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Gene Frequencies (gene + frequency)
Selected AbstractsLymphocyte antigens in sheep: linkage to the MHC class II DRB1 geneINTERNATIONAL JOURNAL OF IMMUNOGENETICS, Issue 4 2001B. M. Jugo Summary In this work a typing battery of sera was developed to test lymphocyte antigens in sheep. Eight antigens were detected in a Latxa sheep sample. The serological determination of these antigens is described. As some of the detected antigens segregated in close linkage with class II DRB1 SSCP patterns in two half-sib families, we can conclude that they are coded by genes located in the MHC. Gene frequencies were very similar in Latxa Mutur Gorria and Latxa Mutur Beltza, the two varieties of the Latxa breed. Although few animals were typed in the comparison with other typing sera, it seems that two of our sera clusters detect the same antigens as those detected by other research groups working in other breeds with their own typing batteries. [source] Identification of ovalbumin phenotypes of the Asian indigenous chicken populations using polymerase chain reaction-restriction fragment length polymorphismANIMAL SCIENCE JOURNAL, Issue 5 2003Keiji KINOSHITA ABSTRACT Three electrophoretic variations (AA, BB and AB) of ovalbumin controlled by codominant alleles OvA and OvB have been observed in various chicken populations. We compared nucleotide sequences of the open reading frame between two alleles of ovalbumin gene. The difference between the two alleles was found as a non-synonymous substitution of asparagine to aspartic acid as a result of AAT to GAT point mutation at position 8032,8034 in exon 8. We developed polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) protocol in combination with Mbo I restriction endnuclease mapping for the detection of this substitution. By the PCR-RFLP the allelic frequency of the OvB was estimated to be within the range of 0.000,0.150 in 11 Asian indigenous chicken populations and 0.000 in four improved breeds used in the present study. Gene frequency, estimated by PCR-RFLP in the present study, paralleled that obtained by protein polymorphisms of egg white. Thus, this study provides, for the first time, information of the occurrence of ovalbumin allele OvA and OvB in Asian indigenous chicken populations. [source] Mortality differences by APOE genotype estimated from demographic synthesisGENETIC EPIDEMIOLOGY, Issue 2 2002Douglas C. EwbankArticle first published online: 10 JAN 200 Abstract The 4 allele of apolipoprotein E (APOE) is associated with increased risk of two major causes of death in low-mortality populations: ischemic heart disease and Alzheimer's disease. It is less common among centenarians than at younger ages. Therefore, it is likely that it is associated with excess risk of death. This article extends demographic models that estimate relative mortality risks from changes in gene frequencies with age. The resulting demographic synthesis combines gene frequencies with data on mortality by genotype from cohort studies. The model was applied to data from Denmark, Finland, France, Italy, Sweden, and the United States. Near age 50, the 3/4 genotype is associated with a risk of death of 1.34 times that of the 3/3 (95% CI 1.18,1.67). The relative risk for 4/4 is the square of the relative risk for 3/4, 1.81. The 2/3 genotype is protective with a relative risk of 0.84 (0.68,0.93) near age 50. These relative risks move toward 1.0 at the oldest ages and APOE genotype is associated with little variation in mortality over age 100. There are no significant differences in the relative risks by sex. There is little evidence of differences within Europe in the effects of APOE. This approach can be generalized to combine data on genetic risk factors for disease from a wide variety of study designs and sample characteristics. Genet. Epidemiol. 22:146,155, 2002. © 2002 Wiley-Liss, Inc. [source] Distribution of killer cell immunoglobulin-like receptor genes in PolesINTERNATIONAL JOURNAL OF IMMUNOGENETICS, Issue 4-5 2008E. Majorczyk Summary Killer cell immunoglobulin-like receptors (KIRs) present on natural killer cells and minor subpopulations of T cells recognize class I human leucocyte antigen (HLA) molecules on the surface of target cells. Humans differ by the presence or absence of some KIR genes on their chromosomes. As KIRs are important for the outcome of tissue transplantation (particularly for haematopoietic stem cell transplantation) and possibly for pregnancy and autoimmune diseases, knowledge of the KIR gene distribution in a given human population is of practical value. Therefore, we tested 363 healthy individuals from Western Poland for the presence or absence of KIR genes. Results are compared with those published for other human populations. KIR