FRESHWATER BIOLOGY, Issue 2 2006
F. AYLLON
Summary 1. Microsatellite and isozyme loci variation were used to study structure and dynamics of a brown trout (Salmo trutta) population heavily affected by damming. The downstream area accessible for spawning was drastically reduced to a stream 1 km long influenced by regulated discharge. 2. Stocking of hatchery-reared juveniles failed and the population is entirely supported by anadromous adults from neighbouring populations. 3. Temporal genetic stability is reported here. Some punctual between-river genetic differences are likely because of different contribution from each neighbouring river through years. 4. High anadromy-mediated gene flow produces a lack of genetic substructure in the region. The role of anadromous brown trout on maintenance of endangered small populations is emphasised. [source]

Population substructures in the soil invertebrate Orchesella cincta, as revealed by microsatellite and TE-AFLP markers

MOLECULAR ECOLOGY, Issue 6 2003
A. W. G. Van Der Wurff
Abstract Microsatellite and three enzyme,amplified fragment length polymorphism (TE-AFLP) DNA markers were used to describe the population genetic structure in the soil dwelling collembolan Orchesella cincta (L.). Two forests were sampled according to a three-level nested hierarchical design, with fixed distances among samples within a parcel and among parcels within a forest. The largest component of variation was found at the smallest scale, within parcels (77,97%), while the smallest component of variation was found between forests. The two different methods to study population structure indicated a similar allocation of variance. Population genetic substructuring was revealed between samples on a scale of 50 m; the degree of substructuring however, varied between parcels and forests. One forest showed a high degree of structure as revealed by microsatellites, while another showed a low degree of structure. A significant deviation from random-mating (average FIS = 0.23) over the two forests was detected. Two of 18 samples showed a difference in population genetic structure between males and females. We discuss the fact that the population genetic structure of O. cincta is significantly affected by long-range dispersal, even though it is a small and wingless insect. This interpretation is supported by observations on tree-climbing behaviour in this species that may facilitate air dispersal. As a consequence, the assumption that migration a priori may be neglected in demographic analysis of O. cincta is incorrect. [source]

EST-derived polymorphic microsatellites from cultivated strawberry (Fragaria×ananassa) are useful for diversity studies and varietal identification among Fragaria species

MOLECULAR ECOLOGY RESOURCES, Issue 4 2006
D. J. GIL-ARIZA
Abstract Microsatellite or simple sequence repeat markers derived from expressed sequence tags (ESTs) provide genetic markers within potentially functional genes, which could be very useful for breeding programs. To date, the development of microsatellite markers in the genus Fragaria has focused mainly on Fragaria vesca. However, most of the interests of breeding programs relate to specific characteristics of cultivated strawberry. Here, we describe a set of 10 EST-derived microsatellites from Fragaria × ananassa. These markers showed high levels of polymorphism within strawberry cultivars and among different Fragaria species, indicating their potential for genetic studies not only on strawberry but also in other species within the genus. [source]

Clonal composition of the peach-potato aphid Myzus persicae (Homoptera: Aphididae) in France and Scotland: Comparative analysis with IGS fingerprinting and microsatellite markers

ANNALS OF APPLIED BIOLOGY, Issue 3 2003
B FENTON
Summary Fourteen colonies of the peach-potato aphid, Myzus persicae, were taken either from French peach trees or weeds in 2001. Thirty five apomictic parthenogenetic lineages (APLs) were established. Ribosomal DNA intergenic spacer (IGS) fingerprinting was used to characterise these and 28 fingerprints were duly obtained. Those lineages with different fingerprints were considered different genotypes and those with the same fingerprint as the same. The genetic identity of APLs was further tested using four microsatellite loci. APLs that differed by IGS fingerprint had distinct microsatellite allele combinations and those that had the same IGS fingerprint had the same microsatellite allele combinations. The results confirmed that IGS types corresponded to different aphid genotypes. Independent APLs with identical IGS and microsatellite genotype were therefore considered different representatives of the same clone. APLs from M. persicae found on Scottish crops in 1995, 1996 and 2001, as well as a long-term laboratory line were also examined by the same methods. Their IGS fingerprints were similar or identical suggesting that they all belonged to the same clone. Microsatellite markers also suggested that these lineages were derived from a single clone. Some field lineages exhibited slight modifications to their IGS fingerprints confirming that the IGS evolves more rapidly than these microsatellite alleles. Thus, IGS will continue to provide a useful marker for aphid fieldwork. [source]

Microsatellite and chromosomal stable colorectal cancers demonstrate poor immunogenicity and early disease recurrence

