Analysis of polymorphism of CTG repetitive sequences in the gene of myotonic dystrophy in human populations of the Volga-Ural region]

Distribution of CTG repetitive sequences in the myotonic dystrophy (MD) gene was analyzed in ten populations of the Volga-Ural region, including Tatars, Chuvashes, Maris, Udmurts, Mordovians, Komis, and four ethnogeographical groups of Bashkirs. A total of 25 alleles were found (9 to 14 in individual populations), with each allele containing 5 to 34 trinucleotide repeats. The allele frequency distribution had two peaks corresponding to alleles with 5 and 11-14 CTG repeats. The frequency of the (CTG)5 allele varied from 0.23 to 0.47 in Maris and Mordovians, respectively. Regarding the (CTG)11-14 alleles, those containing 13 and 12 trinucleotides were most frequent in all populations; their frequencies varied from 0.15 in Mordovians to 0.24 in Maris and Bashkirs from the Abzelilovskii raion (district). Alleles with large numbers of repeats (more than 30) were only found in Tatars and Bashkirs from the Abzelilovskii raion, where their frequency was 0.01. The data obtained were compared with those on other human populations from various regions of the world. In general, the populations of the Volga-Ural region took an intermediate position between European and Asian populations (although were somewhat more similar to the latter ones) with respect to the distribution of allelic frequencies of the CTG repetitive sequences. In individual populations, the number of genotypes varied from 13 to 27 in Mordovians and Bashkirs from the Ilishevskii raion, respectively. The observed heterozygosity was the highest (91%) in Udmurts and the lowest (58%) in Mordovians; the average heterozygosity was 81%. Such a high heterozygosity, as well as the revealed differentiation of the populations with respect to the distribution of the allelic frequencies of CTG repetitive sequences in the MD gene, allow this polymorphic DNA locus to be considered a highly informative genetic marker of populations.     

VNTR-polymorphism of the PAH, e-NOS genes and deletion of the CCR5 gene in populations in the northern Caucasus

VNTR allelic polymorphism at the phenylalanine hydroxilase (PAH) and endothelial constitutive nitric oxide synthase (eNOS) genes and the prevalence of the CCR5 chemokine receptor gene 32-bp deletion were examined in four indigenous populations of Northern Caucasus, Adygs, Kumyks, Karachais, and Nogais (Kuban and Karanogais). Population-specific features of the allele and genotype frequency distribution patterns of the polymorphisms examined were described. The data obtained were compared to those obtained from literature. The results of the study confirmed that the frequency and occurrence of the PAH polymorphic alleles exhibit substantial interpopulation differences. In the populations of Northern Caucasus, the eNOS minisatellite polymorphism alleles and genotypes frequency distribution patterns were close to those described earlier for populations of the Volga-Ural region (VUR), and also for the Australian Caucasoids, Japanese, and Turks. In the populations examined, the mean frequency of the CCR5 gene deletion was 0.055, which was somewhat lower than in the populations of VUR (0.07) and Europe (0.081), and practically identical to that in Asian populations (0.050). For each population observed and expected heterozygosities at each locus were calculated. In general, the gene pool of Northern Caucasian populations showed substantial differentiation at the loci examined: the GST value was 0.0274. The data for individual loci showed that the greater contribution to the interpopulation diversity was made by the differences in the PAH VNTR allele frequencies (GST = 0.04), while the differences at the eNOS and CCR5 loci were small (GST = 0.0025 and GST = 0.0039, respectively).     

Analysis of Apolipoprotein E gene polymorphism in populations of the Volgo-Ural region]

Polymorphism at the apolipoprotein E gene (ApoE) in populations of the Volga-Ural region was studied by means of polymerase chain reaction. In the region examined the population-specific patterns of the ApoE alleles and genotypes frequency distribution were established. The results obtained were compared with the literature data on the ApoE polymorphism in other world populations. Substantial heterogeneity of different ethnic populations in respect to the ApoE genotypes distribution and frequency was revealed.     