gene frequencies in Poles are close to these in other Caucasoids but different from those in Asian and African populations, and particularly distant from those in Australian Aborigines. [source] Haptoglobin: a review of the major allele frequencies worldwide and their association with diseasesINTERNATIONAL JOURNAL OF LABORATORY HEMATOLOGY, Issue 2 2007KYMBERLEY CARTER Summary Haptoglobin (Hp) is a plasma ,2 -glycoprotein which binds free haemoglobin, thus preventing oxidative damage. The complex is rapidly removed from the circulation by a specific receptor (CD163) found on macrophages. Three major subtypes, Hp1-1, Hp2-1 and Hp2-2 are the product of two closely related genes HP1 and HP2. The frequency of the HP1 and HP2 genes varies worldwide depending on racial origin: the HP1frequency varying from about 0.07 in parts of India to over 0.7 in parts of West Africa and South America. Both HP1 and HP2 have been linked to susceptibility to various diseases. Such associations may be explained by functional differences between the subtypes in the binding of Hb and its rate of clearance from the plasma. However, there are also corresponding negative reports for disease associations. The conflicting evidence on disease association and the lack of association between disease and particular populations, despite the wide range of HP1 and HP2 gene frequencies across the world, may indicate that any associations are marginal. [source] Genetic discontinuities and disequilibria in recently established populations of the plant pathogenic fungus Mycosphaerella fijiensisMOLECULAR ECOLOGY, Issue 18 2010F. HALKETT Abstract Dispersal processes of fungal plant pathogens can be inferred from analysis of spatial genetic structures resulting from recent range expansion. The relative importance of long-distance dispersal (LDD) events vs. gradual dispersal in shaping population structures depends on the geographical scale considered. The fungus Mycosphaerella fijiensis, pathogenic on banana, is an example of a recent worldwide epidemic. Founder effects in this species were detected at both global and continental scale, suggesting stochastic spread of the disease through LDD events. In this study, we analysed the structure of M. fijiensis populations in two recently (,1979,1980) colonized areas in Costa Rica and Cameroon. Isolates collected in 10,15 sites distributed along a ,250- to 300- km-long transect in each country were analysed using 19 microsatellite markers. We detected low-to-moderate genetic differentiation among populations in both countries and isolation by distance in Cameroon. Combined with historical data, these observations suggest continuous range expansion at the scale of banana-production area through gradual dispersal of spores. However, both countries displayed specific additional signatures of colonization: a sharp discontinuity in gene frequencies was observed along the Cameroon transect, while the Costa Rican populations seemed not yet to have reached genetic equilibrium. These differences in the genetic characteristics of M. fijiensis populations in two recently colonized areas are discussed in the light of historical data on disease spread and ecological data on landscape features. [source] Isolation by distance and sharp discontinuities in gene frequencies: implications for the phylogeography of an alpine insect species, Carabus solieriMOLECULAR ECOLOGY, Issue 7 2004S. GARNIER Abstract Analysis of genetic isolation by distance (IBD) is of prime importance for the study of processes responsible for spatial population genetic structure and is thus frequently used in case studies. However, the identification of a significant IBD pattern does not necessarily imply the absence of sharp discontinuities in gene frequencies. Therefore, identifying barriers to gene flow and/or secondary contact between differentiated entities remains a major challenge in population biology. Geographical genetic structure of 41 populations (1080 individuals) of an alpine insect species, Carabus solieri, was studied using 10 microsatellite loci. All populations were significantly differentiated and spatially structured according to IBD over the entire range. However, clustering analyses clearly identified three main clusters of populations, which correspond to geographical entities. Whereas IBD also occurs within each cluster, population structure was different according to which group of populations was considered. The southernmost cluster corresponds to the most fragmented part of the range. Consistently, it was characterized by relatively high levels of differentiation associated with low genetic diversity, and the slope of the regression of genetic differentiation against geographical distances was threefold those of the two other clusters. Comparisons