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1.
As a consequence of the close integration of horses into human society, equine DNA analysis has become relevant for forensic purposes. However, the information content of the equine Short Tandem Repeat (STR) loci commonly used for the identification or paternity testing has so far not been fully characterized. Population studies were performed for 17 polymorphic STR loci (AHT4, AHT5, ASB2, ASB17, ASB23, CA425, HMS1, HMS2, HMS3, HMS6, HMS7, HTG4, HTG6, HTG7, HTG10, LEX3 and VHL20) including 8641 horses representing 35 populations. The power of parental exclusion, polymorphic information content, expected and observed heterozygosity and probability of identity were calculated, showing that the set of 17 STRs has sufficient discriminating power for forensic analysis in almost all breeds. We also explored the reliability of individual assignment tests in identifying the correct breeds of origin for unknown samples. The overall proportion of individuals correctly assigned to a population was 97.2%. Finally, we demonstrate the phylogenetic signal of the 17 STR. We found three clusters of related breeds: (i) the cold-blooded draught breeds Haflinger, Dutch draft and Friesian; (ii) the pony breeds Shetland and Miniature horse with the Falabella, Appaloosa and Icelandic; and (iii) The Warmblood riding breeds, together with the hot-blooded Standard-bred, Thoroughbred and Arabian. 相似文献
2.
In this study, a proposal is presented for the allele nomenclature of 16 polymorphic short tandem repeat (STR) loci ( BM1824 , BM2113 , ETH10 , ETH225 , INRA023 , SPS115 , TGLA122 , TGLA126 , TGLA227 , ETH3 , TGLA53 , BM1818 , CSRM60 , CSSM66 , HAUT27 and ILSTS006 ) for bovine genotyping ( Bos taurus ). The nomenclature is based on sequence data of the polymorphic region(s) of the STR loci as recommended by the DNA commission of the International Society of Forensic Genetics for human DNA typing. To cover commonly and rarely occurring alleles, a selection of animals homozygous for the alleles at these STR loci were analysed and subjected to sequence studies. The alleles of the STR loci consisted either of simple or compound dinucleotide repeat patterns. Only a limited number of alleles with the same fragment size showed different repeat structures. The allele designation described here was based on the number of repeats including all variable regions within the amplified fragment. The set of 16 STR markers should be propagated for the use in all bovine applications including forensic analysis. 相似文献
3.
Genetic variation of endangered Bi?goraj horses and two common Polish horse breeds was compared with the use of 12 microsatellite loci (AHT4, AHT5, ASB2, HMS2, HMS3, HMS6, HMS7, HTG4, HTG6, HTG7, HTG10, VHL20). Lower allelic diversity was detected in all investigated populations in comparison to other studies. Large differences in the frequencies of microsatellite alleles between Bi?goraj horses and two other horse breeds were discovered. In all polymorphic loci all investigated breeds were in the Hardy-Weinberg equilibrium. Mean Fis values and the results of a test for the presence of a recent bottleneck were non-significant in all studied populations. Comparable values of observed and expected gene diversity indicate no substantial loss of genetic variation in the Bi?goraj population and two other breeds. The lowest variability observed in the investigated group of Thoroughbred horses was confirmed. About 10% of genetic variation are explained by differences between breeds. Values of pairwise Fst and two measures of genetic distance demonstrated that Bi?goraj horses are distantly related to both common horse breeds. 相似文献
4.
To determine the genetic diversity and validate the pedigree record of Chinese Guanzhong horse, 67 individuals were genotyped with eight microsatellite markers. In our study, the mean observed and expected heterozygosities were 0.51 and 0.66, respectively. The mean observed number of alleles for the Guanzhong horse was 3.88. Nonetheless, the total value of FST multiloci clearly indicates that about 0.5% of overall genetic variation is due to line founder differences, while differences among individuals are responsible for the remaining 99.5%. In addition, the polymorphic information content (PIC) result showed that five loci (HTG7, HMS7, HMS2, AHT4, and HMS6) were highly polymorphic (PIC?>?0.5) and three loci (HMS3, HTG6, and COR071) were moderate polymorphic (PIC?>?0.25). Genetic distances and cluster analysis showed that the genetic relationship among 67 Guanzhong horse was generally consistent with pedigree recorded. Our results not only evaluated the genetic diversity of Chinese Guanzhong horse, but also suggested that the eight microsatellite markers might be used as subservient markers for parentage verification and individual identification in the Guanzhong horse. 相似文献
5.
