Allele Frequency Distribution Patterns Research Articles

Leaf shredding as an alternative strategy for managing apple scab resistance to demethylation inhibitor fungicides

Within integrated apple scab control there is a strong focus on reduction of Venturia inaequalis primary inoculum. The hypothesis that leaf shredding as an orchard sanitation practice would reduce the effective population size of the fungus (resulting in lower genetic variation due to reduction in sexual offspring) was tested. Assuming the allele causing fungicide resistance is already present in the population, it will be widely distributed at the end of the season, since selection occurs when the demethylation inhibitor (DMI) fungicide was applied. For short-term disease management a reduction of inoculum size, (i.e. potential ascospore dose) is most important. In the long-term resistant isolates/genotypes would be less likely to survive the winter and/or to infect in the spring, if that inoculum (i.e. in fallen leaves) has been removed. To sustain the use of highly effective synthetic fungicides, such as the DMIs, fungicide resistance management practices have to be evaluated. Fungicide resistance, which negatively affects pathogen fitness, is hypothetically reversible, if the selection pressure by the fungicide is removed. This study quantified the effect of leaf shredding on changes in the pathogen’s flusilazole sensitivity and population genetic structure using SSR markers. Venturia inaequalis populations in orchard trials, where sanitation practices had been applied, were tested for flusilazole sensitivity in planta and in vitro. Significant shifts towards flusilazole resistance were identified in orchards with a history of DMI application without sanitation treatment, with a mean sensitivity of EC50= 0.208 ug/ml (n=49) compared to an unexposed V. inaequalis population (EC50= 0.104 ug/ml, n=55). However, the isolates from the same sanitation trial orchards, from leaf shredding treatment in combination with a fungicide spray programme, had a mean EC50 of 0.110 ug/ml (n=41), similar to an unexposed V. inaequalis population. Furthermore, V. inaequalis offspring after sanitation treatment, showed shifts in microsatellite allele frequency distribution patterns used as an indicator of sexual reproduction. This study concludes that sanitation treatments, i.e. leaf shredding, impact on fungicide sensitivity and therefore effectively contributes to fungicide resistance management.

Allele and genotype frequencies of CYP3A4, CYP3A5, CYP3A7, and GSTP1 gene polymorphisms among mainland Tibetan, Mongolian, Uyghur, and Han Chinese populations.

Over 50% prescribed drugs are metabolised by cytochrome P450 3A (CYP3A) and glutathione S-transferase pi (GSTP1) adds a glutathione to the oxidative products by CYP3A, which increases the hydrophilic property of metabolites and facilitates the excretion. Single nucleotide polymorphisms (SNPs) of CYP3A and GSTP1show a diverse allele and genotype frequencies distribution among the world populations. The present study aimed to investigate the genotype and allele frequency distribution patterns of CYP3A4, CYP3A5, CYP3A7 and GSTP1 polymorphisms among healthy participants in mainland Tibetan, Mongolian, Uyghur, and Han Chinese populations. Blood samples were collected from 842 unrelated healthy subjects (323Tibetan, 134Mongolian, 162 Uyghur, and 223 Han) for genotyping analysis. Variant allele frequencies of CYP3A4 rs2242480, CYP3A5 rs776746, CYP3A7 rs2257401, and GSTP1 Ile105Val were observed in Han (0.253, 0.686, 0.312 and 0.188), Tibetan (0.186, 0.819, 0.192 and 0.173), Mongolian (0.198, 0.784, 0.228 and 0.235) and Uyghur (0.179, 0.858, 0.182 and 0.250) respectively. The allele frequency of CYP3A7*1C in Uyghur (0.019) was higher than that in Tibetan (0.002, p<0.01). There was a strong linkage disequilibrium between CYP3A4 rs2242480, CYP3A5 rs776746, and CYP3A7 rs2257401 among the four ethnic groups. The results might be useful for the precise medication in the Chinese populations.

Genomic and Phenotypic Diversity of Cultivated and Wild Tomatoes with Varying Levels of Heat Tolerance.

