efficient animal breeding and conservation management programs. However, MHC genetic information on king penguins (Aptenodytes patagonicus; Appa) in captivity remains limited. Here, we developed a Next Generation Sequencing (NGS)-based genotyping method to characterize MHC class IIB (Appa-CIIB) polymorphisms in 99 king penguins housed at Adventure World (Wakayama, Japan), identifying 72 novel Appa-CIIB alleles, each encoding a distinct amino acid sequence. Phylogenetic analysis classified these alleles into two major and one minor lineage, with peptide-binding regions in the main lineages showing signatures of positive selection. Thirty-four Appa-CIIB haplotypes composed of one to three Appa-CIIB loci, were inferred using individual management records (IMRs) from 123 individuals. Pedigree analysis revealed that 114 individuals belonged to a single extended family encompassing up to five generations, with the founders representing the first generation. Despite over 30 years of captive maintenance, population genetic analyses indicated that this population has retained high genetic diversity. The identification of multiple Appa-CIIB loci and copy number variations suggests that the Appa-CIIB region has undergone gene duplication and recombination events during evolution. These findings provide valuable insights into the genetics and evolutionary characteristics of Appa-CIIB genes and offer a practical framework for managing king penguin gene diversity in captivity, supporting future breeding programs that minimize inbreeding depression and maintain healthy populations.
The human leukocyte antigen (HLA) system underpins allorecognition and shapes the response to infection, autoimmunity, and treatment response. Technological advances from serology to next-generation sequencing now enable full-gene characterization and four-field HLA nomenclature, while artificial intelligence (AI) and machine learning are transforming the data generation, interpretation, and clinical use. This review summarizes the progress on the technical developments in the HLA era, which could be evaluated in three perspectives. First, we survey AI for antigen processing and T-cell recognition, including HLA–peptide binding, presentation, and T cell receptor (TCR)–epitope models, and outline their effects on applications like neoantigen discovery, vaccine design, and tolerance induction. Since there are still persistent gaps in immunogenicity prediction and coverage of rare alleles, secondly, we evaluated HLA imputation from the single nucleotide polymorphism (SNP) arrays and low-coverage whole-genome sequencing, highlighting deep learning models that improve accuracy for common and low-frequency alleles, and the critical role of diverse reference panels. Third, we assessed the AI-enabled transplant decision support: survival and graft-versus-host disease forecasting from registry data, donor ranking beyond simple allele match, and crossmatch compatibility prediction. We integrate emerging biology, non-classical HLA molecules, allele-specific expression, and HLA loss of heterozygosity, as key modulators of immune activation and evasion with implications for donor selection, infectious diseases, vaccinology, inflammatory disease, and cancer therapy. To accelerate safe clinical translation, we need to have standards for data governance, fairness auditing, validation and calibration, explainability, robustness, monitoring, and human oversight. By bridging core HLA principles with recent biological insights and AI innovations, we outline a path toward reproducible and equitable clinical translation to immunogenomics in transplantation, infectious, inflammatory, oncologic diseases, and precision vaccinology.
Chemokine receptor type 1 (CCR1) is expressed on several immune cells, including neutrophils, monocytes, and T cells. In rodents, a paralog of CCR1 was identified and called CCR1L1. Here, we studied the evolution of the CCR1 gene in mammals. Our results show that CCR1L1 is restricted to specific mammalian lineages, with muroids and ruminants each harbouring two CCR1-related paralogs. Topology tests do not unambiguously discriminate between independent duplications and an ancestral duplication followed by lineage-specific losses. Branch-site analyses revealed episodic positive selection acting on CCR1L1 lineages, including the basal branches of the two CCR1L1 clades. Moreover, we observed that selective regimes differ between the two CCR1L1 mammalian groups, with evidence for a shift in selection intensity in ruminants but not in muroids. We identified several amino acid changes in the structural components of chemokine receptors that are likely to impact the Ruminants CCR1L1 function. In Bos javanicus and Moschus berezovskii, CCR1L1 pseudogenes with premature stop codons were identified. Expression data indicate that Bos taurus, CCR1 is expressed in at least seven tissues, whereas CCR1L1 is only expressed in the lung. Together, these results suggest a complex evolutionary history for CCR1L1, involving duplication, lineage-specific selection, and, in some species, pseudogenization.