COLORECTAL DISEASE, Issue 6 2009
A. Banerjea
Abstract Objective, Colorectal cancers may demonstrate chromosomal instability (CSI) or microsatellite instability (MSI-H). A third group of microsatellite and chromosome stable (MACS) colorectal cancer has been described more recently. Patients with MSI-H colorectal cancers demonstrate improved outcome and a pronounced inflammatory infiltrate. Enhanced host immune response and increased immunogenicity might explain these observations. This study aims to further characterize colorectal cancer immunogenicity. Method, Microsatellite stability status was determined in resected tumour samples. Microsatellite stable (MSS) tumour samples were stratified by DNA ploidy status, as determined by flow cytometry into aneuploid MSS (CSI) and diploid MSS (MACS) cancers. Lymphocyte proliferation, quantified by bromodeoxyuridine incorporation assays assessed tumour protein immunogenicity and ELISA assays quantified inflammatory cytokine release. Kaplan,Meier survival curves and multivariate analyses were used to determine prognostic value. Results, Patients with MSI-H colorectal cancer had improved outcome but those with MACS cancers undergoing curative surgery had significantly poorer disease-free survival (P = 0.002). The MACS phenotype was an independent predictor of poor outcome (HR = 2.44, 1.33,4.47, P = 0.004). Lymphocyte proliferation assays confirmed enhanced immunogenicity of MSI-H proteins and reduced immunogenicity of MACS proteins (P < 0.0001). In vitro levels of IFN-, (P = 0.004) and IL-18 (P < 0.0001) mirrored these differences in lymphocyte activity. Conclusions, Stratification of colorectal cancer by MSI and ploidy status may have prognostic value in patients undergoing curative surgery. MSI-H cancers display enhanced immunogenic properties but the immune response to MACS cancers appears to be absent and this may contribute to their poor prognosis. [source]

Human ameloblastin gene: genomic organization and mutation analysis in amelogenesis imperfecta patients

EUROPEAN JOURNAL OF ORAL SCIENCES, Issue 1 2001
Carina Kärrman Mårdh
A gene encoding the enamel protein ameloblastin (AMBN) was recently localized to a region on chromosome 4q21 containing a gene for the inherited enamel defect local hypoplastic amelogenesis imperfecta (AIH2). Ameloblastin protein is located at the Tomes processes of secretory ameloblasts and in the sheath space between rod-interrod enamel, and the AMBN gene therefore represents a viable candidate gene for local hypoplastic amelogenesis imperfecta (AI). In this study, the genomic organization of human AMBN was characterized. The gene was shown to consist of 13 exons and 12 introns. An alternatively spliced 45 bp sequence was shown not to represent a separate exon and is most likely spliced by the use of a cryptic splice site. The finding that there were no recombinations between an intragenic microsatellite and AIH2 encouraged us to evaluate this gene's potential role as a candidate gene for local hypoplastic AI. Mutation screening was performed on all 13 exons in 20 families and 8 sporadic cases with 6 different forms of AI. DNA variants were found but none that was associated exclusively with local hypoplastic AI or any of the other variants of AI in the identified Swedish families. This study excludes the coding regions and the splice sites of AMBN from a causative role in the pathogenesis of AIH2. [source]

WHEN VICARS MEET: A NARROW CONTACT ZONE BETWEEN MORPHOLOGICALLY CRYPTIC PHYLOGEOGRAPHIC LINEAGES OF THE RAINFOREST SKINK, CARLIA RUBRIGULARIS

EVOLUTION, Issue 7 2004
Ben L. Phillips
Abstract Phylogeographic analyses of the fauna of the Australian wet tropics rainforest have provided strong evidence for long-term isolation of populations among allopatric refugia, yet typically there is no corresponding divergence in morphology. This system provides an opportunity to examine the consequences of geographic isolation, independent of morphological divergence, and thus to assess the broader significance of historical subdivisions revealed through mitochondrial DNA phylogeography. We have located and characterized a zone of secondary contact between two long isolated (mtDNA divergence > 15%) lineages of the skink Carlia rubrigularis using one mitochondrial and eight nuclear (two intron, six microsatellite) markers. This revealed a remarkably narrow (width<3 km) hybrid zone with substantial linkage disequilibrium and strong deficits of heterozygotes at two of three nuclear loci with diagnostic alleles. Cline centers were coincident across loci. Using a novel form of likelihood analysis, we were unable to distinguish between sigmoidal and stepped cline shapes except at one nuclear locus for which the latter was inferred. Given estimated dispersal rates of 90,133 m X gen,1/2 and assuming equilibrium, the observed cline widths suggest effective selection against heterozygotes of at least 22,49% and possibly as high as 70%. These observations reveal substantial postmating isolation, although the absence of consistent deviations from Hardy-Weinberg equilibrium at diagnostic loci suggests that there is little accompanying premating isolation. The tight geographic correspondence between transitions in mtDNA and those for nuclear genes and corresponding evidence for selection against hybrids indicates that these morphologically cryptic phylogroups could be considered as incipient species. Nonetheless, we caution against the use of mtDNA phylogeography as a sole criterion for defining species boundaries. [source]

THE AFRICANIZATION OF HONEYBEES (APIS MELLIFERA L.) OF THE YUCATAN: A STUDY OF A MASSIVE HYBRIDIZATION EVENT ACROSS TIME

EVOLUTION, Issue 7 2002
Kylea E. Clarke
Abstract Until recently, African and European subspecies of the honeybee (Apis mellifera L.) had been geographically separated for around 10,000 years. However, human-assisted introductions have caused the mixing of large populations of African and European subspecies in South and Central America, permitting an unprecedented opportunity to study a large-scale hybridization event using molecular analyses. We obtained reference populations from Europe, Africa, and South America and used these to provide baseline information for a microsatellite and mitochondrial analysis of the process of Africanization of the bees of the Yucatan Peninsula, Mexico. The genetic structure of the Yucatecan population has changed dramatically over time. The pre-Africanized Yucatecan population (1985) comprised bees that were most similar to samples from southeastern Europe and northern and western Europe. Three years after the arrival of Africanized bees (1989), substantial paternal gene flow had occurred from feral Africanized drones into the resident European population, but maternal gene flow from the invading Africanized population into the local population was negligible. However by 1998, there was a radical shift with both African nuclear alleles (65%) and African-derived mitochondria (61%) dominating the genomes of domestic colonies. We suggest that although European mitochondria may eventually be driven to extinction in the feral population, stable introgression of European nuclear alleles has occurred. [source]

