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1

Combining microsatellite and pedigree data to estimate relationships among Skyros ponies

100%
Bomcke E., Gengler N.
Journal of Applied Genetics
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2009
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vol. 50
|
issue 2
133-143
EN
The main objective of this study was to develop a new method to estimate relationship coefficients by combining molecular with pedigree data, which is useful for specific situations where neither pedigree nor molecular data are complete. The developed method was applied to contribute to the conservation of the Skyros pony breed, which consists of less than 200 individuals, divided into 3 main herds or subpopulations. In this study, relationships between individuals were estimated using traditional estimators as well as the newly developed method. For this purpose, 99 Skyros ponies were genotyped at 16 microsatellite loci. It appeared that the limitation of the most common molecular-based estimators is the use of weights that assume relationships equal to 0. The results showed that, as a consequence of this limitation, negative relationship values can be obtained in small inbred populations, for example. By contrast, the combined estimator gave no negative values. Using principal component analysis, the combined estimator also enabled a better graphic differentiation between the 3 subpopulations defined previously. In conclusion, this new estimator can be a promising alternative to traditionally used estimators, especially in inbred populations, with both incomplete pedigree and molecular information.
2

Horse breed discrimination using machine learning methods

100%
Burocziova M., R?ha J.
Journal of Applied Genetics
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2009
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vol. 50
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issue 4
375-377
EN
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.
3

Divergent selection for skeletal malformations in chickens alters polymorphism at microsatellite loci

100%
Wardecka B., Jaszczak K., Pierzchala M., Parada R., Korczak M.
Journal of Applied Genetics
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2004
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vol. 45
|
issue 1
61-71
EN
The objective of this study was to determine microsatellite polymorphism in Rhode Island Red (RIR) and Sussex (SX) chickens, divergently selected over six generations for high (H) or low (L) incidence of skeletal defects in embryos (30.7% for H lines, 3.7% for L lines). The polymorphism analysis covered 15 microsatellite markers within four lines (a total of 60 individuals). Eight alleles were identified as specific to H lines and six alleles as specific to L lines. The selection for skeletal malformation appears to have affected the frequency of microsatellite alleles. The experimental material examined constitutes a valuable source for identification of real genes causing skeletal defects.
4

Haplotypes of microsatellite markers of the CFTR gene in Polish and German CF chromosomes suggest an ancient origin of the most frequent cystic fibrosis mutations

100%
Witt M., Varon M. R., Reis A., Rutkiewicz E.
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issue 3
329-334
EN
In this study we have analysed haplotypes of microsatellite markers of the CFTR gene: IVS8CA, IVS17BTA, IVS17BCA in 17 CF chromosomes of Polish origin and in 19 chromosomes of German origin bearing CF mutations other than DF508. In the Polish population, the G542X mutation is connected with haplotypes 16/17 28/32/38 13; in the German population, a more diverse haplotype association has been detected (23 33 13 and 16 32 13). The 1717 1G >A mutation is associated with the 15/16 7 13 haplotype in the Polish population, like the G551D mutation in Germany. The only analysed case of N1303K of Polish origin is connected with the 23 30 13 haplotype, like in the German population. One N1303K chromosome of an entirely different haplotype (16 29 17) turned out to be of Greek origin. These data suggest an ancient, Palaeolithic or Neolithic origin of these mutations in the territory of current Northern Europe.
5

Genetic variation of Polish endangered Bilgoraj horses and two common horse breeds in microsatellite loci

100%
Zabek T., Nogaj A., Radko A., Nogaj J., Slota E.
Journal of Applied Genetics
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2005
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vol. 46
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issue 3
295-305
EN
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.
6

Evaluation of the genetic profile of the Pulawska breed

100%
Babicz M., Kuryl J., WalkiewiczA.
Journal of Applied Genetics
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2003
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vol. 44
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issue 4
497-508
EN
An assessment was made of the genetic variation of the Pulawska pig through the determination of polymorphism of 6 genes and 14 microsatellite sequences. The examinations covered 52 gilts included in a preservation breeding project. The identification of the alleles at microsatellite loci was performed in an ABI PRISM 310 GENETIC ANALYZER. Gene polymorphism was established by the PCR-RLFP method. On the basis of the variation of 6 genes and 14 microsatellites the mean value of the heterozygosity coefficient was estimated at 0.61, while the value of the corresponding PIC coefficient (polymorphism information content) amounted to 0.55. The probability that the genotypes of two randomly chosen individuals in a population are identical was: 6.95 ? 10?3 (based on gene allele frequency) and 1.23 ? 10?14 (based on microsatellite allele frequency).
7