Assessment of genetic variability in heat-tolerant tomato germplasm is a pre-requisite to improve yield and fruit quality under heat stress. We assessed the population structure and diversity in a panel of three Solanum pimpinellifolium (wild tomatoes) and 42 S. lycopersicum (cultivated tomatoes) lines and accessions with varying heat tolerance levels. The DArTseq marker was used for the sequencing and 5270 informative single nucleotide polymorphism (SNP) markers were retained for the genomic analysis. The germplasm was evaluated under two heat stress environments for five yield and flower related traits. The phenotypic evaluation revealed moderate broad-sense heritabilities for fruit weight per plant and high broad-sense heritabilities for fruit weight, number of inflorescences per plant, and number of flowers per inflorescence. The hierarchical clustering based on identity by state dissimilarity matrix and UPGMA grouped the germplasm into three clusters. The cluster analysis based on heat-tolerance traits separated the germplasm collection into five clusters. The correlation between the phenotypic and genomic-based distance matrices was low (r = 0.2, p < 0.05). The joint phenotypic and genomic-based clustering grouped the germplasm collection into five clusters well defined for their response to heat stress ranging from highly sensitive to highly tolerant groups. The heat-sensitive and heat-tolerant clusters of S. lycopersicum lines were differentiated by a specific pattern of minor allele frequency distribution on chromosome 11. The joint phenotypic and genomic analysis revealed important diversity within the germplasm collection. This study provides the basis for efficient selection of parental lines to breed heat-tolerant varieties.

WGVD: an integrated web-database for wheat genome variation and selective signatures.

Bread wheat is one of the most important crops worldwide. With the release of the complete wheat reference genome and the development of next-generation sequencing technology, a mass of genomic data from bread wheat and its progenitors has been yield and has provided genomic resources for wheat genetics research. To conveniently and effectively access and use these data, we established Wheat Genome Variation Database, an integrated web-database including genomic variations from whole-genome resequencing and exome-capture data for bread wheat and its progenitors, as well as selective signatures during the process of wheat domestication and improvement. In this version, WGVD contains 7 346 814 single nucleotide polymorphisms (SNPs) and 1 044 400 indels focusing on genic regions and upstream or downstream regions. We provide allele frequency distribution patterns of these variations for 5 ploidy wheat groups or 17 worldwide bread wheat groups, the annotation of the variant types and the genotypes of all individuals for 2 versions of bread wheat reference genome (IWGSC RefSeq v1.0 and IWGSC RefSeq v2.0). Selective footprints for Aegilops tauschii, wild emmer, domesticated emmer, bread wheat landrace and bread wheat variety are evaluated with two statistical tests (FST and Pi) based on SNPs from whole-genome resequencing data. In addition, we provide the Genome Browser to visualize the genomic variations, the selective footprints, the genotype patterns and the read coverage depth, and the alignment tool Blast to search the homologous regions between sequences. All of these features of WGVD will promote wheat functional studies and wheat breeding.Database URL http://animal.nwsuaf.edu.cn/code/index.php/Wheat

Identifying QTL–allele system of seed protein content in Chinese soybean landraces for population differentiation studies and optimal cross predictions

Soybean originated in ancient China has been quickly extended globally as a major protein and oil crop. The QTL–allele constitution of seed protein content (SPC) in the Chinese soybean landrace population (CSLRP) was studied using a representative sample composed of 365 accessions tested under multiple environments and analysed under the novel restricted two-stage multi-locus genome-wide association study (RTM-GWAS) procedure based on 29,121 SNPLDB (single nucleotide polymorphism linkage disequilibrium blocks) markers. The SPC varied from 37.51 to 50.46% among accessions, for which 89 QTLs, each with 2–9 alleles in a total of 255 alleles were identified, accounting for 83.16% of the phenotypic variation covering most of the genetic variation (h2 = 84.31%). The QTL–alleles of the 365 landraces were organized into a 255 × 365 QTL–allele matrix as the compact form of SPC genetic constitution in CSLRP. Of the 89 QTLs, 53 showed significantly differentiated allele frequency distribution patterns among geographic eco-regions (sub-populations). There were 32.09% alleles not common among sub-populations but found only in some sub-populations; new allele(s) emerged on some loci in some respective sub-populations, with Eco-region III showing less but Eco-region VI more emergence. The QTL–allele matrix was also used for prediction of optimal crosses for breeding purpose to reach a 99th percentile potential of up to 54.81%, more than the highest accession (50.46%). From the 89 QTLs, 59 SPC candidate genes involving biological processes, cellular components and molecular functions were annotated. Among them, Glyma18g13574 and Glyma20g21370 were inferred as two of the major SPC genes in the whole genome.

