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Results for “Genomic inbreeding coefficient”

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PubMed2026

Genomic inbreeding coefficients and inbreeding depression of semen production traits at genome-wide and chromosomal levels in Japanese Holstein bulls.

We aimed to estimate inbreeding coefficients and the effects of inbreeding depression on semen production traits at both the genome-wide and chromosomal levels. We utilized pedigree data for 19,921 animals, single nucleotide polymorphism (SNP) data on 5700 Japanese Holstein bulls, and 52,193 semen collection records from 775 bulls. We estimated 4 different inbreeding coefficients, namely a pedigree-based coefficient (FPED) and 3 genomic coefficients derived from SNP data. The genomic coefficients consisted of one based on the genomic relationship matrix (FGRM), one based on runs of homozygosity (ROH), and one based on homozygous-by-descent (HBD) segments (FHBD). These genomic coefficients were estimated at both the genome-wide and chromosomal levels. Furthermore, we investigated the effects of these coefficients on semen production traits: semen volume (VOL), sperm concentration (CON), sperm number (NUM), and sperm motility (MOT). In the genome-wide-level analysis, inbreeding coefficients increased markedly in bulls born after 2009, coinciding with the introduction of genomic selection. Significant inbreeding depression of VOL was found. At the chromosomal level, the inbreeding coefficients for most chromosomes showed a similar trend to the genome-wide metrics, although some (e.g., chr10 and chr20) exhibited a more pronounced trend. Suggestive inbreeding effects were detected on specific chromosomes for all traits (chr1 and chr22 for VOL, chr24 and chr29 for CON, chr1, chr12, and chr27 for NUM, chr10 and chr18 for MOT), including the traits that were not significant at the genome-wide level. Our results highlight that chromosomal-level analysis provides information complementary to whole-genome metrics, offering a more detailed perspective for managing inbreeding effects. To mitigate the adverse effects of inbreeding on semen production traits, future breeding programs would benefit from the control of inbreeding effects on high-risk chromosomal regions.

Genomic inbreeding coefficient↗

PubMed2024

Detecting inbreeding depression in structured populations.

Measuring inbreeding and its consequences on fitness is central for many areas in biology including human genetics and the conservation of endangered species. However, there is no consensus on the best method, neither for quantification of inbreeding itself nor for the model to estimate its effect on specific traits. We simulated traits based on simulated genomes from a large pedigree and empirical whole-genome sequences of human data from populations with various sizes and structures (from the 1,000 Genomes project). We compare the ability of various inbreeding coefficients ([Formula: see text]) to quantify the strength of inbreeding depression: allele-sharing, two versions of the correlation of uniting gametes which differ in the weight they attribute to each locus and two identical-by-descent segments-based estimators. We also compare two models: the standard linear model and a linear mixed model (LMM) including a genetic relatedness matrix (GRM) as random effect to account for the nonindependence of observations. We find LMMs give better results in scenarios with population or family structure. Within the LMM, we compare three different GRMs and show that in homogeneous populations, there is little difference among the different [Formula: see text] and GRM for inbreeding depression quantification. However, as soon as a strong population or family structure is present, the strength of inbreeding depression can be most efficiently estimated only if i) the phenotypes are regressed on [Formula: see text] based on a weighted version of the correlation of uniting gametes, giving more weight to common alleles and ii) with the GRM obtained from an allele-sharing relatedness estimator.

Humans↗

PubMed2026

Genotypic and phenotypic consequences of domestication in dogs.

Runs of homozygosity (ROH) are genomic regions that arise when identical haplotypes are inherited from a shared ancestor. In this study, we explored ROH across 556 whole-genome sequences from domesticated and non-domesticated dogs. Then, we leveraged ROH from 466 breed dogs, representing 13 breed groups and 13 phenotypic traits, to investigate associations between genetic diversity and non-disease phenotypes. We identified significant associations between the ROH-based inbreeding coefficient (FROH) and multiple phenotypes. These include three quantitative traits (height, weight, lifespan) and ten morphological and coat-related traits. After correcting for population structure, we identified more than 45 genes associated with quantitative traits that exceeded suggestive or genome-wide significance (GWS) thresholds. We also observed distinct patterns of inbreeding across dog populations, including elevated levels of long ROH in modern breed dogs relative to more ancient breeds, consistent with intensive breeding practices during Victorian-era breed formation. Together, our results demonstrate how domestication, demographic bottlenecks, and selective breeding have shaped patterns of homozygosity and contributed to the genetic architecture of complex traits in dogs, highlighting an important role for non-additive genetic variation and polygenicity.

