GENETIC ANALYSIS GERMAN SHEPHERD BREED DOGS USING MICROSATELLITE DNA MARKERS

2016 ◽  
Vol 52 ◽  
pp. 166-171
Author(s):  
V. V. Dzitsiuk ◽  
S. G. Kruhlyk ◽  
V. G. Spyrydonov
Keyword(s):  
Genetic Diversity ◽  
Genetic Analysis ◽  
Microsatellite Markers ◽  
Dna Markers ◽  
Microsatellite Loci ◽  
Genetic Evaluation ◽  
German Shepherd ◽  
Genetic Characteristics ◽  
Expected Heterozygosity ◽  
The Impact

Modern methods of breeding dogs are based on getting of stable phenotypic uniformity by using close inbreeding or breeding by one line, but such strategy leads to a loss of genetic diversity, and as a result there are genetic defects in breeds which have no external manifestations or manifest in adulthood of dogs and are transmitted from generation to generation. Therefore, to prevent use of dogs with genetic abnormalities in breeding, and to develop standards for a breed and make an accurate pedigree, must carry out the genetic evaluation of animals. One of the modern tools for dogs’ genetic evaluation is DNA-testing using microsatellite loci permitting to match the parental couple effectively, identify (to certify) animals, undertake a comprehensive assessment for heterozygous and homozygous genotypes in populations, permitted for use in the selection process, and illustrate clearly the impact of artificial selection on the genetic characteristics of breeds. The study was conducted in Ukrainian Laboratory of Quality and Safety of Agricultural Products in Department of Molecular Biology Research. For the genetic analysis 42 German Shepherd dogs, used for breeding in kennels of Ukrainian Kennel Union (UKU), were selected. The material for the research was DNA isolated from dogs’ buccal epithelium cells and blood. Genomic DNA was extracted using a standard set of reagents for DNA isolation. Level of theoretically expected heterozygosity (Hexp) varied between 0.385 (PEZ1) to 0.835 (PEZ8). On average theoretically expected heterozygosity with coefficient of 0.657 had not significant advantage over value of actual heterozygosity (0.629), it also shows that the status of the sample of dogs is close to balance. The same is observed in actual and expected heterozygosity for PEZ 6 (0.629) and PEZ 8 (0.657) loci, which also shows the balance. For FHC2010 loci actual heterozygosity is higher than expected, indicating increasing the number of heterozygous individuals. For FHC2054 locus, by contrast, theoretically expected heterozygosity (0.670) dominates the actual (0.429), indicating the lack of heterozygous genotypes in this micropopulation. The value of PIC (polymorphism information content) of the analysed loci ranged from 0.325 to 0.740 with average value 0.574. PEZ6, PEZ8, FHC 2010 and FHC 2054 loci optimally meets their suitability for genetic certification of genotypes because their frequency varies from 0.587 to 0.740. The reduced average index of polymorphism for PEZ1 locus with coefficient of 0.325 confirmed the insufficient level of its polymorphism for full genetic evaluation of the micropopulation of German Shepherd dogs (PIC < 0.500), as confirmed by Chinese researcher J.-H. Ye, according to his data PIC value for PEZ1 locus was 0,320, which correlates with our results. And PIC value for PEZ8 locus was 0.740 in our studies, whereas according to J.-H. Ye – 0,720, which, by contrast, indicates high polymorphism and confirms the effectiveness of its use in genotyping of dogs. Probability of exclusion of accidental allele coincidence (PE), which is 0.675 on average, indicates a lack of the number and informativeness of the selected microsatellite markers for German Shepherd as in this case a combined probability (CPE) of accidental allele coincidence is 0.933886 or 93.3%. The chosen microsatellite loci to study the genetic structure of the German Shepherd dog population, show a sufficiently high informativeness of chosen system of molecular genetic DNA markers. However, there is the need for using additional microsatellite markers which will increase the combined probability of accidental allele coincidence (CPE) from 93.3% to 99.9%. The analysis of heterozygosity is important in studying the dynamics of genetic processes in populations, because heterozygosity has an effect on many factors, including mutations, selection, non-random mating, genetic drift, etc., so continuous monitoring of genetic diversity is required for their timely identification and development of measures to improve breeding work on biodiversity in different dog breeds.

