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 Regional Polymorphism Assessment of Myanmar ‘Sein Ta Lone’ Mango (Mangifera indica Linn) from Sintgaing Township Based on Microsatellite Markers

1970 ◽  
pp. 17-22
Author(s):  
May Sandar Kyaing ◽  
Sein Sandar May Phyo
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Genetic Variation ◽  
Microsatellite Markers ◽  
Mangifera Indica ◽  
Germplasm Management ◽  
Upgma Dendrogram ◽  
Expected Heterozygosity ◽  
Upgma Cluster Analysis ◽  
Relationship Of

This study was conducted to explore the genetic diversity and relationship of Sein Ta Lone mango cultivars among 20 commercial orchards in Sintgaing Township, Mandalay region. Nine microsatellite (SSR) markers were used to detect genetic polymorphism in a range from (3 to 6) alleles with (4.33) alleles per marker in average. Six out of nine microsatellite markers gave the PIC values of greater than (0.5). Among them, SSR36 held the highest PIC values of (0.691) while MiSHRS39 and MN85 possessed the least PIC values of (0.368) and (0.387) respectively. The genetic diversity was expressed as unbiased expected heterozygosity (UHe) value with an average of (0.561). The genetic relationship was revealed by (UPGMA) dendrogram in a range of (0.69 to 1.00). Based on UPGMA cluster analysis, three main clusters were classified among three different locations. This study was intended to help cultivar characterization and conservation for proper germplasm management with the estimation of genetic variation and relationship in the existing population of Sein Ta Lone mangoes in Sintgaing Township by microsatellite markers.  

scholarly journals Assessment of Genetic Diversity and Relationship of the Two Sanga Type Cattle of Botswana Based on Microsatellite Markers

2021 ◽  
Author(s):  
Tirelo Bakae ◽  
Phetogo Ineeleng Monau ◽  
James Nsoso ◽  
Patrick Monametsi Kgwatalala
Keyword(s):  
Genetic Variation ◽  
Microsatellite Markers ◽  
Polymorphic Information Content ◽  
Allelic Diversity ◽  
Inbreeding Coefficient ◽  
Analysis Of Molecular Variance ◽  
Expected Heterozygosity ◽  
Hardy Weinberg Equilibrium ◽  
Almost All ◽  
Relationship Of

Abstract The study was performed to evaluate genetic variation on two Sanga type cattle found in Botswana; Tswana and Tuli using twelve microsatellite markers. All amplified loci were polymorphic with 75 and 77 alleles genotyped in the Tswana and Tuli populations, respectively. The total number of alleles per locus ranged from 2 (BM1818) to 10 (TGLA227) with total mean of 6.25 for Tswana and 6.43 for Tuli population. Almost all the markers showed high polymorphic information content (PIC) apart from BM1818 (0.375) and INTRA23 (0.393) which were moderately informative in Tswana population. Most of the markers were in Hardy-Weinberg equilibrium except for CSSRM60 and CSSM66 loci in Tswana population and ETH10, ETH225 and CSSM66 loci in Tuli population. A total of 103 unique alleles were genotyped across the two breeds with 49-shared, and 26 and 28 were unique to Tswana and Tuli populations, respectively. The expected heterozygosity (He) values were higher than the observed heterozygosity (Ho) in both populations; Tswana (He=0.7895±0.033 vs Ho=0.631±0.091) and Tuli (He=0.8123±0.033 vs Ho=0.556±0.021). The inbreeding coefficient was 0.200±0.002 and 0.332±0.001 in Tswana and Tuli populations, respectively. Analysis of molecular variance revealed 6.8% of the total genetic variation corresponding to differences between the two breeds and 93.2% within populations. The genetic identity between the two breeds was 56% and there were similar levels of multilocus heterozygosity and allelic diversity in the two breeds. The use of Tswana and Tuli breeds in a crossbreeding program is likely to result in minimal heterosis and therefore not recommended.

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 An Evaluation of the Genetic Structure of Geese Maintained in Poland on the Basis of Microsatellite Markers

Animals ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 737 ◽  
Author(s):  
Warzecha ◽  
Oczkowicz ◽  
Rubis ◽  
Fornal ◽  
Szmatoła ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Genetic Variability ◽  
Microsatellite Markers ◽  
Polymorphism Information Content ◽  
Population Studies ◽  
Molecular Level ◽  
Microsatellite Data ◽  
Expected Heterozygosity ◽  
First Time