Haplotype and Allelic Variations at Dopamine Receptor Gene (DRD2) among six Austro-Asiatic Speaking Tribal Groups of Central India

Central India is mainly constituted by two states, namely; Madhya Pradesh and Chhattisgarh that are homeland of several caste and tribal groups speaking diverse language belongs to Indo-European, Dravidian and Austro-Asiatic thus makes it an important place for testing several language-gene interaction models. Various archaeological evidences indicated that the Narmada region has played a significant role in initial peopling of the Asian subcontinent. There is a necessity to fill the big lacuna by inclusion of this region to reveal a continuous picture of the origin and genetic affinity of the Indian population. It is hypothesized that Austro-Asiatic speaking tribes are autochthonous to India. The present study was conducted to examine the haplotype variations at Dopamine Receptor Gene (DRD2) in the Austro-Asiatic Speaking Tribal Groups of Central India. Haplotypes provide information on evolutionary histories, beyond what can be learned from individual marker. A total of 327 unrelated samples belonging to Birhor, Gadaba, Kol, Hill korwa, Saora and Baiga were analyzed for three selected TaqI sites of DRD2 gene using Polymerase chain reaction (PCR). All the loci were found to be polymorphic among the studied populations. The frequency of ancestral allele B2 is less than 50% in all six populations (41.4-49.2%) while D2 allele exhibit frequency of 15.3-44.8%. A1 allele observed with a frequency ranging from 36.2-48.2%. The average heterozygosity ranged from 0.417 in Baiga to 0.501 in Kol. The ancestral haplotype (B2D2A1) in all six populations exhibit 0% frequency. LD values calculated for the three bi-allelic sites, TaqIB, TaqID, and TaqIA are low, i.e., below 0.8 with respect to all populations in each pair. Overall, allele frequency distribution patterns and high average heterozygosity values, suggest a genetic proximity among the studied populations. Low recurrence of genealogical alleles and nonattendance of familial haplotype in the examined populace bunches, demonstrating towards indigenous inception of Central Indian Austro-Asiatic talking tribes.

Genetic differentiation and population structure of five ethnic groups of Punjab (North-West India)

The state of Punjab in the North-West part of India has acted as the main passage for all the major human invasions into the Indian subcontinent. It has resulted in the mixing of foreign gene pool into the local populations, which led to an extensive range of genetic diversity and has influenced the genetic structure of populations in Punjab, North-West India. The present study was conducted to examine the genetic structure, relationships, and extent of genetic differentiation in five Indo-European speaking ethnic groups of Punjab. A total of 1021 unrelated samples belonging to Banias, Brahmins, Jat Sikhs, Khatris, and Scheduled castes were analyzed for four human-specific Ins/Del polymorphic loci (ACE, APO, PLAT, and D1) and three restriction fragment length polymorphisms ESR (PvuII), LPL (PvuII), and T2 (MspI) using Polymerase chain reaction (PCR). All the loci were found to be polymorphic among the studied populations. The frequency of the Alu insertion at APO locus was observed to exhibit the highest value (82.6-96.3%), whereas D1 exhibited the lowest (26.5-45.6%) among all the ethnic groups. The average heterozygosity among the studied populations ranged from 0.3816 in Banias to 0.4163 in Khatris. The FST values ranged from 0.0418 to 0.0033 for the PLAT and LPL loci, respectively, with an average value being 0.0166. Phylogenetic analysis revealed that Banias and Khatris are genetically closest to each other. The Jat Sikhs are genetically close to Brahmins and are distant from the Banias. The Jat Sikhs, Banias, Brahmins, and Khatris are genetically very distant from the Scheduled castes. Overall, Uniform allele frequency distribution patterns, high average heterozygosity values, and a small degree of genetic differentiation in this study suggest a genetic proximity among the selected populations. A low level of genetic differentiation was observed in the studied population groups indicating that genetic drift might have been small or negligible in shaping the genetic structure of North-West Indian Populations.

