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At least 19 recordsLinked to original sources
PubMed2026

Host genetic regulation of xylem-resident Pseudomonas enhances cucumber growth.

BACKGROUND: Although endophytic microorganisms play a critical role in plant growth and stress resilience, the genetic basis underlying host selection of beneficial microbiota-particularly within the xylem-remains poorly understood. Cucumber (Cucumis sativus), as a crop model with a well-developed system for studying vascular biology, offers a valuable system to investigate the host genetic determinants of xylem microbiome assembly. RESULTS: By conducting population-level microbiome profiling across 109 cucumber accessions, we identified a conserved xylem microbiota dominated by Proteobacteria. Within this community, 20 core amplicon sequence variants (ASVs) were consistently present in xylem sap. Genome-wide association mapping identified a host genetic locus, CsXPR1, which encodes a tetratricopeptide repeat protein that regulates the abundance of the dominant xylem-colonized Pseudomonas ASV_4. Colonization patterns of ASV_4 varied across host genotypes and were correlated with CsXPR1 expression levels, suggesting a precision genetic regulation of bacterial entry into vascular tissues. Pseudomonas fulva strain 220, with 97% 16S rRNA gene identity with ASV_4, could colonize in cucumber xylem by inoculation of either roots or leaves. Genome analysis and plate assays revealed the biosynthesis of indole-3-acetic acid (IAA), solubilization of phosphate, and a range of plant beneficial traits in strain 220. Inoculation with strain 220 significantly enhanced growth in cucumber, but only in CsXPR1 haplotype that exhibited high gene expression and higher recruitment capacity of the strain. These benefits included notable increases in plant height (38%), stem diameter (36%), leaf area (61%), fresh and dry weight (51% and 85%, respectively), and a 4.57-fold increase in 4-methyleneglutamine content within the xylem sap. CONCLUSION: Our findings reveal a complete "gene-to-function" pathway where the host gene CsXPR1 mediates a genotype-dependent growth promotion. It achieves this by regulating the xylem colonization of a beneficial bacterium, Pseudomonas fulva, which in turn enhances plant growth by enriching the xylem sap with the key metabolite 4-methyleneglutamine. Video Abstract.

Cucumis sativus↗
PubMed2026

Can host genetics transform the sustainable control of tropical theileriosis? Insights from the Tick-Theileria interface.

Tropical theileriosis, caused by the tick-transmitted apicomplexan parasite Theileria annulata, remains a major constraint on cattle production across North Africa, the Mediterranean basin, the Middle East and South Asia. Current control depends on acaricides, the theilericidal drug buparvaquone and live attenuated schizont vaccines, but acaricide resistance, buparvaquone-resistance mutations and the logistical demands of vaccination are eroding the sustainability of these tools. Host genetics offers a complementary and durable alternative. Indigenous Bos indicus breeds are consistently more resistant to ticks and tolerate T. annulata infection better than exotic Bos taurus cattle, and this advantage has a measurable heritable component. Unlike previous reviews, which treat tick resistance, T. annulata immunobiology and livestock genomic selection as separate subjects, we integrate all three and assess host genetics specifically against the failure modes of current control. We review the tick, parasite and host interface, the evidence for natural resistance, and the genetic and immunological mechanisms involved, including signal-regulatory protein, bovine major histocompatibility complex class II and inflammatory pathway genes. We then assess whether genomic selection, multi-omics, machine learning and gene editing can translate these mechanisms into resistant cattle, and we weigh the biological, economic and infrastructural barriers to implementation. The evidence indicates that host genetics will not replace existing control but could reduce reliance on acaricides and chemotherapy. That contribution remains prospective rather than demonstrated: no resistance marker for T. annulata has yet been validated, prediction accuracies are moderate and transfer poorly between breeds, and no endemic production system has implemented selection for resistance.

Animals↗
PubMed2025

Host genetics predominates over gut microbiota in serum copper levels in boars.