Genetic relationships and population structure of 8 horse breeds in the Czech and Slovak Republics were investigated using
classification methods for breed discrimination. To demonstrate genetic differences among these breeds, we used genetic information
— genotype data of microsatellite markers and classification algorithms — to perform a probabilistic prediction of an individual’s
breed. In total, 932 unrelated animals were genotyped for 17 microsatellite markers recommended by the ISAG for parentage
testing (AHT4, AHT5, ASB2, HMS3, HMS6, HMS7, HTG4, HTG10, VHL20, HTG6, HMS2, HTG7, ASB17, ASB23, CA425, HMS1, LEX3). Algorithms
of classification methods — J48 (decision trees); Naive Bayes, Bayes Net (probability predictors); IB1, IB5 (instance-based
machine learning methods); and JRip (decision rules) — were used for analysis of their classification performance and of results
of classification on this genotype dataset. Selected classification methods (Naive Bayes, Bayes Net, IB1), based on machine
learning and principles of artificial intelligence, appear usable for these tasks. 相似文献
6.
Machado FB de Vasconcellos Machado L Bydlowski CR Bydlowski SP Medina-Acosta E 《Molecular biology reports》2012,39(2):1447-1452
Validation of parentage and horse breed registries through DNA typing relies on estimates of random match probabilities with
DNA profiles generated from multiple polymorphic loci. Of the twenty-seven microsatellite loci recommended by the International
Society for Animal Genetics for parentage testing in Thoroughbred horses, eleven are located on five chromosomes. An important
aspect in determining combined exclusion probabilities is the ascertainment of the genetic linkage status of syntenic markers,
which may affect reliable use of the product rule in estimating random match probabilities. In principle, linked markers can
be in gametic phase disequilibrium (GD). We aimed at determining the extent, by frequency and strength, of GD between the
HTG4 and HMS3 multiallelic loci, syntenic on chromosome 9. We typed the qualified offspring (n
1 = 27; n
2 = 14) of two Quarter Bred stallions (registered by the Brazilian Association of Quarter Horse Breeders) and 121 unrelated
horses from the same breed. In the 41 informative meioses analyzed, the frequency of recombination between the HTG4 and HMS3
loci was 0.27. Consistent with genetic map distances, this recombination rate does not fit to the theoretical distribution
for independently segregated markers. We estimated sign-based D′ coefficients as a measure of GD, and showed that the HTG4 and HMS3 loci are in significant, yet partial and weak, disequilibrium,
with two allele pairs involved (HTG4*M/HMS3*P, D′(+) = 0.6274; and HTG4*K/HMS3*P, D′(−) = −0.6096). These results warn against the inadequate inclusion of genetically linked markers in the calculation of combined
power of discrimination for Thoroughbred parentage validation. 相似文献
7.
Li SL Yamamoto T Yoshimoto T Uchihi R Mizutani M Kurimoto Y Tokunaga K Jin F Katsumata Y Saitou N 《Human genetics》2006,118(6):695-707
We have analyzed 105 autosomal polymorphic short tandem repeat (STR) loci for nine East and South-eastern Asian populations
(two Japanese, five Han Chinese, Thai, and Burmese populations) and a Caucasian population using a multiplex PCR typing system.
All the STR loci are genomewide tetranucleotide repeat markers of which the total number of observed alleles and the observed
heterozygosity were 756 and 0.743, respectively, for Japanese populations. Phylogenetic analysis for these allele frequency
data suggested that the Japanese populations are more closely related with southern Chinese populations than central and/or
northern ones. STRUCTURE program analysis revealed the almost clearly divided and accountable population structure at K=2–6, that the two Japanese populations always formed one group separated from the other populations and never belong to different
groups at K≥3. Furthermore, our new allele frequency data for 91 loci were analyzed with those for 52 worldwide populations published
by previous studies. Phylogenetic and multidimensional scaling (MDS) analyses indicated that Asian populations with large
population size (six Han Chinese, three Japanese, two Southeast Asia) formed one distinct cluster and are closer to each other
than other ethnic minorities in east and Southeast Asia. This pattern may be the caviar of comparing populations with greatly
differing population sizes when STR loci were analyzed. 相似文献
8.
