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.     

Analysis of the AluPolymorphism in the Buryat Populations

Polymorphism of three populations of the Buryat Republic and a population from Aginskii Buryat Autonomous okrug of Chita oblast was examined using a set of five autosomal Aluinsertions at theACE, PLAT, PV92, APOA1,and F13Bloci. The allele frequency distribution patterns revealed in Buryat populations were typical to other Asian populations. Buryats were characterized by relatively low level of intrapopulation diversity (0.369 in the pooled population sample). Analysis of autosomal Aluinsertions suggests the uniformity of the Buryat gene pool. The coefficient of genetic differentiation in the four populations studied was 0.8%.     

Genetic Differentiation of the Population of Central Asia Inferred from Autosomal Markers

The gene pool of five ethnic groups of the Central Asian population was characterized using nine human-specific polymorphic insertion/deletion loci (ACE, PLAT, APOA1, PV92, F13B, A25, B65, CD4, Mt-Nuc). It has been shown for the first time that at the CD4 locus, the frequency of Alu(–) is inversely related to the Mongoloid component of the population. For the Central Asian populations, the lowest and highest frequencies of the Alu deletion at locus CD4 were recorded respectively in Dungans (0.04), immigrants from China, and Tajiks (0.15). The coefficient of gene differentiation in the Central Asian populations for all the genes was 2.8%, which indicates a relatively low level of population genetic subdivision in this region. The unity of the gene pool of the Central Asian Caucasoids was shown.     

Analysis of Ethnogeographic Groups of Kazakhs Based on Nuclear Genome DNA Polymorphism

Eight nuclear DNA loci, including six Alu insertions (ACE, APOA1, PV92, TPA25, Ya5NBC27, and Ya5NBC148), 32-bp deletion in the CCR5 gene, and VNTR locus at the eNOS gene, were examined in three ethnogeographic groups of Kazakhs (342 individuals). The individuals examined lived in southeastern, central, and southwestern regions of Kazakhstan, and according to their tribal attribution, belonged to the Senior, Middle, and Junior Zhuzes. The Alu insertions appeared to be polymorphic in all populations examined: the insertion frequency varied from 0.264 in the populations of the Senior and Middle Zhuzes at the Ya5NBC27 and Ya5NBC148 loci, to 0.827 in Kazakhs of the Middle Zhuz at the APOA1 locus. In Kazakh groups examined only two alleles of the eNOS VNTR locus were detected with the number of repeats constituting four (A) and five (B) copies. The highest frequency of A allele was found in Kazakhs from the Junior Zhuz (0.113), while the highest frequency of B allele was detected in population of the Senior Zhuz (0.893). The frequency of the 32-bp deletion in the chemokine receptor CCR5 gene varied from 0.027 in the Junior Zhuz to 0.045 in the Senior Zhuz. Kazakhs showed high genetic diversity (H _ex = 0.376). In general, in three ethnogeographic groups of Kazakhs, the coefficient of gene differentiation (G _ST) over eight diallelic markers of nuclear genome constituted 1.1%. The differences in the Alu insertions made the highest contribution to the among-population diversity (G _ST = 1.2%).__________Translated from Genetika, Vol. 41, No. 7, 2005, pp. 973–980.Original Russian Text Copyright © 2005 by Salimova, Kutuev, Khusainova, Akhmetova, Svyatova, Berezina, Khusnutdinova.     

Analysis of Alu-polymorphism in Buryat populations]

Polymorphism of three populations of the Buryat Republic and a population from Aginskii Buryat Autonomous okrug of Chita oblast 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 Buryat populations were typical to other Asian populations. Buryats were characterized by relatively low level of intrapopulation diversity (0.369 in the pooled population sample). Analysis of autosomal Alu insertions suggests the uniformity of the Buryat gene pool. The coefficient of genetic differentiation in the four populations studied was 0.8%.     

Genetic Structure of the Volga–Ural and Central Asian Populations Inferred from the Data on Alu Polymorphism

NineAlu 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 (F _st = 0.061) was higher than for the populations of Central Asia (F _st = 0.024), Europe (F _st = 0.02), and Southeastern Asia (F _st = 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.     