scholarly journals Development of microsatellite markers for the Japanese endemic conifer Thuja standishii and transfer to other East Asian species

2019 ◽  
Author(s):  
James Raymond Peter Worth ◽  
K. S. Chang ◽  
Y.-H. Ha ◽  
Aili Qin
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Microsatellite Loci ◽  
East Asian ◽  
Clonal Reproduction ◽  
Sister Species ◽  
Asian Species ◽  
Expected Heterozygosity ◽  
Polymorphic Microsatellite ◽  
Diversity Structure

Abstract Objective: Design polymorphic microsatellite loci that will be useful for studies of the genetic diversity, structure and reproduction in the Japanese endemic conifer Thuja standishii and test the transferability of these loci to the two other East Asian species, T. sutchuenensis and T. koraiensis . Results: Fifteen loci were developed which displayed 3 to 21 alleles per locus (average = 9.2) among 97 samples from three populations of T. standishii . Observed heterozygosity for all samples varied between 0.33-0.75 (average 0.54) while expected heterozygosity values were higher with an average over the 15 loci of 0.62 (0.37-0.91). Low multi-locus probability of identity values (< 0.00001) indicate that these markers will be effective for identifying individuals derived from clonal reproduction. All 15 loci amplified in 13 samples of T. sutchuenensis , the sister species of T. standishii , with 1 to 11 alleles per locus (average = 4.33) while 13 loci amplified in four samples of the more distantly related T. koraiensis with 1 to 5 alleles per locus (average = 2.15).

scholarly journals Interspecies and intraspecies genetic diversity of Ongole Grade cattle and Madura cattle based on microsatellite DNA markers

2018 ◽  
Vol 19 (4) ◽  
pp. 1593-1600
Author(s):  
SUTARNO . ◽  
NINA KURNIANINGRUM ◽  
ELISA HERAWATI ◽  
AHMAD DWI SETYAWAN
Keyword(s):  
Genetic Diversity ◽  
Dna Sequences ◽  
Dna Markers ◽  
Microsatellite Loci ◽  
Microsatellite Dna ◽  
Polymorphic Information Content ◽  
Entire Genome ◽  
Genetic Characteristics ◽  
Microsatellite Dna Markers ◽  
The Mean

Sutarno, Kurnianingrum N, Herawati E, Setyawan AD. 2018. Interspecies and intraspecies genetic diversity of Ongole Gradecattle and Madura cattle based on microsatellite DNA markers. Biodiversitas 19: 1593-1600. DNA microsatellite has been extensivelyemployed for estimating the degree of kinship between genotypes and improving the quality of cattle products. Microsatellite markersare short-patterned DNA sequences and repeated tandem (sequentially) with 2-5 nucleotide units scattering the entire genome. Thepurpose of this study was to investigate the genetic characteristics of inter and intraspecies of Ongole Grade cattle and Madura cattleusing microsatellite DNA markers. Blood samples from 20 individuals of each species were extracted by the method referring to WizardGenomic DNA Purification Kit (Promega, USA) and PCR amplification was performed using 5 microsatellite loci, i.e., BM1824,ETH225, INRA005, MM12, and TGLA227. Results of the genetic characteristics of both species were calculated using the POPGENEprogram version 1.31. The data suggest that there is a genetic diversity of inter and intraspecies of Ongole Grade cattle and Maduracattle. The average value of Shannon's Information Index (I) at all microsatellite loci for Ongole Grade cattle was 0.76 and for Maduracattle was 1.12. Meanwhile, the average interspecies I value was 1.03. The mean intraspecies Polymorphic Information Content (PIC) ofOngole Grade and Madura cattle was 0.43, and 0.63, respectively, and the mean interspecies PIC value was 0.57. The data altogethersuggest that all loci meet the standards as being informative markers in the assessment of genetic population because it has a PIC value>0.5 especially for intraspecies of Madura cattle.

