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 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 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.

Genetic diversity and molecular markers of five snapper species

2007 ◽  
Vol 4 (1) ◽  
pp. 39-46 ◽  
Author(s):  
Liu Li ◽  
Liu Chu-Wu
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Simple Sequence Repeats ◽  
Microsatellite Loci ◽  
Random Amplified Polymorphic Dna ◽  
Genetic Distances ◽  
The Other ◽  
Information Contents ◽  
The Mean ◽  
Simple Sequence

AbstractIn order to protect and develop valuable snappers (Lutjanus spp.), genetic diversity and molecular markers of five species (Lutjanus vitta, L. fulvus, L. fulviflamma, L. sebae and L. stellatus) were detected and analysed using random amplified polymorphic DNA (RAPD) and simple sequence repeats (SSR) techniques. The polymorphic loci ratio (P) (86.00–92.11%), the mean intraspecies genetic distances (D) (0.1775–0.3431) and the intraspecies genetic diversity indexes (Hi) (0.1022–0.1634) were calculated using the RAPD technique. The genetic diversities of L. fulviflamma and L. vitta were richest in terms of P, and D and Hi, respectively. The results of SSR showed that low effective numbers of alleles (1.7893–3.6591), medium average heterozygosities (0.332–0.676) and medium polymorphism information contents (PIC) (0.302–0.641) occurred in five species of snappers, indicating comparatively rich genetic diversity among these fish. Nine molecular markers in the products amplified by primers OPA8 and OPP10, and six molecular markers in 11 microsatellite loci were found to be useful as specific markers to identify five species of snappers. Two neighbour-joining (NJ) dendrograms based on the results of RAPD and SSR suggested that L. stellatus and L. sebae are closely related and clustered in one branch, with L. vitta, L. fulviflamma and L. fulvus in the other.

Genetic variation in 26 populations of Racospermaauriculiforme and Racospermamangium using allozymes

1994 ◽  
Vol 24 (6) ◽  
pp. 1123-1132 ◽  
Author(s):  
P.D. Khasa ◽  
W.M. Cheliak ◽  
J. Bousquet
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Unknown Origin ◽  
Population Level ◽  
Genetic Distances ◽  
Starch Gel Electrophoresis ◽  
Introduced Populations ◽  
Linear Relationships ◽  
Starch Gel ◽  
The Mean

Racospermaauriculiforme (Cunn. ex Benth.) Pedley and Racospermamangium (Willd.) Pedley are two fast-growing multipurpose leguminous species that have great potential for reforestation in the subhumid and humid tropics. The level and distribution of genetic variability were evaluated among and within 13 populations of each species at 18 loci encoding 10 enzymes, using starch gel electrophoresis. At the population level, the mean number of alleles per locus, the mean percentage of polymorphic loci, and mean expected heterozygosity were, respectively, 1.9, 52.1%, and 0.122 for R. auriculiforme, and 1.5, 24.3%, and 0.064 for R. mangium. Therefore, R. mangium appeared genetically depauperate compared with R. auriculiforme. The proportion of the total genetic diversity that resided among populations in R. auriculiforme (18%) was twice that in R. mangium (9%). No linear relationships were detected between genetic and geographic distances among populations. Cluster analysis of Nei's genetic distances and discriminant analysis did not show any significant geographic pattern of population differentiation for R. mangium. These same analyses revealed two distinct clusters of populations for R. auriculiforme, one in Queensland, Australia, and Papua New Guinea, and the other in the Northern Territory of Australia and Indonesia. For both taxa, seed of unknown origin of some introduced populations in Zaire and Congo could be identified. The genetic distance between the two species (D = 0.097) was, as expected, much larger than the average intraspecific genetic distance derived from comparisons of conspecific populations (D = 0.034 for R. auriculiforme and D = 0.007 for R. mangium). However, the amplitude of the interspecific genetic distance calculated is representative of divergence levels usually observed among subspecific taxa. Based on this, and the lower levels of genetic diversity found in R. mangium, it is suggested that R. mangium derived recently from R. auriculiforme.

High level of genetic diversity among spelt germplasm revealed by microsatellite markers

Genome ◽  
2004 ◽  
Vol 47 (6) ◽  
pp. 1043-1052 ◽  
Author(s):  
P Bertin ◽  
D Grégoire ◽  
S Massart ◽  
D de Froidmont
Keyword(s):  
Genetic Diversity ◽  
Triticum Aestivum L ◽  
Genetic Distances ◽  
Group Method ◽  
Germplasm Collections ◽  
Pair Group ◽  
Genetic Diversity And Structure ◽  
The Mean ◽  
High Level ◽  
Shared Alleles

The genetic diversity of spelt (Triticum aestivum (L.) Thell. subsp. spelta (L.) Thell.) cultivated presently is very narrow. Although the germplasm collections of spelt are extensive, the related genetic knowledge is often lacking and makes their use for genetic improvement difficult. The genetic diversity and structure of the spelt gene pool held in gene banks was determined using 19 simple sequence repeat (SSR) markers applied to 170 spelt accessions collected from 27 countries and 4 continents. The genetic distances (1 – proportion of shared alleles) were calculated and an unweighted pair-group method with arithmetic averaging (UPGMA)-based dendrogram was generated. The genetic diversity was high: 259 alleles were found and the mean interaccession genetic distance was 0.782 ± 0.141. The dendrogram demonstrated the much higher genetic diversity of spelt held in germplasm collections than in the currently used genotypes. Accessions with the same geographical origin often tended to cluster together. Those from the Middle East were isolated first. All but one of the Spanish accessions were found in a unique subcluster. Most accessions from eastern Europe clustered together, while those from northwestern Europe were divided into two subclusters. The accessions from Africa and North America were not separated from the European ones. This analysis demonstrates the extent of genetic diversity of spelts held in germplasm collections and should help to widen the genetic basis of cultivated spelt in future breeding programs.Key words: spelt, SSR, microsatellites, genetic diversity, germplasm.