Animals↗

PubMed2026

Targeted population genomics uncovers demographic history and genetic divergence in north American wild cranberry.

Wild populations of North American cranberry (Vaccinium macrocarpon Aiton) are reservoirs of genetic variation that may contribute to the improvement of breeding-relevant traits. However, the extent to which wild genetic variation is geographically structured and represented in elite germplasm remains unclear. We analysed 179 wild cranberry accessions from the upper Midwest and Eastern North America to estimate nucleotide diversity (π), population structure, and loci associated with genetic differentiation and environmental variables using a genome-informed targeted genotyping panel. Additionally, 14 demographic scenarios were evaluated using site-frequency-spectrum-based inference to identify historical events that could explain current genetic diversity. We observed extremely low nucleotide diversity within the targeted panel (π = 5 × 10-6). Rare allele distributions strongly influenced π and Tajima's D values, suggesting constrained diversity in the genomic regions assayed that is not captured by heterozygosity-based estimates alone. However, we interpreted these results as conservative lower bounds on genome-wide neutral diversity because the targeted panel is enriched for genic and conserved regions. A clear separation between the Midwest and East populations was observed, with inbreeding coefficients ranging from -0.13 to 0.15. Furthermore, site frequency spectrum inference from the targeted panel supported a demographic scenario consistent with a significant population reduction ≈15-14 thousand years ago (kya), followed by a divergence between the two regions ≈12 kya, and an asymmetric gene flow ≈1.3 kya. We detected 254 candidate loci showing regional allele-frequency differentiation. Several of these loci colocalized with candidate genes linked to stress response, development, and metabolic processes. To evaluate the representation of geographically differentiated wild alleles in a breeding context, we analysed Rutgers breeding materials (n = 484) and found that this panel is enriched for common alleles in Eastern wild populations. These findings indicate regionally structured allele-frequency variation in wild cranberry, with potential relevance to environmental response and breeding. This study extends prior wild cranberry population-genetic research by providing targeted-panel estimates of diversity, comparisons of demographic models, and breeding insights on geographically differentiated alleles, while highlighting the importance of conserving wild cranberry germplasm for use in modern breeding programs.

Journal Article↗

PubMed2008

Runs of homozygosity in European populations.

Estimating individual genome-wide autozygosity is important both in the identification of recessive disease variants via homozygosity mapping and in the investigation of the effects of genome-wide homozygosity on traits of biomedical importance. Approaches have tended to involve either single-point estimates or rather complex multipoint methods of inferring individual autozygosity, all on the basis of limited marker data. Now, with the availability of high-density genome scans, a multipoint, observational method of estimating individual autozygosity is possible. Using data from a 300,000 SNP panel in 2618 individuals from two isolated and two more-cosmopolitan populations of European origin, we explore the potential of estimating individual autozygosity from data on runs of homozygosity (ROHs). Termed F(roh), this is defined as the proportion of the autosomal genome in runs of homozygosity above a specified length. Mean F(roh) distinguishes clearly between subpopulations classified in terms of grandparental endogamy and population size. With the use of good pedigree data for one of the populations (Orkney), F(roh) was found to correlate strongly with the inbreeding coefficient estimated from pedigrees (r = 0.86). Using pedigrees to identify individuals with no shared maternal and paternal ancestors in five, and probably at least ten, generations, we show that ROHs measuring up to 4 Mb are common in demonstrably outbred individuals. Given the stochastic variation in ROH number, length, and location and the fact that ROHs are important whether ancient or recent in origin, approaches such as this will provide a more useful description of genomic autozygosity than has hitherto been possible.

Adolescent↗

PubMed2025

Genomic diversity and selection signatures in Asian Zebu Cattle: insights into adaptation and genetic erosion.

