scholarly journals Genetic diversity revealed by AFLP markers in Albanian goat breeds

2012 ◽  
Vol 64 (2) ◽  
pp. 799-807 ◽  
Author(s):  
Anila Hoda ◽  
Lumturi Sena ◽  
Gentian Hykaj
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Fragment Length Polymorphism ◽  
Similarity Index ◽  
Shannon Index ◽  
Upgma Tree ◽  
Expected Heterozygosity ◽  
The Mean ◽  
High Level ◽  
Aflp Technique

The amplified fragment length polymorphism (AFLP) technique with three EcoRI/TaqI primer combinations was used in 185 unrelated individuals, representative of 6 local goat breeds of Albania, and 107 markers were generated. The mean Nei?s expected heterozygosity value for the whole population was 0.199 and the mean Shannon index was 0.249, indicating a high level of within-breed diversity. Wright?s FST index, Nei?s unbiased genetic distance and Reynolds? genetic distance were calculated. Pairwise Fst values among the populations ranged from 0.019 to 0.047. A highly significant average FST of 0.031 was estimated, showing a low level of breed subdivision. Most of the variation is accounted for by differences among individuals. Cluster analysis based on Reynolds? genetic distance between breeds and PCA were performed. An individual UPGMA tree based on Jaccard?s similarity index showed clusters with individuals from all goat breeds. Analysis of population structure points to a high level of admixture among breeds.

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 Is it possible to obtain zero estimates of genetic diversity? A case study of the Nigerian indigeneous goat breeds at the β-lactoglobulin gene locus

2017 ◽  
Vol 33 (4) ◽  
pp. 375-388
Author(s):  
Emeka Ezewudo ◽  
Geka Abubakar ◽  
Sunday Egena ◽  
Olushola Alabi
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Gene Locus ◽  
Polymorphic Locus ◽  
Information Index ◽  
Expected Heterozygosity ◽  
Goat Population ◽  
The Mean ◽  
Β Lactoglobulin

The current investigation was conducted to appraise the genetic diversity and genetic distance of three goat populations namely; Red Sokoto, Sahel and West African Dwarf (WAD), in Nigeria, making use of blood samples collected from 20, 20 and 20 individual from which blood DNAs were extraction, respectively. The DNAs extracted were used to study polymorphism at the ?-lactoglobulin gene locus using RLFP-PCR process. Results revealed that the mean total number of alleles was 1 while the effective number of alleles was also 1. The percentage of polymorphic locus was 0% while Shannon?s information index, observed homozygousity, expected heterozygosity, unbiased expected heterozygosity and inbreeding coefficient (F) were all observed to be 0.000. The pairwise Fst was 0.000 between all the breeds of goats. Variation within and between the populations of goats was 0% at p>0.05. The genetic distance between the goat breeds was 0.000. The present study revealed that RLFP-PCR may not be a powerful tool for the study of the ?-lactoglobulin gene locus and hence other methodologies should be employed for a broader judgment on the genetic status of the goat population at the locus.

scholarly journals Genetic Diversity of Populations of Akhal-Teke Horses from the Czech Republic, Russia, Estonia and Switzerland

2016 ◽  
Vol 64 (2) ◽  
pp. 461-466 ◽  
Author(s):  
Iva Jiskrová ◽  
Irena Vrtková ◽  
Michaela Prausová
Keyword(s):  
Genetic Diversity ◽  
Czech Republic ◽  
Genetic Distance ◽  
Genetic Parameters ◽  
Inbreeding Coefficient ◽  
The Other ◽  
Effective Number ◽  
The Czech Republic ◽  
Expected Heterozygosity ◽  
The Mean

Our research objective was to evaluate the genetic parameters in the populations of Akhal-Teke horses in 4 countries: Czech Republic, Russia, Estonia and Switzerland. The experiment involved a total of 325 Akhal-Teke horses; 121 horses came from the Czech Republic, 152 were from Russia, 28 were from Estonia and 24 horses came from Switzerland. For the divided database of micro satellites we evaluated the following parameters: effective number of alleles, frequency of alleles for the groups of horses; the observed heterozygosity (HO); the expected heterozygosity (HE); the inbreeding coefficient (Fis); and the genetic distance. The researched population is polymorphous. The population in the Czech Republic differs from the other three countries in the numbers of alleles per locus. The Czech population also includes Akhal-Teke horses which are not purebred Akhal-Teke horses. A confirmation of this fact is the effective number of alleles. The population in the Czech Republic exhibits the highest mean number of effective alleles. The Akhal-Teke population in Estonia exhibits the highest mean observed heterozygosity. By contrast, the population in the Czech Republic exhibits the lowest mean observed heterozygosity. In the Czech Republic the mean Fis value is a positive number indicating a reduced number of heterozygotes in the Czech Akhal-Teke population. The genetic distance is the highest between populations of horses bred in Russia and Estonia. The genetic distance is the lowest between populations of Akhal-Teke horses bred in Russia and in the Czech Republic.

