Search results for "LOCUS"

Second generation sequencing of three STRs D3S1358, D12S391 and D21S11 in Danes and a new nomenclature for sequenced STR alleles

2014

Second generation sequencing (SGS) may revolutionize the field of forensic STR typing. Two of the essential requirements for implementation of an SGS based approach for forensic investigations are (1) establishment of adequate frequency databases and (2) adoption of a new STR nomenclature. We report the STR sequences and allele frequencies of three STR loci: D3S1358, D12S391 and D21S11 in 197 unrelated Danes. We used a new STR nomenclature that depicts the locus name used in forensic genetics, the length of the repeat region divided by the repeat length (typically 4 nucleotides) and detailed sequence information of possible sub-repeats and SNPs within the amplified fragment.

Primers for nine microsatellite loci in the hermaphroditic snailLymnaea stagnalis

2003

Variation in and amplification conditions for nine polymorphic microsatellite loci identified from Lymnaea stagnalis , a hermaphroditic pulmonate snail, are described. Eight populations from central Finland were studied, which varied in terms of both observed polymorphism and heterozygosity. The number of alleles at each locus is moderate (two to seven), except for one exceptional locus having 16 alleles, and for which null alleles are possible. There is no evidence for genotypic disequilibrium in the populations for all pairs of loci. Heterozygosity levels are indicative of outcrossing in L. stagnalis , whose mating system will be characterized further using these markers.

Distortion of symmetrical introgression in a hybrid zone: evidence for locus-specific selection and uni-directional range expansion

2006

The fate of species integrity upon natural hybridization depends on the interaction between selection and dispersal. The relative significance of these processes may be studied in the initial phase of contact before selection and gene flow reach equilibrium. Here we study a hybrid zone of two salamander species, Lyciasalamandra antalyana and Lyciasalamandra billae, at the initial phase of hybridization. We quantify the degree and mode of introgression using nuclear and mtDNA markers. The hybrid zone can be characterized as an abrupt transition zone, the central hybrid zone being only c. 400 m, but introgressed genes were traced up to 3 km. Introgression was traced in both sexes but gene flo…

Development and characterization of microsatellite markers in the Colorado potato beetle, Leptinotarsa decemlineata

2006

The characterization of 11 Leptinotarsa decemlineata microsatellite loci isolated using the fast isolation by AFLP of sequences containing repeats (FIASCO) protocol is reported. Three to 15 alleles per locus were detected in 54 beetles collected from four populations of L. decemlineata. The mean number of alleles was 7.4 ± 3.2 and the level of expected heterozygosity ranged from 0.451 to 0.798. The total exclusionary probabilities using these loci for the first and the second parent were 0.982 and 0.999, respectively. These are the first microsatellite loci characterized from the Colorado potato beetles that can be used for estimating genetic diversity, population structure and parentage an…

Chimerism and genetic diversity within the cultivar group of pinots

2002

Three clones of Vitis vinifera cv. pinot gris were analysed at 50 microsatellite loci to assess the presence of intra-varietal genetic variability. Two clones revealed a polymorphism expressed by the presence of three alleles at 5 loci instead of the two expected for a diploid species. By sequencing the three alleles amplified at two loci, we confirm that they correspond to different allelic states of the same locus but differ in their number of repeat units. Such tri-allelic profiles could reveal periclinal chimeras in which the two cell layers of the apical meristem are genetically different. For two clones, this periclinal chimeric state has been deduced from the comparison of the genoty…

Morphological characteristics, microsatellite fingerprinting and determination of incompatibility genotypes of Sicilian sweet cherry cultivars

2007

Sicily has extensive germplasm of diploid sweet cherry (Prunus avium L.) that has not been well studied. In this investigation, 39 cherry accessions, selected from collections and farms, were analysed using molecular markers and characterised for various morphological and other agronomic characters such as flesh colour, fruit size, quality and, in some cases, ripening periods. Thirteen Simple Sequence Repeat (SSR) primer pairs, as well as two primer pairs for the incompatibility (S) locus, which amplified across the first intron of the S-RNase gene and across the intron of the SFB gene, were used in three multiplexed reactions to analyse the accessions. The number of alleles per SSR locus r…

Sequence characterization of the melanocortin 1 receptor (MC1R) gene in sheep with different coat colour and identification of the putative e allele …

2010

Abstract Sequence of the melanocortin 1 receptor (MC1R) gene (the Extension locus) was obtained from a panel of 73 animals belonging to 9 Italian sheep breeds or populations (Appenninica, Bergamasca, Comisana, Cornigliese-like, Delle Langhe, Massese, Merinizzata Italiana, Sarda and Valle del Belice) with different coat colours. Evaluation of the identified polymorphisms on this phenotype was reported with in silico predictions and comparative approaches within and across breeds and across species. Five novel single nucleotide polymorphisms (SNPs), organized in three haplotypes, were detected. Another haplotype, including the two missense mutations already described for the ED allele, was id…

Localization of MRX82: A new nonsyndromic X-linked mental retardation locus to Xq24-q25 in a Basque family

2004

Clinical and molecular studies are reported on a Basque family (MRX82) with nonsyndromic X-linked mental retardation (XLMR) in five affected males. A total of 38 microsatellite markers were typed. The XLMR locus has been linked to DXS8067, DXS1001, DXS425, DXS7877, and DXS1183 with a maximum LOD score of 2.4. The haplotype studies and multipoint linkage analysis suggest a localization of the MRX82 locus to an interval of 7.6 Mb defined by markers DXS6805 and DXS7346, in Xq24 and Xq25, respectively. No gene contained in this interval has been so far associated with nonsyndromic mental retardation, except for GRIA3, disrupted by a balanced translocation in a female patient with bipolar affect…

102 NOVEL SUSCEPTIBILITY LOCI FOR PRIMARY SCLEROSING CHOLANGITIS IDENTIFIED BY GENOME-WIDE ASSOCIATION AND REPLICATION ANALYSIS

2011

Validation and casework testing of the BioPlex-11 for STR typing of telogen hair roots.

2005

A new STR typing strategy has been developed allowing the simultaneous amplification and subsequent analysis of 11 polymorphic systems with amplicon sizes smaller than 270 bp. The multiplex amplification reaction includes six STR loci from the European standard set of loci (ESS) for DNA databases (D3S1358, D8S1179, D21S11, THO1, FGA and VWA) as well as four additional STR systems selected for their robustness (D2S1338, D12S391, TPOX and D5S818) together with the sex-specific locus amelogenin. After PCR amplification, the multiplex reaction is splitted into two sets of STR multiplexes by using biotin labelled primers only for one set. Using streptavidin-coated Sepharose beads five STR system…