DNA microsatellite analysis in families with autosomal dominant polycystic kidney disease (ADPKD): the first Polish study

100%
Binczak-Kuleta A., Rozanski J., Domanski L., Myslak M., Ciechanowski K., Ciechanowicz A.
Journal of Applied Genetics
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2006
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vol. 47
|
issue 4
383-389
EN
Autosomal dominant polycystic kidney disease (ADPKD) is one of the most common inherited renal disorders with genetic heterogeneity. Mutations of two known genes are responsible for this disease: PKD1 at 16p13.3 and PKD2 at 4q21?23. A majority of cases (85%) are caused by mutations in PKD1. Because direct mutation screening remains complex, we describe here the application of an efficient approach to studies based on highly informative dinucleotide and tetranucleotide repeats flanking genes PKD1 and PKD2. Methods: For this study a series of microsatellites closely linked to locus PKD1 (D16S291, D16S663, D16S665, D16S283, D16S407, D16S475) and to locus PKD2 (D4S1563, D4S2929, D4S414, D4S1534, D4S423) were selected. Short (81-242 bp) DNA fragments containing the tandem repeats were amplified by polymerase chain reaction (PCR). The number of repeat units of microsatelite markers was determined by fluorescent capillary electrophoresis. DNA microsatellite analysis was performed in 25 Polish ADPKD families and established the type of disease (21 families PKD1-type, 1 family PKD2-type). While a disease-causing mutation in the PKD1 and PKD2 genes cannot be identified, DNA microsatellite analysis provided an early diagnosis and may be considered in ADPKD families.
8

Polymorphism of nine canine-derived microsatellites in farm silver foxes (Vulpes fulvus)

88%
Zajac M., Klukowska J., Slomski R., Switonski M.
Journal of Applied Genetics
|
2000
|
vol. 41
|
issue 1
43-50
EN
Polymorphism of nine canine-derived microsatellites (CPH1, CPH3, CPH6, CPH11, 2004, 2010, 2140,2168 and 2319) was studied in a group of 91 unrelated silver foxes kept on a commercial farm. Among the studied microsatellites two appeared to be dimorphic (CPH1 and 2140) and another two (2010 and 2319) were highly polymorphic, with PIC (Polymorphic Information Content) values of 0.775 and 0.692, respectively. Other five microsatellites demonstrated medium polymorphism and the PIC values ranged from 0.548 to 0.616. It was calculated that if all the studied markers were applied for paternity testing, then combined exclusion probability would be 0.989. Microsatellite polymorphisms in the silver fox, blue fox and dog were compared and tendency toward longer alleles in the dog was revealed. It was confirmed that canine-derived microsatellites can be successfully applied for parentage control and genome mapping in silver foxes.
9

Bi-paternal litter in Finn raccoon (Nyctereutes procyonoides Gray 1834) detected by polymorphic DNA markers

88%
Slaska B., Jezewska G.
Folia Biologica
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2008
|
vol. 56
|
issue 3-4
193-195
EN
The present paper demonstrates novel results confirming the phenomenon of multipaternity in Finn raccoons. The purpose of the study was to affirm the occurrence of bi-paternal litters in Finn raccoons using polymorphic microsatellite markers. The study was carried out on 37 Finn raccoon females, males that mated with them and the resulting offspring (176 individuals). The offspring came from females mating with two or three different males during one estrus. Parentage testing of 15microsatellites was used inthe present study. Based on genetic analysis including the control of the origin of the Finn raccoons, it was observed that in the case of double-mating with two different males, as well as triple-mating with three different males, there were 47.06% and 54.55%, respectively, of maternal half-sibs, i.e., animals born in one litter but with different fathers. Paternity was wrongly ascribed in 18.2% of the offspring in the examined Finn raccoon population. The conducted research indicates a necessity to check the origin of young animals selected for breeding stock in Finn raccoon breeding farms.
10

