scholarly journals Allelic polymorphism of microsatelite DNA locі of egg chikens

2020 ◽  
pp. 22-27
Author(s):  
A.V. Shelyov ◽  
◽  
K.V. Kopylov ◽  
N.P. Prokopenko ◽  
S.S. Kramarenko ◽  
...  
Keyword(s):  
Data Analysis ◽  
International Society ◽  
Microsatellite Dna ◽  
Statistical Processing ◽  
Allelic Polymorphism ◽  
Specific Character ◽  
Allelic Variants ◽  
Mutation Model ◽  
Allelic Variability ◽  
Stepwise Mutation

The analysis of allelic polymorphism of five industrial egg crosses of chickens by five microsatellite DNA loci (ADL0268, MCW216, LEI0094, ADL0278, and MCW248) was carried out. DNA loci were chosen according to the recommendations of the International Society for Animal Genetics (ISAG). Based on the results of mathematical-statistical processing and data analysis, the spectra and frequencies of allelic variability, the peculiarities of allele pools, were identified, and unique alleles were identified. In general, the species Gallus gallus is characterized by a specific character of allelic spectra for all investigated microsatellite DNA loci (P <0.001). The highest rates of allelic variability were recorded in brown crosses "Lohmann brown" and "Hisex brown" (Na (LimNa)=(9.2 (5-17) and 7.4 (6-11), respectively). The studied crosses were characterized by a shift in allelic spectra towards a decrease in the fragment length. “Lohmann white” stands out among the birds of other crosses by high consolidation for individual alleles for all studied microsatellites (from ADL278114 – 0.343 and ADL268108 – 0.485 to LEI094259 – 0.720, MCW0248213 – 0.785 and MCW0216137 – 0.920). Unique alleles with the highest frequency were found in brown cross chickens, and in the “Hy-Line W-98” bird, they were not found. The number of unique alleles identified varied from 1 ("Hisex white") to 11 ("Lohmann brown"). Locus LEI094 turned out to be the most polymorphic in terms of the number of unique alleles – 10 such allelic variants were identified for it. No unique alleles were identified at the ADL0268 locus. The obtained estimates criterion χ2 of K. Pearson indicate significant differences in the frequency distribution of alleles for all studied loci. When using the MICROSATELLITE ANALYSER software, it was found that the nature of the variability of the studied microsatellite DNA loci in five industrial crosses of the egg chickens, both in the number of identified alleles and in the nature of their distribution, corresponded to the stepwise mutation model (SMM).

Expert survey and analysis of the results

2019 ◽  
Vol 85 (7) ◽  
pp. 73-82
Author(s):  
Vladimir O. Tolcheev
Keyword(s):  
Data Analysis ◽  
Research University ◽  
Statistical Processing ◽  
Educational Process ◽  
Expert Survey ◽  
Educational Modules ◽  
Training Modules ◽  
Engineering Institute ◽  
Good Agreement ◽  
Statistical Criteria

The issues of organizing an expert survey and carrying out statistical processing and analysis of the results are considered. The experts are the fifth-year students undergoing training at the Department of Management and Informatics «Moscow Power Engineering Institute» of the National Research University. The goal of the survey is revealing the disciplines that are most useful for employment in their specialty. We discuss the special features of the survey and a concept of «work in the specialty», with due regard for statistical reliability of the results. Data of written questionnaire gained in 2018 were processed and analyzed using cluster analysis (construction of dendrograms and application of the K-means method) and non-parametric statistical criteria (Friedman and Mann – Whitney – Wilcoxon). Data processing is implemented in the program STATISTICA. The analysis is carried out to reveal significant differences between the educational courses and assess the degree of consistency of the respondents to divide them into clusters that unite the students with similar judgments. Data analysis revealed that experts’ estimates in 2018 are in fairly good agreement with the estimates of previous studies; among the respondents there are three coalitions corresponding to the training modules «Software», «Management Theory», «Data Analysis»; the overall consistency of students in the two groups is very low (and, on the contrary, high in the identified clusters); grades are homogeneous and do not depend on training groups (and employment – unemployment of the respondents). The obtained results allow us to address a number of important questions regarding the ways of improving the educational process, e.g., to optimize yearly course hours for different educational modules.