Integrating whole-genome sequencing with single-cell RNA-seq data enhances the current understanding of how genomic differences across humans contribute to variations in gene activity. eQTL discovery offers a potent method for decoding genomic regulation and identifying population-specific genomic variants associated with gene expression differences. The current development of single-cell sequencing technologies provides a significant opportunity for precise and detailed profiling of both major and minor cell states, facilitating the identification of genomic variants and their effects within specific cellular contexts. Therefore, this study aims to investigate the combined analysis of paired whole-genome and single-cell RNA-seq data from 230,000 peripheral blood mononuclear cells (PBMCs) across 30 individuals. Overall, 1,233,644 cis-eQTLs were identified across 18 cell types in PBMCs. The results were thoroughly evaluated through conservation analysis, revealing that the most statistically significant eQTLs are associated with less conserved genomic regions and are concentrated in the regulatory areas of more divergent genes. Using deep learning-based cis-regulatory models, cis-eQTLs were further investigated to reveal the cell-type-specific context of variant activity. The analysis revealed how eQTLs influence the expression of key immune-related genes (NKG7, HLA, MIF, MS4A1), identifying transcription factors whose binding sites are disrupted by genomic variants. This study integrates genetics, single-cell transcriptomics, and deep learning models to reveal and understand the role of genomic variants in gene expression regulation.
Within the bovine immune response, a distinct type of immunoglobulin (Ig), known as ultralong complementarity-determining region 3 (CDR3) antibodies, coexists alongside canonical Igs. These ultralong heavy chains (HC) feature a remarkable structure with a lengthened CDR3 of the heavy chain (CDR H3), allowing them to adopt either a smaller and more extended paratope than canonical antibodies. However, very little is known about the distribution of ultralong CDR H3s in cattle tissues and which isotypes they are ultimately associated with. This study analyzed and quantified the amplicons of the five immunoglobulin isotypes (IgM, IgD, IgG, IgA, and IgE) for both the canonical and ultralong CDR H3 throughout 24 Bos taurus tissues. IgH amplicons analysis identified an extensive repertoire of expressed canonical and ultralong CDR H3s of each isotype in most tissues. Ultralong cattle Igs were preferentially switched to the IgG isotype, especially in the medial retropharyngeal lymph node draining the immunization site. Additionally, B cells producing canonical Igs in bone marrow switched most to the IgG isotype. These data suggest that ultralong CDR H3 may be uniquely qualified to handle some antigens. A more comprehensive understanding of isotype and tissue-specific immune responses of these unusual antibodies can provide a deeper insight into their function within the overall cattle immune system, offering unique opportunities for innovations for in both bovine health and human immunotherapeutics.