Usefulness of microsatellite markers in identification of family members carrying a mutation of the b-myosin heavy chain gene in families with hypertrophic cardiomyopathy

88%
Smolik S., Domal-Kwiatkowska D.-K. D., Domal-Kwiatkowska D., Mazurek M. U., Mazurek U., Moric M. E., Moric E., Nowalany-Kozielska N.-K. E., Nowalany-Kozielska E., Glanowska G. G., Glanowska G., Kozakiewicz K. K., Kozakiewicz K., Wodniecki W. J., Wodniecki J., Tendera T. M., Tendera M., Wilczok W. T., Wilczok T.
Journal of Applied Genetics
|
2000
|
vol. 41
|
issue 3
199-208
EN
Familial hypertrophic cardiomyopathy (FHC) is characterised by autosomal dominant transmission, left ventricular hypertrophy and myocardial disarray. Genetic assessment is of special importance in this disease. Missense mutations of the gene coding for the b-myosin heavy chain (bMHC) have been identified as statistically the most important cause of the disease. Identification of specific mutations may be difficult, thus a simpler method of disease carrier identification is needed. We performed haplotype analysis of six Polish families (47 individuals) with three microsatellite markers located at the bMHC locus. Linkage of the disease locus to the bMHC gene was excluded in 4 out of the 6 families analysed. In 2 families particular haplotypes were coinherited with the disease phenotype. Microsatellite markers allowed identification of 2 carriers of the disease gene in these families among children of the patients.
11

Polymorphism of the porcine growth hormone gene and its linkage to hormone gene and its linkage to microsatellites S0083 and S0090

88%
Korwin-Kossakowska A., Pierzchala M., Kuryl J., Zwierzchowski L., Cymerowska-Prokopczyk I., SiadkowskaE.
|
1999
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vol. 40
|
issue 2
85-91
EN
Polymorphism of microsatellites S0083 and S0090 as well as of the second exon and second intron of the pGH (porcine growth hormone) gene was determined for 293 pedigrees obtained from crossing of 12 F1 (Zlotnicka Spotted x Polish Large White) boars with 64 F1 (Zlotnicka Spotted x Polish Large White) sows, experimental material arranged for a QTL mapping project. Microsatellites were genotyped by capillary electrophoresis of PCR products in an ABI PRISM 310 Genetic Analyser PERKIN-ELMER. The PCR-RFLP polymorphism of the GH gene was identified using HaeII and MspI restriction endonucleases. The following order of linked loci was established: GH-S0083-S0090. This is important information for the mapping of QTLs on chromosome 12.
12

Relationship between microsatellite marker alleles on chromosomes 1-5 originating from the Rhode Island Red and Green-legged Partrigenous breeds and egg production and quality traits in F2 mapping population

88%
Wardecka B., Olszewski R., Jaszczak K., Zieba G., Pierzchala M., Wicinska K.
|
EN
The objective of this study was to determine the relationship between the origin of marker alleles from the Rhode Island Red (RIR) and Green-legged Partrigenous (GlP) breeds and chosen egg production and quality traits in F2 generation consisting of 10 full-sib families. Polymorphism analysis of 23 microsatellite markers within the mapping population (519 F2) was made. In parental generation 17 alleles were identified as specific for the GlP and 23 for the RIR. The least squares method was used to evaluate the significance of effects of genotype (GlP/GlP, RIR/RIR, GlP/RIR) on the analysed quantitative traits. Thirty traits of egg production and quality were measured during the laying period. It was shown that the effects of the genotype (GlP/GlP, RIR/RIR, GlP/RIR) at the loci on analysed traits of F2 animals were diversified. Significant effects were found for 16 traits. These results confirm that the analysed microsatellite loci may be linked to the genes affecting egg production and quality traits. The loci examined and the experimental population constitutes a valuable material for QTL mapping (linkage analysis).
13

Microsatellite DNA polymorphism divergence in Chinese wheat (Triticum aestivum L.) landraces highly resistant to Fusarium head blight