Human Dopamine Receptor D2 (DRD2) Polymorphisms among Four Tribal Populations of Chhattisgarh, India

Dopamine receptor gene plays an important role in central nervous system and helps in the proper functioning of neural circuits in the human brain. Polymorphisms of this gene affect the functioning of brain activities. Association of Dopamine receptor D2 gene (DRD2) polymorphisms with cognitive disorders and alcoholism has been reported in various studies now-a-days. The interest on DRD2 polymorphism is not only limited to psychiatric disorders or alcoholic behaviors or pharmacology but it is also a promising gene for evolutionary genetic studies and studies on genetic variations among populations. The present study is an attempt to understand the extent of genetic variations in four tribal populations by using the allele frequencies, haplotype frequencies and the distribution patterns of the three Taq I polymorphic sites of DRD2 gene. 197 unrelated blood samples were collected with individual informed consent and analysed by using standard protocols. All the three sites were found to be polymorphic among the four studied populations. The allele frequency distribution patterns and sharing of haplotypes in this study suggest genetic proximity among the populations.

Molecular genetic polymorphism of androgen receptor gene (AR) in African populations of Hadza and Datoga

The molecular genetic analysis of the polymorphic variants of the CAG repeat-containing locus of the andro- gen receptor (AR) gene was performed in the populations of Hadza and Datoga. Allele frequency distribution patterns were established. Alleles containing 20-25 repeats were the most abundant in both populations were the. The populations studied were compared with Asians (Han), white Americans, and Africans (Ariaal). Sta- tistically significant difference between populations of Hadza and Datoga in the distribution of the AR allelic variants was demonstrated.

A Preliminary Study of Copy Number Variation in Tibetans

Genetic features of Tibetans have been broadly investigated, but the properties of copy number variation (CNV) have not been well examined. To get a preliminary view of CNV in Tibetans, we scanned 29 Tibetan genomes with the Illumina Human-1 M high-resolution genotyping microarray and identified 139 putative copy number variable regions (CNVRs), consisting of 70 deletions, 61 duplications, and 8 multi-allelic loci. Thirty-four of the 139 CNVRs showed differential allele frequencies versus other East-Asian populations, with P values <0.0001. These results indicated a distinct pattern of CNVR allele frequency distribution in Tibetans. The Tibetan CNVRs are enriched for genes in the disease class of human reproduction (such as genes from the DAZ, BPY2, CDY, and HLA-DQ and -DR gene clusters) and biological process categories of “response to DNA damage stimulus” and “DNA repair” (such as RAD51, RAD52, and MRE11A). These genes are related to the adaptive traits of high infant birth weight and darker skin tone of Tibetans, and may be attributed to recent local adaptation. Our results provide a different view of genetic diversity in Tibetans and new insights into their high-altitude adaptation.

Polymorphisms of cytochrome p450 genes in three ethnic groups from Russia.

