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.     

DNA polymorphism in the Mongolian population. Restriction fragment length polymorphism analysis of DNA at seven loci of the nuclear genome]

Seven DNA markers from five genes and one chromosomal region were analysed in Mongolian population using the polymerase chain reaction. The frequencies of alleles of the polymorphisms detected with HindIII in the HBG-2, AvaII in the HBB, MspI and XbaI in the Apo-B, PstI in the D7S8, HincII in the LDLR and allele frequency of the minisatellite fragment in the AT-3 have been determined. The results of the RELP for Apo-B(MspI), LDLR, D7S8 and AT-3 are obtained for the first time among Mongoloids. DNA markers studied demonstrated high level of polymorphisms in the population of Mongolia, except for XbaI and MspI restriction sites at the Apo-B locus. The data obtained for Mongolian population and the literature data were compared.     

DNA polymorphism in the Russian population. Analysis of dna restriction fragment length polymorphism in seven loci of the nuclear genome]

Using the method for polymerase chain reaction the polymorphism of eight markers of the nuclear DNA was studied. In a sample of Russians taken at random (N = 118) from predominantly southern and central regions of Russia, allele frequencies were determined for restriction sites HindIII at HBG-2 and PAH loci, AvaII at the HBB locus, MspI at the ApoB locus, PstI at D7S8, HincII at LDLR, TaqI and BamHI at the DSX164. Comparative data for different world regions are presented.     

DNA polymorphism at the casein loci in sheep

By using seven endonucleases and four bovine cDNA probes specific for alpha S1-, alpha S2-, beta-, and kappa-casein genes, nine restriction fragment length polymorphisms (RFLPs) have been found in the sheep orthologous DNA regions. In contrast to the low level of variation observed at the protein level, these DNA polymorphisms determine a high level of heterozygosity and, therefore, represent useful tools for genetic analyses since they can also be obtained without the need for gene expression. In fact, informative matings suggest that in sheep, as in cattle, the four loci are linked.     

Population study of the Udmurt population: Analysis of ten polymorphic DNA loci of the nuclear genome

Genetic structure of Southern and Northern ethnographic groups of the Udmurt population from six regions of the Republic of Udmurtia has been studied. All the samples were examined using ten polymorphic DNA loci: VNTR/PAH, VNTR/ApoB, VNTR/DATI, VNTR/eNOS, ACE, CCR5 Δ32, KM19, IVS6a, THOI, and FABP2. Allelic and genotype frequencies were estimated for each of the six populations. The average heterozygosity for these ten polymorphic loci varied from 0.47 in Udmurts from Glazovskii region to 0.53 in Udmurts from Malopurginskii region. The level of genetic variation (F _ST) between populations of Udmurts was 0.0048. Ethnographic subdivision of the population into Northern and Southern Udmurts is in good agreement with the values of genetic distances and phylogenetic analysis.     

Syrian hamster DNA shows limited polymorphism at class I-like loci

The class I gene products of the Syrian hamster major histocompatibility complex are unique in that they lack functionally detectable polymorphism. Mouse cDNA and hamster genomic probes were used to analyze the hamster class I gene family using genomic Southern hybridization. These studies revealed that the hamster possesses a complex class I multigene family and that it shares extensive sequence homology with the corresponding mouse sequences. Unlike the mouse, however, the Syrian hamster demonstrates only limited restriction endonuclease polymorphism in these genes. These results suggest that the lack of detectable polymorphism in this species is directly related to limited DNA polymorphism. The data presented here support the hypothesis that this species has undergone an evolutionary bottleneck, i. e., that all surviving members of the species arose from a limited number of progenitors.Abbreviations used in this paper MHC major histocompatibility complex - MLR mixed lymphocyte reactions - SSC saline sodium citrate - kbp kilobase pairs - SDS sodium dodecyl sulfate     

Population-genetic structure of Chuvashia (from data on eight DNA loci in the nuclear genome)

Population-genetic study of indigenous populations representing three ethnic Chuvash group: highland (Cheboksarsk and Morgaush district), lowland (Kanash district) and mid-lowland (Marposad district). Eight polymorphic DNA loci of the nuclear genome (VNTR/PAH, STR/PAH, VNTR/ApoB, VNTR/DAT1, APF, VNTR/eNOS, IVS6aGATT, and KM.19/PstI) were examined in the population of each district. For each of the four population, we estimated the allele and genotype frequency distributions at each polymorphic system, heterozygosities HS and between-population differences FST. In the combined Chuvash sample, HS = 0.464 and FST = 0.006. Loci VNTR(DAT) and VNTR(ApoB) showed highest between-population differentiation (0.009 < or = FST < or = 0.012), and loci IVS6aGATT, APF, VNTR/eNOS, and D7S23 (KM.19), lowest differentiation (0.001 < or = FST < or = 0.003). Analysis of genetic distances revealed somewhat higher genetic similarity between the Cheboksarsk and Morgaush populations belonging to the highland Chuvash group, whereas the highland Chuvash population from the Marposad district, which belong to the mid-lowland group, was more distant from the former populations.     