The aim of this study was to evaluate the genetic variability of the White Kołuda® goose and 12 conservative flocks: Kielecka, Podkarpacka, Garbonosa, Pomerian, Rypinska, Landes, Lubelska, Suwalska, Kartuska, Romanska, Slowacka, and Kubanska, maintained in Poland using microsatellite data. The genetic diversity of geese kept in Poland remains poorly analyzed at the molecular level. In total 392 samples were examined with the usage of 15 microsatellite markers. 119 alleles were identified and the number of alleles per locus ranged from 1 to 13. The highest number of alleles was observed in TTUCG5 (16) and the lowest in CAUD-G007 (2), while CKW47 was monomorphic. The lowest value of expected heterozygosity (He) was observed in Landes, while the highest in Romanska. Similarly, the observed heterozygosity (Ho) was the lowest in Landes but the highest in Kartuska. The polymorphism information content (PIC) indicates loci TTUCG5 as the most valuable microsatellite marker among those examined. The Structure software was used for the first time to identify goose populations, revealing high admixture between breeds and their close genetic propinquity. Moreover, the presented panel of microsatellite markers remained polymorphic and is useful for population studies of geese and assessment of genetic diversity.

scholarly journals Diversity and genetic relatedness among genotypes of Vitis spp. using microsatellite molecular markers

2013 ◽  
Vol 35 (3) ◽  
pp. 799-808 ◽  
Author(s):  
Patrícia Coelho de Souza Leão ◽  
Cosme Damião Cruz ◽  
Sérgio Yoshimitsu Motoike
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Molecular Markers ◽  
Microsatellite Markers ◽  
Information Content ◽  
Genetic Relatedness ◽  
Polymorphic Information Content ◽  
Germplasm Bank ◽  
Expected Heterozygosity ◽  
Vitis Spp

The purpose of this research was to study the genetic diversity and genetic relatedness of 60 genotypes of grapevines derived from the Germplasm Bank of Embrapa Semiárido, Juazeiro, BA, Brazil. Seven previously characterized microsatellite markers were used: VVS2, VVMD5, VVMD7, VVMD27, VVMD3, ssrVrZAG79 and ssrVrZAG62. The expected heterozygosity (He) and polymorphic information content (PIC) were calculated, and the cluster analysis were processed to generate a dendrogram using the algorithm UPGMA. The He ranged from 81.8% to 88.1%, with a mean of 84.8%. The loci VrZAG79 and VVMD7 were the most informative, with a PIC of 87 and 86%, respectively, while VrZAG62 was the least informative, with a PIC value of 80%. Cluster analysis by UPGMA method allowed separation of the genotypes according to their genealogy and identification of possible parentage for the cultivars 'Dominga', 'Isaura', 'CG 26916', 'CG28467' and 'Roni Redi'.

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 Microsatellite-Based Genetic Structure and Hybrid Detection in Alpacas Bred in Poland

Animals ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 2193
Author(s):  
Angelika Podbielska ◽  
Katarzyna Piórkowska ◽  
Tomasz Szmatoła
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
First Generation ◽  
Expected Heterozygosity ◽  
Hybrid Detection ◽  
Average Coefficient ◽  
Mixed Origin ◽  
Generation Hybrid

This study aimed to characterize the population structure and genetic diversity of alpacas maintained in Poland using 17 microsatellite markers recommended by the International Society for Animal Genetics. The classification of llamas, alpacas, and hybrids of both based on phenotype is often difficult due to long-term admixture. Our results showed that microsatellite markers can distinguish alpacas from llamas and provide information about the level of admixture of one species in another. Alpacas admixed with llamas constituted 8.8% of the tested individuals, with the first-generation hybrid displaying only 7.4% of llama admixture. The results showed that Poland hosts a high alpaca genetic diversity as a consequence of their mixed origin. More than 200 different alleles were identified and the average observed heterozygosity and expected heterozygosity values were 0.745 and 0.768, respectively, the average coefficient of inbreeding was 0.034, and the average polymorphism information content value was 0.741. The probability of exclusion for one parent was estimated at 0.99995 and for two parents at 0.99999.

scholarly journals Genetic variability and relationship among different accessions of Froriepia subpinata Bail (Gijavash) an endangered medicinal plant from Iran revealed by ISSR and IRAP markers

2021 ◽  
Vol 35 (1) ◽  
Author(s):  
Abbas Jorkesh ◽  
Yousef Hamidoghli ◽  
Jamalali Olfati ◽  
Habibollah Samizadeh ◽  
Davood Bakhshi
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Genetic Variability ◽  
Medicinal Plant ◽  
Genetic Information ◽  
Conservation Strategies ◽  
Polymorphic Band ◽  
Mean Values ◽  
Endangered Medicinal Plant ◽  
Irap Markers

The genetic variability of Froriepia subpinata Ledeb. Bail., an endangered Iranian endemic species, has been estimated with a total of 52 accessions using 20 markers including ISSR and IRAP. The results showed the polymorphic band produced by primers was 82.3%. The best mean values of genetic diversity parameters observed in ISSRs markers, being UBC873, UBC811, and UBC873 the best primers tested. The similarity range among accessions was 34.45% to 93.3%. The cluster analysis classified the accessions into five main groups that in totally, accessions with similarity in region generally were clustered in the same group. Overall, present study could provide elementary information for formulation of conservation strategies and invaluable elementary genetic information for next breeding or designing conservation programs.

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 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).

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