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 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 Genetic diversity and relationships of Chinese donkeys using microsatellite markers

2019 ◽  
Vol 62 (1) ◽  
pp. 181-187 ◽  
Author(s):  
Lulan Zeng ◽  
Ruihua Dang ◽  
Hong Dong ◽  
Fangyu Li ◽  
Hong Chen ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Genetic Relationships ◽  
Mean Value ◽  
Principal Coordinates Analysis ◽  
Expected Heterozygosity ◽  
Principal Coordinates ◽  
Baseline Information ◽  
Grouping Pattern ◽  
The Mean

Abstract. Donkeys are one important livestock in China because of their nourishment and medical values. To investigate the genetic diversity and phylogenetic relationships of Chinese donkey breeds, a panel of 25 fluorescently labeled microsatellite markers was applied to genotype 504 animals from 12 Chinese donkey breeds. A total of 226 alleles were detected, and the expected heterozygosity ranged from 0.6315 (Guanzhong) to 0.6999 (Jiami). The mean value of the polymorphism information content, observed number of alleles, and expected number of alleles for all the tested Chinese donkeys were 0.6600, 6.890, and 3.700, respectively, suggesting that Chinese indigenous donkeys have relatively abundant genetic diversity. Although there were abundant genetic variations found, the genetic differentiation between the Chinese donkey breeds was relatively low, which displayed only 5.99 % of the total genetic variance among different breeds. The principal coordinates analysis clearly splits 12 donkey breeds into two major groups. The first group included Xiji, Xinjiang, Liangzhou, Kulun, and Guanzhong donkey breeds. In the other group, Gunsha, Dezhou, Biyang, Taihang, Jiami, Qingyang, and Qinghai donkeys were clustered together. This grouping pattern was further supported by structure analysis and neighbor-joining tree analysis. Furthermore, genetic relationships between different donkey breeds identified in this study were corresponded to their geographic distribution and breeding history. Our results provide comprehensive and precise baseline information for further research on preservation and utilization of Chinese domestic donkeys.

scholarly journals Genetic diversity of different breeds of Kazakh sheep using microsatellite analysis

2019 ◽  
Vol 62 (1) ◽  
pp. 305-312
Author(s):  
Kairat Dossybayev ◽  
Zarina Orazymbetova ◽  
Aizhan Mussayeva ◽  
Naruya Saitou ◽  
Rakhymbek Zhapbasov ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Microsatellite Loci ◽  
Allelic Diversity ◽  
Genetic Distances ◽  
Sheep Breed ◽  
Expected Heterozygosity ◽  
The Mean ◽  
High Level ◽  
Short Tandem

Abstract. A total of 75 individuals from five sheep populations in Kazakhstan were investigated based on 12 STR (short tandem repeat, also known as microsatellite) markers in order to study their genetic structure and phylogenetic relationship based on genetic distances. These sheep had a high level of genetic diversity. In total, 163 alleles were found in all the populations using 12 microsatellite loci. The mean number of alleles, effective number of alleles, and polymorphism information content (PIC) values per loci were 13.4, 5.9, and 0.78, respectively. Comparing the allelic diversity between the populations, the highest genetic diversity was observed in the Edilbay-1 sheep breed (8.333±0.644), and the lowest parameter was for Kazakh Arkhar-Merino (7.083±0.633). In all populations, there is a deficiency of heterozygosity. The largest genetic diversity was found in loci INRA023 and CSRD247 with 16 alleles, and the smallest polymorphism was noted for the locus D5S2 with 8 alleles. The level of observed heterozygosity was in the range 0.678±0.051 for Kazakh Arkhar-Merino and 0.767±0.047 for Kazakh fat-tailed coarse wool. The expected heterozygosity level range was from 0.702±0.033 for Kazakh Arkhar-Merino to 0.777±0.023 for Edilbay-1. When 12 microsatellite loci are compared, the OarFCB20 locus showed the highest level of genetic variability. Excess of heterozygosity was observed at three loci; MAF065, McM042, and OarFCB20. The highest genetic distance was observed between Kazakh Arkhar-Merino and Edilbay-1, whereas the genetic distance between Edilbay-1 and Edilbay-2 is the smallest using Nei's standard genetic distance. The Edilbay-1 sheep breed possesses the largest genetic diversity among these five populations.