To determine the prevalence of the most common allelic variants of CYP1A1, CYP1A2, CYP1B1, CYP2C9, CYP2E1, CYP2F1, CYP2J2 and CYP2S1 in a representative sample of the three ethnic groups (Russians, Tatars and Bashkirs) from Republic of Bashkortostan (Russia), and compare the results with existing data published for other populations. CYPs genotypes were determined in 742 DNA samples of healthy unrelated individuals representative of three ethnic groups. The CYPs gene polymorphisms were examined using the PCR-RLFP method. Analysis of the CYP1A1 (rs1048943, rs4646903), CYP1A2 (rs762551), CYP2E1 (rs2031920) allele, genotype and haplotype frequencies revealed significant differences among healthy residents of the Republic of Bashkortostan of different ethnicities. Distribution of allele and genotype frequencies of CYP1A2 (rs35694136), CYP1B1 (rs1056836), CYP2C9 (rs1799853, rs1057910), CYP2F1 (rs11399890), CYP2J2 (rs890293), CYP2S1 (rs34971233, rs338583) genes were similar in Russians, Tatars, and Bashkirs. Analysis of the CYPs genes allele frequency distribution patterns among the ethnic groups from the Republic of Bashkortostan in comparison with the different populations worldwide was conducted. The peculiarities of the allele frequency distribution of CYPs genes in the ethnic groups of the Republic of Bashkortostan should be taken into consideration in association and pharmacogenetic studies. The results of the present investigation will be of great help in elucidating the genetic background of drug response, susceptibility to cancer and complex diseases, as well as in determining the toxic potentials of environmental pollutants in our region.

A combined DPA1∼DPB1 amino acid epitope is the primary unit of selection on the HLA-DP heterodimer

Here, we present results for DPA1 and DPB1 four-digit allele-level typing in a large (n = 5,944) sample of unrelated European American stem cell donors previously characterized for other class I and class II loci. Examination of genetic data for both chains of the DP heterodimer in the largest cohort to date, at the amino acid epitope, allele, genotype, and haplotype level, allows new insights into the functional units of selection and association for the DP heterodimer. The data in this study suggest that for the DPA1-DPB1 heterodimer, the unit of selection is the combined amino acid epitope contributed by both the DPA1 and DPB1 genes, rather than the allele, and that patterns of LD are driven primarily by dimer stability and conformation of the P1 pocket. This may help explain the differential pattern of allele frequency distribution observed for this locus relative to the other class II loci. These findings further support the notion that allele-level associations in disease and transplantation may not be the most important unit of analysis, and that they should be considered instead in the molecular context.Electronic supplementary materialThe online version of this article (doi:10.1007/s00251-012-0615-3) contains supplementary material, which is available to authorized users.

Haptoglobin polymorphism among the tribal groups of southern Gujarat.

BACKGROUND:Gujarat is located at the western most point of the Indian subcontinent. Valsad and Surat districts are part of the ‘tribal belt’of Gujarat and constitute 29.1% of total tribal population of Gujarat. These tribal populations are a rich source of gaining insights in the patterns of genetic diversity and genetico-environmental disorders against the back drop of their ecological, historical and ethnographic aspects.AIM:The objectives were to find out a) the genetic diversity among the tribes of Gujarat with reference to haptoglobin (Hp) locus b) the relationship between Hp polymorphism and sickle cell anemia/trait.MATERIALS AND METHODS:431 individuals belonging to eight tribal groups were studied for Hp polymorphism using polyacrylamide disc gel electrophoresis (PAGE). Hb*S was screened by dithionate tube turbididy (DTT) test and confirmed using cellulose acetate membrane electrophoresis (CAME).STATISTICAL ANALYSIS:Allele frequency was calculated by direct gene counting method. Average heterozygosity and gene diversity were computed using software DISPAN. Analysis of molecular variance (AMOVA) was estimated using software ARLEQUIN version 3.1.RESULTS AND CONCLUSIONS:Pattern of allele frequency distribution showed preponderance of Hp2 allele in all the eight tribal groups, which is in accordance with its frequency in different populations of Indian subcontinent. Total average heterozygosity (HT) was found to be low (0.160) but the level of genetic differentiation (GST) was found to be moderately high (5.6%). AMOVA analysis indicated least among group variance between west and south Indian populations (-0.04%) indicating the affinities of the tribes of Gujarat with that of Dravidian speaking groups. Analysis of Hp phenotypes among sickle cell anemia/ trait individuals revealed a high frequency of Hp 0-0 phenotype (92.7%) among SS individuals as opposed to only 9.7% among AS individuals, reaffirming the selective advantage of HbAS state in relation to hemolytic disorders.