Genetic Structure and Diversity among Species of Salacia: An Endangered Medicinal Herb of Western Ghats, India

2019 ◽  
Vol 9 (1) ◽  
pp. 23-33
Author(s):  
Chandrashekhar G Patil ◽  
Sheetal Ganapati Kamat ◽  
R Vasudeva
Keyword(s):  
Genetic Diversity ◽  
Southern China ◽  
Issr Marker ◽  
Group Method ◽  
Population Genetic Differentiation ◽  
Expected Heterozygosity ◽  
Marker Analysis ◽  
Endangered Medicinal Herb ◽  
High Level ◽  
Genetic Structure And Diversity

Salacia is one of the medicinally valuable genus, distributed throughout tropical areas which include India, Sri Lanka, Southern China and other Southern Asian Countries. The genus Salacia is represented by 21 species in India, among them eight species are recorded from the state of Karnataka in the Southern part of India. Despite its pharmaceutical importance, very little information exists about the genetic diversity of Salacia at molecular level. Hence the present study was carried out to evaluate the genetic among six species of Salacia namely S. chinensis, S. malabarica, S. oblonga, S. macrosperma, S. reticulata and S. gambleana with the help of ISSR marker analysis. Dendrogram and genetic distance were generated adopting Unweighted Paired Group Method with Arithmetic mean (UPGMA) in the NTSYS-pc software. Basic genetic parameters were calculated by analysing the genetic data with Pop gene 1.32 and GenAlEx 6.2 software. The overall polymorphism across the ten primers screened revealed 26 % polymorphism. A 60% polymorphism was scored for the primer UBC 841, whereas, no polymorphism was observed for primer UBC 840 and ISSR 6. The average observed heterozygosity was more than expected heterozygosity. Observed heterozygosity (Ho) ranged from 0.15 (UBC 841) to 0.38 (ISSR 6) with an average of 0.25, whereas expected heterozygosity (He) ranged from 0.10 (UBC 843) to 0.35 (ISSR 6) with an average of 0.23 for Salacia species. The higher heterozygosity pointed towards increased genetic diversity amongst the species. ISSR marker analysis showed high level of inter and intra population genetic differentiation.

scholarly journals Genetic diversity and structure of Dorstenia elata (Moraceae) in an Atlantic Forest remnant

Rodriguésia ◽  
2021 ◽  
Vol 72 ◽  
Author(s):  
Liliana Aparecida Ribeiro Martins ◽  
Rodrigo Monte Lorenzoni ◽  
Ronald Martins Pereira Júnior ◽  
Fábio Demolinari de Miranda ◽  
Milene Miranda Praça Fontes ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Atlantic Forest ◽  
Shannon Index ◽  
The Road ◽  
Expected Heterozygosity ◽  
Forest Remnant ◽  
Genetic Diversity And Structure ◽  
Native Populations ◽  
The Matrix ◽  
Issr Primers

Abstract Plant species that show gregarious spatial distribution and endemism to the Atlantic Forest, such as Dorstenia elata, are particularly sensitive to the effects of genetic diversity loss. In the present study, we aimed to quantify the genetic diversity in native populations of this species in an Atlantic Forest remnant. The sample included three aggregates of individuals, and molecular characterization was performed with twelve ISSR primers. Intrapopulation analyses were based on the calculation of the Shannon index; total expected heterozygosity and the matrix of distances between pairs of individuals were also calculated. The obtained grouping dendrogram evinced the formation of two groups. Interpopulation investigations were based on the analysis of molecular variance and the estimate of historical gene flow. The results demonstrate that one group comprised the genotypes from two subpopulations, and the other contained exclusively the genotypes of a third subpopulation. The greatest genetic variability was observed within rather than among populations, indicating that the geographical distance and the road that divides the studied populations are not causing loss of genetic diversity.

scholarly journals Genetic diversity in Brazilian tall coconut populations by microsatellite markers

2013 ◽  
Vol 13 (4) ◽  
pp. 356-362 ◽  
Author(s):  
Francisco Elias Ribeiro ◽  
Luc Baudouin ◽  
Patricia Lebrun ◽  
Lázaro José Chaves ◽  
Claudio Brondani ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Cape Verde ◽  
Coconut Palm ◽  
Different Populations ◽  
The Mean ◽  
High Level ◽  
Brazilian Populations