Association of vasopressin 1a receptor levels with a regulatory microsatellite and behavior

GENES, BRAIN AND BEHAVIOR, Issue 5 2005
E. A. D. Hammock
Vasopressin regulates complex behaviors such as anxiety, parenting, social engagement and attachment and aggression in a species-specific manner. The capacity of vasopressin to modulate these behaviors is thought to depend on the species-specific distribution patterns of vasopressin 1a receptors (V1aRs) in the brain. There is considerable individual variation in the pattern of V1aR binding in the brains of the prairie vole species, Microtus ochrogaster. We hypothesize that this individual variability in V1aR expression levels is associated with individual variation in a polymorphic microsatellite in the 5, regulatory region of the prairie vole v1ar gene. Additionally, we hypothesize that individual variation in V1aR expression contributes to individual variation in vasopressin-dependent behaviors. To test these hypotheses, we first screened 20 adult male prairie voles for behavioral variation using tests that measure anxiety-related and social behaviors. We then assessed the brains of those animals for V1aR variability with receptor autoradiography and used polymerase chain reaction to genotype the same animals for the length of their 5, microsatellite polymorphism in the v1ar gene. In this report, we describe the results of this discovery-based experimental approach to identify potential gene, brain and behavior interrelationships. The analysis reveals that V1aR levels, in some but not all brain regions, are associated with microsatellite length and that V1aR levels in those and other brain regions correlate with anxiety-related and social behaviors. These results generate novel hypotheses regarding neural control of anxiety-related and social behaviors and yield insight into potential mechanisms by which non-coding gene polymorphisms may influence behavioral traits. [source]

Multiple forms of genetic instability within a 2-Mb chromosomal segment of 3q26.3,q27 are associated with development of esophageal adenocarcinoma

GENES, CHROMOSOMES AND CANCER, Issue 4 2006
Lin Lin
Gene amplification is one of the mechanisms to activate oncogenes in many cancers, including esophageal adenocarcinoma (EA). In the present study, we used two-dimensional restriction landmark genome scanning to clone a NotI/DpnII fragment that showed increased genomic dosage in 1 of 44 EAs analyzed. This fragment maps to 3q26.3,q27, and subsequent experiments identified two intrachromosomal amplicons within a 10-Mb DNA segment in 7 of 75 (9%) EAs. The distal amplified-core region maps centromeric to the PIK3CA locus, and a microsatellite (D3S1754) within this region exhibited significant instability (MSI), in stark contrast to the genomewide microsatellite stability found in EA. D3S1754-MSI arises in premalignant Barrett's dysplastic cells and preceded amplification of the nascent MSI allele in the corresponding EA. Seven ESTs within the amplified-core were overexpressed in amplicon-containing EAs. One of these, EST AW513672, represents a chimeric transcript that initiated from an antisense promoter sequence in the 5,UTR of a full-length LINE-1 element (L1-5,ASP). Similar chimeric transcripts encoding portions of the MET oncogene and the BCAS3 gene also were overexpressed in EAs, suggesting that L1-5,ASP activation may occur at a broad level in primary EAs. Thus, the fine dissection of a 2-Mb amplified DNA segment in 3q26.3,q27 in EA revealed multiple genetic alterations that had occurred sequentially and/or concurrently during EA development. This article has supplementary material, available at http://www.interscience.wiley.com/jpages/1045-2257/suppmat. © 2005 Wiley-Liss, Inc. [source]

Microsatellites versus single-nucleotide polymorphisms in confidence interval estimation of disease loci

GENETIC EPIDEMIOLOGY, Issue 1 2006
Charalampos Papachristou
Abstract With cost-effective high-throughput Single Nucleotide Polymorphism (SNP) arrays now becoming widely available, it is highly anticipated that SNPs will soon become the choice of markers in whole genome screens. This optimism raises a great deal of interest in assessing whether dense SNP maps offer at least as much information as their microsatellite (MS) counterparts. Factors considered to date include information content, strength of linkage signals, and effect of linkage disequilibrium. In the current report, we focus on investigating the relative merits of SNPs vs. MS markers for disease gene localization. For our comparisons, we consider three novel confidence interval estimation procedures based on confidence set inference (CSI) using affected sib-pair data. Two of these procedures are multipoint in nature, enabling them to capitalize on dense SNPs with limited heterozygosity. The other procedure makes use of markers one at a time (two-point), but is much more computationally efficient. In addition to marker type, we also assess the effects of a number of other factors, including map density and marker heterozygosity, on disease gene localization through an extensive simulation study. Our results clearly show that confidence intervals derived based on the CSI multipoint procedures can place the trait locus in much shorter chromosomal segments using densely saturated SNP maps as opposed to using sparse MS maps. Finally, it is interesting (although not surprising) to note that, should one wish to perform a quick preliminary genome screening, then the two-point CSI procedure would be a preferred, computationally cost-effective choice. Genet. Epidemiol. 30:3,17, 2006. © 2005 Wiley-Liss, Inc. [source]

Comparison of single-nucleotide polymorphisms and microsatellite markers for linkage analysis in the COGA and simulated data sets for Genetic Analysis Workshop 14: Presentation Groups 1, 2, and 3