Copper is an essential trace element in numerous biological processes; maintaining its homeostasis is crucial for pig health and productivity. In this study, we employed a mixed-effects model to investigate the contributions of host genetics, gut microbiota, and their interactions with serum copper levels in pigs. We further explored potential candidate genes and microbiota associated with copper metabolism. The results demonstrated that host genetics exert a dominant influence on serum copper regulation compared to the effects of the gut microbiota. Furthermore, genome-wide association analysis identified 4 candidate genes, CPHL1, CP, NCEH1, and PDE10A, strongly linked to copper metabolism. By applying multiple association approaches, 10 bacterial genera, such as Blautia, Lachnospiraceae UCG-008, and Ruminococcaceae UCG-007 were found to be significantly correlated with serum copper levels. This research offers novel insights into the genetic and microbial determinants of copper variation in pigs, establishing a foundation for future genetic and microbiota-based strategies aimed at enhancing copper homeostasis and overall livestock health.

Animals↗
PubMed2026

Impacts of host genetics on gut microbiome composition in Alzheimer's disease.

BACKGROUND: Host-microbiome interactions play essential roles in the development of Alzheimer's disease (AD), yet the host genetic impacts on gut microbial alterations in AD remain poorly understood. RESULTS: Here, we simultaneously profiled host genotype and gut microbiome in 252 Chinese individuals with varying degrees of cognitive disability. Using the latent Dirichlet allocation topic model, we identified the Anaerostipes-enriched enterosignature (ES-Ana) at the microbial subgroup level as significantly negatively associated with cognitive disability, which could be recapitulated in external cohorts. With the whole-genome sequencing data, we performed microbiome genome-wide association studies for the ES-Ana relative abundance. We prioritized 41 lead genetic variants and confirmed that the high ES-Ana relative abundance showed a negative correlation with the polygenic risk score of AD, indicating its protective effect against AD. Furthermore, we identified 174 ES-Ana-associated genes, which are enriched in AD-related biological functions and phenotypes, and exhibite pervasive underexpression in glial cells during brain aging. CONCLUSIONS: In summary, our study reveals the complex genetic effects on the gut microbiota in AD, and provides novel evidence for the roles of the gut-brain axis in AD. Video Abstract.

Alzheimer Disease↗
PubMed1989

Host genetic control of incubation periods of Creutzfeldt-Jakob disease in mice.

Host genetic control of the incubation period of Creutzfeldt-Jakob disease (CJD) was studied using various inbred strains of mice, including B10 congenic strains. Various incubation periods were found in mice injected either intracerebrally or intraperitoneally with the Fukuoka 1 strain of the CJD agent; NZW/Sea and A/JJms had the shortest, and B10.AKM/Ola and C57BL/6J the longest, incubation periods. Length of the CJD incubation period did not correlate with the genetic markers tested, i.e. the murine major histocompatibility (H-2) complex (which has previously been reported to be linked to a gene influencing CJD incubation period in mice), coat colour or sex genes. In NZW/Sea x C57BL/6J F1 hybrid mice the CJD incubation periods were similar to that of the parent with the longest incubation period. Incubation periods of the backcross progeny from F1 and NZW/Sea were intermediate between those of the parental mice and had a unimodal distribution pattern. A similar observation was made on the progeny of the A/JJms x C57BL/6J mating. On the other hand, the length of incubation period for the NZW/Sea x B10.AKM/Ola F1 hybrid fell between those for the two parents and the NZW/Sea x A/JJms F1 hybrid had a significantly longer incubation period than those of the two parents. These results suggest that polygenes probably control the length of the CJD incubation period in mice.

Alleles↗
PubMed1978

Host genetic factors influencing the occurrence of leukemoid reaction in BALB/cMk mice bearing transplanted tumors.

Host genetic factors influencing the occurrence of leukemoid reaction in BALB/cMk strain mice bearing transplanted tumors were studied. A Mendelian hybridization experiment was performed with BALB/cMk and C57BL/6 strains, and their strain hybrids; the first filial (F1) generation hybrids; the second filial (F2) generation hybrids; and the backcrosses to the two parental strains. The results of these studies suggested a genetic regulation of leukemoid reaction occurrence in BALB/cMk mice bearing transplanted tumors. Genes permissive to the occurrence of the reaction seemed to be dominant to their nonpermissive alleles.

Animals↗
PubMed2025

Host Genetic Factors and Clinical Comorbidities Associated With Tuberculosis Risk.

