scholarly journals Review: Genetic diversity studies using microsatellite markers and their contribution in supporting sustainable sheep breeding programs

2017 ◽  
Vol 1 (01) ◽  
pp. 46-51
Author(s):  
OUMER SHERIFF ◽  
KEFYALEW ALEMAYEHU
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Polymorphic Information Content ◽  
Domestic Sheep ◽  
Breeding Programs ◽  
Sheep Breeding ◽  
Population Structures ◽  
The Mean ◽  
Tree Building ◽  
Diversity Studies

Sheriff O, Alemayehu K. 2017. Review: Genetic diversity studies using microsatellite markers and their contribution in supporting sustainable sheep breeding programs. Asian J Agric 1: 46-51. Microsatellites have been widely accepted and employed as useful molecular markers for measuring genetic diversity and divergence within and among populations. The various parameters developed so far to measure genetic diversity within and among populations are observed and expected heterozygosities (Ho and He), the mean number of alleles per locus (MNA),polymorphic information content (PIC), genetic distance and phylogenetic or tree building approach.The objective of thisreview was therefore to quantifythe genetic diversity studies of domestic sheep populations using microsatellite markersand their contribution in supporting sustainable sheep breeding programs. From the review, it is possible to see that there was high within population genetic variations in all the studied sheep populations, poor level of population differentiations and high levels of inbreeding. On the other hand, low estimates of hetrozygosities and mean number of alleles and employing only few and weak markers were observed in some of the studies. The gaps observed in the previous genetic diversity studies of the sheep populations may demand further works to reveal more information on the population structures andto start appropriate and sustainable breeding programs.

Analysis of genetic diversity of four quails by microsatellite markers

2016 ◽  
Author(s):  
Jun.Yan. Bai ◽  
You.Zhi. Pang ◽  
Sheng.Jun. Wu ◽  
Mei.Qin. Yu ◽  
Xiao.Hui. Zhang
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Microsatellite Markers ◽  
Egg Production ◽  
Total Population ◽  
Polymorphic Information Content ◽  
Scientific Basis ◽  
Protection And Utilization ◽  
The Mean ◽  
Population Genetic Variation

Genetic diversity of four quail populations, including Korean quails (maroon quails), Peking white quails, Chinese yellow quails and Chinese black quails, were analyzed by microsatellite markers, aiming to provide scientific basis for new breeds of Chinese black quails for egg production as well as the assessment, protection and utilization of Chinese quail’s genetic resources. The results showed that 48 alleles were detected by nine microsatellite markers in the four quail populations, with the mean of 5.33 alleles in each locus. The average effective number of alleles marked by the nine microsatellite markers in Chinese black quails, Peking white quails, Chinese yellow quails and maroon quails were 3.5338, 3.6135, 4.0312 and 3.6508 respectively. The average heterozygosity of the four quail populations were 0.6952, 0.7046, 0.7353 and 0.7096 respectively. The average polymorphic information content of nine microsatellite loci in four quail populations were 0.6204, 0.6587, 0.6942 and 0.6639, respectively, all of which were greater than 0.5, indicating the four populations’ copious genetic diversity. In this study, the average genetic differentiation coefficient among populations was 0.0349, so the genetic variation among populations accounted for 3.49%, which demonstrated that genetic variation among populations was just a small proportion of the total population genetic variation, and there was little differentiation among the four populations. Cluster analysis indicated that Chinese black quails and Peking white quails were firstly clustered, and then Chinese yellow quails and maroon quails were clustered, and finally the two were clustered together.

scholarly journals Use of Microsatellites in Genetic Diversity Assessment, Parentage Testing and Individual Identification of the Kangal Shepherd Dog

2020 ◽  
Vol 70 (2) ◽  
pp. 170-181
Author(s):  
Dimitrijević Vladimir ◽  
Ristanić Marko ◽  
Stanisić Ljubodrag ◽  
Drobnjak Darko ◽  
Urosević Milivoje ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Polymorphic Information Content ◽  
Mean Value ◽  
Individual Identification ◽  
Parentage Testing ◽  
Diversity Assessment ◽  
Study Population ◽  
The Mean ◽  
Matching Probability

AbstractThe Kangal Shepherd Dog is considered the most common dog breed of Turkish origin. This study investigated variations in ten autosomal microsatellite markers (PEZ01, PEZ03, PEZ05, PEZ06, PEZ08, PEZ12, PEZ20, FHC2010, FHC2054 and FHC2079) for the purposes of genetic diversity assessment of the Kangal breed. In addition, the use of markers was assessed in parentage testing and individual identification within the Kangal breed. The microsatellite markers were typed in 51 Kangal dogs. The total number of alleles in the study population was 69. The mean number of alleles per locus was 6.9, and varied from four (FHC2079) to 12 (PEZ12). The polymorphic information content (PIC) ranged from 0.52 (FHC2079) to 0.87 (PEZ12), with the mean value for all loci of 0.717. Power of exclusion (PE) in 10 microsatellites investigated varied between 0.143 (FHC2054) and 0.472 (PEZ08) per locus. In order to determine the efficiency of using microsatellites for individual identification in the Kangal breed, power of discrimination (PD) and matching probability (MP) were calculated for each microsatellite marker. The panel achieved high combined MP (6.77 × 10-10) and high combined PD value of 99.99999%. The obtained results may contribute to further recognition of the Kangal breed, and confirm that the investigated microsatellites enable a reliable parentage testing and individual identification of the breed.