Genetic differentiation of residents of Central Asia from autosomal marker data

The gene pool of five ethnic groups of the Central Asian population was characterized using nine human-specific polymorphic insertion/deletion loci (ACE, PLAT, APOA1, PV92, F13B, A25, B65, CD4, Mt-Nuc). It has been shown for the first time that at the CD4 locus, the frequency of Alu(-) is inversely related to the Mongoloid component of the population. For the Central Asian populations, the lowest and highest frequencies of the Alu deletion at locus CD4 were recorded respectively in Dungans (0.04), immigrants from China, and Tajiks (0.15). The coefficient of gene differentiation in the Central Asian populations for all the genes was 2.8%, which indicates a relatively low level of population genetic subdivision in this region. The unity of the gene pool of the Central Asian Caucasoids was shown.     

The russian gene pool: the gene geography of Alu insertions (ACE, APOA1, B65, PV92, TPA25)

For the first time, an analysis of five Alu insertion loci (ACE, APOA1, B65, PV92, TPA25) has been carried out in 10 Russian populations (1088 individuals) covering the whole historical area of the Russian ethnos. Depending on the locus, Russian populations exhibit similarity to their Western (European populations) or Eastern (populations of the Ural region) neighbors. Considering the frequencies of the studied Alu-insertions, the Russian gene pool exhibits low variation: average interpopulation variation (d) was 0.007, whereas on classical markers, mtDNA and Y chromosome, heterogeneity of the Russian gene pool is essentially higher (0.013, 0.033, 0.142, respectively). Therefore, on the intra-ethnic level, this set of five Alu insertions has low variation. However, a clear pattern was obtained in inter-ethnic comparison of 13 East European ethnic groups, which formed three clusters in accordance with their historical and geographical position: East Slavic, Caucasian and South Ural clusters. The obtained data confirm the efficiency of using Alu insertions for studying genetic differentiation and gene pool history of East European populations.     

Phylogenetic signals from point mutations and polymorphic Alu

Allelic frequency data derived from five polymorphic Alu insertion loci and five point mutation polymorphic loci were compared to determine their ability to infer phylogenetic relationships among human populations. While point mutation polymorphisms inferred a monophyletic Caucasian clade that is corroborated by other studies, these data failed to support the generally accepted monophyly of Orientals with native Americans. In addition, there is less statistical bootstrap support for the maximum-likelihood tree derived from the point mutation polymorphisms as compared to those generated from either the Alu insertion data or the combined Alu insertion+point mutation data. The Alu data and the combined Alu insertion+point mutation data inferred a monophyletic relationship among the Oriental and native American populations. The Alu insertion data and the combined Alu insertion+point mutation data also displayed two separate, well defined, tight clusters of the Caucasian and the Oriental+native American populations which was not inferred from the point mutation data. These findings indicate greater phylogenetic information contained in Alu insertion frequencies than in allelic frequencies derived from point-mutations. This revised version was published online in July 2006 with corrections to the Cover Date.     

Analysis of the genetic structure of Tuvinian short-fat-tailed sheep populations with the use of the ISSR-PCR method

The genetic structure of populations of the Tuvinian short-fat-tailed sheep was studied with the use of the ISSR-PCR (Inter Simple Sequence Repeats) method in 18 farms of Tyva. Data on the spectrum of ISSR fragments of DNA were obtained using the (AG)₉C primer. Analysis of intermicrosatellite polymorphism permitted us to determine genomic characteristics of the populations, their genealogical relations, and the parameters of genetic diversity within the populations and the breed as a whole. Three genetic notions were considered on the basis of the results of this analysis: gene pool profile, gene pool standard, and breed-specific pattern. The data obtained can be used to carry out population genetic monitoring, to develop a breeding strategy, and to conserve in situ the Tuvinian sheep breed and breeds of other domesticated species.     