scholarly journals Evaluation of genetic diversity and population structure of five Chinese indigenous donkey breeds using microsatellite markers

2017 ◽  
Vol 62 (No. 5) ◽  
pp. 219-225 ◽  
Author(s):  
R. Di ◽  
Q.Y. Liu ◽  
F. Xie ◽  
W.P. Hu ◽  
X.-Y. Wang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Microsatellite Markers ◽  
Principal Component ◽  
Principal Component Analysis Plot ◽  
Animal Conservation ◽  
Mean Values ◽  
Expected Heterozygosity ◽  
The Mean ◽  
Near Future

China had the largest population of raising donkeys in the world, however the number of Chinese indigenous donkey decreased dramatically due to the increase of agriculture mechanization in the last century. The species has still been important in China because of its edible and medical value, therefore the survey on its genetic diversity in China is necessary for its conservation and utilization. In this study, 15 microsatellite markers were used to evaluate genetic diversity and population structure of five Chinese indigenous donkey breeds. The mean values of expected heterozygosity, allelic richness, and total number of alleles for all the tested Chinese donkeys were 0.70, 6.04, and 6.28 respectively, suggesting that the genetic diversity of Chinese indigenous donkeys is rich. The Bayesian analysis and principal component analysis plot yielded the same clustering result, which revealed that Guanzhong donkey was the most differentiated breed in all detected samples, and Jinnan (JN) and Guangling (GL) were genetically closed together. Additionally, our results indicated that the heterozygote deficit was severe in two Chinese indigenous donkey breeds (GL and JN), and it warned us that animal conservation activities on this species should be considered carefully in near future.

scholarly journals Genetic diversity of Tibetan goats of Plateau type using microsatellite markers

2011 ◽  
Vol 54 (2) ◽  
pp. 188-197 ◽  
Author(s):  
Y. Wang ◽  
J. Wang ◽  
X.-D. Zi ◽  
C.-R. Huatai ◽  
X. Ouyang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Information Content ◽  
Microsatellite Loci ◽  
Polymorphism Information Content ◽  
The Other ◽  
Allele Number ◽  
The Mean ◽  
Black Goat ◽  
Historical Origins

Abstract. The 10 microsatellite markers (XBM7, XBM11, XBM16, XBM19, XBM24, XBM31, XBM84, TGLA53, SRCRSP-10 and ILS005) were selected to investigate the genetic diversity of Tibetan goat of Plateau type (NM, n=108), and the other 5 goat populations, i.e., Tibetan goat of Valley type (TG, n=36), Baiyu black goat (BY, n=36), Jianchang black goat (JC, n=36), Meigu goat (MG, n=36) and Xinjiang goat (XJ, n=32) were served as control. The mean polymorphism information content, heterozygosity and effective allele number of these 6 populations were 0.660/0.777/4.476, 0.716/0.797/4.9416, 0.631/0.673/3.061, 0.649/0.680/3.125, 0.629/0.680/3.125 and 0.561/0.793/4.840 respectively. The allele frequencies of Tibetan goat of plateau type in 10 microsatellite loci were greatly different with other 5 goat populations. The 6 goat populations were grouped into three distinct clusters: the Tibetan goat cluster (NM goat and TG goat), Sichuan goat cluster (JC goat, MG goat and BY goat), and Xinjiang goat cluster (XJ goat). These 3 distinct clusters were finally clustered together. The genetic differences among populations were in accordance with their geographical and historical origins.