ANALYSIS OF GENETIC STRUCTURE OF DOGS OF FRENCH BULLDOG BREED USING MICROSATELLITE DNA MARKERS

2018 ◽  
Vol 51 ◽  
pp. 185-192
Author(s):  
S. Kruhlyk ◽  
V. Dzitsiuk ◽  
V. Spyrydonov
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Dna Markers ◽  
Microsatellite Dna ◽  
High Variability ◽  
Molecular Diagnostic ◽  
Allelic Variants ◽  
Microsatellite Dna Markers ◽  
Gene Complexes ◽  
French Bulldog

Genetic variability of domestic dogs is a source for effective process of breed formation and creating unique gene complexes. In the world, for preservation of genetic resources of dogs, there are dog training associations which have great confidence: American Club Dog Breeders (AKC), the British Kennel Club (KC) and the Federation Cynologique Internationale (FCI), aimed at protecting breeding dogs, standards creation, registration of a breed, and issuance of accurate pedigrees. Evaluation of the genetic diversity of dog breeds is able to significantly complement and improve their breeding programs. Since breeds of dog differ in morphological and economic characteristics, the problem of finding of the breed features in the genome of animals is becoming more topical. From this point of view, French Bulldog is an interesting breed of dog (FRANC.BULLDOGGE, FCI standard number 101) which belongs by the classification of breeds, adopted in FCI, to the group IX – a dog-companion for health and fun, but to a subgroup of fighting dogs of a small format. French Bulldog breed has been researched slightly not only in Ukraine and also abroad, as the main work of all dog association is focused on solving theoretical and practical issues of breeding, keeping, feeding, veterinary protection and others. The study was conducted at Research Department of Molecular Diagnostic Tests of Ukrainian Laboratory of Quality and Safety of Agricultural Products. 33 animals of French Bulldog breed, admitted to use in dog breeding of Ukrainian Kennel Union (UKU), were involved for the genetic analysis using DNA markers. The materials of the research were buccal epithelial cells, selected before the morning feeding of animals by scraping mucous membrane of oral cavity with disposable, dry, sterile cotton swab. Genomic DNA was extracted using KIT-set of reagents for DNA isolation according to the manufacturer's instructions. PEZ1, PEZ3, PEZ6, PEZ8, FHC 2010, FHC 2054 markers, recommended by International Society for Animal Genetics (ISAG), ACN, КC and FCI, were used for research. As a result of research 25 alleles for all the loci were detected in the experimental sample of dogs. The average number of alleles at the locus Na, obtained by direct counting, was 4.16. The most polymorphic loci for this breed were PEZ6 and PEZ3 with 8 and 6 allelic variants. Monomorphic loci were PEZ8 and FHC 2054 which had 4 and 3 alleles and the lowest level of polymorphism was observed for PEZ 1 and FHC 2010 loci in which only 2 alleles were identified. On analyzing the molecular genetic characteristics of dogs of French Bulldog breed, we found a high variability of genotype on rare alleles, which included alleles: M, C, D, E, J, K, L, O, N and representing 60% of the total number of the identified alleles. C, D, E alleles for PEZ3 locus and O allele at PEZ6 locus are unique to the sampling of dogs because they are not repeated in other loci. Typical alleles: N, F, R, I, P, K, M are 40% of the total. But F, R alleles for PEZ3 locus and P allele for locus PEZ6 are not repeated either in standard allelic variants or in rare one, indicating a high information content of these alleles and loci to be used for further monitoring of allele pool, genetic certification and identification of dogs. Microsatellite DNA loci were analyzed as a result of investigations of French Bulldogs and the most informative: PEZ3, PEZ6 and PEZ8 were found, which have high efficiency in individual and breed certification of dogs due to high variability. These data allow further monitoring of the state of genetic diversity of the breed and the development of measures for improvement of breeding to preserve the structure of breeding material. The study of individual and population genetic variability is advisable to continue for breeding of French Bulldogs "in purity" and preserving valuable gene complexes. The results are the basis for further monitoring of the proposed informative panels of microsatellite DNA markers for genotyping dog of French Bulldog breed and their complex evaluation.

scholarly journals An evaluation of genetic distances for use with microsatellite loci.