Genetic Peculiarity of the Yakut Population as Inferred from Autosomal Loci

The autosomal gene pool of Yakuts was analyzed with a panel of polymorphic Alu insertions. The observed allele frequencies were typical for other Asian ethnic groups. Genetic differentiation of three Yakut populations was relatively high, 2%. East Siberian ethnic groups were shown to have a common gene pool and to experience no intense gene flow from other populations. Development of the Yakut gene pool was assumed to involve no substantial genetic effect of neighboring populations. The results fit both autochthonous and southern origin hypotheses.     

Analysis of Gene Complexes Predisposing to Coronary Atherosclerosis

The following seven polymorphic marker loci of genes responsible for predisposition to coronary atherosclerosis (CAS) were studied: the ACE locus responsible for angiotensin-converting enzyme insertion/deletion polymorphism for the presence or absence of the Alu insertion in the gene; the F13,PLAT, and APOA1 loci, controlling the clotting factor 13, plasminogen-activating tissue factor, and apolipoprotein A, respectively; the MTHFR and AGT polymorphic loci responsible for point mutations in methylenetetrahydrofolate reductase and those in angiotensinogen, respectively, and the NOS3 locus controlling the number of tandem repeats in the nitric oxide synthase gene. These loci are located on different chromosomes and encode products involved into various metabolic pathways leading to CAS. In the populations studied, significant differences between healthy subjects and patients predisposed to cardiovascular diseases were revealed with regard to the above seven markers. The 174M allele (T174M polymorphism in the AGT gene) was significantly associated with coronary atherosclerosis. It was found that specific gene combinations are involved in the CAS development and determine variation in the pathogenetically important quantitative traits.     

Analysis of eight polymorphic Alu elements in the Teleuts population

Allele frequencies and genetic diversity in the population of Teleuts were assessed by the Alu repeat polymorphism at eight autosomal loci (ACE, APOA1, PLAT, F13, PV92, A25, CD4, D1). For comparison, the study included previously obtained data on the Alu polymorphism in 19 indigenous populations of Siberia. On the dendrogram of genetic distances, the Teleut population is located in the cluster of Siberian ethnic groups, which are similar in origin, geography, and cultural traditions.     

Distribution and frequency of a polymorphicAlu insertion at the plasminogen activator locus in humans

We have investigated the frequency distribution, across a broad range of geographically dispersed populations, of alleles of the polymorphic Alu insertion that occurs within the 8th intron of the tissue plasminogen activator gene (PLAT). This Alu is a member of a recently derived subfamily of Alu elements that has been expanding during human evolution and continues to be transpositionally active. We used a “population tube” approach to screen 10 chromosomes from each of 19 human populations for presence or absence of this Alu in the PLAT locus and found that all tested populations are dimorphic for presence/absence of this insertion. We show that the previously published EcoRI, HincII, PstI, TaqI, and XmnI polymorphisms at the PLAT locus all result from insertion of this Alu and we use both restriction fragment length polymorphism and polymerase chain reaction analysis to examine the frequency of Alu(+) and Alu(–) alleles in a sample of 1003 individuals from 27 human populations and in 38 nonhuman primates. Nonhuman primates are monomorphic for the Alu(–) allele. Human populations differ substantially in allele frequency, and in several populations both alleles are common. Our results date the insertion event prior to the spread and diversification of modern humans. Received: 10 July 1995 / Revised: 17 November 1995     

An Alu insertion polymorphism in a baboon hybrid zone

A novel polymerase chain reaction (PCR) primer pair was used to analyze the frequency of insertion of the first described, nonhuman, baboon-specific Alu repetitive element in populations from the Papio hamadryas anubis and the Papio hamadryas hamadryas subspecies, and from a number of anubis-hamadryas hybrids. The Alu insertion is found in intron 7 of the baboon lipoprotein lipase (LPL) gene. Each of the populations had different frequencies for the insertion, and the hybrids examined had a frequency intermediate to that of the parental populations. All hybrids and all P. h. anubis groups except the group of anubis sampled in 1973 exhibited higher-than-expected heterozygosity, while P. h. hamadryas and 1973 P. h. anubis showed lower-than-expected heterozygosity, supporting behavioral and other genetic observations of greater anubis outbreeding relative to hamadryas. This may include asymmetric introgression of the Alu insertion from hamadryas to the anubis population due to hybridization. Am J Phys Anthropol 109:1–8, 1999. © 1999 Wiley-Liss, Inc.     