Genetic analysis of ten sheep breeds using microsatellite markers

2000 ◽  
Vol 80 (1) ◽  
pp. 9-17 ◽  
Author(s):  
A. Farid ◽  
E. O'Reilly ◽  
C. Dollard ◽  
C.R. Kelsey Jr.
Keyword(s):  
North America ◽  
Genetic Variability ◽  
Genetic Analysis ◽  
Genetic Distance ◽  
Microsatellite Markers ◽  
Microsatellite Loci ◽  
Narrow Range ◽  
The Other ◽  
The North ◽  
Expected Heterozygosity

The genetic variability of 257 sheep from 10 breeds; North Country Cheviot (NCC), Cheviot (CHE), Dorset (DOR), Suffolk (SUF), Scottish Blackface (SBF), Texel (TEX), Romanov (ROM), Finnish Landrace (FIN), Icelandic (ICE) and Red Masai (MAS) was assessed using 10 microsatellite loci. The average number of alleles per locus was 4.3 in ROM, 5.0 in MAS, and spanned a narrow range (5.4 to 6.0) in the other breeds. Estimates of expected heterozygosity (HE) of the breeds varied within 0.05 point of each other (0.62 in FIN to 0.67 in CHE), except for ROM (0.53) which was lower (P < 0.05) than those of the other breeds, and in MAS (0.57), which was lower (P < 0.05) than those of NCC, CHE and SBF. Estimates of observed heterozygosity (HO) of the breeds were the lowest in MAS, ROM and SUF (0.50 to 0.53) and the highest in NCC and CHE (0.64 and 0.67). The HE was greater (P < 0.01) than HO only in SUF. The results suggest that there have not been drastic losses of genetic variability in the intensely selected breeds. The low genetic variability of ROM was probably due to a small number of animals imported to North America. The British breeds (NCC, CHE, SUF, DOR, SBF) were genetically close to each other, as were the North European breeds (ROM, ICE, FIN). MAS was remotely related to the British breeds, but it was surprisingly close to the North European breeds. TEX was more closely related to the British breeds than to the North European breeds. More than 90% of 1000 simulated individuals from each breed were assigned to the correct breed, indicating that this panel of markers is useful for the identification of breed membership of individual animals, and could be used to protect the integrity of registered breeds. Key words: Sheep, genetic variability, genetic distance, microsatellites

scholarly journals Development of microsatellite markers for the Japanese endemic conifer Thuja standishii and transfer to other East Asian species

2019 ◽  
Author(s):  
James Raymond Peter Worth ◽  
K. S. Chang ◽  
Y.-H. Ha ◽  
Aili Qin
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Microsatellite Loci ◽  
East Asian ◽  
Clonal Reproduction ◽  
Sister Species ◽  
Asian Species ◽  
Expected Heterozygosity ◽  
Polymorphic Microsatellite ◽  
Diversity Structure

Abstract Objective: Design polymorphic microsatellite loci that will be useful for studies of the genetic diversity, structure and reproduction in the Japanese endemic conifer Thuja standishii and test the transferability of these loci to the two other East Asian species, T. sutchuenensis and T. koraiensis . Results: Fifteen loci were developed which displayed 3 to 21 alleles per locus (average = 9.2) among 97 samples from three populations of T. standishii . Observed heterozygosity for all samples varied between 0.33-0.75 (average 0.54) while expected heterozygosity values were higher with an average over the 15 loci of 0.62 (0.37-0.91). Low multi-locus probability of identity values (< 0.00001) indicate that these markers will be effective for identifying individuals derived from clonal reproduction. All 15 loci amplified in 13 samples of T. sutchuenensis , the sister species of T. standishii , with 1 to 11 alleles per locus (average = 4.33) while 13 loci amplified in four samples of the more distantly related T. koraiensis with 1 to 5 alleles per locus (average = 2.15).