Indigenous cattle breeds in Asia are highly adapted to their local environments providing essential commodities such as meat, milk and draught power while also playing a key role in traditional ceremonies, and sports. Despite ongoing efforts to characterize and conserve these breeds, the increasing trend of indiscriminate crossbreeding of Zebu cattle with high-yielding taurine breeds, threatens their genetic diversity. This study investigates the population structure, inbreeding levels, effective population size, gene flow and identification of selection footprints of Asian Zebu (Bos indicus) cattle. Using an Axiom 60 K SNP chip, we analyzed genotypes from 1303 cattle across 36 populations in nine countries, including seven taurine outgroups and 29 Zebu populations from Bangladesh, Cambodia, India, Myanmar, Pakistan, and Sri Lanka. Zebu populations demonstrated moderate genetic diversity, with heterozygosity levels averaging 0.356, inbreeding coefficients ranging from 0.026 to 0.074 and genetic differentiation (FST) varied between 0.01 and 0.11. Breed clusters aligned closely with their geographic locations except for Achai (Pakistan) and Baru Harak (Sri Lanka) breeds that appeared in both Zebu and taurine clusters indicating evidence of taurine admixture. Genomic analyses identified regions under selection using extended haplotype homozygosity (EHH) and fixation index (FST) methods. Candidate genes associated with key biological functions related to environmental responsiveness, including heat tolerance (HSP90AA1), immunity (RIPK3), metabolism and fertility (REC8, CLIC4, TSSK4), were identified, reflecting adaptive traits critical for Zebu survival and utility across diverse environments. These findings provide valuable insights for conservation and management strategies aimed at preserving the unique genetic diversity of Asian Bos indicus breeds.

Animals↗

PubMed2025

Genotypic and phenotypic consequences of domestication in dogs.

Runs of homozygosity (ROH) are genomic regions that arise when two copies of identical haplotypes are inherited from a shared common ancestor. In this study, we leverage ROH to identify associations between genetic diversity and non-disease phenotypes in Canis lupus familiaris (dogs). We find significant association between the ROH inbreeding coefficient (FROH) and several phenotypic traits. These traits include height, weight, lifespan, muscled, white coloring of the head and chest, furnishings, and fur length. After correcting for population structure, we identified more than 45 genes across the examined quantitative traits that exceed the threshold for suggestive significance. We observe distinct distributions of inbreeding and elevated levels of long ROH in modern breed dogs compared to more ancient breeds, which aligns with breeding practices during Victorian era breed establishment. Our results highlight the impact of non-additive variation and of polygenicity on complex quantitative phenotypes in dogs due to domestication and the breed formation bottleneck.

GWAS↗

PubMed2026

Genomic diversity, inbreeding, and selection signatures in duroc, landrace, and yorkshire pigs from a long-term closed breeding system.

Duroc (DD), Landrace (LL), and Yorkshire (YY) are among the most widely used commercial pig breeds, having undergone intense long-term selection within closed breeding systems. This study presents a comprehensive genomic analysis of genetic diversity, inbreeding patterns, and selection signatures in DD, LL, and YY populations that have been subject to close breeding for over 15 years. Genomic and pedigree data were available for 1,088 animals (DD = 348, LL = 276, YY = 464), genotyped using the GenoBaits® Porcine 100 K SNP panel. Principal component analysis and genetic diversity metrics revealed distinct population structures among the three breeds. Pairwise genetic differentiation supported this pattern, with DD showing the greatest divergence from LL (0.34 ± 0.24) and YY (0.33 ± 0.24), while LL and YY were more closely related (FST = 0.22 ± 0.19). Linkage disequilibrium (LD) analysis further confirmed these differences, as DD exhibited the highest average r² (0.34), followed by LL (0.28) and YY (0.25). Within-breed genetic diversity metrics, including observed heterozygosity (HO: 0.37 in DD, 0.39 in LL, 0.38 in YY), expected heterozygosity (HE: 0.36 in DD, 0.37 in LL, 0.38 in YY), and minor allele frequency (MAF: 0.27 in DD, 0.28 in LL, 0.29 in YY), indicated greater genetic variability in LL and YY compared to DD. Runs of homozygosity (ROH) analyses revealed different patterns of autozygosity, with DD exhibiting more long ROH indicative of recent inbreeding, while YY harbored a higher number of short ROH, suggestive of more ancient demographic events. ROH-based inbreeding coefficients (FROH) consistently exceeded pedigree-based estimates (FPED) across all breeds, highlighting the presence of recent or unrecorded inbreeding that pedigree data may not fully capture. According to Generation Proxy Selection Mapping (GPSM), 17, 1, and 12 significant SNPs were detected in DD, LL, and YY, respectively. Functional annotation of ROH islands and GPSM-significant loci revealed both breed-specific and overlapping QTLs related to traits such as growth, reproduction, and carcass. In general, the findings of this study contribute to a deeper understanding of the genomic consequences of long-term closed breeding and provide reference information to support consideration of breeding strategies that balance continued selection for productivity with the maintenance of genetic diversity in modern commercial pig populations.