The immunopolymorphism database (IPD) provides a single nomenclature for alleles at the major histocompatibility complex (MHC)
loci for a range of different species. The minimum requirements for inclusion of a sheep class II DRB1 sequence is a submission that includes all polymorphic sites within the second exon from at least two independent polymerase
chain reactions (PCR). In order to meet these requirements, we have developed a DNA-based genotyping method for the rapid
analysis of allelic diversity at the DRB1 locus in domestic sheep, Ovis aries. Using a series of primers located within introns flanking exon 2 and genomic DNA from a cohort of 214 sheep representing
15 different breeds and crossbreeds, the complete exon 2 sequences of 38 Ovar-DRB1 alleles were obtained. This sequence resource allowed the development of a generic set of locus-specific primers which amplify
a fragment that includes all polymorphic sites within the second exon. Bidirectional sequence analysis of the PCR product
provides a composite sequence where each polymorphic site is represented by the corresponding International Union of Biochemistry
nucleotide code. A Basic Local Alignment Search Tool search of alleles held within the IPD or National Center for Biotechnology
Information databases allows individual allele sequences to be identified. Low levels of homozygosity (7.48%) within the cohort
and verification of previously genotyped samples confirmed the broad allelic specificity of this method. It improves on currently
available methods and is broadly applicable to the analysis of MHC diversity in studies investigating linkages with resistance
or susceptibility to disease. 相似文献
9.
T. A. Borodina D. V. Ivanov E. K. Khusnutdinova V. A. Spitsyn A. V. Baranova N. K. Yankovsky 《Russian Journal of Genetics》2001,37(1):102-104
Using polymerase chain reaction (PCR) DNA samples of unrelated subjects from the Volga-Ural region of Russia were examined to study allele polymorphism of the pentanucleotide repeat (TTGTG)
g
localized to an intron of the tumor suppressor gene ING1. STR marker was registered in the EMBL database with the accession number AJ277387. In a sample of 119 individuals, three pentanucleotide alleles consisting of seven, eight, and nine repeated monomers were revealed. The allele frequencies were 0.24, 0.74, and 0.02, respectively. Heterozygosity was 0.45. On the basis of these data, the repeat can be regarded as a polymorphic STR marker for the ING1 gene and used in population and clinical studies. 相似文献
10.
Yoo SY Cho NS Park MJ Seong KM Hwang JH Song SB Han MS Lee WT Chung KW 《Molecules and cells》2011,32(1):15-19
Genotyping of highly polymorphic short tandem repeat (STR) markers is widely used for the genetic identification of individuals
in forensic DNA analyses and in paternity disputes. The National DNA Profile Databank recently established by the DNA Identification
Act in Korea contains the computerized STR DNA profiles of individuals convicted of crimes. For the establishment of a large
autosomal STR loci population database, 1805 samples were obtained at random from Korean individuals and 15 autosomal STR
markers were analyzed using the AmpFlSTR Identifiler PCR Amplification kit. For the 15 autosomal STR markers, no deviations
from the Hardy-Weinberg equilibrium were observed. The most informative locus in our data set was the D2S1338 with a discrimination
power of 0.9699. The combined matching probability was 1.521 × 10−17. This large STR profile dataset including atypical alleles will be important for the establishment of the Korean DNA database
and for forensic applications. 相似文献
11.
Primers were developed for 14 microsatellite or simple sequence repeat (SSR) loci identified from a Prunus avium‘Charger’ genomic DNA library. In a survey of 16 wild cherry accessions 10 of the loci revealed polymorphisms of between two and six alleles. The remaining loci were found to be monomorphic. Seven polymorphic loci identified in this study and four polymorphic loci previously reported in sweet cherry were mapped and found to be unlinked. Two multiplex polymerase chain reactions (PCR) were optimized to enable the characterization of all 11 unlinked, polymorphic SSR loci. 相似文献
12.
Seong Yeon Yoo Sang Hyun An Ji Hye Park Na Yeon Kim Young Ae Lee Jong Jin Kim Ki Won Park Ki Wha Chung 《Genes & genomics.》2014,36(3):355-363
Short tandem repeats (STRs) loci are very useful genomic markers with high power of individual discrimination, thus, they have been used for population genetics, forensic application and complex kinship analyses. In this study, we examined allele frequencies and forensic parameters for a total of 23 STR loci, that is, 17 established STRs with 13 CODIS core STR loci and D2S1338, D19S433, Penta E, and Penta D loci, and 6 new STRs (D10S1248, D22S1045, D2S441, D1S1656, D12S391, and SE33) in a sample of 545 unrelated individuals in South Korea. All loci were highly polymorphic and no significant departure from Hardy–Weinberg equilibrium was observed. The addition of 6 new loci to the 17 established STRs increased their power of discrimination by almost eight orders of magnitude (2.52 × 10?20–4.44 × 10?28) and improved the specificity of missing children database searches. Furthermore, we found several microvariant alleles at D2S441 and SE33 loci that have not been reported in the Korean population. We believe that this analysis will be useful for forensic application, deficiency paternity testing and expanding previously established Korean DNA databases. 相似文献
13.