scholarly journals Cross-Species Amplification of Microsatellite Loci for the Endangered Conifer, Taxus chinensis var. mairei (Taxaceae)

2012 ◽  
Vol 61 (1-6) ◽  
pp. 287-291 ◽  
Author(s):  
Y. Wen ◽  
K. Uchiyama ◽  
G. Xu ◽  
S. Ueno ◽  
W. Han ◽  
...  
Keyword(s):  
Endangered Species ◽  
Genetic Analysis ◽  
Microsatellite Markers ◽  
Microsatellite Loci ◽  
Rare Species ◽  
Null Allele ◽  
Null Alleles ◽  
Taxus Chinensis ◽  
Congeneric Species ◽  
Expected Heterozygosity

AbstractBeing an economical and endangered species, microsatellite markers of Taxus chinensis var. mairei were very limited. We have developed a set of microsatellite markers, which was benefit for future genetic analysis of this rare species. Polymorphic loci were developed from congeneric species by cross-species amplification methods, and new primers were redesigned to test for potential null alleles. 15 loci showed polymorphism. The number of alleles per locus varied from 2 to 23 tested in 48 individuals. The observed heterozygosity (Ho) and expected heterozygosity (He) values ranged form 0.000 to 0.854 and 0.082 to 0.827, respectively. Newly redesigned primer confirmed that no null allele existed in most suspected loci. These microsatellite markers will be useful for future genetic analysis and conservation of this endangered species.

scholarly journals Development of microsatellite markers for the Japanese endemic conifer Thuja standishii and transfer to other East Asian species

2019 ◽  
Author(s):  
James Raymond Peter Worth ◽  
K. S. Chang ◽  
Y.-H. Ha ◽  
Aili Qin
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Microsatellite Loci ◽  
East Asian ◽  
Clonal Reproduction ◽  
Sister Species ◽  
Asian Species ◽  
Expected Heterozygosity ◽  
Polymorphic Microsatellite ◽  
Diversity Structure

Abstract Objective Design polymorphic microsatellite loci that will be useful for studies of the genetic diversity, structure and reproduction in the Japanese endemic conifer Thuja standishii and test the transferability of these loci to the two other East Asian species, T. sutchuenensis and T. koraiensis. Results Fifteen loci were developed which displayed 3 to 21 alleles per locus (average = 9.2) among 97 samples from three populations of T. standishii . Observed heterozygosity for all samples varied between 0.33-0.75 (average 0.54) while expected heterozygosity values were higher with an average over the 15 loci of 0.62 (0.37-0.91). Low multi-locus probability of identity values (< 0.00001) indicate that these markers will be effective for identifying individuals derived from clonal reproduction. All 15 loci amplified in T. sutchuenensis, the sister species of T. standishii, with 1 to 11 alleles per locus (average = 4.33) while 13 loci amplified in the more distantly related T. koraiensis with 1 to 5 alleles per locus (average = 2.15).

scholarly journals Development of EST microsatellite markers for the Tasmanian palaeoendemic conifer Lagarostrobos franklinii (Hook. f.) Quinn (Podocarpaceae)

2020 ◽  
Vol 69 (1) ◽  
pp. 1-5
Author(s):  
James R. Marthick ◽  
Matthew J. Larcombe ◽  
James R. P. Worth
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Expressed Sequence Tag ◽  
Genetic Studies ◽  
Expected Heterozygosity ◽  
Rnaseq Data ◽  
Lagarostrobos Franklinii ◽  
The Impact ◽  
Expressed Sequence