of within-cluster and between-cluster IBD patterns revealed barriers to gene flow. A comparison of the two approaches, IBD and clustering analyses, provided us with valuable information with which to infer the phylogeography of the species, and in particular to propose postglacial colonization routes from two potential refugia located in Italy and in southeastern France. Our study highlights strongly the possible confounding contribution of barriers to gene flow to IBD pattern and emphasizes the utility of the model-based clustering analysis to identify such barriers. [source] Genetic similarity of polyploids: a new version of the computer program POPDIST (version 1.2.0) considers intraspecific genetic differentiationMOLECULAR ECOLOGY RESOURCES, Issue 5 2009JÜRGEN TOMIUK Abstract For evolutionary studies of polyploid species estimates of the genetic identity between species with different degrees of ploidy are particularly required because gene counting in samples of polyploid individuals often cannot be done, e.g., in triploids the phenotype AB can be genotypically either ABB or AAB. We recently suggested a genetic distance measure that is based on phenotype counting and made available the computer program POPDIST. The program provides maximum-likelihood estimates of the genetic identities and distances between polyploid populations, but this approach is not informative for populations within species that only differ in their allele frequencies. We now close this gap by applying the frequencies of shared ,bands' in both populations to Nei's identity measure. Our simulation study demonstrates the close correlation between the band-sharing identity and the genetic identity calculated on the basis of gene frequencies for any degree of ploidy. The new extended version of POPDIST (version 1.2.0) provides the option of choosing either the maximum-likelihood estimator or the band-sharing measure. [source] Ethics and Genetic Selection in Purebred DogsREPRODUCTION IN DOMESTIC ANIMALS, Issue 1 2003VN Meyers-Wallen Contents There is an ongoing revolution in medicine that is changing the way that veterinarians will be counselling clients regarding inherited disorders. Clinical applications will emerge rapidly in veterinary medicine as we obtain new information from canine and comparative genome projects (Meyers-Wallen 2001: Relevance of the canine genome project to veterinary medical practice. International Veterinary Information Service, New York). The canine genome project is described by three events: mapping markers on canine chromosomes, mapping gene locations on canine chromosomes (Breen et al. 2001: Genome Res. 11, 1784,1795), and obtaining the nucleotide sequence of the entire canine genome. Information from such research has provided a few DNA tests for single gene mutations [Aguirre 2000: DNA testing for inherited canine diseases. In: Bonagura, J (ed), Current Veterinary Therapy XIII. Philadelphia WB Saunders Co, 909,913]. Eventually it will lead to testing of thousands of genes at a time and production of DNA profiles on individual animals. The DNA profile of each dog could be screened for all known genetic disease and will be useful in counselling breeders. As part of the pre-breeding examination, DNA profiles of prospective parents could be compared, and the probability of offspring being affected with genetic disorders or inheriting desirable traits could be calculated. Once we can examine thousands of genes of individuals easily, we have powerful tools to reduce the frequency of, or eliminate, deleterious genes from a population. When we understand polygenic inheritance, we can potentially eliminate whole groups of deleterious genes from populations. The effect of such selection on a widespread basis within a breed could rapidly improve health within a few generations. However, until we have enough information on gene interaction, we will not know whether some of these genes have other functions that we wish to retain. And, other population effects should not be ignored. At least initially it may be best to use this new genetic information to avoid mating combinations that we know will produce affected animals, rather than to eliminate whole groups of genes from a population. This is particularly important for breeds with small gene pools, where it is difficult to maintain genetic diversity. Finally, we will eventually have enough information about canine gene function to select for specific genes encoding desirable traits and increase their frequencies in a population. This is similar to breeding practices that have been applied to animals for hundreds of years. The difference is that we will have a large pool of objective data that we can use rapidly on many individuals at a time. This has great potential to improve the