Home About us Contact
|
Home About us Contact | ||
|
|
||
Heterozygosity Values (heterozygosity + value)
Selected AbstractsA new autosomal STR nineplex for canine identification and parentage testingELECTROPHORESIS, Issue 2 2009Barbara van Asch Abstract A single multiplex PCR assay capable of simultaneously amplifying nine canine-specific autosomal STR markers (FH3210, FH3241, FH2004, FH2658, FH4012, REN214L11, FH2010, FH2361 and the newly described C38) was developed for individual identification and parentage testing in domestic dogs. In order to increase genotyping efficiency, amplicon sizes were optimized for a 90,350,bp range, with fluorescently labelled primers for use in Applied Biosystems, Inc., platforms. The performance of this new multiplex system was tested in 113 individuals from a case-study population and 12 random dogs from mixed-breed origin. Co-dominant inheritance of STR alleles was investigated in 101 father, mother and son trios. Expected heterozygosity values vary between 0.5648 for REN214L11 and 0.9050 for C38. The high level of genetic diversity observed for most markers provides this multiplex with a very high discriminating power (matching probability=1.63/1010 and matching probability among siblings=4.9/103). Allele sequences and a proposal for standardized nomenclature are also herein presented, aiming at implementing the use of this system in forensic DNA typing and population genetic studies. This approach resulted in an optimized and well-characterized canine DNA genotyping system that is highly performing and straightforward to integrate and employ routinely. Although this STR multiplex was developed for use and tested in a case-study population, the Portuguese breed Cão de Gado Transmontano, it proved to be useful for general identification purposes or parentage testing. [source] Characteristics of 11 polymorphic microsatellite markers in the red imported fire ant, Solenopsis invicta BurenMOLECULAR ECOLOGY RESOURCES, Issue 3 2009RAJESH B. GARLAPATI Abstract We have characterized 11 polymorphic microsatellite loci in the invasive ant Solenopsis invicta. Primer pairs were evaluated on fire ants collected from monogyne mounds in Lauderdale County, Mississippi. The observed and effective number of alleles ranged from two to six and from 1.31 to 2.64, respectively. The observed and expected heterozygosity values ranged from 0.1613 to 0.7826 and from 0.1491 to 0.6242, respectively. The polymorphism information content of the microsatellites ranged from 0.1482 to 0.6208. Probability tests indicated significant deviations from the Hardy,Weinberg equilibrium at three loci. Pairwise tests did not detect linkage disequilibrium between any pair of loci. [source] PERMANENT GENETIC RESOURCES: Isolation and characterization of 12 microsatellite markers in the middle-spotted woodpecker (Dendrocopos medius)MOLECULAR ECOLOGY RESOURCES, Issue 2 2008M. VILA Abstract Twelve polymorphic microsatellite loci were developed for Dendrocopos medius. Polymorphism was assessed for 27 individuals from the southwesternmost population of this woodpecker species. The number of alleles per locus ranged from three to seven, with observed heterozygosity values from 0.444 to 0.852. Genotypic frequencies conformed to Hardy,Weinberg equilibrium, and no evidence for linkage disequilibrium was observed. Multilocus genotypes resulting from this set of markers will be useful to determine genetic diversity and differentiation within and among habitat patches inhabited by D. medius. Three of the loci were polymorphic for Picoides articus. [source] Microsatellite markers for the endangered European mink (Mustela lutreola) and closely related mustelidsMOLECULAR ECOLOGY RESOURCES, Issue 6 2007M. T. CABRIA Abstract The European mink (Mustela lutreola L., 1761) is an endangered carnivore species whose populations suffered a severe decline during the last century. The genotyping of eight polymorphic microsatellite loci revealed a relatively low number of alleles per locus (two to eight), as well as low levels of polymorphism (observed and expected heterozygosity values per locus were 0.49 and 0.54, respectively). Cross-specific polymerase chain reaction amplifications were successful in seven closely related mustelid species suggesting that these loci may be useful not only for assessing genetic variability in European mink populations but also for determining potential hybridization events between M. lutreola and other mustelid species. [source] PRIMER NOTE: Isolation and characterization of microsatellite loci in the flat-headed bat (Tylonycteris pachypus)MOLECULAR ECOLOGY RESOURCES, Issue 3 2007P. Y. HUA Abstract Microsatellite loci were developed in the flat-headed bat (Tylonycteris pachypus) from genomic DNA using an enriched library method. Nine loci were tested on 48 individuals sampled from Guangxi Province, China. The mean number of observed alleles per locus was 6.4 (range 4,12). Observed and expected heterozygosity values ranged from 0.24 to 0.83 and from 0.30 to 0.89, respectively. One locus revealed significant departure from Hardy,Weinberg equilibrium and no significant linkage disequilibrium was detected between loci pairs. These markers will be used to examine genetic structure and parentage analysis in this species. [source] Isolation, characterization and evaluation of 11 autosomal STRs suitable for population studies in black and gold howler monkeys Alouatta carayaMOLECULAR ECOLOGY RESOURCES, Issue 1 2007LUCIANA I. OKLANDER Abstract We identified 11 polymorphic microsatellite markers for Alouatta caraya. Three markers were isolated from an enriched genomic library of A. caraya (AC14, AC17, AC45), five were previously described in Homo sapiens (TGMS1, TGMS2, D5S117, D8S165, D17S804), and