AbstractNuclear Expressed Sequence Tag (EST) microsatellite markers were developed for the Tasmanian palaeoendemic conifer Lagarostrobos franklinii (Hook.-f.) Quinn for genetic studies. RNAseq data was mined for EST microsatellites, and primer pairs were synthesised from 70 contigs with 50 producing amplification products. Of these 50, 10 reliably amplified and displayed polymorphism across 8 samples representing the entire species range. The genetic diversity of these 10 loci was then examined in three wild populations (84 samples). The number of alleles varied from two to thirteen per locus with the average number of alleles per population ranging between 3.0 – 4.7. Observed and expected heterozygosity ranged from 0.34 – 0.42 and 0.37 – 0.44, respectively. Marker cross-amplification was tested in the New Zealand sister species Manoao colensoi (Hook. f.) Molloy, but no markers amplified reliably, which possibly reflects the age of divergence between these species (~64 million years). These are the first microsatellite markers developed for the monotypic genus Lagarostrobos. They will be valuable for assessing the species extant genetic diversity, the impact of past climatic perturbations and human disturbance and the role of clonal propagation in recruitment.

scholarly journals Development of microsatellite markers for the Japanese endemic conifer Thuja standishii and transfer to other East Asian species

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
James R. P. Worth ◽  
K. S. Chang ◽  
Y.-H. Ha ◽  
Aili Qin
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Microsatellite Markers ◽  
Microsatellite Loci ◽  
East Asian ◽  
Clonal Reproduction ◽  
Sister Species ◽  
Asian Species ◽  
Expected Heterozygosity ◽  
Polymorphic Microsatellite

Abstract Objective Design polymorphic microsatellite loci that will be useful for studies of the genetic diversity, gene-flow and reproduction in the Japanese endemic conifer Thuja standishii and test the transferability of these loci to the two other East Asian species, T. sutchuenensis and T. koraiensis. Results Fifteen loci were developed which displayed 3 to 21 alleles per locus (average = 9.2) among 97 samples from three populations of T. standishii. Observed heterozygosity for all samples varied between 0.33 and 0.75 (average = 0.54) while expected heterozygosity values were higher with an average over the 15 loci of 0.62 (0.37–0.91). Low multi-locus probability of identity values (< 0.00002) indicate that these markers will be effective for identifying individuals derived from clonal reproduction. All 15 loci amplified in 13 samples of T. sutchuenensis, the sister species of T. standishii, with 1 to 11 alleles per locus (average = 4.33) while 13 loci amplified in four samples of the more distantly related T. koraiensis with 1 to 5 alleles per locus (average = 2.15).

Genetic Diversity of Six Duck Populations in India

2021 ◽  
Author(s):  
P. Veeramani ◽  
R. Prabakaran ◽  
S.N. Sivaselvam ◽  
T. Sivakumar ◽  
S.T. Selvan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Microsatellite Loci ◽  
Tamil Nadu ◽  
Expected Number ◽  
Pekin Ducks ◽  
Expected Heterozygosity ◽  
Chicken Population ◽  
The Mean ◽  
Substantial Degree