Genetics ◽  
1995 ◽  
Vol 139 (1) ◽  
pp. 463-471 ◽  
Author(s):  
D B Goldstein ◽  
A Ruiz Linares ◽  
L L Cavalli-Sforza ◽  
M W Feldman
Keyword(s):  
Microsatellite Loci ◽  
Phylogenetic Reconstruction ◽  
Genetic Distances ◽  
Stepwise Mutation Model ◽  
Mutation Model ◽  
Stepwise Mutation ◽  
The Difference ◽  
Nei's Distance ◽  
Infinite Alleles Model ◽  
Overall Reliability

Abstract Mutations of alleles at microsatellite loci tend to result in alleles with repeat scores similar to those of the alleles from which they were derived. Therefore the difference in repeat score between alleles carries information about the amount of time that has passed since they shared a common ancestral allele. This information is ignored by genetic distances based on the infinite alleles model. Here we develop a genetic distance based on the stepwise mutation model that includes allelic repeat score. We adapt earlier treatments of the stepwise mutation model to show analytically that the expectation of this distance is a linear function of time. We then use computer simulations to evaluate the overall reliability of this distance and to compare it with allele sharing and Nei's distance. We find that no distance is uniformly superior for all purposes, but that for phylogenetic reconstruction of taxa that are sufficiently diverged, our new distance is preferable.

scholarly journals Dynamics of Microsatellite Divergence Under Stepwise Mutation and Proportional Slippage/Point Mutation Models

Genetics ◽  
2001 ◽  
Vol 159 (2) ◽  
pp. 839-852 ◽  
Author(s):  
Peter P Calabrese ◽  
Richard T Durrett ◽  
Charles F Aquadro
Keyword(s):  
Point Mutations ◽  
Genetic Distances ◽  
Mutational Bias ◽  
Human Populations ◽  
Mutation Model ◽  
Perfect Repeat ◽  
Stepwise Mutation ◽  
Equilibrium Distributions ◽  
Theoretical Results ◽  
Polymerase Slippage

Abstract Recently Kruglyak, Durrett, Schug, and Aquadro showed that microsatellite equilibrium distributions can result from a balance between polymerase slippage and point mutations. Here, we introduce an elaboration of their model that keeps track of all parts of a perfect repeat and a simplification that ignores point mutations. We develop a detailed mathematical theory for these models that exhibits properties of microsatellite distributions, such as positive skewness of allele lengths, that are consistent with data but are inconsistent with the predictions of the stepwise mutation model. We use our theoretical results to analyze the successes and failures of the genetic distances (δμ)2 and DSW when used to date four divergences: African vs. non-African human populations, humans vs. chimpanzees, Drosophila melanogaster vs. D. simulans, and sheep vs. cattle. The influence of point mutations explains some of the problems with the last two examples, as does the fact that these genetic distances have large stochastic variance. However, we find that these two features are not enough to explain the problems of dating the human-chimpanzee split. One possible explanation of this phenomenon is that long microsatellites have a mutational bias that favors contractions over expansions.

Allelic polymorphism of six microsatellite DNA Loci in populations of Sakha (Yakutia)

2011 ◽  
Vol 45 (2) ◽  
pp. 221-228 ◽  
Author(s):  
V. V. Zhirkova ◽  
S. A. Fedorova ◽  
V. L. Akhmetova ◽  
L. A. Zhivotovsky ◽  
E. K. Khusnutdinova
Keyword(s):  
Microsatellite Dna ◽  
Allelic Polymorphism

scholarly journals VNTR allele frequency distributions under the stepwise mutation model: a computer simulation approach.