Investigation of monoamine oxidase gene restriction polymorphism in male populations of the Volga-Ural region

Restriction polymorphism at the monoamine oxidase A (MAO A) gene was typed in eight male populations of the Volga-Ural region (Bashkirs, Chuvashes, Tatars, Udmurts, Maris, Mordovians, Komis, and Russians inhabiting the Republic of Bashkortostan). Analysis of the MAO A alleles frequency distribution patterns did not reveal statistically significant differences between the Volga-Ural populations examined. The results obtained suggest genetic homogeneity of the populations described in respect of the polymorphic locus examined.     

Molecular-genetic analysis of polymorphism of the DXS532 locus in people from the Volga-Ural region]

The DXS52 polymorphic locus mapping to the 5'-region of the blood-clotting factor VIII gene on the X chromosome was genotyped in seven Volga-Ural ethnic groups (Bashkirs, Tatars, Chuvashes, Maris, Mordovians, Udmurts, and Komis). A total of 47 different genotypes and 15 allelic variants of this locus were described. Substantial intra- and interpopulation heterogeneity of the ethnic groups studied in respect to frequency and distribution of the DXS52 alleles and genotypes was demonstrated. The unimodal DXS52 allele frequency distribution pattern with the peak at 1690 bp was typical to Mordovians and Komis. Chuvashes and Maris, as well as Udmurts, were characterized by bimodal frequency distribution patterns, with the peaks at 1690 and 670 bp, and 1690 and 1390 bp, respectively. Moreover, Bashkirs and Tatars displayed trimodal DXS52 allele frequency distribution patterns with the peaks at 1690, 1390, and 670 bp. The DXS52 allele frequency distribution patterns described in populations of the Volga-Ural region were found to be remarkably different from those established for the mixed Moscow population and the population of Western Europe. These data indicate that the DXS52 locus is highly informative, and this polymorphic system can serve as a molecular marker for population genetic studies.     

Analysis of polymorphic loci of Huntington genes in peoples from the Volga-Ural region

Eleven populations of the Volga-Ural region were analyzed with respect to three intragenic polymorphisms of the Huntington disease gene (IT15), including highly polymorphic (CAG)n and moderately polymorphic (CCG)n of exon 1 and neutral del2642 of exon 58. In the case of (CAG)n, 101 genotypes were observed, with genotype number varying from 15 in Southeastern Bashkirs to 34 in Mari. Allele diversity RS ranged from 9.70 in Southeastern Bashkirs to 18.00 in Chuvash, averaging 13.79 +/- 2.12. The (CAG)n allele frequency distribution was unimodal and had a maximum at (CAG)17. In the case of (CCG)n, six alleles with 6-10 or 12 repeats were observed. RS was 4.13 +/- 0.44, ranging from 3.73 in Udmurts to 4.99 in Tatars. In the case of del2642, allele del- was detected at a frequency 0.830 in Mari to 0.932 in Udmurts. Of all Volga-Ural ethnic populations, Finno-Ugric ones proved to be most heterogeneous with respect to the three polymorphisms, whereas Turkic populations and, in particular, Bashkirs were homogeneous. Micro-differentiation of the Volga-Ural populations corresponded to the European type.     

A population genetic study of six VNTR loci in three ethnically defined populations.

To investigate the population genetic characteristics of VNTR polymorphisms in human populations, we have studied the allele frequency distribution of six VNTR loci (D1S57, RB1, D1S77, D1S61, alpha-globin 5'HVR, D1S76) in three well-defined populations (Kachari of Northeast India; Dogrib Indian of Canada; and New Guinea Highlander of Papua New Guinea). Even though the number of alleles sampled is limited, 48 to 92 alleles per locus per population, significant variation is noticed in the number of alleles per locus for all the populations. Using alternate summary measures, we have observed that genotype distributions at the six VNTR loci apparently conform to their respective Hardy-Weinberg predictions. Multilocus genotype profiles of the individuals in each of the three populations suggest that the VNTR alleles are independently segregating with the exception of the two linked loci D1S76 and D1S77. Lack of fit of all VNTR loci to one particular model of mutational change, either the Infinite Allele Model or the Stepwise Mutation Model, suggests more than one mechanism for production of new VNTR alleles. This study also indicates that increased heterozygosity at VNTR loci in comparison to protein and blood group loci may lead to more accurate estimates of genetic distance.     