The association between HLA-A alleles and an Alu dimorphism near HLA-G

The AluYb8 sequences are a subfamily of short interspersed Alu retroelements that have been amplified within the human genome during recent evolutionary time and are useful polymorphic markers for studies on the origin of human populations. We have identified a new member of the Yb8 subfamily, AluyHG, located between the HLA-H and -G genes and 88-kb telomeric of the highly polymorphic HLA-A gene within the alpha block of the major histocompatibility complex (MHC). The AluyHG element was characterised with a view to examining the association between AluyHG and HLA-A polymorphism and reconstructing the history of the MHC alpha block. A specific primer pair was designed for a simple PCR assay to detect the absence or presence (dimorphism) of the AluyHG element within the DNA samples prepared from a panel of 46 homozygous cell-lines containing complete or recombinant ancestral haplotypes (AH) of diverse ethnic origin and 92 Caucasoid and Asian subjects on which HLA-A typing was available. The AluyHG insertion was most strongly associated with HLA-A2 and, to a lesser degree with HLA-A1, -A3, -A11, and A-19. The gene frequency of the AluyHG insertion for 146 Caucasians and 94 Chinese-Han was 0.30 and 0.32 and there was no significant difference between the observed and expected frequencies. The results of the association studies and the phylogenetic analysis of HLA-A alleles suggest that the AluyHG sequence was integrated within the progenitor of HLA-A2, but has been transferred by recombination to other human ancestral populations. In this regard, the dimorphic AluyHG element is an important diagnostic marker for HLA association studies and could help in elucidating the evolution and functions of the MHC alpha block and polymorphism within and between ancestral haplotypes. Received: 7 December 2000 / Accepted: 28 February 2001     

Polymorphism of the Y-Chromosome Diallelic Loci in Ethnic Groups of the Altai–Sayan Region

Using the data on five diallellic Y-chromosome loci (DYS199,92R7, SRY1532, RBF5, and DYS287) polymorphism, genetic structures of the five Turkic-speaking ethnic groups of the Altai–Sayan upland (Tuvinians, Sojots, Shorians, Khakassians, and Southern Altaians (Altai-Kizhi), were described. The gene pools of the populations examined were characterized by the presence of pronounced paleo-Caucasoid component (92R7-T-lineages). The frequency of this component increased westward, reaching more than 70% in Shorians and Southern Altaians. Haplotype TAT-C (RBF5 locus) was observed in all populations, except Shorians, with the frequencies varying from 5.4% in Altai-Kizhi to 18.8% in Khakassians. The Alu-insertion in the DYS287 locus was revealed only in the Altaian sample with the frequency of 3.3%. It was established that the Altai–Sayan populations studied split into two statistically significantly different groups. One of the groups was represented by Tuvinians, Sojots, and Khakassians, while another one was comprised of Shorians and Altaians.     

Genomic diversity and affinities in population groups of North West India: An analysis of Alu insertion and a single nucleotide polymorphism

