scholarly journals Phenotypic and genotypic variability between two Nigerian indigenous goat population

2020 ◽  
Vol 45 (1) ◽  
pp. 1-8
Author(s):  
O. A. Ojo ◽  
G. N. Akpa ◽  
M. Orunmuyi ◽  
I. A. Adeyinka
Keyword(s):  
Microsatellite Markers ◽  
Tissue Sample ◽  
Shannon Index ◽  
Inbreeding Coefficient ◽  
Genotypic Variability ◽  
Tissue Samples ◽  
Expected Heterozygosity ◽  
Goat Population ◽  
The Mean ◽  
Phenotypic And Genotypic Variability

In order to estimate the future breeding potential of a livestock breed, it is necessary to estimate the level of genetic diversity within the breed. Thus, this study was conducted to determine the phenotypic and genotypic variability within the West African dwarf (WAD) goats and a non-descript goat population. The WAD goats were obtained from Bodija market Ibadan, Oyo state, while the non-descript goats were obtained from the Animal Science Departmental Farm in Zaria, Kaduna State. Random collection of tissue samples was carried out on each goat population using an all flex ear punch tissue sample collector and aliquoted into plastic tubes containing the all flex preservative. DNA extraction, amplification and sequencing were carried out at the International Livestock Research Institute (ILRI), Nairobi, Kenya. DNA was extracted from the tissue cells using the Pure Link™ Genomic DNA-minikit according to the manufacturer's specifications and protocol and 25 microsatellite markers as recommended by FAO/ISAG were used for genotyping. Twenty three of the 25 microsatellite markers used in this analysis had four or more alleles. The mean Shannon index (I), observed (Ho) and expected heterozygosity (He) and inbreeding coefficient (Fis) for the WAD goats were 1.568, 0.584, 0.679 and 0.167, respectively. For the non-descript goats, the mean Shannon index, observed and expected heterozygosity and inbreeding coefficient (Fis) were 1.607, 0.678, 0.721 and 0.041, respectively. The microsatellite markers used in this study showed their suitability for analysis of genetic variability in this population as demonstrated by the high mean Shannon index. This study has shown that these two goat populations are significantly different phenotypically and genetically. Also, both populations showed significant deviations (P<0.01) from Hardy-Weinberg expectations.  

Molecular genetic studies on Nellore and Deccani sheep using microsatellite markers

2017 ◽  
Author(s):  
P. Amareswari ◽  
M. Gnana Prakash ◽  
B. Ekambaram ◽  
M. Mahendar ◽  
Ch Hari Krishna
Keyword(s):  
Microsatellite Markers ◽  
Genetic Architecture ◽  
Molecular Genetic ◽  
Inbreeding Coefficient ◽  
Conservation Priority ◽  
Genetic Studies ◽  
Sheep Breeds ◽  
Expected Heterozygosity ◽  
The Mean ◽  
Nellore Sheep

The study was undertaken to understand the genetic architecture of Deccani and Nellore sheep breeds and to assess the genetic distance between the breeds. Allele diversity, genetic variability and population structure in the two breeds were estimated using 30 microsatellite markers. A total of 100 sheep, 50 each from Deccani and Nellore breeds were genotyped. The total number of alleles observed was 254 and 260 in Deccani and Nellore, respectively. The mean expected heterozygosity among the breeds ranged from 0.79 (Deccani) to 0.80 (Nellore) whereas the mean observed heterozygosity levels ranged from 0.77 in Deccani to 0.78 in Nellore sheep. The overall mean inbreeding coefficient was 0.029 in Deccani and 0.031 in Nellore sheep and of the 30 loci studied, 14 loci in Deccani and 16 loci in Nellore sheep showed negative inbreeding coefficient indicating the presence of outbreeding. However, eight loci (BM1314, BM6506, BM8125, ILSTS28, MAF70, MCM140, OarCB226 and OarFCB128) showed positive, mild to moderate inbreeding ranging from 0.007 to 0.25 in Deccani and 0.066 to 0.37 in Nellore sheep studied. The FIS values ranged from -0.372 to 0.74, FST values ranged from 0.001 to 0.172 and FIT values ranged from -0.370 to 0.728 between the Deccani and Nellore sheep breeds studied. The PIC values ranged from 0.498 to 0.886 with a mean of 0.773 in Deccani and from 0.574 to 0.894 with a mean of 0.777 in Nellore breed. The information generated from the present study will be valuable for setting conservation priority of these two 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.

scholarly journals Testing the breeding strategy of Hungarian Bronze turkey strains for maintaining genetic diversity with microsatellites