CATHERINE J. HITCHCOCK SUSAN M. CHAMBERS JOHN W. G. CAIRNEY 《Molecular ecology resources》2006,6(2):443-445
Six polymorphic simple sequence repeat (SSR) markers were developed for the ectomycorrhizal fungus Pisolithus microcarpus. A polymerase chain reaction (PCR)‐based technique was used in which random amplified polymorphic DNA (RAPD) fingerprints were probed with labelled SSR oligonucleotides by southern hybridization. The number of alleles per locus ranged from two to nine with expected heterozygosity values from 0.33 to 0.76. These loci will be potentially useful for genetic structure and gene flow studies of P. microcarpus populations. Cross‐species amplification with Pisolithus albus isolates at all loci was also observed. 相似文献
14.
Limonium dufourii is an endemic plant from the eastern Mediterranean coast of Spain with a triploid chromosome number and apomictic reproduction. We have isolated and characterized 13 polymorphic microsatellite loci from an enriched library in order to investigate its population genetic structure. Simple sequence repeat (SSR) loci were screened in 120 individuals from the six extant populations of this species. They show an average of 5.76 alleles per locus, ranging from 2 to 18, with seven loci exhibiting heterozygosities larger than 0.60. Three loci present one single allele in each individual, whereas one locus presents three alleles in every individual analysed. 相似文献
15.
Kahraman Gürcan Shawn A. Mehlenbacher 《Molecular breeding : new strategies in plant improvement》2010,26(3):551-559
Polymorphic microsatellite markers were developed for European hazelnut (Corylus
avellana L.) from the sequences of inter-simple sequence repeat (ISSR) fragments and flanking regions. Twenty-five ISSR primers were
used to generate fragments for cloning. Of the 520 unique sequences obtained, 41 contained long internal repeats (≥20 bp)
with flanking sequences sufficient for primer design. From these, we developed 23 new polymorphic microsatellite loci. The
flanking sequences were obtained for fragment ends by chromosome walking, and an additional 47 polymorphic markers were developed.
Two additional polymorphic markers were developed from a GA-enriched library. The 72 new marker loci were characterized using
50 diverse hazelnut accessions. For the internal repeat loci, the number of alleles per locus ranged from 2 to 16, with a
mean of 7.52. Mean values for expected heterozygosity (He), observed heterozygosity (Ho), and polymorphism information content (PIC) were 0.62, 0.59, and 0.58, respectively. The estimated frequency of null alleles
(r) was ≥0.05 at six of the 23 loci. For the 47 marker loci developed from fragment ends, the number of alleles per locus ranged
from 2 to 16, with a mean of 7.30. Mean values for He, Ho, and PIC were 0.62, 0.47, and 0.58, respectively. The estimated frequency of null alleles (r) was ≥0.10 at 18 of the 47 loci. Of the 70 loci developed from ISSR and flanking sequences, 50 segregated in our mapping
population and were assigned to linkage groups. 相似文献
16.
Intrinsic polymorphism of variable number tandem repeat loci in the human genome. 总被引:1,自引:0,他引:1 下载免费PDF全文
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. 相似文献
17.
Eight short tandem repeat markers included in the International Society for Animal Genetics panel of 24 loci investigated in canine comparison tests were analysed in a sample of pure-breed dogs, with the purpose of defining an allele nomenclature based on the number of repeats. A regression analysis of the raw data produced by the sequencer, coupled with the direct sequencing of selected alleles, allowed us to propose a system of nomenclature for six of the eight loci (four di-nucleotidic: AHT121, AHTh137, REN169018 and REN64E19, and two tetra-nucleotidic: FH2001 and FH2328). The remaining two loci (INU055 and FH2848) showed a pattern of fragments that did not resolve in a simple allele series. This work may be useful to establish a basis for comparing data across different laboratories for a set of validated canine markers, which can be used in population genetics, forensics and other analyses. 相似文献
18.