Allele frequency distributions of Apo B VNTR locus in Cukurova, Turkey

The highly polymorphic minisatellites contain a variable number of tandemly repeated (VNTR) DNA sequences. They are extremely useful and informative markers to study genetic variation among human populations. We have analysed the allele frequency distribution at the highly polymorphic apolipoprotein B (Apo B) VNTR locus in order to obtain the population data for the Cukurova region in Turkey by using the polymerase chain reaction and polyacrylamide gel electrophoresis. We observed 10 different alleles and 21 genotypes in a sample of 100 unrelated individuals. The allele frequencies ranged from 0.01 to 0.4, with an expected heterozygosity of 0.69 for the Apo B locus. Alleles 37 (frequency = 0.4) and 35 (frequency = 0.17) were the most common in the Cukurova population. There was a significant deviation from the Hardy-Weinberg equilibrium (HWE) for genotype frequencies (chi2 = 29.12; df = 1; p = 0.000). This study possesses novelty as it is the first DNA polymorphism study conducted at the Cukurova population using an Apo B minisatellite locus.     

Genetic structure of the Sardinian population at the D1S80 VNTR locus and population diversity

We typed the Sardinian population at the D1S80 VNTR locus. Nineteen alleles were detected in a sample of 92 unrelated individuals, allele frequency distribution showing a modal pattern mostly in agreement with other Caucasoid populations. A high degree of heterozygosity (observed value=80.4%) was present. Goodness-of-fit tests demonstrated no departure from Hardy-Weinberg expectations. Data regarding heterozygosity, number of alleles and singletons appeared in accordance with the IAM mutation-drift equilibrium model and showed no evidence of hidden substructuring. Allele 34 exhibited in Sardinians the highest frequency never observed in Caucasians. Nonetheless, the comparison with other European populations did not disclose Sardinian genetic peculiarity. Indeed, measures of genetic divergence among Europeans demonstrated definitely smaller values at the D1S80 locus in comparison with those calculated over a high number of (pre-DNA) polymorphic loci. High mutation rate and selective neutrality typical of VNTRs could account for the observed moderate genetic divergence. Isolation and genetic drift, on the other hand, may have determined certain deviations in allele frequency distribution, as occurred to allele 34 in the Sardinian population.     

VNTR loci reveal differentiation between and structure within populations of the eastern barred bandicoot Perameles gunnii

The Eastern Barred Bandicoot Perameles gunnii has declined in abundance within mainland south-eastern Australia, to a relict wild population of less than 100 individuals in Hamilton, Victoria. It is more common, but is also declining in Tasmania. Genomic DN A variability was compared within and between surviving populations of P. gunnii using variable number of tandem repeat (VNTR) markers in one of two ways. First, average percentage differences (APDs) were determined between profiles for two VNTR probe—endonuclease combinations. Secondly, because one of these combinations revealed two multiallelic VNTR loci, genotypes were assigned and analysed for homogeneity of allele frequencies among subpopulations, for deviation of heterozygosity from Hardy-Weinberg equilibrium within populations and for genetic structuring among individuals from different subpopulations. The results of both the APD and defined locus approaches showed consistent trends within and between populations. Genetic variability was higher among mainland P. gunnii than in Tasmanian populations (higher APDs, number of alleles, and heterozygosity at one locus), despite the known decline and subdivision of the Hamilton population. Eleven per cent of the variability detected in Hamilton was attributed to genetic differentiation between east and west subdivisions of the population. Departure from random mating indicating local inbreeding within collecting localities was evident for one locus in both north and south Tasmania, particularly at one locality. AH alleles at both loci were unique to either Hamilton or Tasmanian P. gunnii. The initial captive colony contains high heterozygosity for these loci. It is concluded that VNTR markers can be of benefit for use in studies of population differentiation and for conservation management.     