Brief communication: Allelic and haplotypic structure at the DRD2 locus among five North Indian caste populations

The dopamine D2 receptor (DRD2) gene, with its known human-specific derived alleles that can facilitate haplotype reconstruction, presents an important locus for anthropological studies. The three sites (TaqIA, TaqIB, and TaqID) of the DRD2 gene are widely studied in various world populations. However, no work has been previously published on DRD2 gene polymorphisms among North Indian populations. Thus, the present study attempts to understand the genetic structure of North Indian upper caste populations using the allele and haplotype frequencies and distribution patterns of the three TaqI sites of the DRD2 gene. Two hundred forty-six blood samples were collected from five upper caste populations of Himachal Pradesh (Brahmin, Rajput and Jat) and Delhi (Aggarwal and Sindhi), and analysis was performed using standard protocols. All three sites were found to be polymorphic in all five of the studied populations. Uniform allele frequency distribution patterns, low heterozygosity values, the sharing of five common haplotypes, and the absence of two of the eight possible haplotypes observed in this study suggest a genetic proximity among the selected populations. The results also indicate a major genetic contribution from Eurasia to North Indian upper castes, apart from the common genetic unity of Indian populations. The study also demonstrates a greater genetic inflow among North Indian caste populations than is observed among South Indian caste and tribal populations.

Do Caucasian and Asian clocks tick differently?

The Period 3 and Clock genes are important components of the mammalian molecular circadian system. Studies have shown association between polymorphisms in these clock genes and circadian phenotypes in different populations. Nevertheless, differences in the pattern of allele frequency and genotyping distribution are systematically observed in studies with different ethnic groups. To investigate and compare the pattern of distribution in a sample of Asian and Caucasian populations living in Brazil, we evaluated two well-studied polymorphisms in the clock genes: a variable number of tandem repeats (VNTR) in PER3 and a single nucleotide polymorphism (SNP) in CLOCK. The aim of this investigation was to search for clues about human evolutionary processes related to circadian rhythms. We selected 109 Asian and 135 Caucasian descendants. The frequencies of the shorter allele (4 repeats) in the PER3 gene and the T allele in the CLOCK gene among Asians (0.86 and 0.84, respectively) were significantly higher than among Caucasians (0.69 and 0.71, respectively). Our results directly confirmed the different distribution of these polymorphisms between the Asian and Caucasian ethnic groups. Given the genetic differences found between groups, two points became evident: first, ethnic variations may have implications for the interpretation of results in circadian rhythm association studies, and second, the question may be raised about which evolutionary conditions shaped these genetic clock variations.

Genetic diversity of European cattle breeds highlights the conservation value of traditional unselected breeds with high effective population size

In times of rapid global and unforeseeable environmental changes, there is an urgent need for a sustainable cattle breeding policy, based on a global view. Most of the indigenous breeds are specialized in a particular habitat or production system but are rapidly disappearing. Thus, they represent an important resource to meet present and future breeding objectives. Based on 105 microsatellites, we obtained thorough information on genetic diversity and population structure of 16 cattle breeds that cover a geographical area from the domestication centre near Anatolia, through the Balkan and alpine regions, to the North-West of Europe. Breeds under strict artificial selection and indigenous breeds under traditional breeding schemes were included. The overall results showed that the genetic diversity is widespread in Busa breeds in the Anatolian and Balkan areas, when compared with the alpine and north-western European breeds. Our results reflect long-term evolutionary and short-term breeding events very well. The regular pattern of allele frequency distribution in the entire cattle population studied clearly suggests conservation of rare alleles by conservation of preferably unselected traditional breeds with large effective population sizes. From a global and long-term conservation genetics point of view, the native and highly variable breeds closer to the domestication centre could serve as valuable sources of genes for future needs, not only for cattle but also for other farm animals.

Frequencies of the DRB1, DQA1, DQB1 and TNFA alleles in immigrant population of west Siberia

Based on population analysis of the DRB1, DQA1, DQB1 and TNFA allele frequency distribution patterns, regional features of immunogenetic structure of the population of West Siberia were investigated. Statistically significant linkage disequilibrium within the HLA class II region, as well as between the TNFA and DRB1, DQA1, and DQB1 was demonstrated. Population frequency distribution patterns of two- and multilocus haplotypes were examined.