The tall coconut palm was introduced in Brazil in 1553, originating from the island of Cape Verde. The aim of the present study was to evaluate the genetic diversity of ten populations of Brazilian tall coconut by 13 microsatellite markers. Samples were collected from 195 individuals of 10 different populations. A total of 68 alleles were detected, with an average of 5.23 alleles per locus. The mean expected and observed heterozygosity value was 0.459 and 0.443, respectively. The number of alleles per population ranged from 36 to 48, with a mean of 40.9 alleles. We observed the formation of two groups, the first formed by the populations of Baía Formosa, Georgino Avelino and São José do Mipibu, and the second by the populations of Japoatã, Pacatuba and Praia do Forte. These results reveal a high level of genetic diversity in the Brazilian populations.

scholarly journals GENOMIC DETERMINATION OF THE MOST IMPORTANT FATHER LINES OF SLOVAK PINZGAU COWS

AGROFOR ◽  
2016 ◽  
Vol 1 (3) ◽  
Author(s):  
Veronika KUKUČKOVÁ ◽  
Nina MORAVČÍKOVÁ ◽  
Radovan KASARDA
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
The State ◽  
Most Probable Number ◽  
Pedigree Data ◽  
Probable Number ◽  
Expected Heterozygosity ◽  
High Level ◽  
The Bayesian Approach

The aim of this study was to assess genetic structure of Slovak Pinzgau populationbased on polymorphism at molecular markers using statistical methods. Femaleoffspring of 12 most frequently used bulls in Slovak Pinzgau breeding programmewere investigated. Pinzgau cattle were found to have a high level of diversity,supported by the number of alleles observed across loci (average 5.31, range 2-11)and by the high within-breed expected heterozygosity (average 0.66, range 0.64-0.73). The state of genetic diversity is satisfying and standard for local populations.Detection of 12 possible subpopulation structures provided us with detailedinformation of the genetic structure. The Bayesian approach was applied, detectingthree, as the most probable number of clusters. The similarity of eachsubpopulation using microsatellites was confirmed also by high-throughputmolecular data. The observed inbreeding (FROH=2.3%) was higher than thatexpected based on pedigree data (FPED=0.4%) due to the limited number ofavailable generations in pedigree data. One of the most important steps indevelopment of efficient autochthonous breed protection programs ischaracterization of genetic variability and assessment of the population structure.The chosen set of microsatellites confirmed the suitability in determination of thesubpopulations of Pinzgau cattle in Slovakia. The state of genetic diversity at moredetailed level was successfully performed using bovineSNP50 BeadChip.

scholarly journals Genetic diversity in wild and hatchery populations of stinging catfish (Heteropneustes fossilis Bloch) revealed by RAPD analysis

2012 ◽  
Vol 19 ◽  
pp. 81-87
Author(s):  
Md Nazrul Islam ◽  
Abhishak Basak ◽  
Dr Ashrafullah ◽  
Md Samsul Alam
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Gene Diversity ◽  
Similarity Index ◽  
Heteropneustes Fossilis ◽  
Wild Populations ◽  
Polymorphic Loci

Context: DNA fingerprinting using genetic markers such as Random Amplification of Polymorphic DNA (RAPD), Restriction Fragment Length Polymorphism (RFLP), microsatellite (Simple sequence repeat), Amplified Fragment Length Polymorphism (AFLP) etc. can be successfully used to reveal genetic variation within and among different populations. Objective: The aim of the present study was to assess genetic diversity in two wild and one hatchery populations of stinging catfish Heteropneustes fossilis by RAPD fingerprinting. Materials and Methods: A total of 90 live fish (H. fossilis), 30 from each source, were collected from a beel in Patuakhali, a beel in Jessore and Rupali Hatchery, Mymensingh. Genomic DNA was extracted from fin tissues. The concentration of DNA was estimated using a spectrophotometer. Fifteen decamer primers of random sequence from three kits (six from kit A, seven from kit B and two from kit C) (Operon technologies, Inc., Alameda, CA, USA) were screened on sub-samples of one randomly chosen H. fossilis DNA sample from the each population to test their suitability for amplifying RAPDs. The amplified products from each sample were separated by electrophoresis on 1.4% agarose gel containing ethidium bromide. The sizes of the bands were calculated using the software DNAFRAG and the sizes in base pair (bp) were used for identification of the bands (RAPD markers). The similarity index values (SI) between the RAPD fingerprint of any two individuals on the same gel were calculated from RAPD band sharing. Results: A total of 28 RAPD bands were obtained using four decamer random primers, among which 21 bands were polymorphic. The percentage of polymorphic loci, intra-population similarity indices and Nei's gene diversity values were 85.71%, 78.75 and 0.304±0.183 for Jessore population, 83.71%, 82.62 and 0.280±0.159 for Patuakhali population, 82.14%, 85.25 and 0.271±0.165 for Rupali hatchery population, respectively. The overall gene flow (Nm) among the populations was 5.755. The highest inter-similarity (Sij) was found between Patuakhali - Rupali hatchery populations. Among the three populations, the highest genetic distance (0.069) was found between Jessore and Patuakhali population. Considering polymorphic loci, intrapopulation similarity index and gene diversity the genetic variation in the Jessore population was higher than the other two populations. The genetic variation of the hatchery population was found to be lower than the two wild populations. Conclusion: The result of the present study can be used as baseline information regarding the genetic variation and population structure before undertaking any breeding programme. Study indicated that the genetic variation in the hatchery populations were slightly lower than those of the wild populations. DOI: http://dx.doi.org/10.3329/jbs.v19i0.13005 J. bio-sci. 19 81-87, 2011