HLA influence the immune response, shaping genetic susceptibility or resistance to tuberculosis (TB). This study aimed to investigate the associations of host genetics and comorbidities with TB infection in Taiwanese populations. This retrospective case-control study utilised data from the Taiwan Precision Medicine Initiative. TB cases and non-TB controls were compared using genome-wide association studies (GWAS), HLA allele typing, and genotype data. Multivariate logistic regression identified independent predictors of TB and interactions between risk factors. A total of 390 TB cases and 3,909 controls were analysed. Risk factors for TB included bronchiectasis (OR&#x2009;=&#x2009;2.76; 95% CI 1.54-4.44; p&#x2009;<&#x2009;0.001), diabetes mellitus (OR&#x2009;=&#x2009;1.30; 95% CI 1.00-1.68; p&#x2009;=&#x2009;0.050), malignancy (OR&#x2009;=&#x2009;1.46; 95% CI 1.15-1.85; p&#x2009;=&#x2009;0.002), smoking (OR&#x2009;=&#x2009;1.42; 95% CI 1.08-1.88; p&#x2009;=&#x2009;0.012), and steroid use (OR&#x2009;=&#x2009;1.66; 95% CI 1.29-2.13; p&#x2009;<&#x2009;0.001). HLA-DRB1*16:02 was associated with a higher frequency in the TB group (OR&#x2009;=&#x2009;1.47; 95% CI 1.04-2.09; p&#x2009;=&#x2009;0.030). Interaction analysis showed HLA-DRB1*16:02 increased TB risk in non-smokers (OR&#x2009;=&#x2009;1.58; 95% CI 1.02-2.46; p&#x2009;=&#x2009;0.042), but not in smokers. HLA-DRB1*16:02 was associated with a higher risk for TB. While carriers of HLA-DRB1*16:02 did not exhibit an increased risk of TB among smokers, we demonstrated a heightened risk among non-smokers.

Humans↗
PubMed1991

Host genetic influences on fetal susceptibility to murine cytomegalovirus after maternal or fetal infection.

Genetically determined resistance to murine cytomegalovirus is observed in adult mice and is mediated in part by genes of the H-2 complex, with the H-2k haplotype conferring resistance. This model was used to examine the effect of primary maternal infection on fetal outcome. The severity of fetal growth retardation and death after primary maternal infection on day 8 of pregnancy was found to be genetically determined. Fetal viability and weight were significantly lower in infected BALB/c mothers (H-2d) than in CBA(H-2k) and BALB.K(H-2k) mothers. However, fetal infection was not detected, suggesting that the resistance mechanisms operate at the level of the mother or placenta. By directly inoculating fetuses in utero, it was shown that genetic factors in the fetus can influence the level of fetal infection and viability. These results point to the possibility that host genetic factors may modulate maternal and fetal cytomegalovirus infections in humans.

Animals↗
PubMed2026

Whole-exome characterization of host genetic variation in HIV-associated genes across the high-prevalence Mizo population, Northeast India.

BACKGROUND: The Mizoram state of Northeast India has one of the highest HIV prevalence rates in Asia, yet the host genetic factors influencing HIV susceptibility in this Tibeto-Burman population remain uncharacterised. METHODS: We performed whole-exome sequencing using Illumina NovaSeq 6000, mean coverage 100X on 76 HIV-negative Mizo individuals. Variants were called using GATK HaplotypeCaller v4.3 against GRCh38p14, annotated with ANNOVAR, and filtered using hard-quality thresholds (QD&#xa0;&#x2265;&#xa0;2, SOR&#xa0;&#x2264;&#xa0;3, MQ&#xa0;&#x2265;&#xa0;40, DP&#xa0;&#x2265;&#xa0;10, GQ&#xa0;&#x2265;&#xa0;20). The allele frequencies were compared against gnomAD v2.1.1 population databases. Hardy-Weinberg equilibrium was assessed using the Wigginton exact test with Bonferroni correction. RESULTS: Post-quality filtering resulted in 12,011 sample-variants across 2,821 unique positions from 36 HIV-associated loci (33 protein-coding genes, 2 chemokine ligands, and 3 lncRNA targets). Of these, 784 observations (51 unique positions) were high-impact nonsynonymous or loss-of-function variants. ADAR rs2229857 (p.K384R, NM_015840) was the most frequently observed variant (Mizo carrier frequency&#xa0;=&#xa0;0.895; 95% CI: 0.806-0.946). CXCR1 rs16858808 (p.R335C) showed the greatest population enrichment (Mizo carrier frequency&#xa0;=&#xa0;0.197; 95% CI: 0.123-0.300; 7.65-fold carrier-frequency enrichment versus gnomAD South Asian; CADD&#xa0;=&#xa0;15.60). Sixteen of 20 tested variants deviated from Hardy-Weinberg equilibrium after Bonferroni correction (p&#xa0;<&#xa0;0.0025), predominantly showing excess homozygosity consistent with the endogamous Mizo population. The protective variant CCR5-&#x394;32 was absent in all the 76 individuals tested. CONCLUSION: This first whole-exome characterization of HIV host genes in the Mizo population identifies CXCR1 rs16858808 as the most population-enriched functional variant and reveals a pervasive endogamy signature. These findings provide a population-specific genetic framework for future HIV susceptibility studies and ART pharmacogenomics research.