Lymphomas are biologically heterogeneous malignancies with multifactorial etiologies involving genetic, environmental, and immune dysregulation. The functional variant rs1049174 SNP in the KLRK1 gene (encoding NKG2D) regulates NKG2D expression and modulates NK cells immune surveillance pathways, which may influence lymphoma susceptibility. We investigated this association through a two-stage case-control study and meta-analysis. First, we analyzed 246 diffuse large B-cell lymphoma (DLBCL) patients and 599 healthy controls (exploratory cohort), followed by a confirmatory cohort of 234 non-Hodgkin lymphoma (NHL)/Hodgkin lymphoma (HL) patients. Genotype frequencies were assessed via chi-square tests, with odds ratios (ORs) calculated for risk associations. A systematic review and meta-analysis of 10 studies, including our cohorts (3,785 cases and 4,129 controls), testing rs1049174 and cancer risk was also conducted. In the exploratory cohort, the GG genotype showed no significant association with overall lymphoma risk (OR = 0.83; 95
In vertebrates, cytidine-to-uracil (C-to-U) editing is mediated by the AID / APOBEC family of deaminases, with APOBEC1 ( A1 ) known to catalyse precise RNA editing of apolipoprotein B (apoB) transcripts in mammals. Despite its well-characterised role in mammals, the evolutionary history and functional divergence of A1 across birds remain underexplored. Here, we investigate the evolutionary trajectory of A1 in birds, where both the presence of the gene and apoB RNA editing activity have been questioned. Through a comprehensive in silico analysis of 81 avian genomes, we identify recurrent disruptions and catalytic inactivation of A1 in multiple lineages. Comparative sequence and structural analyses reveal a lack of domains and key residues essential for RNA binding, dimerisation, and cofactor interaction, suggesting a role in DNA editing. Furthermore, genome-wide screening for A1 -associated G-to-A mutations in long terminal repeat (LTR) retrotransposons demonstrates that species with higher endogenous retrovirus (ERV) loads retain more DNA editing signatures, consistent with a defensive role of A1 against retroelements. In contrast, species with low ERV content exhibit relaxed selection and frequent A1 pseudogenisation. Together, these findings support the hypothesis that DNA editing represents the ancestral function of A1 , with RNA editing in mammals evolving later as an exaptation following the expansion of A3 and changes in retroviral pressures.
The major histocompatibility complex (MHC) plays a central role in immune responses, with strong links to both infectious disease resistance and autoimmune conditions. In typical mammals, such as humans, the MHC is large and complex, comprising many genes and exhibiting weak associations with infectious diseases, but strong associations with autoimmunity. In contrast, the chicken MHC is small and simple, with only one dominantly-expressed class I and class II gene, and strong associations with resistance to infectious pathogens; however, its role in autoimmunity is less well understood. This raises a question: Does the simplicity of the chicken MHC reduce the risk of autoimmunity? In this speculative review, we explore the question by comparing chickens and typical mammals, and by considering the spectrum of MHC alleles from promiscuous generalists to fastidious specialists. We suggest that comparing the spectrum of alleles within a single species, such as chickens, may offer a way to test the link between MHC complexity and autoimmunity. Although much work remains, this approach could provide new insights into the balance between immune protection and self-tolerance.
Non-human primates are important for preclinical vaccine evaluation. In depth characterization of the antibody response requires representative immunoglobulin (IG) germline gene databases for correct gene and allele assignments and assessment of affinity maturation of antigen-specific antibodies. Current IG-reference databases do not cover the genetic diversity observed in frequently used macaque species and it is unclear to what extent closely related animals express shared alleles at similar levels. Here, IG-germline alleles of sixteen cynomolgus macaques (CynoSet), some of which were related, were characterized and compared with previously described Mauritian and Indonesian origin cynomolgus macaque datasets. Although the CynoSet showed more overlap with the Mauritian origin dataset, compared to an Indonesian origin dataset, there were clear differences in allelic expression patterns, independent of family relationship. Calculation of somatic hypermutation levels in post-infection influenza hemagglutinin-specific B cells demonstrated the need for individualized IG-genotyping for accurate evaluation of the antigen-specific B cell response.
The Sterile Alpha Motif Domain-containing 9 (SAMD9) and SAMD9-like (SAMD9L) are two paralogous genes responsible for important antiviral and antitumoral functions. While their functions and mechanisms have become well defined throughout years of research, research into their evolution has seemingly stagnated. In this work, we analysed the evolution of these two genes in primates. We have found that the evolutionary history of these two genes in primates is remarkably variable, with genome deletions, gene duplications, pseudogenes and translocations being identified, with roughly half of all analysed primate species having lost functional copies of one of these genes. Microcebus murinus lacks functional copies of both genes, having undergone a deletion of SAMD9L and the pseudogenization of SAMD9, making it the only currently known mammal to have no functional copy of either SAMD9 or SAMD9L. Hominidae and Cercopithecinae were found to be the only two primate families to have maintained both SAMD9 and SAMD9L in their functional forms, while the remaining primate families and wider clades preserved only one gene in its functional form: Colobinae have one functional SAMD9L and a pseudo-SAMD9; Platyrrhini have SAMD9L and lost SAMD9 and Strepsirrhini have lost SAMD9L, while preserving their SAMD9. Interestingly, SAMD9 underwent deletions and pseudogenizations multiple times in Haplorhini. We hypothesise that the frequent loss of primate SAMD9s may be related to their proviral effects in certain primate viruses, such as HIV-1, although functional studies must be performed to test our hypothesis.