Genetic structure of people from the Volga-Ural region and Central Asia from data of Alu-polymorphism

Nine Alu loci (Ya5NBC5, Ya5NBC27, Ya5NBC148, Ya5NBC182, YA5NBC361, ACE, ApoA1, PV92, TPA25) were analyzed in six ethnic populations (Trans-Ural Bashkirs, Tatars-Mishars, Mordovians-Moksha, Mountain Maris, Udmurts, and Komi-Permyaks) of the Volga-Ural region and in three Central Asian populations (Uzbeks, Kazakhs, and Uigurs). All Alu insertions analyzed appeared to be polymorphic in all populations examined. The frequency of insertion varied from 0.110 in Mountain Maris at the Ya5NBC5 locus to 0.914 in Tatars at the ApoA1 locus. The data on the allele frequency distribution at nine loci point to the existence of substantial genetic diversity in the populations examined. The value of the observed heterozygosity averaged over nine Alu insertions varied from 0.326 in Mountain Maris to 0.445 in Kazakhs and Uigurs. The level of the interpopulation genetic differences for the Volga-Ural population (Fst = 0.061) was higher than for the populations of Central Asia (Fst = 0.024), Europe (Fst = 0.02), and Southeastern Asia (Fst = 0.018). The populations examined were highly differentiated both in respect of linguistic characteristics and the geographical position. The data obtained confirmed the effectiveness of the marker system used for the assessment of genetic differentiation and the relationships between the ethnic groups.     

Analysis of the angiotensinogen gene T174M polymorphism in populations of the Volga-Ural region

The method of polymerase chain reaction was used to analyze T174M polymorphism at the angiotensinogen (AGT) gene in a number of populations of the Volga-Ural region, belonging to Finno-Ugric (Komi-Permyaks, Maris, Mordovians, and Udmurts), Turkic (Chuvashes, Tatars, and Bashkirs), and Eastern-Slavic (Russians) ethnic groups. Population-specific patterns of the polymorphic alleles and genotypes frequency distribution were established. Comparison of the results with the literature data on the AGT gene polymorphism in different world populations provided identification of specific trends in the changes of genotype frequency of the AGT gene depending on the ethnicity of the populations.     

DAT1 VNTR allele frequencies in the Omani population

To determine the genetic variability at the human DAT1 VNTR locus, we screened 110 healthy Omani blood donors using the polymerase chain reaction (PCR) and agarose gel electrophoresis. Two common alleles (DAT1*9 and DAT1*10) were observed with a frequency of 0.332 and 0.609, respectively. There were also five rare alleles (*3, *6, *7, *8, and *11). The frequency of the observed genotypes was not significantly different from the expected Hardy-Weinberg distribution. We compared the Omani DAT1 alleles with similar data from other populations.     

Characteristics of polymorphism at a VNTR locus 3' to the apolipoprotein B gene in five human populations.

We have analyzed the allele frequency distribution at the hypervariable locus 3' to the apolipoprotein B gene (ApoB 3' VNTR) in five well-defined human populations (Kacharis of northeast India, New Guinea Highlanders of Papua New Guinea, Dogrib Indians of Canada, Pehuenche Indians of Chile, and a relatively homogeneous Caucasian population of northern German extraction) by using the PCR technique. A total of 12 segregating alleles were detected in the pooled sample of 319 individuals. A fairly consistent bimodal pattern of allele frequency distribution, apparent in most of these geographically and genetically diverse populations, suggests that the ApoB 3' VNTR polymorphism predates the geographic dispersal of ancestral human populations. In spite of the observed high degree of polymorphism at this locus (expected heterozygosity levels 55%-78%), the genotype distributions in all populations (irrespective of their tribal or cosmopolitan nature) conform to their respective Hardy-Weinberg predictions. Furthermore, analysis of the congruence between expected heterozygosity and the observed number of alleles reveals that, in general, the allele frequency distributions at this locus are in agreement with the predictions of the classical mutation-drift models. The data also show that alleles that are shared by all populations have the highest average frequency within populations. These findings demonstrate the potential utility of highly informative hypervariable loci such as the ApoB 3' VNTR locus in population genetic research, as well as in forensic medicine and determination of biological relatedness of individuals.     