Animals↗

PubMed2026

Genetic diversity of Plasmodium falciparum helical interspersed subtelomeric (phistb) gene in Tanzania and neighboring countries.

BACKGROUND: Lysine-rich membrane associated Plasmodium helical interspersed subtelomeric gene (phistb) is a member of the phist family of genes which encodes exported proteins essential for the parasite's survival within infected red blood cells. Recent studies suggest the phistb gene as a promising malaria vaccine candidate, however, its genetic diversity remains understudied. This study assessed the genetic diversity of the phistb gene in regions of varying malaria transmission aiming to generate data and improve our understanding of this promising malaria vaccine candidate gene. METHODS: Genomic data from 1472 Plasmodium falciparum samples from Tanzania, Kenya, Uganda, and Ethiopia were retrieved in variant Calling file format (VCF) format from the MalariaGEN Pf7 database. Variants were filtered to include only biallelic Single Nucleotide Polymorphism (SNPs) with Variant Quality Score Log- Odds (VQSLOD) > 1 and "PASS" status. Genetic diversity, differentiation, and selection signatures were analyzed using population genetics metrics. RESULTS: After filtering, 1312 samples were retained. Wright's inbreeding coefficient (Fws) showed that 875 (66.7%) samples had monoclonal infections, with the highest proportion of monoclonal infections in Ethiopia (95.3%), followed by Tanzania (67.2%), Kenya (65.7%), and Uganda (50%). Among the 875 monoclonal samples, 88 haplotypes were identified, with Hap_1 (renamed PF3D7) and Hap_13 comprising 37.9 and 21.5 of the samples, respectively. Nucleotide and haplotype diversity were relatively higher in Kenya with 0.097, and 0.88 respectively, compared to the other study populations. The overall fixation index (Fst) was < 0.05, and Principal Component Analysis revealed no clear population sub-structure among countries. Negative Tajima's D values in Tanzania, Kenya, and Ethiopia indicated an excess of low-frequency alleles. CONCLUSION: This study reports low genetic diversity of the phistb gene in the four countries despite varying malaria transmission intensities among them, thus making it a suitable candidate gene for malaria vaccine. Further studies should be conducted to assess individual antibodies recognition of the phistb variants and the ability to elicit cross reactivity to further support its potential as a vaccine candidate.

Plasmodium falciparum↗

PubMed2026

Fine-Scale Population Genomics Reveals Genetic Differentiation in the Brooding Amphipod Cheirimedon femoratus Across the South Shetland Islands, Antarctica.

Antarctic marine ecosystems are sensitive to environmental change, and impacts on processes such as population connectivity will play a fundamental role in future population dynamics and persistence, affecting short-term demography and long-term evolution. We investigated the population genomics of the common benthic brooding Antarctic amphipod Cheirimedon femoratus (Pfeffer, 1888), using 8837 high-quality single-nucleotide polymorphisms (SNPs) from 87 individuals collected at 4 sites in the South Shetland Islands, separated by up to 200 km: Deception Island, King George Island, Livingston Island, and Snow Island. While Admixture, F ST, principal component analysis (PCA), and demographic (Ne) analyses revealed a generally weak population genetic structure, Livingston Island emerged as a distinct population, especially compared to King George Island. All populations showed a heterozygote deficit with positive inbreeding coefficients (F IS), particularly high in the Snow Island population (~0.55). Tajima's D test suggested overall neutral evolution, although slight variation was observed among sites. Despite the limited dispersal potential of this brooding species, the observed connectivity may be maintained through passive dispersal, likely via floating macroalgae or ice-rafted debris, facilitated by prevailing regional ocean currents. This may enhance the population resilience of Antarctic benthic communities under environmental change, including regional warming and shifts in ocean circulation, compared to more isolated populations. Our findings underscore the complex interplay between passive connectivity and fine-scale differentiation in shaping Antarctic benthic invertebrate diversity.

Amphipoda↗