Mitochondrial DNA insertions in the nuclear horse genome

The insertion of mitochondrial DNA in the nuclear genome generates numts, nuclear sequences of mitochondrial origin. In the horse reference genome, we identified 82 numts and showed that the entire horse mitochondrial DNA is represented as numts without gross bias. Numts were inserted in the horse nuclear genome at random sites and were probably generated during the repair of DNA double-strand breaks. We then analysed 12 numt loci in 20 unrelated horses and found that null alleles, lacking the mitochondrial DNA insertion, were present at six of these loci. At some loci, the null allele is prevalent in the sample analysed, suggesting that, in the horse population, the number of numt loci may be higher than 82 present in the reference genome. Contrary to humans, the insertion polymorphism of numts is extremely frequent in the horse population, supporting the hypothesis that the genome of this species is in a rapidly evolving state.     

Intrinsic polymorphism of variable number tandem repeat loci in the human genome.

In the human genome, short tandem repetitive (STR) DNA sequences often show restriction fragment length polymorphisms (RFLPs) due to variation in the number of copies of the repeat unit. For a subset of these sequences known as minisatellites or variable number tandem repeat loci (VNTR), it has been proposed that a homologous "core" sequence of 10-12 nucleotides is involved in the mechanism(s) generating the polymorphism. In our present study we have prepared oligonucleotide probes complementary to one or two repeat units of several VNTR loci. Under stringent hybridization and wash conditions these probes hybridize locus specifically thus allowing the evaluation of the intrinsic polymorphism of individual loci. Our results indicate that not all of the loci having STR DNA sequences are polymorphic despite the fact that they share the "core" sequence. This suggests that more than the DNA sequence of the locus is involved in the mechanism(s) generating the polymorphism.     

Enzymatic variation at seven loci in nine natural populations of Drosophila melanogaster

Allozyme polymorphisms at seven loci have been studied in nine natural populations of Drosophila melanogaster from the Saône and Rhône valleys sampled in 1973 and 1974. A great deal of polymorphism was observed; an individual was on the average heterozygous at 20.2% of its loci. The populations were genetically very homogeneous throughout the region sampled. The number of ovariolae per female varied from one group of populations to another depending on their geographical separation. Yet the number of ovariolae remained constant from one year to the next. The results show that migration alone cannot explain the homogeneity of the allozyme frequencies. It seems reasonable to conclude that selection plays a major role in maintaining the homogeneity of populations living in proximal biotopes.E.R.A. No. 406: Analyse et mécanismes de maintien du polymorphisme.     

Analysis of DNA polymorphism in populations of the Volga-Ural region using genome fingerprinting with phage M13 DNA]

The hyperpolymorphism of minisatellite DNA hybridizing with DNA of bacteriophage M13 was analyzed in seven Turkic and Finno-Ugric populations from the Volga-Urals region. In total, hybridization revealed 80 BspRI genomic DNA fragments ranging in size from 1.7 to 10 kb; the average frequency of an individual fragment was 0.299 +/- 0.020. The average number of hybridization fragments per pattern (varying from 14 to 20 in different populations) and frequencies of individual fragments showed significant interpopulation differences. Parameters of this polymorphic system were assumed to reflect phenotypic diversity of populations. Genome fingerprinting with the use of phage M13 can be employed in the studies of population genetic structure and differentiation and in forensic medicine, for more accurate personal identification.     

Genetic polymorphism of six DNA loci in six population groups of India

The genetic profile based on autosomal markers, four microsatellite DNA markers (D8S315, FES, D8S592, and D2S1328) and two minisatellite DNA markers (TPMT and PDGFA), were analyzed in six endogamous populations to examine the effect of geographic and linguistic affiliation on the genetic affinities among the groups. The six populations are from three different states of India and are linguistically different. Marathas from western India speak Marathi, an Indo-European language. Arayas, Muslims, Ezhavas, and Nairs from Kerala state of South India speak Malayalam, and Iyers from Tamil Nadu state speak Tamil. Genomic DNA was extracted from peripheral blood samples of random, normal, healthy individuals. Locus-specific PCR amplification was carried out, followed by electrophoresis of the amplicons and genotyping. All the loci were highly polymorphic and followed Hardy-Weinberg equilibrium, except for loci D8S315 and PDGFA in Iyers and Marathas, respectively. All six loci had high heterozygosity (average heterozygosity ranged from 0.73 to 0.76) and high polymorphism information content (0.57-0.90). The extent of gene differentiation among the six populations (G(ST) = 0.030) was greater than that for four Kerala populations (G(ST) = 0.011), suggesting proximity between the four Kerala populations. This result conforms with the cultural and linguistic background of the populations. The extent of diversity found among the populations probably resulted from the strict endogamous practices that they follow.     