GENETIC EPIDEMIOLOGY, Issue S1 2005
Marsha A. Wilcox
Abstract The papers in presentation groups 1,3 of Genetic Analysis Workshop 14 (GAW14) compared microsatellite (MS) markers and single-nucleotide polymorphism (SNP) markers for a variety of factors, using multiple methods in both data sets provided to GAW participants. Group 1 focused on data provided from the Collaborative Study on the Genetics of Alcoholism (COGA). Group 2 focused on data simulated for the workshop. Group 3 contained analyses of both data sets. Issues examined included: information content, signal strength, localization of the signal, use of haplotype blocks, population structure, power, type I error, control of type I error, the effect of linkage disequilibrium, and computational challenges. There were several broad resulting observations. 1) Information content was higher for dense SNP marker panels than for MS panels, and dense SNP markers sets appeared to provide slightly higher linkage scores and slightly higher power to detect linkage than MS markers. 2) Dense SNP panels also gave higher type I errors, suggesting that increased test thresholds may be needed to maintain the correct error rate. 3) Dense SNP panels provided better trait localization, but only in the COGA data, in which the MS markers were relatively loosely spaced. 4) The strength of linkage signals did not vary with the density of SNP panels, once the marker density was ,1 SNP/cM. 5) Analyses with SNPs were computationally challenging, and identified areas where improvements in analysis tools will be necessary to make analysis practical for widespread use. Genet. Epidemiol. 29:(Suppl. 1): S7,S28, 2005. © 2005 Wiley-Liss, Inc. [source]

Parent-of-origin, imprinting, mitochondrial, and X-linked effects in traits related to alcohol dependence: Presentation Group 18 of Genetic Analysis Workshop 14

GENETIC EPIDEMIOLOGY, Issue S1 2005
Konstantin Strauch
Abstract The participants of Presentation Group 18 of Genetic Analysis Workshop 14 analyzed the Collaborative Study on the Genetics of Alcoholism data set to investigate sex-specific effects for phenotypes related to alcohol dependence. In particular, the participants looked at imprinting (which is also known as parent-of-origin effect), differences between recombination fractions for the two sexes, and mitochondrial and X-chromosomal effects. Five of the seven groups employed newly developed or existing methods that take imprinting into account when testing for linkage, or test for imprinting itself. Single-marker and multipoint analyses were performed for microsatellite as well as single-nucleotide polymorphism markers, and several groups used a sex-specific genetic map in addition to a sex-averaged map. Evidence for paternal imprinting (i.e., maternal expression) was consistently obtained by at least two groups at genetic regions on chromosomes 10, 12, and 21 that possibly harbor genes responsible for alcoholism. Evidence for maternal imprinting (which is equivalent to paternal expression) was consistently found at a locus on chromosome 11. Two groups applied extensions of variance components analysis that model a mitochondrial or X-chromosomal effect to latent class variables and electrophysiological traits employed in the diagnosis of alcoholism. The analysis, without using genetic markers, revealed mitochondrial or X-chromosomal effects for several of these traits. Accounting for sex-specific environmental variances appeared to be crucial for the identification of an X-chromosomal factor. In linkage analysis using marker data, modeling a mitochondrial variance component increased the linkage signals obtained for autosomal loci. Genet. Epidemiol. 29(Suppl. 1):S125,S132, 2005. © 2005 Wiley-Liss, Inc. [source]

Cross-species amplification of Lolium microsatellites in Poa ssp

GRASSLAND SCIENCE, Issue 3 2006
Bryan Kindiger
Abstract Cross-species amplification of 47 Lolium ssp. microsatellite primers were evaluated across eight Poa species or subspecies. Of the 47 evaluated Lolium simple sequence repeat (SSR) primer pairs examined, 18 generated one or more amplification products. Of these, only two resulted in the identification of Poa ssp. microsatellite motifs, of which only one was complementary to the microsatellite motif identified in Lolium. Though few Poa ssp. microsatellite regions were identified, several of the amplification products were polymorphic within and across the Poa ssp. and could be utilized as markers in Poa ssp. intergeneric hybrid studies. Results of the research suggest the use of Lolium microsatellite derived primers to identify complementary SSR regions in Poa is not an effective approach for the development of microsatellite markers in Poa. [source]

Narrowing of the regions of allelic losses of chromosome 1p36 in meningioma tissues by an improved SSCP analysis

INTERNATIONAL JOURNAL OF CANCER, Issue 8 2008
Yanlei Guan
Abstract Mapping loss of heterozygosity (LOH) regions in the genomes of tumor tissues is a practical approach for identifying genes whose loss is related to tumorigenesis. Conventional LOH analyses using microsatellite or single nucleotide polymorphism (SNP) markers require the simultaneous examination of tumor- and matched normal-DNA. Here, we improved the previously developed SNP-based LOH assay using single strand conformation polymorphism (SSCP) analysis, so that LOH in tumor samples heavily contaminated with normal DNA can now be precisely estimated, even when matched normal DNA is not available. We demonstrate the reliability of the improved SSCP-based LOH detection method, called the LOH estimation by quantitative SSCP analysis using averaged control (LOQUS-AC), by comparing the results with those of the previous "LOH estimated by quantitative SSCP assay" (LOQUS) method. Using the LOQUS-AC assay, LOH was detected at a high consistency (98.1%) with the previous LOQUS method. We then applied this new method to characterize LOH profiles in 130 meningiomas, using 68 SNPs (i.e., a mean inter-SNP interval of 441 kbp) that are evenly distributed throughout chromosome 1p36. Benign, atypical and anaplastic meningiomas exhibited 1p36 LOH at frequencies of 48.39, 84.62 and 100.00%, respectively, using LOQUS-AC. Subsequently, we detected a candidate common LOH region on 1p36.11 that might harbor tumor suppressor genes related to malignant progression of meningioma. © 2007 Wiley-Liss, Inc. [source]