health of the dog population as a whole. However, if we or our breeder clients make an error, we can inadvertently cause harm through massive, rapid selection. Therefore, we should probably not be advising clients on polygenic traits or recommend large scale changes in gene frequencies in populations until much more knowledge of gene interaction is obtained. By then it is likely that computer modelling will be available to predict the effect of changing one or several gene frequencies in a dog population over time. And as new mutations are likely to arise in the future, these tools will be needed indefinitely to detect, treat and eliminate genetic disorders from dog populations. Information available from genetic research will only be useful in improving canine health if veterinarians have the knowledge and skills to use it ethically and responsibly. There is not only a great potential to improve overall canine health through genetic selection, but also the potential to do harm if we fail to maintain genetic diversity. Our profession must be in a position to correctly advise clients on the application of this information to individual dogs as well as to populations of dogs, and particularly purebred dogs. [source] Length variability and interspersion patterns of the HRAS1 minisatellite: a new approach for the reconstruction of human population relationshipsANNALS OF HUMAN GENETICS, Issue 4 2001A. VEGA During recent years the HRAS1 minisatellite has been analysed by several authors because of its putative association with cancer susceptibility. The aim of this report is to test the usefulness of this minisatellite in investigating human population relationships. We have studied 370 chromosomes from two well-differentiated populations: Galicia (North-west Iberia) and South-east Africa, as well as available data on allele length gene frequencies. The fragment analysis results show a strong tendency to differentiate between non-African and African populations. In spite of the usefulness of fragment analysis, the minisatellite variant repeat (MVR) approach of the HRAS1 minisatellite appears to be a more powerful method for use in human population studies, due to the high level of diversity of its interspersion pattern structures. In addition, this approach has allowed us to define some new structural characteristics of this minisatellite. Four different major groups of human HRAS1 minisatellite alleles could be distinguished following a structural criterion based on the MVR code. Furthermore, the characterisation of the HRAS1 minisatellite in chimpanzees revealed clear differences when compared to humans, not only with respect to the allele size but also to the internal structure. [source] Linkage disequilibrium and natural selection for mimicry in the Batesian mimic Hypolimnas misippus (L.) (Lepidoptera: Nymphalidae) in the AfrotropicsBIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 1 2010IAN J. GORDON On two occasions, on opposite sides of the African continent (Cape Coast, Ghana, and Dar es Salaam, Tanzania), high adult population densities in the polymorphic butterfly Hypolimnas misippus (a presumed mimic of Danaus chrysippus) were followed by linkage disequilibrium in combinations of fore- and hindwing colour patterns. On both occasions, disequilibrium was caused by significant changes in morph frequencies favouring rarer and more mimetic forms. Recaptures were too few for analysis at Dar, although the changes there took place within a single generation and must have been the result of differential survival. Recapture rate data and survival rate estimates at Cape Coast support the hypothesis that selective predation was responsible, as does the observation of synchronous linkage disequilibrium at Dar in the model D. chrysippus, indicating parasitic mimicry. There was clear selection for the perfection of mimicry for forewings at Dar and for hindwings at Cape Coast. Disequilibrium is also reported for two other sites, Legon (Ghana) and Boksburg (South Africa) and, in all four sites, it was associated with an increase in the most mimetic forms. New chemical evidence is presented to support the contention that D. chrysippus is a defended model. Although all the evidence leads to the conclusion that H. misippus is a Batesian mimic of D. chrysippus, many questions remain, particularly with regard to the identity of predators, the episodic nature of selective predation events, and their apparent lack of lasting and significant impact on overall gene frequencies. We conclude that H. misippus presents both challenges and opportunities for studies on mimicry, and we suggest that linkage disequilibrium can be a useful generic indicator for Gestalt predation on polymorphic prey. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 100, 180,194. [source] Expression of low-frequency Ala108Pro substitution in the platelet glycoprotein Ib, geneINTERNATIONAL JOURNAL OF IMMUNOGENETICS, Issue 2 2003S. Kunishima Summary We determined the gene frequency of the glycoprotein (GP) Ib, Ala108Pro substitution. The Pro108 allele was not found in 208 healthy Japanese and 200 healthy Caucasians. In vitro expression studies showed surface expression of the GPIb, Pro108 variant, suggesting the possibility of the involvement of the substitution as an alloantigen. [source] Determination of the inheritance pattern of hyperthelia in cattle by maximum likelihood analysis 1JOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 6 2000M. Brka Summary A previously published data-set with observations on supernumerary teats (hyperthelia) in dual-purpose Simmental was reanalysed by maximum-likelihood. The data comprised 537 unrelated animals and 614 members of 27 paternal half-sib families with known phenotype of each sire. The frequency of hyperthelia was 58% in unrelated animals, 51% in families with unaffected sire, and 73% in families with affected sires. Six different cases of single-gene inheritance were considered. The highest log-likelihood was obtained for additive inheritance and for a recessive pattern with 100% penetrance for recessive homozygotes and 32% for both other genotypes. Estimates for the gene frequency of the favourable allele were 0.34 and 0.29, respectively. Simple dominance or recessiveness with full or incomplete penetrance could be excluded. The possibility of finding paternal half-sib families with a heterozygous sire as a resource for a mapping experiment seem to be good in German Simmental. Zusammenfassung Untersuchung des Erbganges für Hyperthelie beim Rind mittels Maximum-Likelihood-Analyse Schon früher veröffentliche Daten mit Beobachtungen zum Auftreten überzähliger Zitzen (Hyperthelie) bei Fleckviehtieren wurden einer Maximum-Likelihood-Analyse unterzogen. Das Material bestand aus 537 unverwandten Tieren und 614 Tieren, die aus 27 verschiedenen väterlichen Halbgeschwistergruppen stammten, wobei der Phänotyp des Vaters jeweils bekannt war. Die relative Häufigkeit überzähliger Zitzen betrug 58% bei unverwandten Tieren, 51% bei Nachkommen von nicht betroffenen Vätern und 73% bei Nachkommen von Vätern, die selbst überzählige Zitzen aufwiesen. Sechs verschiedene Möglichkeiten monogener Vererbung wurden untersucht. Die höchsten Werte für die log-likelihood ergaben sich für einen additiven Erbgang sowie für eine Variante mit 100% Penetranz für die rezessiv Homozygoten und jeweils 32% Penetranz für die beiden anderen Genotypen. Für das erwünschte Allel wurde in beiden Varianten eine ähnliche Frequenz von 34% bzw. 29% geschätzt. Einfache dominante oder rezessive Erbgänge, auch mit unvollständiger Penetranz, konnten ausgeschlossen werden. Die Aussicht, für Kartierungsexperimente geeignete väterlichen Halbgeschwisterfamilien zu finden, scheint für die Rasse Fleckvieh günstig zu sein. [source] Estimation of gene frequency and heterozygosity from pooled samplesMOLECULAR ECOLOGY RESOURCES, Issue 3 2002K. Ritland Abstract Pooling of DNA samples can significantly reduce the effort of population studies with DNA markers. I present a statistical model and numerical method for estimating gene frequency when pooled DNA is assayed for the presence/absence of alleles. Analytical and Monte-Carlo methods examined estimation variance and bias, and hence optimal pool size, under a triangular allele frequency distribution. For gene frequency of rarer alleles, the optimal number of pooled individuals is approximately the inverse of the gene frequency. For heterozygosity, the optimal pool is approximately half the allele number; this results in pools containing, on average, 60% of possible alleles. [source] ,-Globin gene cluster haplotypes and ,-thalassemia in sickle cell disease patients from TrinidadAMERICAN JOURNAL OF HUMAN BIOLOGY, Issue 3 2008Altheia Jones-Lecointe In this study, we have determined the frequency of ,S haplotypes in 163 sickle cell disease patients from Trinidad. The ,3.7 globin gene deletion status was also studied with an observed gene frequency of 0.17. Among the 283 ,S chromosomes analyzed, the Benin haplotype was the most prevalent (61.8%) followed by Bantu (17.3%), Senegal (8.5%), Cameroon (3.5%), and Arab-Indian (3.2%), while 5.7% of them were atypical. This ,S haplotypes distribution differed from those previously described in other Caribbean islands (Jamaica, Guadeloupe, and Cuba), in agreement with the known involvement of the major colonial powers (Spain, France, and Great Britain) in the slave trade in Trinidad and documented an Indian origin of the ,S gene. Am. J. Hum. Biol., 2008. © 2008 Wiley-Liss, Inc. [source] | |||||||||||||||||||||||||