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PubMed2002

[Origin of caucasoid-specific mitochondrial DNA lineages in the ethnic populations of the Altai-Sayan region].

The data on sequence variation in the first hypervariable segment (HVSI) of human mitochondrial DNA (mtDNA) representing Caucasoid mtDNA lineages in the gene pools of Altaians and Khakassians are presented. Identification of the subgroups of Caucasoid mtDNA lineages found in the gene pools of the ethnic populations of the Altai-Sayan region and the adjacent territories, Altaians, Khakassians, Tuvinians, Buryats, and Yakuts was carried out. All Caucasoid mtDNA lineages belonged to groups H, HV1, J*, J1, J1b1, T1, T4, U1a, U2, U3, U4, U5a1, I, X and N1a. Taking into consideration possible contribution of southern Caucasoid and eastern European components to the formation of the anthropological type of Altai-Sayan ethnic populations, distribution of the revealed Caucasoid mtDNA lineages among the ethnic populations of the Central Asia, Western Asia, Caucasus, and Eastern Europe was examined. The applied approach permitted identification of 60% of mtDNA types the majority of which had southern Caucasoid origin. Less than 10% of mtDNA types were of eastern European origin. The gene pools of Altaians and Khakassians displayed the presence of autochthonous components represented by mtDNA types from subgroups U2 and U4.

Asian People↗

PubMed1999

[Evaluation of the relative contribution of Caucasoid and Mongoloid components in the formation of ethnic groups of the Volga-Ural region according to data of DNA polymorphism].

For the first time, an attempt was made to quantitatively estimate the relative contributions of major racial components to populations of the Volga-Ural region based on the data on allelic polymorphisms of nine loci of the mitochondrial and nuclear genomes. Comparison of the proportions of Caucasoid and Mongoloid characteristics in the gene pools of Bashkirs, Tatars, Chuvashes, Maris, Mordovians, Udmurts, and Komi revealed a heterogeneous pattern. Data on the proportions of major racial components in the nuclear genome indicated that the Caucasoid component was maximum in Mordovians, Komis, and Udmurts. Mongoloid characters were most prevalent in Bashkirs, Maris, Tatars, and Chuvashes. Data on restriction-deletion polymorphism of mitochondrial DNA (mtDNA) also indicated an increased Caucasoid contribution to Mordovian, Udmurt, and Komi gene pools and an increased Mongoloid component in Chuvashes and Tatars. In general, the results obtained agree with ethnic anthropological data indicating the greatest Caucasoid contribution to the Mordovian and Komi gene pools and an increased Mongoloid component in Turkic populations of the Volga-Ural region (Bashkirs, Tatars, and Chuvashes).

Asian People↗

PubMed2003

Genetic structure and diversity among maize inbred lines as inferred from DNA microsatellites.

Two hundred and sixty maize inbred lines, representative of the genetic diversity among essentially all public lines of importance to temperate breeding and many important tropical and subtropical lines, were assayed for polymorphism at 94 microsatellite loci. The 2039 alleles identified served as raw data for estimating genetic structure and diversity. A model-based clustering analysis placed the inbred lines in five clusters that correspond to major breeding groups plus a set of lines showing evidence of mixed origins. A "phylogenetic" tree was constructed to further assess the genetic structure of maize inbreds, showing good agreement with the pedigree information and the cluster analysis. Tropical and subtropical inbreds possess a greater number of alleles and greater gene diversity than their temperate counterparts. The temperate Stiff Stalk lines are on average the most divergent from all other inbred groups. Comparison of diversity in equivalent samples of inbreds and open-pollinated landraces revealed that maize inbreds capture <80% of the alleles in the landraces, suggesting that landraces can provide additional genetic diversity for maize breeding. The contributions of four different segments of the landrace gene pool to each inbred group's gene pool were estimated using a novel likelihood-based model. The estimates are largely consistent with known histories of the inbreds and indicate that tropical highland germplasm is poorly represented in maize inbreds. Core sets of inbreds that capture maximal allelic richness were defined. These or similar core sets can be used for a variety of genetic applications in maize.

Alleles↗

PubMed1976

Blood polymorphism frequencies in the Sara Majingay of Chad.

Blood samples of 258 Sara Majingay of Ndila (Southern Chad) were analysed. Phenotype and allele frequencies are given for 22 polymorphisms. For each of these, the Majingay are compared to a number of other African populations. Then they are included in a set of 8 African populations between which multivariate distances for 25 alleles at 9 loci are computed. A two-dimensional representation is derived from the matrix of distances, and is discussed. It bears the stamp of gene flow in central Ethiopia, where an Arab admixture is evident, and in Southern Africa, where a reciprocal gene flow has marked the gene pools of Khoisan and Bantu speakers to a varying degree. The Majingay stand relatively near to the Bedik, another population of West-Central Africa. The non-Arab or non-Khoisan components of the gene pool of the other populations do not seem to differ largely from the gene pools of the West-Central African populations.