Utility of nuclear DNA intron markers at lower taxonomic levels: phylogenetic resolution among nine Tragelaphus spp

Phylogenetic relationships among the nine spiral-horn antelope species of the African bovid tribe Tragelaphini are controversial. In particular, mitochondrial DNA sequencing studies are not congruent with previous morphological investigations. To test the utility of nuclear DNA intron markers at lower taxonomic levels and to provide additional data pertinent to tragelaphid evolution, we sequenced four nuclear DNA segments (MGF, PRKCI, SPTBN, and THY) and combined these data with mitochondrial DNA sequences from three genes (cytochrome b, 12S rRNA, and 16S rRNA). Our molecular supermatrix comprised 4682 characters which were analyzed independently and in combination. Parsimony and model based phylogenetic analyses of the combined nuclear DNA data are congruent with those derived from the analysis of mitochondrial gene sequences. The corroboration between nuclear and mtDNA gene trees reject the possibility that genetic processes such as lineage sorting, gene duplication/deletion and hybrid speciation account for the conflict evident in the previously published phylogenies. It suggests rather that the morphological characters used to delimit the Tragelaphid species are subject to convergent evolution. Divergence times among species, calculated using a relaxed Bayesian molecular clock, are consistent with hypotheses proposing that climatic oscillations and their impact on habitats were the major forces driving speciation in the tribe Tragelaphini.     

Multiple nuclear pseudogenes of mitochondrial DNA exist in the canine genome

Many copies of nuclear counterparts of mitochondrial DNA (mtDNA) were found in nuclear DNA from sperm heads of the domestic dog, Canis familiaris, by DNA-DNA hybridization and DNA sequencing. Nuclear counterparts homologous to the mtDNA D-loop region were cloned into lambda phage vectors (EMBL4 and lambda gt11), and nucleotide sequences of seven different mtDNA pseudogenes were then determined. The seven pseudogenes were E3 (474 bp; 82% homology with canine mtDNA), E13 (1867 bp; 67%), 8B (2375 bp; 78%), 12A (2650 bp; 79%), 33 (4131 bp; 86%), 47 (4251 bp; 86%), and E17 (5721 bp; 71%). These seven mtDNA pseudogenes corresponded to portions of cytoplasmic mtDNA containing the genes ile, ND1, leu, 16S rRNA, val, 12S rRNA, phe, D-loop, pro, thr, cytb, and glu. A neighbor-joining phylogenetic tree constructed from 12S rRNA sequences in mtDNA pseudogenes 8B, 33, 47, and E17 and in 10 mtDNA fragments from other species showed that these four pseudogenes form a monophyletic clade with canine mtDNA. A neighbor-joining phylogenetic tree based on the 318-bp cytb region showed that the canine pseudogenes existed before the divergence of 17 related canids, and their divergence dates were calculated at around 4.4 to 8.6 million years ago.     

Extensive chromosomal polymorphism revealed by ribosomal DNA and satellite DNA loci in 13 Citrus species

Little is known about the chromosomal variability and polymorphism existing in mitotic chromosomes of Citrus, mainly due to lack of reliable chromosomal markers and small chromosome size. To test the hypothesis of chromosomal polymorphism and provide the foundation of the genome organization in the Citrus cultivars, we have developed molecular cytogenetic markers for 13 Citrus species collected from Jeju island, Korea. In this study, we demonstrated that the chromosomal locations of cytogenetic markers are quite variable and extremely polymorphic, in contrast to the previous studies. The data obtained in this study will be of utmost importance in cytological systematics and karyotyping of the Citrus species.     

C-banding polymorphism and linkage of nonhomoeologous RFLP loci in the D genome progenitor of wheat.

Chromosomes from four different accessions of Triticum tauschii, used as parents in generating F2 populations for RFLP genetic linkage map construction, were analyzed by C-banding. The accessions consist of the varietal taxa strangulata (AUS 21929) and meyeri (AUS 18911), and two genotypes of var. typica (AUS 18902 and CPI 110730 from Iran and Afghanistan, respectively). Chromosomes 1D and 7D of T. tauschii var. typica AUS 18902 are involved in a reciprocal interchange forming translocated chromosomes, T1DS.7DL and T7DS.1DL, with tbe breakpoints being located within the centrometric region. The formation of quadrivalent configuration in F1 hybrids provided further confirmation of the reciprocal translocation. Genetic linkage mapping of additional RFLP markers located on homoeologous group 1 and 7 chromosomes showed consistent linkage to a composite group of proximal markers on chromosomes 1D and 7D of a previously published map derived from the F2 progeny of AUS 18902 x AUS 18911. A high frequency of RFLP genotypes transmitted by the translocation parent was prevalent in the proximal regions of chromosomes 1D and 7D. Genotypic frequencies expected of the nontranslocated parental RFLP markers was evident only in the distal regions of these chromosomes.