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 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.

scholarly journals Intra-line and inter-line genetic diversity in sire lines of the Old Kladruber horse based on microsatellite analysis of DNA

2011 ◽  
Vol 56 (No. 4) ◽  
pp. 163-175 ◽  
Author(s):  
L. Vostrý ◽  
O. Kracíková ◽  
B. Hofmanová ◽  
V. Czerneková ◽  
T. Kott ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Dna Analysis ◽  
Genetic Difference ◽  
Principal Component ◽  
Genetic Distances ◽  
Mean Value ◽  
Pedigree Information ◽  
Mean Values ◽  
The Mean ◽  
Coefficient Of Relationship

The Old Kladruber horse is the oldest original Czech horse breed &ndash; gene resource, with pedigree records spanning three centuries. Because the population is closed, there is a concern about the loss of genetic variation. The genetic diversity within and amongst sire lines was evaluated using microsatellite markers and based on pedigree information. The DNA analysis, covering 16 microsatellite loci, revealed that the genetic diversity (observed heterozygosity = 0.637, genetic diversity = 0.678 and the mean number of alleles = 8.25) for the Old Kladruber horse is consistent with other populations of horses. Inter-line genetic difference in sire lines reached the mean value (the F<sub>ST</sub> values ranged from 0.020 to 0.017). Differences amongst the sire lines were identified using genetic distances and principal component analysis. One gene cluster comprised black variation sire lines, while the second cluster included the sire lines of the grey variation. In the subjects monitored, the average inbreeding coefficient of 0.076 was estimated on the basis of pedigree information. The highest mean values of the coefficient of relationship were estimated within the colour variations. When comparing the genetic distance and the average coefficient of relationship, differences were found out. These results are useful for the development of breeding strategies which consider classical horse breeding as well as recent achievements of population and conservation genetics.

scholarly journals Genetic diversity and population structure of four cattle breeds raised in Turkey using microsatellite markers

2019 ◽  
Vol 64 (No. 10) ◽  
pp. 411-419 ◽  
Author(s):  
Eymen Demir ◽  
Murat Soner Balcioğlu
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Microsatellite Markers ◽  
Factorial Correspondence Analysis ◽  
Cattle Breeds ◽  
Expected Heterozygosity ◽  
Bottleneck Analysis ◽  
Holstein Friesian ◽  
Native Cattle ◽  
Marker Level

In the present study, genetic diversity and population structure of Holstein Friesian and three native cattle breeds of Turkey including Turkish Grey Steppe, Eastern Anatolian Red and Anatolian Black were assessed. Totally 120 individuals of 4 breeds were genotyped using 20 microsatellite markers and 204 different alleles, of which 31 were private alleles, were detected. The average observed and expected heterozygosity values were 0.63 and 0.74, respectively. Observed heterozygosity at the marker level ranged from 0.30 (DRBP1) to 0.88 (ILSTS011), while expected heterozygosity ranged from 0.51 (INRABERN172) to 0.88 (SPS113). Inbreeding coefficient values for Turkish Grey Steppe, Eastern Anatolian Red, Anatolian Black and Holstein Friesian were 0.216, 0.202, 0.128 and 0.069, respectively. The lowest pairwise F<sub>ST</sub> value (0.030) was detected between Turkish Grey Steppe and Anatolian Black breeds, while the highest value (0.070) was detected between Turkish Grey Steppe and Holstein Friesian. Results of structure and factorial correspondence analysis revealed that Turkish native cattle breeds and Holstein Friesian were genetically different enough to separate the two breeds. Results of bottleneck analysis indicated heterozygosity deficiency in Turkish Grey Steppe (P &lt; 0.05).

scholarly journals Assessment of genetic diversity and differentiation of two major camel ecotypes (<i>Camelus dromedarius</i>) in Sudan using microsatellite markers

2015 ◽  
Vol 58 (2) ◽  
pp. 269-275 ◽  
Author(s):  
M. Eltanany ◽  
O. Elfaroug Sidahmed ◽  
O. Distl
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Microsatellite Markers ◽  
Inbreeding Coefficient ◽  
Mean Values ◽  
Significant Differentiation ◽  
Expected Heterozygosity ◽  
Admixed Population ◽  
Relationship Of ◽  
First Time

Abstract. Although Sudan has the second largest camel population in Africa, it has not yet been genetically differentiated. The present study was undertaken to evaluate, for the first time, the genetic diversity and relationship of two major camel ecotypes representing the eastern (Butana) and western (Darfur) regions of Sudan using 12 microsatellite markers. A total of 107 samples of study ecotypes were investigated displaying high mean values of genetic diversity (mean number of alleles: 11.5 ± 1.45; polymorphism information content: 0.67 ± 0.04; observed heterozygosity: 0.69 ± 0.05; expected heterozygosity: 0.72 ± 0.04). The global inbreeding coefficient (FIT = 0.041 ± 0.03, P > 0.05) was attributed to substantial and non-significant within-population inbreeding (FIS = 0.034 ± 0.03) and scarce but highly significant differentiation between ecotypes (FST = 0.008 ± 0.00; P < 0.0001). Multivariate analysis indicated a historical intermixing between different genealogical lineages making up the current admixed gene pool of the geographically divergent ecotypes. Consistent with this, STRUCTURE cluster analysis showed these ecotypes to be one mosaic admixed population. The results showed abundant genetic diversity within Sudanese dromedaries. Our study indicates that the two Sudanese camel ecotypes (Butana and Darfur) appear as an admixture of two geographical branches and do not support the contemporary division of Sudanese dromedaries into their respective socio-ethno-geography.