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 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 Microsatellite based genetic variation among the buffalo breed populations in Pakistan

2017 ◽  
Vol 61 (4) ◽  
pp. 535-542 ◽  
Author(s):  
Tanveer Hussain ◽  
Masroor Ellahi Babar ◽  
Akhtar Ali ◽  
Asif Nadeem ◽  
Zia Ur Rehman ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Polymorphic Information Content ◽  
Mean Value ◽  
Diversity Analysis ◽  
Phenotypic Differentiation ◽  
Genetic Diversity Analysis ◽  
Expected Heterozygosity ◽  
The Mean ◽  
Average Gene

AbstractIntroduction: Eight microsatellite loci were used to define genetic diversity among five native water buffalo breeds in Pakistan.Material and Methods: Blood samples (10 mL) from 25 buffaloes of each of the Nili, Ravi, Nili-Ravi, Kundhi, and Azi-Kheli breeds were collected aseptically from the jugular vein into 50 ml Falcon tubes containing 200 μl of 0.5 M EDTA. The phenol-chloroform method was used to extract DNA and the regions were amplified for microsatellite analysis. The eight microsatellite markers ETH10, INRA005, ILSTS029, ILSTS033, ILSTS049, ILSTS052, ETH225, and CSSM66 were analysed.Results: The effective number of alleles across all loci was as usual lower than the observed values with a mean value of 2.52 alleles per locus. The overall allele frequency varied from 0.0041 for alleles B, I, and J over respective loci ILSTS052, INRA005, and ILSTS029 to 0.80 for allele H over locus ILSTS029. The average observed and expected heterozygosity values across all polymorphic loci in all studied buffalo breeds were 0.43 and 0.53, respectively. The overall value for polymorphic information content of considered microsatellite markers was 0.53, suggesting their appropriateness for genetic diversity analysis in buffalo. The mean Fis value was 0.13 and all loci except ILSTS049 were found significantly deviated from HWE, most likely due to non-random breeding. The five buffalo populations were genetically less diverse as indicated by a small mean Fst value (0.07). The average gene flow (Nm) indicative for population migration was calculated as 3.31. Nei’s original measures of genetic distance (Ds) revealed ancient divergence of the Nili and Azi-Kheli breeds (Ds = 0.1747) and recent divergence of the Nili and Ravi breeds (Ds = 0.0374).Conclusion: These estimates of genetic diversity were seen to coincide with phenotypic differentiation among the studied buffalo breeds. The present study reports the first microsatellite marker-based genetic diversity analysis in Pakistani buffalo breeds, and might facilitate similar studies in other livestock breeds of Pakistan.

scholarly journals Evaluation of Genetic Diversity and Structure of Turkish Water Buffalo Population by Using 20 Microsatellite Markers

Animals ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 1067
Author(s):  
Emel Özkan Ünal ◽  
Raziye Işık ◽  
Ayşe Şen ◽  
Elif Geyik Kuş ◽  
Mehmet İhsan Soysal
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Water Buffalo ◽  
Polymorphic Information Content ◽  
Breeding Strategy ◽  
Weinberg Equilibrium ◽  
Expected Heterozygosity ◽  
Genetic Diversity And Structure ◽  
Hardy Weinberg Equilibrium ◽  
The Mean

The present study was aimed to investigate the genetic diversity among 17 Turkish water buffalo populations. A total of 837 individuals from 17 provincial populations were genotyped, using 20 microsatellites markers. The microsatellite markers analyzed were highly polymorphic with a mean number of alleles of (7.28) ranging from 6 (ILSTS005) to 17 (ETH003). The mean observed and expected heterozygosity values across all polymorphic loci in all studied buffalo populations were 0.61 and 0.70, respectively. Observed heterozygosity varied from 0.55 (Bursa (BUR)) to 0.70 (Muş (MUS)). It was lower than expected heterozygosity in most of the populations indicating a deviation from Hardy–Weinberg equilibrium. The overall value for the polymorphic information content of noted microsatellite loci was 0.655, indicating their suitability for genetic diversity analysis in buffalo. The mean FIS value was 0.091 and all loci were observed significantly deviated from Hardy–Weinberg Equilibrium (HWE), most likely based on non-random breeding. The 17 buffalo populations were genetically less diverse as indicated by a small mean FST value (0.032 ± 0.018). The analysis of molecular variance (AMOVA) analysis indicated that about 2% of the total genetic diversity was clarified by population distinctions and 88 percent corresponded to differences among individuals. The information produced by this study can be used to establish a base of national conservation and breeding strategy of water buffalo population in Turkey.

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.

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