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.

Microsatellite marker-based estimation of the genetic diversity of cattle in Chongqing

2018 ◽  
Author(s):  
Weiwei Ni ◽  
An Jiang ◽  
Jian Zhang ◽  
Guangxin E ◽  
Yongfu Huang
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Microsatellite Marker ◽  
Weinberg Equilibrium ◽  
The Future ◽  
Hardy Weinberg Equilibrium ◽  
The Mean ◽  
Coefficient Of Inbreeding

Cattle are the main source of meat in Chongqing. This study investigated the genetic diversity of cattle native to Chongqing and 4 introduced breeds. A total of 96 individuals from 5 breeds were genotyped using six microsatellite markers. Five markers were highly polymorphic within the breed populations, and one marker had moderate levels of polymorphism. Heterozygosity ranged from 0.5379±0.0434 in Simmental to 0.6667±0.0559 in Charolais. The heterozygosity deficit was significant in all populations analyzed compared with the expected level of heterozygosity. In addition, two microsatellite markers (TGLA53 and OarFCB20) deviated from Hardy-Weinberg equilibrium across populations (except in cattle native to Chongqing). The mean number of alleles ranged from 6.00±2.37 in Angus to 7.17±2.14 in Droughtmaster across six markers. The coefficient of inbreeding ranged from 0.0017 in Simmental and Droughtmaster to 0.0367 in Angus. Pairwise difference analyses revealed that Simmental and Droughtmaster were the most differentiated (FST= 0.06861) from each other, whereas cattle native to Chongqing and Charolais were the least differentiated (FST= 0.00557). In summary, this study showed that cattle native to Chongqing and 4 introduced breeds were genetically well protected in Chongqing, and information from this study would be helpful for guiding hybridization and genetic improvements in the future.

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 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.

Genetic variability of sheep populations of Saudi Arabia using microsatellite markers

2018 ◽  
Author(s):  
Ahmed H. Mahmoud ◽  
Faisal M. Abou Tarboush ◽  
Ahmed Rady ◽  
Khalid M. Al-Anaz Mohammad Abul Farah ◽  
Osama B. Mohammed
Keyword(s):  
Genetic Diversity ◽  
Saudi Arabia ◽  
Genetic Variability ◽  
Microsatellite Markers ◽  
Population Differentiation ◽  
Genomic Dna ◽  
Mean Value ◽  
Weinberg Equilibrium ◽  
Expected Heterozygosity ◽  
Hardy Weinberg Equilibrium

The present study was conducted to know the genetic diversity of three Saudi sheep populations; Naeimi (NM), Herri (H) and Najdi (NJ). Genomic DNA was extracted from 156 animals of sheep comprising 47 Naeimi, 47 Herri and 62 Najdi breeds using 18 microsatellite markers. A total of 212 alleles were generated with a mean value of 11.80 alleles per locus, with a range of observed and expected heterozygosity of 0.505 to 0.875 and 0.595 to 0.854, respectively. Eleven of the microsatellites loci studied in NM, three loci in H and fifteen loci in NJ were observed to be deviated from Hardy-Weinberg equilibrium. The fixation genetic indices (Fst) among the three sheep populations were very low, ranging from 0.017 (between NJ and H) to 0.033 (between NJ and NM), indicating low population differentiation among the three sheep populations studied. The present study showed that the microsatellite markers are powerful tool in determining genetic diversity among sheep populations.

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 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.

scholarly journals Microsatellite Markers in Hazelnut: Isolation, Characterization, and Cross-species Amplification

2005 ◽  
Vol 130 (4) ◽  
pp. 543-549 ◽  
Author(s):  
Nahla V. Bassil ◽  
R. Botta ◽  
S.A. Mehlenbacher
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Geographical Origin ◽  
Genome Mapping ◽  
Polymorphic Information Content ◽  
Corylus Avellana ◽  
Expected Heterozygosity ◽  
Gaa Repeats ◽  
Microsatellite Alleles ◽  
Simple Sequence

Three microsatellite-enriched libraries of the european hazelnut (Corylus avellana L.) were constructed: library A for CA repeats, library B for GA repeats, and library C for GAA repeats. Twenty-five primer pairs amplified easy-to-score single loci and were used to investigate polymorphism among 20 C. avellana genotypes and to evaluate cross-species amplification in seven Corylus L. species. Microsatellite alleles were estimated by fluorescent capillary electrophoresis fragment sizing. The number of alleles per locus ranged from 2 to 12 (average = 7.16) in C. avellana and from 5 to 22 overall (average = 13.32). With the exception of CAC-B110, di-nucleotide SSRs were characterized by a relatively large number of alleles per locus (≥5), high average observed and expected heterozygosity (Ho and He > 0.6), and a high mean polymorphic information content (PIC ≥ 0.6) in C. avellana. In contrast, tri-nucleotide microsatellites were more homozygous (Ho = 0.4 on average) and less informative than di-nucleotide simple sequence repeats (SSRs) as indicated by a lower mean number of alleles per locus (4.5), He (0.59), and PIC (0.54). Cross-species amplification in Corylus was demonstrated. These microsatellite markers were highly heterozygous and polymorphic and differentiated among genotypes of C. avellana irrespective of geographical origin. They will aid in fingerprinting genotypes of the european hazelnut and other Corylus species, genome mapping, and genetic diversity assessments.

scholarly journals Genetic Polymorphism of Calpastatin (CAST) Gene in Pasundan Cattle

2018 ◽  
Vol 42 (4) ◽  
Author(s):  
Slamet Diah Volkandari ◽  
Aina Nadila ◽  
Nani Radiastuti ◽  
Endang Tri Margawati
Keyword(s):  
Genetic Diversity ◽  
Information Content ◽  
Polymorphic Information Content ◽  
Fresh Blood ◽  
Weinberg Equilibrium ◽  
Pcr Rflp ◽  
Hardy Weinberg Equilibrium ◽  
Pcr Method ◽  
Variant Alleles ◽  
Cast Gene

The aim of this study was to determine genetic diversity of Calpastatin gene (CAST) in Pasundan cattle. Forty-four fresh blood samples were collected from UPTD BPPT Beef Cattle Ciamis West Java. Genomic DNA samples were extracted using High Salt method. A 523 bp fragment of Calpastatin gene was successfully amplified using PCR method. Genotyping of CAST gene was conducted by PCR-RFLP method using RsaI restriction enzyme (GT^AC). Genotypes and alleles were analyzed using software Cervus 3.0.7. Parameters were observed i.e genotypes and alleles frequencies, heterozygosity observed (Ho) and expected (He), Hardy Weinberg Equilibrium (HWE), and Polymorphic Information Content (PIC). Result showed that three variant genotypes of GG, GC and CC were found and two variant alleles of G and C. Allele G was found higher (0.77) than allele C (0.23). Population of Pasundan cattle was found polymorphism and in the Hardy Weinberg Equilibrium. Polymorphic Information Content (PIC) value showed in a moderate (0.290) condition. Values of Heterozygosity observed and expected were 0.409 and 0.355 respectively. This research concludes that there is polymorphism of CAST gene in Pasundan cattle population and has genetic diversity. This result could be used as early genetic information in exploration of Pasundan cattle.

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 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.

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