Acid Phosphatase↗

PubMed2005

Comparative genomics of Helicobacter pylori isolates recovered from ulcer disease patients in England.

BACKGROUND: Genomic diversity of H. pylori from many different human populations is largely unknown. We compared genomes of 65 H. pylori strains from Nottingham, England. Molecular analysis was carried out to identify rearrangements within and outside the cag-pathogenicity-island (cag PAI) and DNA sequence divergence in candidate genes. Phylogenetic analysis was carried out based on various high-resolution genotyping techniques. RESULTS: Analyses of virulence genes (cagT, cagE, cagA, vacA, iceA, oipA and babB) revealed that H. pylori strains from England are genetically distinct from strains obtained from other countries. The toxigenic vacA s1m1 genotype was found to be less common and the plasticity region cluster was found to be disrupted in all the isolates. English isolates showed a predominance of iceA1 alleles and a functional proinflammatory oipA gene. The English H. pylori gene pool revealed several Asian/oriental features. This included the predominance of cagA - glr (cagA right junction) motif types III and II (up to 42%), presence of vacA m1c alleles and phylogenetic affinity towards East Asian / Amerindian gene pools based on fluorescent amplified fragment length polymorphism (FAFLP) analysis and glmM sequence analysis. CONCLUSION: Overall, our results demonstrated genetic affinities of H. pylori in England with both European and the Asian gene pools and some distinctive genetic features of virulence genes that may have evolved in this important European population.

Bacterial Proteins↗

PubMed1985

Usefulness and limitations of the species concept for plant viruses.

Continuing concerns among virologists are what range of isolates is covered by one virus name and whether such names relate to categories broadly equivalent to biological species of higher organisms. In the potyviruses, tobamoviruses, and probably other groups of plant viruses with monopartite RNA genomes, exchange of genetic information among isolates is not known to occur; our ability to delineate separate viruses apparently depends on the extent to which biological fitness involves several correlated changes in the genomes of variant clones. Although some such correlated changes are found where viruses infect different plant families, intergrading forms occur in many instances where the host ranges of variants overlap. In plant viruses with multipartite RNA or DNA genomes, the extent of gene pools can be assessed from the ability of isolates to form pseudo-recombinants by reassortment of their genome parts. In the nepoviruses, clusters of virus strains sharing a gene pool resemble, but seem more sharply delimited than, the clusters based on nucleotide sequence homology or serological specificity. In the tobraviruses gene pools do not coincide with serological groupings, and in the geminiviruses biologically very distinct entities have much genome homology and are closely related serologically. The biological species concept seems inappropriate or impractical for many plant viruses, and a more flexible and pragmatic approach to assigning virus isolates to nameable categories is advocated.

Cloning, Molecular↗

PubMed2004

Sequence diversity analysis of dihydroflavonol 4-reductase intron 1 in common bean.

Variation in common bean (Phaseolus vulgaris L.) was investigated by sequencing intron 1 of the dihydroflavonol 4-reductase (DFR) gene for 92 genotypes that represent both landraces and cultivars. We were also interested in determining if introns provide sufficient variation for genetic diversity studies and if the sequence data could be used to develop allele-specific primers that could differentiate genotypes using a standard PCR assay. Sixty-nine polymorphic sites were observed. Nucleotide variation (pi/bp) was 0.0481, a value higher than that reported for introns from other plant species. Tests for significant deviation from the mutation drift model were positive for the population as a whole, the cultivar and landrace subsets, and the Middle American landrace set. Significant linkage disequilibrium extended about 300 nucleotides. Twenty haplotypes were detected among the cultivated genotypes. Seven recombination events were detected for the whole population, and six events for the landraces. Recombination was not observed among the landraces within either the Middle American or Andean gene pools. Evidence for hybridization between the two gene pools was discovered. Five allele-specific primers were developed that could distinguish 56 additional genotypes. The allele-specific primers were used to map duplicate DFR genes on linkage group B8.

Alcohol Oxidoreductases↗

PubMed1990

[Gene geography of human population: computer-generated regional genogeographic atlas].