The comparison of RFLP,RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis 总被引:71,自引:0,他引:71
Wayne Powell Michele Morgante Chaz Andre Michael Hanafey Julie Vogel Scott Tingey Antoni Rafalski 《Molecular breeding : new strategies in plant improvement》1996,2(3):225-238
The utility of RFLP (restriction fragment length polymorphism), RAPD (random-amplified polymorphic DNA), AFLP (amplified fragment length polymorphism) and SSR (simple sequence repeat, microsatellite) markers in soybean germplasm analysis was determined by evaluating information content (expected heterozygosity), number of loci simultaneously analyzed per experiment (multiplex ratio) and effectiveness in assessing relationships between accessions. SSR markers have the highest expected heterozygosity (0.60), while AFLP markers have the highest effective multiplex ratio (19). A single parameter, defined as the marker index, which is the product of expected heterozygosity and multiplex ratio, may be used to evaluate overall utility of a marker system. A comparison of genetic similarity matrices revealed that, if the comparison involved both cultivated (Glycine max) and wild soybean (Glycine soja) accessions, estimates based on RFLPs, AFLPs and SSRs are highly correlated, indicating congruence between these assays. However, correlations of RAPD marker data with those obtained using other marker systems were lower. This is because RAPDs produce higher estimates of interspecific similarities. If the comparisons involvedG. max only, then overall correlations between marker systems are significantly lower. WithinG. max, RAPD and AFLP similarity estimates are more closely correlated than those involving other marker systems.Abbreviations RFLP
restriction fragment length plymorphism
- RAPD
random-amplified polymorphic DNA
- AFLP
amplified fragment length polymorphism
- SSR
simple sequence repeat
- PCR
polymerase chain reaction
- TBE
Tris-borate-EDTA buffer
- MI
marker index
- SENA
sum of effective numbers of alleles 相似文献
19.
Thirty-four microsatellite DNA loci were developed for grass carp (Ctenopharyngodon idella) and used to determine the diversity of 42 individuals of grass carp and 16 individuals of black carp collected from Jingzhou
fragment (the middle reach) of Yangtze River. All the 34 loci were polymorphic in grass carp. The number of alleles found
in grass carp at these loci ranged from 2 to 24. The observed and expected heterozygosities varied from 0.238 to 1.000 and
from 0.162 to 0.945, respectively. Thirty of the 34 loci cross-amplified the DNA of black carp (Mylopharyngodon piceus), and 21 of them revealed polymorphism (more than one allele each locus). 相似文献
20.
Carriero F Fontanazza G Cellini F Giorio G 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2002,104(2-3):301-307
A small insert genomic library of Olea europaea L., highly enriched in (GA/CT)n repeats, was obtained using the procedure of Kandpal et al. (1994). The sequencing of 103 clones randomly extracted from
this library allowed the identification of 56 unique genomic inserts containing simple sequence repeat regions made by at
least three single repeats. A sample of 20 primer pairs out of the 42 available were tested for functionality using the six
olive varieties whose DNA served for library construction. All primer pairs succeeded in amplifying at least one product from
the six DNA samples, and ten pairs detecting more than one allele were used for the genetic characterisation of a panel of
20 olive accessions belonging to 16 distinct varieties. A total of 57 alleles were detected among the 20 genotypes at the
ten polymorphic SSR loci. The remaining primer pair allowed the amplification of a single SSR allele for all accessions plus
a longer fragment for some genotypes. Considering the simple sequence repeat polymorphism, 5.7 alleles were scored on average
for each of the ten SSR loci. A genetic dissimilarity matrix, based on the proportion of shared alleles among all the pair-wise
combinations of genotypes, was constructed and used to disentangle the genetic relationships among varieties by means of the
UPGMA clustering algorithm. Graphical representation of the results showed the presence of two distinct clusters of varieties.
The first cluster grouped the varieties cultivated on the Ionian Sea coasts. The second cluster showed two subdivisions: the
first sub-cluster agglomerated the varieties from some inland areas of Calabria; the second grouped the remaining varieties
from Basilicata and Apulia cultivated in nearby areas. Results of cluster analysis showed a significant relationship between
the multilocus genetic similarities and the geographic origin of the cultivars.
Received: 2 February 2001 / Accepted: 1 June 2001 相似文献