Background: The variety of indigenous duck germplasm contribute maximum to the poultry industry in India, besides chicken population. In southern part of India, the available duck genetic resource, particularly Arni ducks (comprises of Sanyasi and Keeri ducks) of Tamil Nadu, has its own characteristics with innate potentiality of higher productivity without any input system of management. Genetic characterization and diversity of indigenous duck genetic resources has not been properly studied. In the present study, the genetic diversity of Arni ducks with other indigenous and exotic duck germplasm were analysed with microsatellite markers. Method: Genomic DNA was isolated from the blood samples of six duck populations. Molecular characterization was carried out with duck specific FAO recommended microsatellite markers. The genotyping of ducks was done based on the size of 4324 PCR amplicons of 23 microsatellite loci, which were subjected to capillary electrophoresis using automatic sequencer.Result: A total of 222 alleles in six duck populations across 23 microsatellite loci with a mean of 9.65 ± 0.95 alleles were found. Kuttanad duck variety had the highest number of alleles (139) followed by Sanyasi (136), Keeri (129), Muscovy (118), Assam (91) and White Pekin (78) ducks. The mean observed number of alleles was 6.04 ± 0.59, 5.91 ± 0.76, 5.61 ± 3.17, 5.13 ± 0.44, 3.96 ± 0.76 and 3.39 ± 0.40 in Kuttanad, Sanyasi, Keeri, Muscovy, Assam and White Pekin ducks respectively. The overall mean polymorphism information content (PIC) values among the six duck populations was 0.6269. In most of the duck populations, the mean PIC value was more than 0.5 except in Assam (0.4815) and White Pekin (0.3725) ducks. The observed heterozygosity was the highest in Keeri ducks (0.5217) and lowest in White Pekin ducks (0.2766), while, the mean expected heterozygosity was the highest in Sanyasi (0.5628) and lowest in White Pekin (0.4038) ducks. The variations in the observed and expected number of alleles, differences in PIC of various microsatellite loci might be attributed to the genetic variability of the duck populations, number and type of microsatellite primers utilised for analysis and the genetic diversity of the duck breeds under study. Higher FST value indicates the substantial degree of breed differentiation among the studied duck populations.

scholarly journals Genetic diversity and population structure of date palms (Phoenix dactylifera L.) in Ethiopia using microsatellite markers

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Workia Ahmed ◽  
Tileye Feyissa ◽  
Kassahun Tesfaye ◽  
Sumaira Farrakh
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Microsatellite Markers ◽  
Information Content ◽  
Date Palm ◽  
Polymorphic Information Content ◽  
Phoenix Dactylifera ◽  
Mean Value ◽  
Date Palms ◽  
Expected Heterozygosity

Abstract Background Date palm tree (Phoenix dactylifera L.) is a perennial monocotyledonous plant belonging to the Arecaceae family, a special plant with extraordinary nature that gives eminent contributions in agricultural sustainability and huge socio-economic value in many countries of the world including Ethiopia. Evaluation of genetic diversity across date palms at DNA level is very important for breeding and conservation. The result of this study could help to design for genetic improvement and develop germplasm introduction programmes of date palms mainly in Ethiopia. Results In this study, 124 date palm genotypes were collected, and 10 polymorphic microsatellite markers were used. Among 10 microsatellites, MPdCIR085 and MPdCIR093 loci showed the highest value of observed and expected heterozygosity, maximum number of alleles, and highest polymorphic information content values. A total of 112 number of alleles were found, and the mean number of major allele frequency was 0.26, with numbers ranging from 0.155 (MPdCIR085) to 0.374 (MPdCIR016); effective number of alleles with a mean value of 6.61, private alleles ranged from 0.0 to 0.65; observed heterozygosity ranged from 0.355 to 0.726; expected heterozygosity varied from 0.669 to 0.906, polymorphic information content with a mean value of 0.809; fixation index individuals relative to subpopulations ranged from 0.028 for locus MPdCIR032 to 0.548 for locus MPdCIR025, while subpopulations relative to total population value ranged from − 0.007 (MPdCIR070) to 0.891 (MPdCIR015). All nine accesstions, neighbour-joining clustering analysis, based on dissimilarity coefficient values were grouped into five major categories; in population STRUCTURE analysis at highest K value, three groups were formed, whereas DAPC separated date palm genotypes into eight clusters using the first two linear discriminants. Principal coordinate analysis was explained, with a 17.33% total of variation in all populations. Generally, the result of this study revealed the presence of allele variations and high heterozygosity (> 0.7) in date palm genotypes. Conclusions Microsatellites (SSR) are one of the most preferable molecular markers for the study of genetic diversity and population structure of plants. In this study, we found the presence of genetic variations of date palm genotypes in Ethiopia; therefore, these genetic variations of date palms is important for crop improvement and conservation programmes; also, it will be used as sources of information to national and international genbanks.

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