MHC microsatellites in a Southern Brazilian population

INTERNATIONAL JOURNAL OF IMMUNOGENETICS, Issue 5 2009
C. Sens-Abuázar
Summary Microsatellites are short tandem repeats of 1,6 bp DNA fragments, which are found throughout the genome. Due to their high levels of polymorphism, many of them are used as markers for population studies. Here we report an investigation on four microsatellites (D6S273, D6S2792, STR_MICA and D6S2810) located within the major histocompatibility complex in a sample of 281 Southern Brazilians of European ancestry. Allelic and haplotypic frequencies are described, as well as linkage disequilibrium (LD) between alleles of these microsatellites and alleles of three HLA genes: HLA-B, HLA-DRB1 and HLA-DQB1. The most polymorphic microsatellite was D6S2810, located close to the HLA-B locus. Strong LD was observed between alleles of microsatellites and HLA genes. The strongest associations occurred among STR_MICA*A5.1,HLA-B*13, STR_MICA*A6,HLA-B*49, STR_MICA*A9,HLA-B*39, STR_MICA*A9,HLAB*57, D6S2810*334,HLA-B*14, D6S2810*334,HLA-B*38, STR_MICA*A5.1,HLA-DRB1*1501,HLA-DQB1*0602 and D6S2810*344,HLA-DRB1*0411,HLA-DQB1*0302. This study contributes with important information on HLA haplotypes, and is potentially useful in resolving cases of low resolution HLA genotyping ambiguities. [source]

MICA and MICB microsatellite alleles in HLA extended haplotypes

INTERNATIONAL JOURNAL OF IMMUNOGENETICS, Issue 5 2001
E. Bolognesi
Summary The present study is a contribution to the definition of the linkage disequilibrium relationship of MICA and MICB with adjacent loci and to the characterization of extended HLA haplotypes. These issues are of importance for the identification of disease associations and for a better definition of donor,recipient compatibility in bone-marrow grafts through the typing of haplospecific markers. The distribution of the five alleles of MICA and the 13 alleles of MICB microsatellites, located, respectively, in MICA transmembrane exon 5 and in MICB intron 1, was examined in 133 healthy Italian individuals previously typed for HLA class I, class II and complement loci and for the TNFa microsatellite. The MICB microsatellite was also analysed in 49 HTCLs for which MICA typing was already available. Very strong linkage disequilibria with HLA-B and TNFa were detected in the Italian population for both MICA and MICB microsatellite alleles, in spite of the high mutability rate of the larger MICB alleles. Some strong associations were also detected between MICB and DRB1. The strongest associations (P < 0.001, D, > 0.7) were those of MICA-A4 with HLA-B18, B27 and TNFa1, MICA-A5 with HLA-B35, B61 and B62, MICA-A5.1 with HLA-B7, B8, B13, B63 and MICB-CA24, MICA-A6 with HLA-B51, MICA-A9 with HLA-B39, B57 and TNFa2, MICB-CA14 with HLA-B14, B27 and TNFa1, MICB-CA15 with HLA-B52, TNFa4 and TNFa13, MICB-CA17 with HLA-B7 and TNFa11, MICB-CA18 with HLA-B13 and TNFa7, MICB-CA22 with HLA-B57, and MICB-CA24 with HLA-B8 and TNFa2. From pairwise associations in the random panel and results for the homozygous cell lines it was possible to deduce the MICA and MICB microsatellite alleles present in many of the well-known Caucasoid extended haplotypes. [source]

Genetic diversity and structure of the West Balkan Pramenka sheep types as revealed by microsatellite and mitochondrial DNA analysis

JOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 6 2008
inkulov
Summary Several different phenotypes of the native Pramenka sheep have been developed in the Balkan region for different environmental and socio-cultural conditions. Animals from seven West Balkan Pramenka sheep types were analysed for 15 microsatellite markers and for mitochondrial DNA (mtDNA) and the results were used to assess genetic variation within and among the types and to infer the genetic population structure of the Pramenka sheep. Mean expected heterozygosity and allelic richness over the microsatellite loci and sheep types were 0.78 and 7.9, respectively. A Bayesian statistical method for estimating hidden genetic structure suggested that a core of the largest panmictic population was formed by Serbian, Kosovan, Bosnian, Montenegrin and Albanian types, while Croatian and Macedonian types comprised two other main populations, respectively. Mitochondrial DNA analysis revealed two mtDNA haplogroups in the Pramenka sheep, B and A, with a frequency of 93.7% and 6.3%, respectively. A total of 60 mtDNA haplotypes were found in 64 animals sequenced, and the mean nucleotide and haplotypic diversities over the types were 0.013 and 0.945, respectively. Molecular analysis suggests that the West Balkan Pramenka sheep types have their origins in two distinct maternal lineages of domestic sheep and different Pramenka phenotypes tend to form few panmictic populations. The Pramenka sheep represents a valuable resource of genetic diversity in sheep. [source]