The North West region of India is extremely important to understand the peopling of India, as it acted as a corridor to the foreign invaders from Eurasia and Central Asia. A series of these invasions along with multiple migrations led to intermixture of variable populations, strongly contributing to genetic variations. The present investigation was designed to explore the genetic diversities and affinities among the five major ethnic groups from North West India; Brahmin, Jat Sikh, Bania, Rajput and Gujjar. A total of 327 individuals of the abovementioned ethnic groups were analyzed for 4 Alu insertion marker loci (ACE, PV92, APO and D1) and a Single Nucleotide Polymorphism (SNP) rs2234693 in the intronic region of the ESR1 gene. Statistical analysis was performed to interpret the genetic structure and diversity of the population groups. Genotypes for ACE, APO, ESR1 and PV92 loci were found to be in Hardy–Weinberg equilibrium in all the ethnic groups, while significant departures were observed at the D1 locus in every investigated population after Bonferroni's correction. The average heterozygosity for all the loci in these ethnic groups was fairly substantial ranging from 0.3927 ± 0.1877 to 0.4333 ± 0.1416. Inbreeding coefficient indicated an overall 10% decrease in heterozygosity in these North West Indian populations. The gene differentiation among the populations was observed to be of the order of 0.013. Genetic distance estimates revealed that Gujjars were close to Banias and Jat Sikhs were close to Rajputs. Overall the study favored the recent division of the populations of North West India into largely endogamous groups. It was observed that the populations of North West India represent a more or less homogenous genetic entity, owing to their common ancestral history as well as geographical proximity.     

Genetic diversity among alfalfa (Medicago sativa) cultivars coming from a breeding program, using SSR markers

Alfalfa (Medicago sativa) is an autotetraploid, allogamous and heterozygous species whose cultivars are synthetic populations. The breeders apply selection pressure for some agronomic traits within a breeding pool to increase the frequency of favorable individuals. The objective of this study was to investigate the differentiation level among seven cultivars originating from one breeding program, and between these cultivars and the breeding pool, with eight SSR markers. These highly polymorphic and codominant markers, together with recent population genetic statistics extended to autotetraploids, offer tools to analyse genetic diversity in alfalfa. The number of alleles per locus varied between 3 and 24. All loci were at a panmictic equilibrium in the cultivars, except one, probably because of null alleles. With seven SSR loci, each cultivar was at panmictic equilibrium. The mean gene diversity was high, ranging from 0.665 to 0.717 in the cultivars. The parameter F _ST indicated a low but significant diversity among cultivars. Among 21 pairs of cultivars, 15 were significantly different. The breeding pool also had a high diversity, and was significantly different from each cultivar except the most recent one. Considering the characteristics of the breeding program and the mode of cultivar elaboration, we found that they were unable to generate a large variety differentiation. Estimation of population genetics parameters at SSR loci can be applied for assessing the differences between cultivars or populations, either for variety distinction or the management of genetic resources.     

Genetic diversity analysis of Hepatacodium miconioides at different altitude in Tiantai Mountain, Zhejiang Province, China and its relationship with environmental factors

The genetic diversity within and among populations of Hepatacodium miconioides collected at three different altitudes in Tiantai Mountain, Zhejiang Province and its relationships to environmental factors were analyzed by random amplified polymorphic DNA (RAPD) technique. Amplification using 12 random primers of 60 plants and 122 repetitive loci were produced. The percentage of polymorphic loci of three populations ranged from 18.85% to 23.77% with an average of 21.86%, indicating the relatively low genetic diversity of H. miconioides. The average Shannon index of phenotypic diversity (0.1329) and Nei index (0.0925) within populations were relatively low. A distinct genetic differentiation existed among populations of H. miconioides in spite of the relatively small geographical distribution. The average genetic diversity within populations of H. miconioides accounted for 33.58% of the total genetic diversity while the genetic diversity among populations accounted for 66.42% as estimated by the Shannon index of phenotypic diversity, The genetic differentiation among populations of H. miconioides was 0.6546, as estimated by Nei index. The gene flow estimated from G _ST was only 0.2656 and it indicated that gene flow among populations of H. miconioides was relatively low. The mean value of the genetic identity among populations of H. miconioides was 0.7126 and the average of genetic distance of H. miconioides was 0.3412. The genetic identity between populations at the elevation of 990 m and at the elevation of 780 m was the highest. The genetic identity between population at the elevation 500 m and other two populations was relatively low. The correlation analysis showed that the genetic diversity within populations was significantly related with the soil total nitrogen. __________ Translated from Journal of Zhejiang University (science Edition) 2005, 32 (4)[译81EA;: 浙江大学学报(理学版), 2005,32(4)]