Humans↗
PubMed1991

Host genetic background effect on the frequency of mouse mammary tumor virus-induced rearrangements of the int-1 and int-2 loci in mouse mammary tumors.

The frequency with which int-1 and int-2 are rearranged in mouse mammary tumors by mouse mammary tumor virus (MMTV)-induced insertional mutagenesis is a consequence of the host genetic background. In 75% of C3H mammary tumors, int-1 is rearranged by MMTV insertion, whereas only 30% of BALB/cfC3H tumors contain a virus-induced rearrangement of int-1. This difference is significant (P less than 0.005) and could not be accounted for by the potentially additive effect of the genetically transmitted Mtv-1-encoded virus in C3H mice. Similarly, MMTV-induced rearrangement of the int-2 gene in mammary tumors of the R111 mouse strain (59%) occurred at a significantly (P less than 0.025) higher frequency than in BALB/cfR111 (25%) mammary tumors. Moreover, in BALB/cfR111 mammary tumors, there is evidence that rearrangement of int-1 and int-2 does not occur independently (P less than 0.025). These results suggest that the long history of inbreeding for high tumor incidence of C3H and R111 mouse strains has selected for the fixation of host mutations which either complement the action of the particular int gene or affect the sensitivity of specific subpopulations of mammary epithelium to infection by particular strains of MMTV.

Animals↗
PubMed2026

Disentangling host genetic variation for avoidance and resistance to pathogens.

BACKGROUND: Hosts can use avoidance (e.g., behavior) to reduce their contact rates with pathogens; after contact, they can use resistance (e.g., immunity) to reduce the establishment and proliferation of an infection. Because both defenses preserve host fitness and reduce pathogen fitness, we expect that their epidemiological and evolutionary effects will be interdependent. This study used a two-locus model to understand the evolution of allelic associations (i.e., linkage disequilibrium or LD) between genes determining levels of avoidance and resistance in the presence of an infectious disease or a parasite. RESULTS: We found that polymorphism in both avoidance and resistance was possible, but only for a limited range of parameter values. At equilibrium within these polymorphic populations, avoidance and resistance alleles were negatively associated (i.e., in negative LD). However, most commonly, polymorphism was only stably maintained at one defense locus, and the other locus became fixed for one allele. CONCLUSIONS: The model shows that avoidance and resistance are likely to influence each other's evolution because of their joint effects on infection and their costs; however, predictions about their relationship are not necessarily straightforward or intuitive. For example, avoidance and resistance may be more likely to covary across than within populations.

Animals↗
PubMed1977

Dietary, bacterial, and host genetic interactions in the pathogenesis of transmissible murine colonic hyperplasia.

Transmissible murine colonic hyperplasia, cuased by a variant of Citrobacter freundii (4280). was shown to be modified by diet and by host strain and species. Four different diets fed to mice inoculated with C frundii 4280 were found to have a significant but varying influence on the severity of hyperplasia. Diet also influenced the colonic crypt height of uninoculated, control mice. F344 rats, Syrian hamsters, and NIH Swiss [N:(S)], C57BL/6J, C3H/HeJ, and DBA/2J mice were inoculated with C freundii 4280. Marked strain differences were noted in the mice in mortality and severity of the colonic hyperplasia. The NIH Swiss mice had the greatest and the C57BL/6J mice had the least mucosal hyperplasia. The rats and hamsters did not develop disease or maintain infection after inoculation with the organism. Twenty isolates of Citrobacter from a range of biologic sources were inoculated into susceptible mice, but only mice inoculated with C freundii 4280 developed the disease.