Gene geography is considered in this work as the instrument for analysis of population's gene pool. To be effective in this analysis, gene geography should move from mapping of gene frequencies for each gene (and phenes) to construction of genogeographical atlas, as a collection of maps generated by computer, following some strongly defined principles and methods, and joined together, according to general task and the programme of investigation. Brief version of regional genogeographical atlas of Mongolians and the other peoples of Central Asia is presented in the article. This atlas includes computer-generated maps of AB0, Hp, Gc, G'3, Tf, GLO, EstD and PGM1 gene frequencies as well as computer-generalized maps of Mongolian gene pool.

Atlases as Topic↗

PubMed1976

Genetic factors and malaria in the Temuan.

The jungle habitat of the Temuan aborigines harbors a variety of infectious diseases, the most notable being malaria. Our study of 15 genetic systems in the Temuan revealed substantial polymorphism and within-population genetic diversity. The polymorphisms for Hb beta, G6PD, and El are of interest in regard to genetic adaptation to malaria. Among the polymorphisms investigated we conclude that G6PD deficiency and elliptocytosis are likely to have malaria-resistant effects as evidenced by their low association with malarial parasitemia or their higher frequency in adults than in children. These findings suggest that the malarial habitat of the Temuans is livable in the long range sense for them because of the cluster of malaria-resistant alleles in their gene pool (G6PD)-, El, and possibly, but not tested here because of its low frequency, Hb beta E). The same condition probably holds for the Semai, the nearest aborigine neighbors of the Temuan (although the Semai have not been tested for malarial parasitemia and for these polymorphisms simultaneously), since the Semai have substantial Hb betaE, G6PD-, and El. The Temuan have a cultural identity system of rituals, beliefs, and certain aspects of language which effectively isolates them genetically from Malays and other nonaborigines. This system hinders the dilution of the malaria-resistant alleles of the Temuan gene pool with the malaria-susceptible alleles of the nonaborigine gene pools.

Carbonic Anhydrases↗

PubMed2002

Genetic variation in populations of Leishmania species in Brazil.

The population structure of strains of Leishmania (Viannia) braziliensis sensu lato from Pará State and Paraná State in Brazil, of L. (V.) shawi and L. (Leishmania) amazonensis from Pará State, and the relationships of type strains of the subgenera L. (Viannia) and L. (Leishmania) were examined by the random-amplified polymorphic deoxyribonucleic acid (RAPD) technique. Four different primers (M13-40, QG1, L15996 and delta gt11R) were used. The bands were analysed using the neighbor-joining (NJ) and unweighted pair-group method with arithmetic averages (UPGMA) algorithms of the MEGA package. The topology of the NJ and UPGMA trees was very similar but they were not always identical. Both trees differentiated the standard strains of the different species. Strains from the same location were grouped together only in the UPGMA phenogram of the M13-40 primer. L. (V.) braziliensis isolates from Paraná State were genetically closer to those from Paragominas, Pará State than to those from the Amazonian regions of Carajás in Pará State and Peru. The relationship was not dependent on geographical distance. It is postulated that the groups arose from different origins, in which the Amazonian stocks were related to Psychodopygus sand flies while the Paraná strains originated from a gene pool transmitted by Lutzomyia sand flies such as Lutzomyia (Nyssomyia) whitmani. Transmission by Ps. complexus in Paragominas is considered to be a secondary adaptation from the Lutzomyia leishmanial gene pool. Although the vectors of L. (V.) braziliensis are poorly known in the Amazon region, there is strong evidence that the major vectors are all Psychodopygus spp. There was a high degree of genetic variability amongst the L. (V.) shawi strains and there was no clear grouping according to the strains' origins. The genetic variability amongst L. (L.) amazonensis strains from the same locations was much lower but they formed 2 groups which coincided with their origin. Our results support the clonal population structure of Leishmania isolates and suggest that their distribution is related to the origin of the gene pool as well as to present vector and reservoir movements.

Animals↗

PubMed2001

[Genetic differentiation of the Tuva population with respect to the Alu insertions].

Polymorphism of three rural populations of the Tuva Republic was examined using a set of five autosomal Alu insertions at the ACE, PLAT, PV92, APOA1, and F13B loci. The allele frequency distribution patterns revealed in Tuvinians were typical to Mongoloid populations of Asia and were characterized by relatively high frequency of the Alu-repeat insertion at the PV92 and F13B loci along with relatively low insertion frequency at the APOA1 locus. With respect to the test systems used, Tuvinian populations examined displayed high levels of genetic diversity. The mean expected heterozygosity values in the populations of Kugurtug, Toora-Khem, and Teeli were 0.433, 0.407, and 0.437, respectively. The level of genetic diversity in the pooled Tuvinian sample was 0.432. The coefficient of genetic differentiation in the three populations studied was 1.45 pointing to relatively low level of genetic subdivision of the indigenous Tuvinian populations. However, estimates of genetic differentiation of the Tuvinian gene pool made by use of the Alu-repeat system were higher compared to those performed using classical protein systems, mtDNA, or Y-chromosomal haplotypes. Even though Tuvinian populations were characterized by common gene pool, some features specific to Western Tuvinian population could be distinguished. These features could be associated with higher contribution of the Caucasian component to the gene pool of this population. Phylogenetic analysis demonstrated close genetic relationships between the Tuvinian and Altaic ethnic populations.