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 Assessment of Genetic Diversity in Indian Spinach (Basella spp L) Accessions Using RAPD Markers

2020 ◽  
pp. 1-8
Author(s):  
Olalekan Ibrahim Sobowale ◽  
Benjamin Oluwole Akinyele ◽  
Alexander Chukwunweike Odiyi ◽  
Adeyela Ibironke Okunlola ◽  
Emmanuel Oluwakayode Ajayi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Random Amplified Polymorphic Dna ◽  
Leafy Vegetables ◽  
Breeding Programs ◽  
Medicinal Value ◽  
The Mean ◽  
And Cluster Analysis

Background: Indian spinach is one of the important underexploited tropical leafy vegetables which have high nutritional and medicinal value. Molecular marker technology has greatly accelerated the process involved in breeding programs for the improvement of various crops and its techniques have been considered to be the most suitable means of estimating genetic diversity. Aim: The study is to determine the genetic diversity among the accessions of Indian spinach collected from South western Nigeria using molecular markers. Methodology: Random amplified polymorphic DNA (RAPD) markers were used to assay 20 accessions of Indian spinach (Basella spp) collected from the south western states of Nigeria (Oyo, Osun, Ogun, Ondo and Ekiti). Results: Results showed that RAPD markers were highly polymorphic and generated alleles ranging from two to eight. The polymorphic information content was highest for the OPT-17 primer (0.757) and the mean average was (4.23) Moreover, gene diversity (0.785) was high, and cluster analysis delineated the accessions into five groups, which indicated that a significant genetic diversity was present among the accessions studied. A dendrogram clustering method revealed five major clusters. Clusters I, II and IV had one accessions each, III had four and V had thirteen accessions. Conclusion: The result revealed that RAPD markers are useful for genetic characterization as they provide information on the interspecific and phylogenetic statuses of the accessions. The markers also showed a genetic variability that could be exploited for varietal delineation and improvement of the vegetable in Nigeria.

scholarly journals Assessment of genetic diversity among wild populations of the striped catfish (Pangasianodon hypophthalmus) by 20 novel microsatellite markers

2021 ◽  
Vol 63 (7) ◽  
pp. 37-41
Author(s):  
Van Sang Nguyen ◽  
◽  
Minh Thanh Nguyen ◽  
Hoang Thong Nguyen ◽  
Hoang Gia Linh Tran ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Polymorphic Information Content ◽  
Draft Genome ◽  
Null Alleles ◽  
Wild Populations ◽  
High Genetic Diversity ◽  
Pangasianodon Hypophthalmus ◽  
Striped Catfish ◽  
The Mean

The striped catfish, Pangasianodon hypophthalmus, is one of the most economically important aquaculture species in Vietnam. This study developed 26 novel microsatellite markers from the draft genome of the striped catfish to assess the genetic diversity of three wild populations of the striped catfish (Bien Ho, Cuu Long, and Kratie) for establishing the breeding program. The study exhibited that 6 out of 26 loci had significantly high null allele frequency and deviated from Hardy - Weinberg equilibrium; thus, they were eliminated for further analysis. Across 20 loci without null alleles, a total of 255 different alleles was identified, ranging from 7 to 21 alleles per locus, with many unique alleles for each population. The results based on 20 loci revealed the mean polymorphic information content PIC=0.783; the mean observed heterozygosity Ho=0.809; the mean expected heterozygosity He=0.812; inbreeding coefficient Fis=-0.0147 (Fis<0). The results indicated that the striped catfish populations have high genetic diversity and are suitable for selective breeding. The Analysis of Molecular Variance (AMOVA) and comparison of genetic distances showed significant genetic differentiation among three populations while the Kratie population was distant from the others.

scholarly journals Molecular Diversity Analysis of Jattal and Dera Din Panah Goat Breeds of Pakistan using Microsatellite Markers

2018 ◽  
Vol 69 (1) ◽  
pp. 791 ◽  
Author(s):  
T. HUSSAIN ◽  
M. SHAHEEN ◽  
M. E. BABAR ◽  
M. M. MUSTHAFA ◽  
A. NADEEM ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Genetic Resource ◽  
Polymorphic Information Content ◽  
Goat Breed ◽  
Expected Heterozygosity ◽  
Animal Genetic Resource ◽  
Wide Range ◽  
The Mean ◽  
Distinct Features

This paper evaluates the genetic diversity of goat breeds in Pakistan, a country blessed with a wide range of goats spread throughout with distinct features contributing to a rich Animal Genetic Resource. The genetic diversity of two goat breeds (Jattal and Dera Din Panah) was assessed with 25 animals representing the two breeds using 16 microsatellite markers. The mean observed and expected heterozygosity of both goat breed populations were observed as 0.83+0.21. The average number of observed alleles was 3.6+1.6 for all loci. The mean polymorphic information content for a goat breed was 0.45, indicating the usefulness of markers panel. Highest Nei’s standard genetic distance (Ds) value of 0.0612 was observed between Jattal and Dera Din Panah goats, and the mean Fst value was 0.013. The measures of genetic variation revealed a good scope for effective improvement, conservation, and designing national breeding policies, in future, for Pakistan goat breeds.

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.

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