Genetic structure and differentiation of 12 African Bos indicus and Bos taurus cattle breeds, inferred from protein and microsatellite polymorphisms

JOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 1 2005
E.M. Ibeagha-Awemu
Summary Level of genetic differentiation, gene flow and genetic structuring of nine Bos indicus and three Bos taurus cattle breeds in Cameroon and Nigeria were estimated using the genetic information from 16 microsatellite, five blood protein and seven milk protein markers. The global heterozygote deficit across all populations (Fit) amounted to 11.7% (p < 0.001). The overall significant (p < 0.001) deficit of heterozygotes because of inbreeding within breeds (Fis) amounted to 6.1%. The breeds were moderately differentiated (Fst = 6%, p < 0.001) with all loci except CSN1S2 contributing significantly to the Fst value. The 12 populations belong to two genetic clusters, a zebu and a taurine cluster. While inferred sub-clusters within the taurine group corresponded extremely well to predefined breed categorizations, no real sub-clusters, corresponding to predefined breeds, existed within the zebu cluster. With the application of prior population information, cluster analysis achieved posterior probabilities from 0.962 to 0.994 of correctly assigning individuals to their rightful populations. High gene flow was evident between the zebu populations. Positive and negative implications of the observed genetic structure of the breeds on their development, improvement and conservation are discussed. The study shows that the breeds are threatened by uncontrolled breeding and therefore are at risk to become genetically uniform in the future. This situation can be avoided by putting in place effective breeding and management measures aimed at limiting uncontrolled mating between the breeds and to preserve special characteristics, genetic as well as breed biodiversity. The first step towards realizing these goals might be to geographically demarcate the breeds. [source]

Comprehensive analysis of 112 melanocytic skin lesions demonstrates microsatellite instability in melanomas and dysplastic nevi, but not in benign nevi

JOURNAL OF CUTANEOUS PATHOLOGY, Issue 7 2001
Mahmoud R. Hussein
Introduction: Alterations in the length of DNA repetitive sequences (microsatellite instability (MSI)) represent distinct tumorigenic pathways associated with several familial and sporadic tumors. Material and methods: To investigate the prevalence and frequency of MSI in melanocytic lesions, the polymerase chain reaction (PCR)-based microsatellite assay was used to examine formalin-fixed, paraffin-embedded tissues of 30 benign melanocytic nevi, 60 melanocytic dysplastic nevi (MDN), and 22 primary vertical growth phase cutaneous malignant melanomas (CMM). Twenty-four microsatellite markers at the 1p, 2p, 3p, 4q and 9p chromosomal regions were used. Results: MSI was found at 1p and 9p in MDN and CMM but not in benign melanocytic nevi. The overall prevalence of MSI was17/60 (28%) in MDN and 7/22 (31%) in CMM. The frequency of MSI ranged from 2/24 (9%) to 4/24 (17%) and was most commonly found at D9S162. There was a statistically significant correlation between degree of atypia and frequency of MSI (p<0.001) in MDN. There were two MSI banding patterns: band shifts and additional bands. Conclusions: The data presented revealed the presence of low-frequency MSI (MSI-L) at the 1p and 9p regions in both MDN and CMM. Whether the MSI-L pattern reflects a defect in mismatch repair genes is still to be determined. [source]

Opposites attract: MHC-associated mate choice in a polygynous primate

JOURNAL OF EVOLUTIONARY BIOLOGY, Issue 1 2010
J. M. SETCHELL
Abstract We investigated reproduction in a semi-free-ranging population of a polygynous primate, the mandrill, in relation to genetic relatedness and male genetic characteristics, using neutral microsatellite and major histocompatibility complex (MHC) genotyping. We compared genetic dissimilarity to the mother and genetic characteristics of the sire with all other potential sires present at the conception of each offspring (193 offspring for microsatellite genetics, 180 for MHC). The probability that a given male sired increased as pedigree relatedness with the mother decreased, and overall genetic dissimilarity and MHC dissimilarity with the mother increased. Reproductive success also increased with male microsatellite heterozygosity and MHC diversity. These effects were apparent despite the strong influence of dominance rank on male reproductive success. The closed nature of our study population is comparable to human populations for which MHC-associated mate choice has been reported, suggesting that such mate choice may be especially important in relatively isolated populations with little migration to introduce genetic variation. [source]

Chromosomal rearrangements and genetic structure at different evolutionary levels of the Sorex araneus group

JOURNAL OF EVOLUTIONARY BIOLOGY, Issue 3 2008
P. BASSET
Abstract Robertsonian (Rb) fusions received large theoretical support for their role in speciation, but empirical evidence is often lacking. Here, we address the role of Rb rearrangements on the genetic differentiation of the karyotypically diversified group of shrews, Sorex araneus. We compared genetic structure between ,rearranged' and ,common' chromosomes in pairwise comparisons of five karyotypic taxa of the group. Considering all possible comparisons, we found a significantly greater differentiation at rearranged chromosomes, supporting the role of chromosomal rearrangements in the general genetic diversification of this group. Intertaxa structure and distance were larger across rearranged chromosomes for most of the comparisons, although these differences were not significant. This last result could be explained by the large variance observed among microsatellite-based estimates. The differences observed among the pairs of taxa analysed support the role of both the hybrid karyotypic complexity and the level of evolutionary divergence. [source]