Alleles↗

PubMedDate not supplied

Saami mitochondrial DNA reveals deep maternal lineage clusters.

The mitochondrial DNA of 62 Saami from the north of Norway was analyzed in the D loop hypervariable region I and II and sequences were compared to other gene pools. Two major (lineage 1 and 2) and two minor (lineage 3 and 4) maternal lineage clusters were found. Lineage 1 (56.9% of all hitherto analyzed Saami samples) contains a substantial number of branching haplotypes which are unknown in European gene pools. Lineage 2 (31.5%) and lineage 4 (3.6%) have few branching points and are present at a low rate throughout European gene pools. Lineage 3 (4.7%) has polymorphisms characteristic of circumpolar lineages.

Base Sequence↗

PubMed2001

High-resolution analysis of Y-chromosomal polymorphisms reveals signatures of population movements from Central Asia and West Asia into India.

Linguistic evidence suggests that West Asia and Central Asia have been the two major geographical sources of genes in the contemporary Indian gene pool. To test the nature and extent of similarities in the gene pools of these regions we have collected DNA samples from four ethnic populations of northern India, and have screened these samples for a set of 18 Y-chromosome polymorphic markers (12 unique event polymorphisms and six short tandem repeats). These data from Indian populations have been analysed in conjunction with published data from several West Asian and Central Asian populations. Our analyses have revealed traces of population movement from Central Asia and West Asia into India. Two haplogrops, HG-3 and HG-9, which are known to have arisen in the Central Asian region, are found in reasonably high frequencies (41.7% and 14.3% respectively) in the study populations. The ages estimated for these two haplogroups are less in the Indian populations than those estimated from data on Middle Eastern populations. A neighbour-joining tree based on Y-haplogroup frequencies shows that the North Indians are genetically placed between the West Asian and Central Asian populations. This is consistent with gene flow from West Asia and Central Asia into India.

Alleles↗

PubMed2002

[Polymorphism of locus COI-COII of mitochondrial DNA in the honeybee Apis mellifera L. from southern Ural region].

In spite of high biodiversity within the honeybee species Apis mellifera L., only one geographical race, the dark-colored forest honeybee A. m. mellifera, is uniquely adapted to severe environmental conditions of Eurasian forest and forest-steppe zones. Within the vast range of this race, only single isolates remain, where the dark forest honeybee is purebred. The Bashkir population is supposed to be one of these isolates. Molecular-genetic assessment of the state of the gene pool of this population revealed that southern honeybee races were introduced into the Bashkortostan Republic with great intensity, which was above the assimilation capacity of the population. The main part of the former range of the Bashkir population represents a hybrid zone with approximately equal ratio between gene pools of local and introduced honeybees. Our studies provide the possibility to single out one extant reserve of A. m. mellifera, Burzyanskii raion, in which the proportion of local bees in the gene pool is 0.98.

Animals↗

PubMed2004

Genetic diversity of taro, Colocasia esculenta (L.) Schott, in Southeast Asia and the Pacific.

The genetic diversity of 255 taro (Colocasia esculenta) accessions from Vietnam, Thailand, Malaysia,Indonesia, the Philippines, Papua New Guinea and Vanuatu was studied using AFLPs. Three AFLP primer combinations generated a total of 465 scorable amplification products. The 255 accessions were grouped according to their country of origin, to their ploidy level (diploid or triploid) and to their habitat--cultivated or wild. Gene diversity within these groups and the genetic distance between these groups were computed. Dendrograms were constructed using UPGMA cluster analysis. In each country, the gene diversity within the groups of wild genotypes was the highest compared to the diploid and triploid cultivars groups. The highest gene diversity was observed for the wild group from Thailand (0.19), the lowest for the diploid cultivars group from Thailand(0.007). In Malaysia there was hardly any difference between the gene diversity of the cultivars and wild groups, 0.07 and 0.08, respectively. The genetic distances between the diploid cultivars groups ranges from 0.02 to 0.10, with the distance between the diploid accessions from Thailand and Malaysia being the highest. The genetic distances between the wild groups range from 0.05 to 0.07. First, a dendrogram was constructed with only the diploids cultivars from all countries. The accessions formed clusters largely according to the country from which they originated. Two major groups of clusters were revealed, one group assembling accessions from Asian countries and the other assembling accessions from the Pacific. Surprisingly, the group of diploid cultivars from Thailand clustered among the Pacific countries. Secondly,a dendrogram was constructed with diploid cultivated,triploid cultivated and wild accessions. Again the division of the accessions into an Asian and a Pacific gene pool is obvious. The presence of two gene pools for cultivated diploid taro has major implications for the breeding and conservation of germplasm.

