scholarly journals Genetic diversity and population structure of indigenous chicken in Rwanda using microsatellite markers

2019 ◽  
Author(s):  
R. Habimana ◽  
T.O. Okeno ◽  
K. Ngeno ◽  
S. Mboumba ◽  
P. Assami ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Genetic Improvement ◽  
Eastern Region ◽  
Indigenous Chicken ◽  
North West ◽  
Ecological Zones ◽  
The North ◽  
Hardy Weinberg Equilibrium ◽  
Private Alleles

AbstractRwanda has about 4.5 million of indigenous chicken (IC) that are very low in productivity. To initiate any genetic improvement programme, IC needs to be accurately characterized. The key purpose of this study was to ascertain the genetic diversity of IC in Rwanda using microsatellite markers. Blood samples of IC sampled from 5 agro-ecological zones were collected from which DNA was extracted, amplified by PCR and genotyped using 28 microsatellite markers. A total of 325 (313 indigenous and 12 exotic) chicken were genotyped and revealed a total number of 305 alleles varying between 2 and 22 with a mean of 10.89 per locus. 186 distinct alleles and 60 private alleles were also observed. The frequency of private alleles was highest in samples from the Eastern region, whereas those from the North West had the lowest. The influx of genes was lower in the Eastern agro-ecological zone than the North West. The mean observed heterozygosity was 0.6155, whereas the average expected heterozygosity was 0.688. The overall inbreeding coefficient among the population was 0.040. Divergence from the Hardy-Weinberg equilibrium was significant in 90% of loci in all the populations. The analysis of molecular variance revealed that about 92% of the total variation originated from variation within populations. Additionally, the study demonstrated that IC in Rwanda could be clustered into four gene groups. In conclusion, there was considerable genetic diversity in IC in Rwanda, which represents a crucial genetic resource that can be conserved or optimized through genetic improvement.

scholarly journals Molecular characterization of Iranian dromedaries using microsatellite markers

2021 ◽  
Vol 69 (4) ◽  
pp. 321-330
Author(s):  
Mohammadreza Mohammadabadi ◽  
Mehrdad Ghasemi Meymandi ◽  
Mahdieh Montazeri ◽  
Volodymyr Afanasenko ◽  
Oleksandr Kalashnyk
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Camelus Dromedarius ◽  
Conservation Strategies ◽  
The North ◽  
Allele Number ◽  
Total Genetic Diversity ◽  
Hardy Weinberg Equilibrium ◽  
Different Populations ◽  
Future Direction

Considering the importance of maintaining the genetic diversity in native animals, this study conducted to analyse genetic diversity in dromedary populations in the north of Kerman province, Iran, using eight autosomal microsatellite markers. Eighty-one blood samples were collected from five different populations and DNA was extracted. The highest and the lowest allele number and effective alleles were shown in YWLL08 (21 and 4) and VOLP32 (14.97 and 3.11), respectively. The expected heterozygosity varied from 0.778 in Sahra-e Jahad population to 0.847 in Nogh population. The test for Hardy-Weinberg equilibrium showed significant deviations in most loci. The mean multilocus FST value (0.057) suggested that differentiation is moderate between populations. From total genetic diversity, only 6% were due to differentiation among populations, while the remaining 94% corresponded to differences among individuals within each population. The results of the current study indicated that the Camelus dromedarius populations in the north of Kerman province have a relativity high genetic variation and the data could be useful for designing the breeding strategies and conservation. The degree of variability demonstrated implies that studied populations are rich reservoirs of genetic diversity that must be preserved. A future direction to our study can be studying all of the Iranian Camelus dromedarius populations to better evaluate the level of inbreeding and establish the appropriate conservation strategies aimed to avoid losses of genetic diversity.

scholarly journals Assessment of Population Structure and Genetic Diversity of 15 Chinese Indigenous Chicken Breeds Using Microsatellite Markers

2008 ◽  
Vol 21 (3) ◽  
pp. 331-339 ◽  
Author(s):  
Guohong Chen ◽  
Wenbin Bao ◽  
Jingting Shu ◽  
Congliang Ji ◽  
Minqiang Wang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Microsatellite Markers ◽  
Indigenous Chicken ◽  
Chicken Breeds

scholarly journals Genetic diversity of Ukrainian local pig breeds based on microsatellite markers

2018 ◽  
Vol 9 (2) ◽  
pp. 177-182 ◽  
Author(s):  
S. S. Kramarenko ◽  
S. I. Lugovoy ◽  
V. R. Kharzinova ◽  
V. Y. Lykhach ◽  
A. S. Kramarenko ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Microsatellite Markers ◽  
Pig Breeds ◽  
Genetic Groups ◽  
The Mean ◽  
Living Material ◽  
The Individual ◽  
High Degree ◽  
Private Alleles