2011 ◽  
Vol 54 (4) ◽  
pp. 419-429
Author(s):  
S. Kusza ◽  
S. Mihók ◽  
L. Czeglédi ◽  
A. Jávor ◽  
M. Árnyasi
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Mating System ◽  
Breeding Strategy ◽  
Shannon Index ◽  
Inbreeding Coefficient ◽  
Control Population ◽  
Conservation Strategies ◽  
The Mean ◽  
Two Populations

Abstract. The aim of the study was to provide information on the genetic variability of the Hungarian Bronze turkey gene reserve population and its difference from the Broad-breasted turkey, and offer guidance and proposals for its future conservation strategies. Altogether, 239 Hungarian Bronze turkeys from 10 strains and 13 Broad-breasted turkeys as a control population were genotyped for 15 microsatellites. All loci were polymorphic with the average number of alleles per locus 3.20±1.146 in the Hungarian Bronze turkey. The mean expected (Hexp) and observed heterozygosity (Hobs) were not different (0.392 and 0.376, respectively) in the overall population, and similar values were obtained for hens and bucks and among hen strains. Inbreeding coefficient (FIS) and Shannon index (I) indicated that there was low inbreeding within hens and bucks. Our results confirm that the genetic diversity in the Hungarian Bronze turkey population has been preserved by the rotational mating system. Differences between the Hungarian Bronze turkey and the Broad-breasted turkey populations were determined. Nei’s unbiased values clearly indicated that the two populations are highly genetically differentiated.

Genetic characterization of local goats of Karnataka by microsatellite marker analysis

2018 ◽  
Author(s):  
R. Jayashree ◽  
M. R. Jayashankar ◽  
C. S. Nagaraja ◽  
Isloor Shrikrishna ◽  
K. Satyanarayana
Keyword(s):  
Microsatellite Marker ◽  
Genomic Dna ◽  
Genetic Characterization ◽  
Expected Heterozygosity ◽  
Marker Analysis ◽  
Goat Population ◽  
Pcr Products ◽  
The Mean ◽  
Microsatellite Marker Analysis

The diversity status of local goats of Karnataka was studied by using microsatellite marker analysis. The genomic DNA from unrelated local goats were PCR- amplified with a panel of 23 microsatellite markers. Microsatellite PCR products were multiplexed and run on capillary based genetic analyser and the raw data obtained was analysed. Totally 158 alleles were observed and the number of alleles ranged from three (ILSTS005 and OarJMP29) to 13 (RM088). The number of effective alleles ranged from 2.25 (ILSTS005) to 8.40 (RM088) in all the 23 loci studied. The mean observed heterozygosity (Ho) was 0.4698±0.2214 [range 0 (ETH225) to 0.8462 (ILSTS034)] and the mean expected heterozygosity (He) was 0.7471± 0.1098 [range 0.5656 (ILSTS005) to 0.9138 (SRCRSP 8)] indicating the heterogenous nature of the local goat population of Karnataka.

Identification and structure analysis of three tilapia species using microsatellite markers

2009 ◽  
Vol 6 (2) ◽  
pp. 119-125
Author(s):  
Song Hong-Mei ◽  
Bai Jun-Jie ◽  
Quan Ying-Chun ◽  
Li Sheng-Jie
Keyword(s):  
Microsatellite Markers ◽  
Clustering Analysis ◽  
Phylogenetic Trees ◽  
Mean Value ◽  
Group Method ◽  
Oreochromis Aureus ◽  
Arithmetic Average ◽  
Pair Group ◽  
Expected Heterozygosity ◽  
The Mean

AbstractSeventeen special loci were selected from 77 microsatellite markers to distinguish three varieties of tilapias, including the six differential loci UNH636, UNH117, UNH172, UNH738, UNH878 and UNH896 in Oreochromis aureus; five differential loci UNH913, UNH907, UNH222, UNH980 and UNH880 in O. niloticus; and six differential loci of UNH876, UNH899, UNH853, UNH932, UNH933 and UNH773 in O. mossambicus. Any one of the 17 loci could amplify particular bands to distinguish one tilapia from the other two. The genetic structure of O. aureus, O. niloticus and O. mossambicus stocks and their phylogenetic relationships were also analysed using these 17 loci. In total 142 alleles were detected, and the average number of alleles per locus was 8.35. Additionally, a clustering analysis was performed based on the result of the Popgen32 software package and phylogenetic trees were constructed by MEGA4 using the unweighted pair group method using arithmetic average (UPGMA). The results showed that the mean value of observed heterozygosity was 0.0941, 0.5490 and 0.2588, the mean value of expected heterozygosity was 0.1089, 0.7230 and 0.1965, and the polymorphism information content was 0.0869, 0.7149 and 0.1643, in O. aureus, O. niloticus and O. mossambicus, respectively. The UPGMA tree demonstrated that O. aureus was more closely related to O. mossambicus than to O. niloticus.

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 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.

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 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.

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