Asia, Southeastern↗

PubMed1991

Comparison of methods of estimating variance components in pigs.

Components of variance due to average effects of genes (sigma 2g), environmental effects common to littermates (sigma 2c), and environmental effects peculiar to individual pigs (sigma 2e) were estimated (--) by the Pseudo Expectation Approach (PE). Data were litter size (LS), backfat (BF; centimeter) and ADG (kilograms/day) collected from the Nebraska Gene Pool swine population between 1967 and 1986. Mean square errors (MSE) for h--2 and c--2 (sigma--2g and sigma--2c divided by phenotypic variance) by PE and nested ANOVA and h2 estimated by offspring on parent regression (REGOP) were evaluated using simulation of 200 repetitions of the Nebraska Gene Pool population. Parameter values for sigma 2g, sigma 2c, and sigma 2e used in simulations were PE estimates from the Gene Pool population. Estimates of h2 from PE were .18 +/- .06 for LS, .56 +/- .06 for BF, and .16 +/- .05 for ADG. Estimates of c2 from PE were .01 +/- .03 for LS, .09 +/- .02 for BF, and .19 +/- .03 for ADG. Compared with REGOP, PE yielded h--2 with smaller MSE for BF and ADG and larger MSE for LS. The MSE of PE was smaller than the MSE of the nested ANOVA estimate for all estimates and traits. These results were interpreted to suggest that considerable gains in precision in estimation of genetic parameters could be achieved by accounting for all relationships in lieu of accounting for only half- and full-sib relationships or parent-offspring relationships.

Adipose Tissue↗

PubMed1992

Biological characterization of Trichinella isolates from various host species and geographical regions.

Forty isolates of Trichinella collected from 5 continents were compared for 7 biological characters: newborn larvae produced per female worm cultured in vitro at the seventh, eighth, and ninth day postinfection, host muscle nurse cell development time, reproductive capacity index in rats and chickens, and resistance of muscle larvae to freezing. The isolates also were compared by analyses of an environmental character of the location from which they were isolated: the isotherms for January and July. By factorial analysis of correspondence of the biological and environmental data, the 40 isolates were grouped into 8 gene pools (T1-T8). The environmental temperature-related distribution was more evident for the sylvatic isolates (T2, T3, T5, T6, T7, T8), than for T1, which was isolated from domestic pigs, and for T4, a bird-adapted, nonencapsulating genetic type. The 8 biological groups correlated closely with the 8 gene pools previously identified on the basis of allozyme analysis. These results support the concept that the genus Trichinella is composed of at least 5 distinct gene pools or sibling species: Trichinella spiralis sensu stricto (T1), Trichinella nativa (T2), Trichinella sp. (T3), Trichinella pseudospiralis (T4), and Trichinella nelsoni (T7), and 3 other groups of uncertain taxonomic status (i.e., T5, T6, and T8).

Animals↗

PubMed1976

[Problems in the genetics of stress. I. Genetic analysis of the behavior of mice in a stressful situation].

Behavior of progeny of complete diallel crossing between 4 inbred strains of mice (BALB/c, C3H/He, C57BL/6, AKR/J) in a stressful situation was studied. As a model of stressful situation, the open field test was used. A statistically significant influence of genotype on the variability of the behaviour characteristics is found. On the basis of analysis of general combining ability of the strains, a hypothesis is made that in the gene pool of BALB/c and C3H/He strains there are concentrated some genes of additive effect, which increase the strength of emotional reactions of mice in a stressful situation, while in the gene pool of C57BL/6 and AKR/J there are genes of opposite effect. An analysis of the specific combining ability demonstrates that an important role in the control of features characterizing the exploratory activity of mice is played by non-additive gene effects, in particular, the effects of over-dominance. Significant genotypic correlations between the rate of sexual maturation of female mice and their behaviour in stressful situation were observed. The mice which mature earlier are more reactive to the stressing effect of a strange environment.

Animals↗