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.

scholarly journals Keragaman Genetik Inbrida Jagung QPM dan Provit-A Berdasarkan Marka SSRs (Simple Sequence Repeats)

2016 ◽  
Vol 35 (2) ◽  
pp. 133
Author(s):  
Nining Nurini Andayani ◽  
M. Yasin H.G ◽  
Marcia B. Pabendon
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Simple Sequence Repeats ◽  
Genetic Similarity ◽  
Genetic Distances ◽  
Large Variability ◽  
Maize Germplasm ◽  
High Level ◽  
Biology Laboratory ◽  
Simple Sequence

Information on genetic diversity of QPM and Provit-A maize germplasm is important to support breeding program, in order to form a high yielding maize hybrid. Simple sequence repeats (SSR) have been extensively utilized as genetic markers to study the genetic diversity, cultivar identification, and gene mapping. The objectives of this research were to investigate the genetic diversity and to obtain information the genetic relationship among 20 maize accessions using 29 SSRs. The research was carried out at the Moleculer Biology Laboratory of Indonesian Cereals Research Institute (ICERI) in Maros, South Sulawesi. Twenty nine polymorphic primers that covered the 10 maize chromosomes were used to fingerprint the genotype of the lines, detecting 83 allels, with an average allel number of 3 allels per locus, ranging from 2 to 6 alleles per locus. The results indicated that polymorphism information content (PIC) ranged from 0.10 (nc133 and phi072) to 0.74 (phi064) with the average of 0.45. Genetic distance based on genetic similarity estimate ranged from 0.39 to 0.92. The high level of PIC values and wide genetic distances indicated the large variability among maize germplasm. Cluster analysis divided the 20 maize accessions into three groups. Coefficient cofenetic value (r) was 0.85 indicated a good fit based on the genetic similarity value. As many as 30 inbred heterotic recombinants were derived by incorporating 20 QPM and Provit-A with genetic distance of ≤0.65. The SSRs proved to be reliable and is practical technique for revealing the relationship among specialty maize genotypes.

scholarly journals Microsatellite-Based Analysis of Genetic Diversity and Population Structure of Rainbow Trout (Oncorhynchus mykiss) Cultured in Ukraine

2020 ◽  
Vol 5 (1) ◽  
pp. 29-39
Author(s):  
Оlena Bielikova ◽  
Serhii Тarasjuk ◽  
Antonina Mruk ◽  
Olga Zaloilo ◽  
Alexander Didenko
Keyword(s):  
Genetic Diversity ◽  
Rainbow Trout ◽  
Allelic Diversity ◽  
Genetic Distances ◽  
Principal Coordinates Analysis ◽  
Rainbow Trout Oncorhynchus Mykiss ◽  
Principal Coordinates ◽  
High Level ◽  
High Degree ◽  
Simple Sequence

The genetic structure of rainbow trout farmed in Ukraine were characterized based on microsatellite loci. The selected set of SSR-markers (Simple-sequence repeatsmarkers) had a high degree of polymorphism that allowed determining the specificity of each local stock (average PIC value = 0.785 ± 0.034). The microsatellite analysis of rainbow trout from the studied stocks showed a high level of genetic diversity (uHe = 0.825 ± 0.030, PIC = 0.785 ± 0.034, I = 1.836 ± 0.127). The level of allelic diversity of the selected loci was high, where the average number of alleles per locus was 7.833, the effective number of alleles per locus was 5.687. The range of amplicon sizes of the studied loci and private alleles for each local group was determined. The cluster analysis showed the presence of three clusters. The range of genetic variability was presented in the graphical interpretation of the principal coordinates analysis (PCoA). Based on unbiased genetic distances, the Kharkiv and Transcarpathian local stocks were found to be the closest, while the Chernivtsi stock was the most distant from them.

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.

Genetic diversity among four short stature cattle populations of India

2008 ◽  
Vol 43 ◽  
pp. 15-23
Author(s):  
M.S. Tantia ◽  
R.K. Vijh ◽  
B. Mishra ◽  
S.T. Bharani Kumar
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Differentiation ◽  
Short Stature ◽  
Correspondence Analysis ◽  
Microsatellite Loci ◽  
South India ◽  
Relative Magnitude ◽  
Expected Heterozygosity ◽  
The Mean

SummaryThe genetic diversity, genetic differentiation and relationship between four short stature cattle populations of south India - Punganur, Iduki, Kasargod and Vatakara - was studied, using 24 microsatellite loci. A total of 164 alleles were observed. The mean number of alleles per locus was 6.58 with mean observed and expected heterozygosity values of 0.70 and 0.75 respectively. The relative magnitude of gene differentiation (FST) was 6% and was significant except between the Iduki and Kasargod populations. The negative FIS values obtained for the majority of loci indicated a lack of population structure in the four populations. Both phylogenetic and correspondence analysis exhibited a closeness between Iduki and Kasargod animals. The results indicated that all four populations were outbred and Kasargod and Iduki animals should be considered as one even though these are reared for different purposes.

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