Variable number of tandem repeats in the growth hormone gene of Sparus aurata: association with growth and effect on gene transcription

JOURNAL OF FISH BIOLOGY, Issue 2004
R. Almuly
The GH gene of Sparus aurata(saGH) contains variable number of tandem repeats (VNTR). The hyper-variable minisatellites in the first and third introns segregate in a Mendelian manner and exhibit numerous alleles. Analysis by PCR and sequencing of the two introns in several wild Sparidae species revealed comparable minisatellites with some variations. ,Zoo blot' with the first intron unit as a probe showed this sequence to be characteristic of several families from the Perciformes order. Unexpectedly, a similar minisatellite was found in the first intron of the GH gene in flounder, which belongs to a different order. Transfection of constructs containing a reporter gene and first intron of different length to four cell lines resulted in an inhibitory effect of the longer intron relative to the short intron. A (CA)n microsatellite (saGHpCA) is found in the GH promoter. A similar repeat at the same location is present in GH promoters of several other fish species. High variability (11 alleles) of the saGHpCA was found in a hatchery population. Full-sib family genotyping showed a Mendelian inheritance of these alleles. A significant association was found between allele distribution and body mass in large and average size fishes from a hatchery population. The intron minisatellites may serve as markers for hybrid population and parental assignment. Its presence in families and orders of the higher teleosts may help solving classification uncertainties. Their conservation and inhibitory effect suggest a biological role. The saGHpCA is correlated with growth and may be a good candidate for predicting growth performance. [source]

Microgeographic population structure of brook charr: a comparison of microsatellite and mark-recapture data

JOURNAL OF FISH BIOLOGY, Issue 3 2003
B. K. Adams
Polymorphism at five microsatellite genetic markers (genotyped n = 496) and mark-recapture tagging data (tagged n = 9813) were used to define the population structure of brook charr, Salvelinus fontinalis from the Indian Bay watershed, Newfoundland, Canada. Despite the absence of physical barriers to migration among lakes, both genetic and tagging data suggest that brook charr in each lake represent reproductively isolated populations. Exact tests comparing allele frequencies, , (global value = 0·063), Rst (global value = 0·052), individual assignment tests, and Nei's genetic distance provided congruent estimates of population subdivision in agreement with the tagging data (only 2·2% of recaptures were lake-to-lake). The genetic structure of the brook charr populations corresponded with the geographic structure of the drainage basin on a qualitative level, although linear distance over water was not significantly correlated with the tagging data or the genetic distance measures. The agreement between the tagging and the genetic data suggest that microsatellite markers can be useful tools for defining real biological units. The results also suggest that brook charr exhibit microgeographic population structure at the watershed scale, and that this is the scale at which conservation and management of this salmonid might best be implemented. [source]

p53 expression, K- ras gene mutation and microsatellite instability in gastric B-cell lymphomas

JOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY, Issue 9 2003
TORU HIYAMA
Abstract Background and Aims:, Genetic mechanisms involved in the development of gastric B-cell lymphomas remain unclear. The aim of the present study was to clarify the roles of mutations of the p53 and K- ras genes, and microsatellite instability (MSI) in the development of gastric B-cell lymphomas. Methods:, We investigated p53 immunoreactivity, mutations of the K- ras gene, and MSI in 27 gastric marginal zone B-cell lymphomas of mucosa-associated lymphoid tissue type (MZBCL) and 24 diffuse large B-cell lymphomas (DLBCL). p53 immunoreactivity was examined using a monoclonal antibody, DO-7. Mutation of the K- ras gene was detected by polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) analysis. MSI was examined at five microsatellite loci with a microsatellite assay. Cases were classified as having high-frequency MSI (MSI-H) (, 2 loci showing instability), low-frequency MSI (MSI-L) (only one locus showing instability), or as microsatellite stable. Results:, p53 immunoreactivity was detected in 1 of 16 (6%) MZBCL and 8 of 19 (42%) DLBCL. Frequency of p53 immunoreactivity in DLBCL was significantly higher than that in MZBCL (P = 0.018). MSI-H was detected only in 1 of 20 (5%) DLBCL. None of the cases examined showed mutation of the K- ras gene. Conclusions:, These data suggest that mutations of the p53 gene may play an important role in the development of gastric DLBCL, and that mutations of the K- ras gene and MSI may be involved in little part of the development of gastric B-cell lymphomas. [source]

A Microsatellite DNA Marker Developed for Identifying Disease-resistant Population of Giant Black Tiger Shrimp, Penaeus monodon

JOURNAL OF THE WORLD AQUACULTURE SOCIETY, Issue 2 2009
Kuntal Mukherjee
White spot disease caused by white spot syndrome virus (WSSV) poses major problems that result in huge economic losses each year in shrimp aquaculture throughout the world. In the present study, microsatellite-based DNA fingerprints have been compared between naturally occurring WSSV disease-resistant and susceptible populations of giant black tiger shrimp, Penaeus monodon, to find DNA markers. For the first time, we report here a microsatellite locus, which, after amplification by polymerase chain reaction, provides a highly statistically significant DNA fingerprint of 71 bp, only in disease susceptible populations but not in disease-resistant shrimp populations, whereas a 317 bp band is common in both. The absence of the former DNA marker will be very useful to identify disease-resistant broodstock of P. monodon for marker-assisted selection in breeding programs to generate disease-free shrimps (P. monodon) in the aquaculture industry. [source]