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 Molecular Characterization of Lates niloticus (Perciformes, Latidae) Populations from three Nigerian Waterbodies using Random Amplified Polymorphic DNA and Microsatellite Markers

2017 ◽  
Vol 51 (1) ◽  
pp. 31-36
Author(s):  
K. E. Ogbuebunu ◽  
M. O. Awodiran
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Flow ◽  
Microsatellite Markers ◽  
Random Amplified Polymorphic Dna ◽  
Population Level ◽  
Effective Number ◽  
Lates Niloticus ◽  
The Mean

Abstract Thirty Lates niloticus (Linnaeus, 1758) from three Nigerian waterbodies were genotyped on six RAPD primers and five microsatellites loci. RAPD revealed that effective number of alleles (AE) at population level per locus was within the range of 1.641 ± 0.066 to 1.645 ± 0.041 while the mean number of alleles (AN) across populations equals 2.000. Characterization on five microsatellites loci revealed genetic diversity within and among studied populations. Observed heterozygousity (HO) was within the range of 0.317 ± 0.335 to 0.523 ± 0.315 while expected heterozygousity (HE) was within the range of 0.414 ± 0.306 to 0.715 ± 0.097. Proportion of differentiation (FST) within populations was 0.236. Overall gene flow (Nm) among populations equals 0.806. This study established the successful use of RAPD and microsatellite as tools for studying population structure of fish species, especially L. niloticus. Thus, it can be concluded that L. niloticus in the three (3) sampled Nigerian waterbodies is undergoing evolution.

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.

scholarly journals Genetic Diversity and Population Structure Analysis of Dalbergia Odorifera Germplasm and Development of a Core Collection Using Microsatellite Markers

Genes ◽  
2019 ◽  
Vol 10 (4) ◽  
pp. 281 ◽  
Author(s):  
Fu-Mei Liu ◽  
Ning-Nan Zhang ◽  
Xiao-Jin Liu ◽  
Zeng-Jiang Yang ◽  
Hong-Yan Jia ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Microsatellite Markers ◽  
Genetic Resources ◽  
Tree Species ◽  
Core Collection ◽  
Southern China ◽  
Breeding Programs ◽  
Expected Heterozygosity ◽  
Dalbergia Odorifera

Dalbergia odorifera T. Chen (Fabaceae) is a woody tree species indigenous to Hainan Island in China. Due to its high medicinal and commercial value, this tree species has been planted over 3500 ha2 in southern China. There is an urgent need for improvement of the D. odorifera germplasm, however, limited information on germplasm collection, conservation, and assessment of genetic resources is available. Therefore, we have built a database of 251 individuals collected across the whole of southern China, which included 42 wild trees and 210 cultivated trees, with the following objectives. (1) Evaluate genetic diversity and population structure of the database using 19 microsatellite markers and (2) develop a core collection for improvement and breeding programs. Totally, the 19 microsatellite markers harbored 77 alleles across the database with the polymorphic information content (PIC) ranging from 0.03 to 0.66. Medium genetic diversity level was inferred by Nei’s gene diversity (0.38), Shannon’s information index (0.65), and observed (0.33) and expected heterozygosity (0.38). Structure analysis showed that four was the optimum cluster size using the model-based Bayesian procedure, and the 251 D. odorifera individuals were grouped into five populations including four pure ones (RP1-4) and one mixed one (MIX) based on their maximum membership coefficients. Among these populations, the expected heterozygosity varied from 0.30 (RP3) to 0.38 (RP4). Analysis of molecular variance (AMOVA) showed 11% genetic variation existed among populations, and moderate population differentiation was inferred by the matrix of pairwise Fst (genetic differentiation among populations), which was in the range of 0.031 to 0.095. Moreover, a core collection of 31 D. odorifera individuals including six wild and 25 cultivated trees was developed, which was only 12.4% of the database but conserved the whole genetic diversity. The results of this study provided additional insight into the genetic structure of the large D. odorifera germplasm, and the core collection will be useful for the efficient and sustainable utilization of genetic resources, as well as efficient improvement in breeding programs.

Isozyme analysis of genetic variability and population structure of Lathyrus sativus L. germplasm

2019 ◽  
Author(s):  
R. H. Sammour ◽  
A-E. Mustafa ◽  
M.- El-Sheikh ◽  
A. A. Alatar ◽  
W. Taher
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variability ◽  
Random Mating ◽  
Lathyrus Sativus ◽  
Isozyme Analysis ◽  
Expected Heterozygosity ◽  
The Mean ◽  
Low Levels ◽  
Lathyrus Sativus L

This work aimed at exploring the genetic variability, population structure and relationships of Lathyrus sativus L. germplasm using isozyme analysis. The data of isozyme analysis revealed 12 putative polymorphic loci of a total 33 alleles, indicating that studied accessions express good allelic richness and had an apparent rate of allogamy. The mean average of the expected heterozygosity (0.483) was more than the mean average of the observed heterozygosity (0.449) suggesting an apparent rate of allogamy taking place in Lathyrus sativus L. The average of total heterozygosity (HT) and intra-accessional genetic diversity (HS) were 0.559 and 0.428 respectively indicating that majority of genetic diversity was intra-accessional. The low levels and non-significant of genetic diversity among accessions (DST = 0.190, X2 = 62.59, p = 0.029) were probably indicative of occurrence of several gene flows. The coefficient of gene differentiation (GST) showed significant variation, suggesting the heterogonous distribution of L. sativus accessions among different geographic regions. The mean average of FST was 0.327, suggesting the occurrence of random mating system for the studied accessions and reflecting adaptation to strong environmental dissimilarities. Cluster analysis based on isozyme data suggested that the environment had no influence on the genetic diversity and confirmed that Lathyrus sativus L. had a polyphyletic origin.

Sign in / Sign up

Export Citation Format

Share Document