three were identified for Lagothix lagotricha (1110, 1118, 157). Forty-eight individuals from one Argentinean population were genotyped, yielding heterozygosity values between 0.146 and 0.792. These markers provide an exclusion power of 0.922 when neither parent is known (0.992 when one parent is known) and are suitable for parentage analysis, population genetics and phylogeographical studies of A. caraya, the southernmost primate in the New World. [source] Characterization of new microsatellite markers in mung bean, Vigna radiata (L.)MOLECULAR ECOLOGY RESOURCES, Issue 4 2006JAE-GYUN GWAG Abstract The present work reports the isolation and characterization of new polymorphic microsatellites in mung bean (Vigna radiata L.). Of 93 designed primer pairs, seven were found to amplify polymorphic microsatellite loci, which were then characterized using 34 mung bean accessions. The number of alleles ranged from two to five alleles per locus with an average of three alleles. Observed and expected heterozygosity values ranged from 0 to 0.088 and from 0.275 to 0.683, respectively. All seven loci showed significant deviations from Hardy,Weinberg equilibrium, whereas only one pairwise combination (GBssr-MB77 and GBssr-MB91) exhibited significant departure from linkage disequilibrium. These newly developed markers are currently being utilized for diversity assessment within the mung bean germplasm collection of the Korean Gene Bank. [source] Isolation and characterization of microsatellite loci in the Alpine leaf beetle, Oreina elongataMOLECULAR ECOLOGY RESOURCES, Issue 2 2005N. MARGRAF Abstract For a study of local adaptations in the Alpine leaf beetle, Oreina elongata, we developed six microsatellite loci and screened them in 305 individuals from 13 populations. All markers were polymorphic with three to 15 alleles per locus. Average observed and expected heterozygosity values were 0.14 and 0.62, respectively. Four markers showed heterozygote deficiency and deviated significantly from Hardy,Weinberg expectations, indicating the presence of null alleles. [source] Polymorphic microsatellite markers for the goosander (Mergus merganser)MOLECULAR ECOLOGY RESOURCES, Issue 1 2005B. GAUTSCHI Abstract To investigate the population genetic structure of the goosander (Mergus merganser) in Europe and to identify populations with a significant conservation value, we isolated nine microsatellite loci, and screened them in the subspecies Mergus merganser merganser and Mergus merganser americanus. All markers were polymorphic with two to 15 alleles per locus. Average observed and expected heterozygosity values were 0.422 and 0.624, respectively, for the European and 0.497 and 0.667, respectively, for the North American subspecies. Only one marker departed significantly from Hardy,Weinberg expectations in both subspecies. This marker was highly variable but homozygous in all females, suggesting a sex-linked inheritance. [source] Development and characterization of novel microsatellite markers from the olive ridley sea turtle (Lepidochelys olivacea)MOLECULAR ECOLOGY RESOURCES, Issue 1 2004Ramesh K. Aggarwal Abstract Olive ridley turtles, although widely distributed globally and in Indian coastal waters, have undergone declines in recent years due to anthropogenic factors, particularly fishery-related mortality. Assessment of genetic variability in existing populations is critical to the development of effective conservation strategies. Here we describe the development of six highly polymorphic microsatellite loci from a simple sequence repeat-enriched genomic DNA library of olive ridley turtle. Characterization of five of these loci using 83 individual olive ridley turtles revealed eight to 24 alleles per locus, high observed and expected heterozygosity values and broad cross-species amplifications. The sixth microsatellite was found to be monomorphic in the olive ridley samples but was polymorphic in two related marine turtle species. These microsatellites thus provide efficient genetic markers to understand the population structure, phylogeography and species relationships of olive ridley and other marine turtle species. [source] Brief communication: Allelic and haplotypic structure at the DRD2 locus among five North Indian caste populationsAMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue 4 2010Kallur N. Saraswathy Abstract 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. Am J Phys Anthropol, 2010. © 2010 Wiley-Liss, Inc. [source] Bioinformatic mining of EST-SSR loci in the Pacific oyster, Crassostrea gigasANIMAL GENETICS, Issue 3 2008Y. Wang Summary A set of expressed sequence tag-simple sequence repeat (EST-SSR) markers of the Pacific oyster, Crassostrea gigas, was developed through bioinformatic mining of the GenBank public database. As of June 30, 2007, a total of 5132 EST sequences from GenBank were downloaded and screened for di-, tri- and tetra-nucleotide repeats, with criteria set at a minimum of 5, 4 and 4 repeats for the three categories of SSRs respectively. Seventeen polymorphic microsatellite markers were characterized. Allele numbers ranged from 3 to 10, and the observed and expected heterozygosity values varied from 0.125 to 0.770 and from 0.113 to 0.732 respectively. Eleven loci were at Hardy,Weinberg equilibrium (HWE); the other six loci showed significant departure from HWE (P < 0.01), suggesting possible presence of null alleles. Pairwise check of linkage disequilibrium (LD) indicated that 11 of 136 pairs of loci showed significant LD (P < 0.01), likely due to HWE present in single markers. Cross-species amplification was examined for five other Crassostrea species and reasonable results were obtained, promising usefulness of these markers in oyster genetics. [source] | ||||||||||