Kinship and social structure of bobcats (Lynx rufus) inferred from microsatellite and radio-telemetry data

JOURNAL OF ZOOLOGY, Issue 4 2006
J. E. Jane
Abstract Kinship analysis using 12 microsatellites was compared with radio-telemetry data to examine the social structure of bobcats Lynx rufus in southern Texas. Genetically identified kinship relationships combined with capture data were used to reconstruct pedigrees. Three family groups were constructed from parent/offspring pairs identified from shared alleles. All parents identified by genetic analysis had established home ranges. Individuals with no distinct home ranges were not genetically observed to have offspring among the bobcats sampled. This suggests that establishing a home range is necessary for bobcats to breed. Of three identified male offspring and three identified female offspring, two female offspring were philopatric. These females became a part of the breeding population in their natal area. Among sibling pairs that included nine female and four male individuals, four females and one male were residents suggesting male-biased dispersal. [source]

Rolling stones and stable homes: social structure, habitat diversity and population genetics of the Hawaiian spinner dolphin (Stenella longirostris)

MOLECULAR ECOLOGY, Issue 4 2010
KIMBERLY R. ANDREWS
Abstract Spinner dolphins (Stenella longirostris) exhibit different social behaviours at two regions in the Hawaiian Archipelago: off the high volcanic islands in the SE archipelago they form dynamic groups with ever-changing membership, but in the low carbonate atolls in the NW archipelago they form long-term stable groups. To determine whether these environmental and social differences influence population genetic structure, we surveyed spinner dolphins throughout the Hawaiian Archipelago with mtDNA control region sequences and 10 microsatellite loci (n = 505). F -statistics, Bayesian cluster analyses, and assignment tests revealed population genetic separations between most islands, with less genetic structuring among the NW atolls than among the SE high islands. The populations with the most stable social structure (Midway and Kure Atolls) have the highest gene flow between populations (mtDNA ,ST < 0.001, P = 0.357; microsatellite FST = ,0.001; P = 0.597), and a population with dynamic groups and fluid social structure (the Kona Coast of the island of Hawai'i) has the lowest gene flow (mtDNA 0.042 < ,ST < 0.236, P < 0.05; microsatellite 0.016 < FST < 0.040, P < 0.001). We suggest that gene flow, dispersal, and social structure are influenced by the availability of habitat and resources at each island. Genetic comparisons to a South Pacific location (n = 16) indicate that Hawaiian populations are genetically depauperate and isolated from other Pacific locations (mtDNA 0.216 < FST < 0.643, P < 0.001; microsatellite 0.058 < FST < 0.090, P < 0.001); this isolation may also influence social and genetic structure within Hawai'i. Our results illustrate that genetic and social structure are flexible traits that can vary between even closely-related populations. [source]

Pedigree reconstruction in wild cichlid fish populations

MOLECULAR ECOLOGY, Issue 20 2008
MARTIN KOCH
Abstract It is common practice to use microsatellites to detect parents and their offspring in wild and captive populations, in order to reconstruct a pedigree. However, correct inference is often constrained by a number of factors, including the absence of demographic data and ignorance regarding the completeness of parental sampling. Here we present a new Bayesian estimator that simultaneously estimates the pedigree and the size of the unsampled population. The method is robust to genotyping error, and can estimate pedigrees in the absence of demographic data. Using a large-scale microsatellite assay in four wild cichlid fish populations of Lake Tanganyika (1000 individuals in total), we assess the performance of the Bayesian estimator against the most popular assignment program, Cervus. We found small but significant pedigrees in each of the tested populations using the Bayesian procedure, but Cervus had very high type I error rates when the size of the unsampled population was assumed to be lower than what it was. The need of pedigree relationships to infer adaptive processes in natural populations places strong constraints on sampling design and identification of multigenerational pedigrees in natural populations. [source]

Extensive spatial genetic structure revealed by AFLP but not SSR molecular markers in the wind-pollinated tree, Fagus sylvatica

MOLECULAR ECOLOGY, Issue 5 2007
ALISTAIR S. JUMP
Abstract Studies of fine-scale spatial genetic structure (SGS) in wind-pollinated trees have shown that SGS is generally weak and extends over relatively short distances (less than 30,40 m) from individual trees. However, recent simulations have shown that detection of SGS is heavily dependent on both the choice of molecular markers and the strategy used to sample the studied population. Published studies may not always have used sufficient markers and/or individuals for the accurate estimation of SGS. To assess the extent of SGS within a population of the wind-pollinated tree Fagus sylvatica, we genotyped 200 trees at six microsatellite or simple sequence repeat (SSR) loci and 250 amplified fragment length polymorphisms (AFLP) and conducted spatial analyses of pairwise kinship coefficients. We re-sampled our data set over individuals and over loci to determine the effect of reducing the sample size and number of loci used for SGS estimation. We found that SGS estimated from AFLP markers extended nearly four times further than has been estimated before using other molecular markers in this species, indicating a persistent effect of restricted gene flow at small spatial scales. However, our SSR-based estimate was in agreement with other published studies. Spatial genetic structure in F. sylvatica and similar wind-pollinated trees may therefore be substantially larger than has been estimated previously. Although 100,150 AFLP loci and 150,200 individuals appear sufficient for adequately estimating SGS in our analysis, 150,200 individuals and six SSR loci may still be too few to provide a good estimation of SGS in this species. [source]