Animals↗
PubMed2025

Identification of Sample Processing Errors in Microbiome Studies Using Host Genetic Profiles.

In microbiome studies, sample processing errors are frequent and difficult to detect, especially in large studies involving multiple sites, personnel, and sample types. We present two complementary approaches to identify such errors using host DNA profiled via metagenomic sequencing of microbiome samples. The first approach compares host SNPs inferred from metagenomics to independently obtained genotypes (e.g., microarray genotypes) to match samples to their donors, while the second method compares metagenomics-inferred SNPs between samples to identify samples supplied by the same donor. Furthermore, we demonstrate that combining these methods with experimental metadata provides greater confidence in the identification of errors. Analyzing a longitudinal vaginal microbiome dataset, we demonstrate the ability of our approach to identify mislabeled samples. Using subsampling, we further show that our methods are robust to low sequencing coverage. Overall, our analysis highlights the frequency of processing errors in microbiome studies. We therefore recommend applying error-detection methods in all studies with suitable data.

Journal Article↗
PubMed1991

Host genetic factors do not account for variation in parasite loads in Strongyloides fuelleborni kellyi.

Previous work in Papua New Guinea has shown considerable variation in egg counts between different people infected with Strongyloides fuelleborni kellyi, although individual egg loads remained relatively constant over a 14-month period. Possible explanations include genetic predisposition, a surprising longevity of the worms, or external auto-infection. We have now analysed the pedigrees of 177 individuals for whom egg counts were available, and find no evidence for polygenic inheritance of factors related to egg counts. The use of genetic models postulating the segregation of a single unknown susceptibility gene did not enable us, using the data available, to distinguish between this hypothesis and environmental determination of egg counts; nor did we find any association between egg load and the class 1 HLA genotype of the host.

Animals↗
PubMed1991

Regression of v-src DNA-induced sarcomas is under host genetic control.

Previous results have established that subcutaneous inoculation of chickens (line SC) with a v-src(+) subviral DNA fragment induces the formation of progressor sarcomas at the wing web site of inoculation. Because the sarcoma cells are incompetent for production of exogenous progeny virus, this system is a useful model of tumor expansion by sarcoma cell division, in the absence of infection-mediated recruitment of new tumor cells. The present study was undertaken to define conditions that modulate the pattern of growth (regression vs progression) of v-src DNA-induced sarcomas. These conditions were found to include the line of chicken or the presence on the subviral v-src(+) DNA fragment of a viral replication-specific sequence that includes env.

Animals↗
PubMed1989

Neural infection in mice after cutaneous inoculation with HSV-1 is under complex host genetic control.

The ability to restrict neural infection with herpes simplex virus is of potential importance because the nervous system is the main reservoir of virus between recrudescences. Genetic control of innate resistance to herpes simplex after intraperitoneal challenge is well established, but this route of infection does not mimic the progress of virus from skin to the sensory nervous system which occurs during natural infection. We show here, by Mendelian analysis, that the control of neural infection after cutaneous inoculation is complex, involving several (perhaps four) genetic loci, and is not accurately represented by genes which determine survival. The results are discussed in relation to possible underlying resistance mechanisms, particularly the control of early interferon production.

Animals↗
PubMed1985

Host genetic regulation of acute MHV-4 viral encephalomyelitis and acute experimental autoimmune encephalomyelitis in (BALB/cKe x SJL/J) recombinant-inbred mice.

In the present report we provide the strain distribution patterns of susceptibility to acute mouse hepatitis virus type-4 (MHV-4) encephalomyelitis, acute experimental allergic encephalomyelitis (EAE) and vasoactive amine sensitivity (VAAS) for 9 (CXJ) recombinant-inbred strains between BALB/cKe (C) and SJL/J(J) mice. We confirm that susceptibility to MHV-4 is not linked to the H-2 complex, and that all strains susceptible to acute EAE have both a responder H-2 haplotype (H-2s or H-2d) and induced (B. pertussis) VAAS. In addition, we provide evidence that susceptibility to acute EAE induction is controlled by an additional presently unmapped locus and that an EAE-like histopathological disease does not usually follow MHV-4 infection intracerebrally in animals susceptible to MHV-4, acute EAE and induced VAAS.

Animals↗