Analysis of polymorphism at nine nuclear genome DNA loci in maris

Population genetic survey of the indigenous populations of the Marii El Republic, represented by the two major ethnographic groups of Maris, Meadow (five samples from Morkinsk, Orshansk, Semursk, Sovetsk, and Zvenigovsk districts) and Mountain (one sample from Gornomariisk district) Maris, was carried out. All Mari groups were examined at nine polymorphic DNA loci of nuclear genome, VNTR(PAH) (N = 422), STR(PAH) (N = 152), VNTR(ApoB) (N= 294), VNTR(DAT1) (N = 363), VNTR(eNOS) (N = 373), ACE (N = 412), IVS6aGATT (N = 513), D7S23(KM.19) (N = 494), and D7S8 (N = 366). Allele and genotype frequency distribution patterns were obtained for individual samples and ethnographic groups, as well as for the ethnic group overall. In each of six Mari samples examined, the deficit of heterozygotes was observed, i.e., the mean observed heterozygosity was lower than the expected one. The indices of mean heterozygosity, Hs = 0.455, and interpopulation differentiation, FST = 0.0024, for the Mari gene pool were obtained using a set of DNA markers analyzed. Analysis of the genetic distances and between population differentiation (FST) showed that the main part of genetic diversity in Maris was determined by the differentiation between the populations of Meadow Maris. The contribution of the differences between the ethnographic groups of Mountain and Meadow Maris to the ethnic gene pool was small. It is suggested that the main role in the formation of the Mari gene pool is played by the geographic factor.     

Analysis of the VNTR locus D1S80 by the PCR followed by high-resolution PAGE.

Allelic data for the D1S80 locus was obtained by using the PCR and subsequent analysis with a high-resolution, horizontal PAGE technique and silver staining. Compared with RFLP analysis of VNTR loci by Southern blotting, the approach described in this paper offers certain advantages: (1) discrete allele resolution, (2) minimal measurement error, (3) correct genotyping of single-band VNTR patterns, (4) a nonisotopic assay, (5) a permanent record of the electrophoretic separation, and (6) reduced assay time. In a sample of 99 unrelated Caucasians, the D1S80 locus demonstrated a heterozygosity of 80.8% with 37 phenotypes and 16 alleles. The distribution of genotypes is in agreement with expected values according to the Hardy-Weinberg equilibrium. Furthermore, the observed number of alleles and the level of heterozygosity, obtained through the protocol described here, were congruent with each other in accordance with the expectation of a mutation-drift equilibrium model for a single, homogeneous, random-mating population. Therefore, the analysis of D1S80 and similar VNTR loci by amplified fragment length polymorphism (AMP-FLP) may prove useful as models for population genetic issues for VNTR loci analyzed by RFLP typing via Southern blotting.     