Analysis of the cytochrome P450 1A1 (CYP1A1) gene polymorphism in the ethnic groups of the republic of Bashkortostan

In three ethnic groups from the Republic of Bashkortostan, Russians (N = 451), Tatars (N= 333), and Bashkirs (N= 171), allele, genotype, and haplotype frequency distribution patterns of the CYP1A1 gene single nucleotide polymorphisms, A2455G and T33801C, were investigated. Substantial interethnic differences in the allele frequency distribution patterns of the CYPIA1 polymorphisms A2455G and T3801C (chi2 = 15.61, d.f. = 2, P = 0.0001; and chi2 = 22.10, d.f. = 2, P = 0.0001, respectively) were observed. Pairwise comparison showed that ethnic groups of Tatars and Russians were similar in the A2455G allele frequencies (chi2 = 1.10, d.f. = 1, P = 0.30). However, in case of the T3801C marker, statistically significant differences were revealed (chi2 = 4.56, d.f. = 1, P = 0.032). At the same time, Bashkir ethnic group was found to be statistically significantly different from Russians and Tatars in the CYP1A1 polymorphic allele frequency distribution patterns (chi2 = 15.74, d.f. = 2, P = 0.0001; and chi2 = 7.47, d.f. = 1, P = 0.024, for A2455G, and chi2 = 6.46, d.f. = 1, P = 0.011; and chi2 = 21.36, d.f. = 1, P = 0.0001, for T3801C). Analysis of the CYP1A1 haplotype diversity showed that in terms of the CYP1A1 haplotype frequency distribution patterns, Bashkir ethnic group was statistically significantly different from both Russians (chi2 = 30.07, d.f. = 3, P = 0.0001) and Tatars (chi2 = 11.28, d.f. = 3, P = 0.013). The differences observed were caused by the high frequency of haplotype CYP1A1*2B, which was represented by a combination of rare alleles of the CYP1A1 polymorphisms A2455G and T3801C in Bashkirs (5.81%). On the other hand, the ethnic groups of Russians and Tatars residing in the Republic of Bashkortostan were characterized by similar frequencies of the CYP1A1 haplotypes (chi2 = 6.322, d.f. = 3, P = 0.127). The data obtained could be used in further investigations of the genetic bases of ecology dependant diseases and in the risk groups in the Republic of Bashkortostan.

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 DRD4 Gene Polymorphism in Populations of Russia and Neighboring Countries

Allele and genotype frequencies of the VNTR polymorphism in the third exon of human DRD4 gene were determined in 544 individuals living in Russia (Russians, Bashkirs, Tatars, and Mordovians) and in the neighboring countries (Kazakhs and Ukrainians). The data obtained were compared with the allele frequency distribution patterns reported for the populations of Eurasia. Similarly to other Eurasian populations, in our population samples R4 allele was prevalent (64 to 87%). The frequency of this allele in the populations of Western Europe constitute 61 to 71%, while in the populations of Asia it varies from 74 to 96%. In this respect, the populations studied occupied the intermediate position. In the samples examined the R7 allele frequency decreased from 7% in Ukrainians to 1% in Bashkirs, while in Kazakhs and Mordovians the allele was absent. This finding was consistent with the R7 allele distribution pattern in the populations of Eurasia, characterized by higher frequency in the West and lower frequency or absence of the allele in the East. In the group of 22 Eurasian populations, the R7 allele frequency negatively correlated with the frequency of the R4 allele (r = -0.86 at P < 0.001). Unlike the R4 and R7 alleles, the frequency of which changed in the eastward direction, the R2 allele frequency distribution displayed slightly expressed latitudinal increase southwards. The DRD4 genotype distribution deviated from the equilibrium in most of the samples examined. In some samples, statistically significant increase of the R2/R2 homozygotes frequency was demonstrated. One of the possible explanations of this phenomenon is assortative mating with respect to phenotypic (behavioral) allele manifestation. The data obtained can serve as the basis for the investigation of the possible role of the DRD4 alleles as the risk factors for the development of alcoholism and other types of addictions.