88%
Wei Y.-M., Hou Y.-C., Yan Z.-H., Wu W., Zhang Z.-Q., Liu D.-C., Zheng Y.-L.
Journal of Applied Genetics
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2005
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vol. 46
|
issue 1
3-9
EN
Genetic differences between 20 Chinese wheat (Triticum aestivum L.) landraces highly resistant to Fusarium head blight (FHB) and 4 wheat lines highly susceptible to FHB were evaluated by means of microsatellite markers, in order to select suitable parents for gene mapping studies. Thirty-nine out of 40 microsatellite markers (97.5%) were polymorphic among the 24 wheat genotypes. A total of 276 alleles were detected at the 40 microsatellite loci. The number of alleles per locus ranged from 1 to 16, with an average of 6.9 alleles. Among these microsatellite loci, the largest polymorphism information content (PIC) value was 0.914 (GWM484), while the lowest PIC value was 0 (GWM24). The mean genetic similarity index among the 24 genotypes was 0.419, ranging from 0.103 to 0.673. Clustering analysis indicated that the highly susceptible synthetic wheat line RSP was less genetically related to and more divergent from the Chinese highly resistant landraces. These results were useful in the identification of suitable parents for the development of mapping populations for tagging the FHB resistance genes among these Chinese wheat landraces.
14

Variety discrimination in pea (Pisum sativum L.) by molecular, biochemical and morphological markers

63%
Smykal P., Horacek J., Dostalova R., Hybl M.
Journal of Applied Genetics
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2008
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vol. 49
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issue 2
155-166
EN
The distinctness, uniformity and stability (DUS) requirements involve expensive, space- and time-consuming measurements of morphological traits. Moreover, for a majority of traits, interactions between genotype and environment complicate the evaluation. Molecular markers have a potential to facilitate this procedure, increase the reliability of decisions, and substantially save the time and space needed for experiments. We chose 25 varieties of pea (Pisum sativum L.) from the list of recommended varieties for cultivation in the Czech Republic, and made both a standard classification by 12 morphological descriptors and a classification by biochemical-molecular markers. Two isozyme systems, 10 microsatellite loci, 2 retrotransposons for multilocus inter-retrotransposon amplified polymorphism (IRAP), and 12 retrotransposon-based insertion polymorphism (RBIP) DNA markers were analysed. The main objective of the study was to examine the potential of each method for discrimination between pea varieties. The results demonstrate a high potential and resolving power of DNA-based methods. Superior in terms of high information content and discrimination power were SSR markers, owing to high allelic variation, which was the only biochemical-molecular method allowing clear identification of all varieties. Retrotransposon markers in RBIP format proved to be the most robust and easy to score method, while multilocus IRAP produced informative fingerprint already in a single analysis. Isozyme analysis offered a fast and less expensive alternative. The results showed that molecular identification could be used to assess distinctness and complement morphological assessment, especially in cases where the time frame plays an important role. Currently developed pea marker systems might serve also for germplasm management and genetic diversity studies.
15

High-quality plant DNA extraction for PCR: an easy approach

63%
Ahmed I., Islam M., Arshad W., Mannan A., Ahmad W., Mirza B.
Journal of Applied Genetics
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2009
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vol. 50
|
issue 2
105-107
EN
Polymerase chain reaction has found wide applications in modern research involving transformations and other genomic studies. For reproducible PCR results, however, the quantity and quality of template DNA is of considerable importance. A simple and efficient plant DNA extraction procedure for isolation of high-quality DNA from plant tissues is presented here. It requires maceration of plant tissue of about 1.0/ cm2 (e.g. of a leaf blade) in DNA extraction buffer (100 mM Tris-HCl, 100 mM EDTA, 250 mM NaCl) using 1.5-mL microfuge tubes, followed by cell lysis with 20% SDS, and DNA extraction with phenol: chloroform: iso-amyl alcohol (25:24:1). Hydrated ether is then used to remove polysaccharides and other contaminants from the DNA preparation. Average DNA yield is 20-30 mug/ cm2 for fresh tissues, and ratio of absorbance at 260 nm to absorbance at 280 nm is 1.5-1.8. The DNA is quite suitable for PCR using microsatellites, RAPD and specific markers for recombinant selection. Amplifications have been obtained for these markers by using template DNA extracted from fresh as well as frozen leaf tissues of various plants, including barley, oat, potato and tomato. DNA stored for more than 2 years has been successfully amplified with microsatellite markers, which shows suitability of this method after long-term storage of DNA. Besides, the ease of use and cost-effectiveness make the procedure attractive.
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