微卫星DNA标记分析野生鲤鱼群体的遗传多样性

利用30个微卫星分子标记对海南鲤(HN)、长江鲤(CY)、月亮湖鲤(YL)、黑龙江鲤(FY)、呼伦湖鲤(ZL)、贝尔湖鲤(BR)6个野生鲤鱼群体的观测杂合度(Ho)、期望杂合度(He)、多态信息含量(PIC)和有效等位基因数(Ae)等进行了遗传检测,根据基因频率计算遗传相似系数和Nei氏标准遗传距离,χ2检验估计Hardy-Weinberg平衡,用近交系数(FST)和基因流(Nm)分析群体的遗传分化及其来源。同时,使用PHYLIP3.63软件绘制基于Nei氏标准遗传距离的UPGMA进化树。6个群体共检测到8,136个扩增片段,长度在125bp～414bp,30个基因座扩增出等位基因数从3～13个不等,共计210个等位基因,平均每个基因座扩增得到7个等位基因。结果显示:(1)6个野鲤群体的多态性指标均适中,多态信息含量依次0.44、0.52、0.53、0.57、0.63和0.64,有效等位基因数1.04～4.72个不等,平均有效等位基因数依次为2.19、2.60、2.42、2.43、2.45和2.33,无偏期望杂合度平均值为0.50、0.59、0.56、0.56、0.57和0.54;(2)遗传相似系数BR与ZL最高(0.8511),BR与HN最低(0.6688),聚类结果与地理分布呈一定相关性。     

Genetic variation in populations of the threatened seagrass Halophila beccarii (Hydrocharitaceae)

Halophila beccarii (Hydrocharitaceae), a small monoecious seagrass, has been listed as a threatened species. In this study, a total of 106 samples were collected from four Chinese populations located at the northern limit of its distribution range. Using six polymorphic microsatellites, we found low genetic variation in this species, in which the mean number of alleles per locus was 2.8, and 16 multi-locus genotypes were revealed. In the four populations, the mean number of alleles per locus ranged from 1.2 to 2, one to eight genotypes were found, and clonal diversity ranged from 0 to 0.23; observed and expected heterozygosity ranged from 0.17 to 0.40 and from 0.09 to 0.24, respectively. Strong genetic differentiation was found among the populations, and the standardized fixation index (F′_ST) was 0.787. Species traits (i.e., clonal growth) and bottleneck effects due to drastic population fluctuation may contribute to the observed low genetic variation.     

A study of the insertion-deletion polymorphism of the serotonin transporter gene in populations from the Volga-Ural region

The insertion-deletion polymorphism of the serotonin transporter gene (SLC6A4) was studied using the polymerase chain reaction (PCR) in eight populations from the Volga-Ural region (the Bashkir, Chuvash, Tatar, Udmurt, Mari, Mordovian, and Komi populations and the population of Russians living in the Arkhangel's skii raion of Bashkortostan). For this polymorphic system, the pattern of distribution of main population parameters was established in the region studied. Depending on population ethnicity, specific trends were revealed in the pattern of frequencies of alleles and genotypes of gene SLC6A4.     

DAT1 VNTR polymorphisms in a European and an African population: identification of a new allele

Polymorphism frequencies of the dopamine transporter gene (DAT1) hypervariable region have been analyzed in a sample of Italian and Ivory Coast individuals. The 3' untranslated region (UTR) of DAT1 includes a variable number of tandem repeats (VNTR) of a 40-bp monomer, ranging from 3 to 13 repeats in Caucasian and African populations. In our sample we found alleles with 3 to 16 repeats, and the most common alleles were the 10-repeat (DAT1*10) and the 9-repeat (DAT1*9) alleles. We also found two rare alleles in the Italian population and four in the Ivory Coast population. For the first time the new allele DAT1*16 is described in the Ivorians. The Ivory Coast population was not in Hardy-Weinberg equilibrium for the DAT1 locus because of a deficit of heterozygote genotypes. The observed heterozygosity of the Ivorian population was half that of the Italians. The lower observed heterozygosity and deviation from Hardy-Weinberg equilibrium could be the result of microevolutionary trends, such as genetic drift and/or inbreeding, acting on the relatively small and isolated population sampled for this study, although some sort of selective pressures acting against the shorter alleles cannot be excluded. This evidence, in association with the reduced polymorphism shown by the DAT1 VNTR compared to other VNTRs, seems to indicate that the DAT1 locus may be under some selective pressure.