Genetic diversity in African yam bean accessions based on AFLP markers: towards a platform for germplasm improvement and utilization

2014 ◽  
Vol 13 (2) ◽  
pp. 111-118 ◽  
Author(s):  
B. D. Adewale ◽  
I. Vroh-Bi ◽  
D. J. Dumet ◽  
S. Nnadi ◽  
O. B. Kehinde ◽  
...  
Keyword(s):  
Fragment Length Polymorphism ◽  
Aflp Markers ◽  
Fixation Index ◽  
Crop Species ◽  
Phenotypic Profile ◽  
African Yam Bean ◽  
Expected Heterozygosity ◽  
Underutilized Crop ◽  
Breeding Programmes ◽  
The Mean

Accurate knowledge of intra-specific diversity of underutilized crop species is a prerequisite for their genetic improvement and utilization. The diversity of 77 accessions of African yam bean (AYB, Sphenostylis stenocarpa) was assessed by amplified fragment length polymorphism (AFLP) markers. A total of EcoRI/MseI primer pairs were selected and 227 AFLP bands were generated, of which 59(26%) were found to be polymorphic in the 77 accessions of AYB. The most efficient primer combination for polymorphic detection was E-ACT/M-CAG with a polymorphic efficiency of 85.5%, while the least efficient was E-AGC/M-CAG with a polymorphic efficiency of 80.6%. The Jaccard genetic distance among the accessions of AYB ranged between 0.048 and 0.842 with a mean of 0.444. TSs98 and TSs104B were found to be the most similar accessions with a genetic similarity of 0.952. The neighbour-joining dendrogram grouped the 77 accessions of AYB into four distinct clusters comprising 8, 20, 21 and 28 accessions. The major clustering of the accessions was not related to their geographical origin. Cluster I was found to be the most diverse. The mean fixation index (0.203) and the mean expected heterozygosity (0.284) revealed a broad genetic base of the AYB accessions. The same germplasm set was previously evaluated for several agro-morphological traits. As the collection of additional AYB germplasm continues, the phenotypic profile, the clustering of the accessions and the AFLP primer combinations from this study can be used to augment breeding programmes.

scholarly journals The Genetic Diversity and Geographic Differentiation of the Wild Soybean in Northeast China Based on Nuclear Microsatellite Variation

2018 ◽  
Vol 2018 ◽  
pp. 1-9
Author(s):  
Hongkun Zhao ◽  
Yumin Wang ◽  
Fu Xing ◽  
Xiaodong Liu ◽  
Cuiping Yuan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Northeast China ◽  
Wild Soybean ◽  
Population Level ◽  
Mantel Test ◽  
Microsatellite Variation ◽  
Information Index ◽  
Ssr Loci ◽  
The Mean

In this study, the genetic diversity and population structure of 205 wild soybean core collections in Northeast China from nine latitude populations and nine longitude populations were evaluated using SSR markers. A total of 973 alleles were detected by 43 SSR loci, and the average number of alleles per locus was 22.628. The mean Shannon information index (I) and the mean expected heterozygosity were 2.528 and 0.879, respectively. At the population level, the regions of 42°N and 124°E had the highest genetic diversity among all latitudes and longitudes. The greater the difference in latitude was, the greater the genetic distance was, whereas a similar trend was not found in longitude populations. Three main clusters (1N, <41°N-42°N; 2N, 43°N-44°N; and 3N, 45°N–>49°N) were assigned to populations. AMOVA analysis showed that the genetic differentiation among latitude and longitude populations was 0.088 and 0.058, respectively, and the majority of genetic variation occurred within populations. The Mantel test revealed that genetic distance was significantly correlated with geographical distance (r=0.207, p<0.05). Furthermore, spatial autocorrelation analysis showed that there was a spatial structure (ω=119.58, p<0.01) and the correlation coefficient (r) decreased as distance increased within a radius of 250 km.

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