The Major Histocompatibility Complex (MHC) is a gene-dense genomic region essential to adaptive immunity, exhibiting both conserved features and lineage-specific rearrangements across jawed vertebrates. Amphibians, as basal tetrapods, offer critical insights into MHC evolution; however, research has largely focused on anurans (e.g., Xenopus), while urodeles remain understudied, primarily due to their exceptionally large genomes. With recent advances in sequencing technologies, chromosome-scale assemblies for urodeles are now becoming available, opening new opportunities to explore their MHC architecture. Yet, the MHC region remains notoriously challenging to annotate due to its complexity, high polymorphism, and dynamic evolutionary history. For instance, the initial annotation of the axolotl (Ambystoma mexicanum) MHC relied heavily on synteny with mammalian genomes, which led to an overestimation of its size and misinterpretation of its structure. These inaccuracies have fueled evolutionary debates regarding the ancestral genomic structure of the MHC. Here, we present a comprehensive re-annotation of the axolotl MHC, revealing a typical organization found in tetrapods other than eutherian mammals: core MHC region with several, expressed MHC class I genes, tightly linked to their antigen processing genes, and to single loci of MHC class II genes. Contrary to the previous report, class I and class II genes are not separated by class III genes, and the overall MHC region is relatively compact (by axolotl genome standards). These findings correct earlier misconceptions and emphasize the need for annotation strategies that reflect the complex and lineage-specific nature of genomic regions rich in immune genes.
The present study aimed to evaluate lymphoid defects in patients with specific IEIs (n = 28) using a 12-antibody 9-color single-tube flow cytometry assay. The lymphoid defects (lymphocyte counts below the reference range) were significantly higher in XLA patients (p-0.0002), CVID patients (p-0.00022), WAS patients (p- < 0.001), HIES patients (p- < 0.001), CHS patients (p < 0.001), and CGD patients (p < 0.0002) than age-matched controls. The lymphoid defects (lymphocyte counts above the reference range) were significantly higher in LAD-1 than age-matched controls (p < 0.001). In patients with XLA, the NK cells were reduced in 50
The chicken major histocompatibility complex (MHC) represents a “minimal essential MHC” consisting of classical class I (BF) and class II (BL) molecules that present peptides to CD8+ cytotoxic and CD4+ helper T cells, respectively. Class I molecules, primarily encoded by the BF2 gene, are central to immune responses against pathogens. Moreover, these molecules show enormous genetic diversity driven by a molecular arms race with pathogens that determines peptide binding to the polymorphic α1 and α2 domains. Genotyping tools such as the 90-single nucleotide polymorphism (SNP) panel for the MHC-B region (BSNP) and the LEI0258 microsatellite marker have revealed MHC diversity in chickens but do not capture the variation within the α1 and α2 domains. In this study, six populations of Korean native chickens (KNC) were analyzed to assess BF2 gene diversity in individuals homozygous for both the BSNP panel and LEI0258 marker. Two standard BF2 alleles, B06 and B09, were identical while seven additional haplotypes showed high similarity to those found in KNC samples. A total of 30 novel SNPs were identified, with over half located in peptide-binding regions. Most variants overlapped with previously reported data from polymerase chain reaction (PCR) and next-generation sequencing (NGS), leading to the identification of four unique BF2 alleles in KNC. There was no clear relationship among BSNP, the LEI0258 marker, and the BF2 gene, but individuals homozygous for the first two markers also had a homozygous BF2 region. These findings provide insights into MHC diversity and immune potential in KNC populations, supporting conservation and breeding strategies for enhanced disease resistance.