Genetics ◽  
1993 ◽  
Vol 134 (3) ◽  
pp. 983-993 ◽  
Author(s):  
M D Shriver ◽  
L Jin ◽  
R Chakraborty ◽  
E Boerwinkle
Keyword(s):  
Tandem Repeats ◽  
Repeat Unit ◽  
Allele Size ◽  
Frequency Distributions ◽  
Mutation Model ◽  
Stepwise Mutation ◽  
One Step ◽  
Simulation Results ◽  
Summary Measures ◽  
The One

Abstract Variable numbers of tandem repeats (VNTRs) are a class of highly informative and widely dispersed genetic markers. Despite their wide application in biological science, little is known about their mutational mechanisms or population dynamics. The objective of this work was to investigate four summary measures of VNTR allele frequency distributions: number of alleles, number of modes, range in allele size and heterozygosity, using computer simulations of the one-step stepwise mutation model (SMM). We estimated these measures and their probability distributions for a wide range of mutation rates and compared the simulation results with predictions from analytical formulations of the one-step SMM. The average heterozygosity from the simulations agreed with the analytical expectation under the SMM. The average number of alleles, however, was larger in the simulations than the analytical expectation of the SMM. We then compared our simulation expectations with actual data reported in the literature. We used the sample size and observed heterozygosity to determine the expected value, 5th and 95th percentiles for the other three summary measures, allelic size range, number of modes and number of alleles. The loci analyzed were classified into three groups based on the size of the repeat unit: microsatellites (1-2 base pair (bp) repeat unit), short tandem repeats [(STR) 3-5 bp repeat unit], and minisatellites (15-70 bp repeat unit). In general, STR loci were most similar to the simulation results under the SMM for the three summary measures (number of alleles, number of modes and range in allele size), followed by the microsatellite loci and then by the minisatellite loci, which showed deviations in the direction of the infinite allele model (IAM). Based on these differences, we hypothesize that these three classes of loci are subject to different mutational forces.

scholarly journals THE STEPWISE MUTATION MODEL: AN EXPERIMENTAL EVALUATION UTILIZING HEMOGLOBIN VARIANTS

Genetics ◽  
1980 ◽  
Vol 94 (1) ◽  
pp. 185-201
Author(s):  
Paul A Fuerst ◽  
Robert E Ferrell
Keyword(s):  
Amino Acid ◽  
Electrophoretic Mobility ◽  
Tertiary Structure ◽  
Stepwise Mutation Model ◽  
Starch Gel Electrophoresis ◽  
Human Hemoglobin ◽  
Net Charge ◽  
Mutation Model ◽  
Stepwise Mutation ◽  
Hemoglobin Variants

ABSTRACT The stepwise mutation model of OHTA and KIMURA (1973) was proposed to explain patterns of genetic variability revealed by means of electrophoresis. The assumption that electrophoretic mobility was principally determined by unit changes in net molecular charge has been criticized by JOHNSON (1974, 1977). This assumption has been tested directly using hemoglobin. Twenty-seven human hemoglobin variants with known amino acid substitutions, and 26 nonhuman hemoglobins with known sequences were studied by starch gel electrophoresis. Of these hemoglobin% 60 to 70% had electrophoretic mobilities that could be predicted solely on the basis of net charge calculated from the amino acid composition alone, ignoring tertiary structure. Only four hemoglobins showed a mobility that was clearly different from an expected mobility calculated using only the net charge of the molecule. For the remaining 30% of hemoglobins studied, mobility was determined by a combination. of net charge and other unidentified components, probably reflecting changes in ionization of some amino acid residues as a result of small alterations in tertiary structure due to the amino acid substitution in the variant. For the nonhuman hemoglobins, the deviation of a sample from its expected mobility increased with increasing amino acid divergence from human hemoglobin A.—It is concluded that the net electrostatic charge of a molecule is the principal determinant of electrophoretic mobility under the conditions studied. However, because of the significant deviation from strict stepwise mobility detected for 30 to 40% of the variants studied, it is further concluded that the infinite-allele model of KIMURA and CROW (1964) or a "mixed model" such as that proposed by LI (1976) may be more appropriate than the stepwise mutation model for the analysis of much of the available electrophoretic data from natural populations.

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