Preserving the current diversity of the living material on Earth is fundamental for the survival of future generations . A study was conducted to investigate the genetic diversity of Ukrainian local pig breeds. A total of 350 pigs representing five local pig breeds from Ukraine (Mirgorod – MIR, Poltava Meat – PM, Ukrainian Meat – UM, Ukrainian White Steppe – UWS and Ukrainian Spotted Steppe – USS) and one commercial breed (Duroc, DUR) were sampled. Twelve microsatellite loci (SW24, S0155, SW72, SW951, S0386, S0355, SW240, SW857, S0101, SW936, SW911 and S0228) were selected and belong to the list of microsatellite markers recommended by ISAG. The results indicate that there exists, in general, a high degree of genetic variability within the five Ukrainian local pig breeds. However, the genetic variability in the MIR and PM breeds was significantly lower (mean Na = 2.92–3.92; Ho = 0.382–0.411; FIS = 0.178–0.184) than in the other three Ukrainian local pig breeds – UM, UWS and USS (mean Na = 5.00–8.42; Ho = 0.549–0.668; FIS = 0.027–0.066). Thirty-four private alleles were identified among the six analyzed genetic groups which were distributed between 11 of the 12 loci. A high number of alleles typical for the breed (private alleles) was observed in Duroc pigs – 9 alleles did not occur in Ukrainian local pig breeds. The HWE test showed that all of the polymorphic loci deviated from HWE (P < 0.05) in at least one population. Loci S0355 (5), S0386 (4) and SW24 (4) presented a higher number of populations in imbalance. The mean FST showed that approximately 77.8% of the genetic variation was within-population and 12.2% was across the populations. The five Ukrainian local breeds were classified into two major groups, according to the phylogenetic tree, which was based on standard genetic distance. Overall, we found that 92.6% of the individual pigs were correctly assigned (324 out of 350) to the respective breed of origin, which is likely a consequence of the well-defined breed structure. Probabilities from the allocation test of individuals for the six pig genetic groups were estimated with Structure Harvester. In cluster 1 the highest grouping probabilities were found for the MIR (0.917) and PM (0.750) breeds. Local breeds UM (0.824) and USS (0.772) were grouped in cluster 2. Cluster 3 was related to the local pig breed USW (0.873). Cluster 4 presented high allocation probabilities for the commercial pig breed Duroc (0.924). The obtained results are important for the future conservation of Ukrainian local pig breeds.

Evaluation of Genetic Diversity and Genetic Distance Between Twelve Chinese Indigenous Chicken Breeds Based on Microsatellite Markers

2006 ◽  
Vol 5 (6) ◽  
pp. 550-556 ◽  
Author(s):  
Yu Ya-Bo . ◽  
Wang Jin-Yu . ◽  
D.M. Mekki . ◽  
Tang Qing-Ping . ◽  
Li Hui-Fang . ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Microsatellite Markers ◽  
Indigenous Chicken ◽  
Chicken Breeds

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.

Evaluation of genetic diversity in Chinese indigenous chicken breeds using microsatellite markers

2006 ◽  
Vol 49 (4) ◽  
pp. 332-341 ◽  
Author(s):  
Lujiang Qu ◽  
Xianyao Li ◽  
Guifang Xu ◽  
Kuanwei Chen ◽  
Hongjie Yang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Indigenous Chicken ◽  
Chicken Breeds

scholarly journals Genetic diversity and genetic relatedness in P. falciparum parasite population in individuals with uncomplicated malaria based on Microsatellite typing in Eastern and Western regions of Uganda, 2019-2020.

2021 ◽  
Author(s):  
Agaba B. Bosco ◽  
Karen Anderson ◽  
Karryn Gresty ◽  
Christiane Prosser ◽  
David Smith ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Genetic Relatedness ◽  
Statistical Testing ◽  
Eastern Region ◽  
Multiplicity Of Infection ◽  
Close Monitoring ◽  
Genetic Sequencing ◽  
Epidemiological Surveys ◽  
High Level

Abstract Background: Genetic diversity and parasite relatedness are essential parameters for assessing impact of interventions and understanding transmission dynamics of malaria parasites however data on its status in P. falciparum populations in Uganda is limited. We used microsatellite markers and DNA sequencing to determine diversity and molecular characterization of P. falciparum parasite populations in Uganda. Methods: A total of 147 P. falciparum genomic DNA samples collected from cross-sectional surveys in symptomatic individuals 2-10 years were characterized by genotyping of seven highly polymorphic neutral microsatellite markers (n=85) and genetic sequencing of the Histidine Rich Protein 2 (pfhrp2) gene (n=62). ArcGIS was used to map the geographical distribution of isolates while statistical testing was done using Student's t-test or Wilcoxon's rank-sum test and Fisher’s exact test as appropriate at P ≤ 0.05. Results: Overall, 75.5% (95% CI: 61.1 - 85.8) and 24.5 % (95% CI:14.2 - 38.9) of parasites examined were of multiclonal (mixed genotype) and single clone infections respectively. Multiclonal infections occurred more frequently in the Eastern region 73.7% (95% CI: 48.8 - 89.1), P<0.05. Overall, multiplicity of infection (MOI) was 1.9 (95% CI: 1.7 - 2.1), P=0.01 that was similar between age groups (1.8 vs 1.9), P=0.60 and regions (1.9 vs 1.8), P=0.43 for the <5 and ≥5 years and Eastern and Western regions respectively. Genomic sequencing of the pfhrp2 exon2 revealed a high level of genetic diversity reflected in 96.8% (60/62) unique sequence types. Repeat type AHHAAAHHATD and HRP2 sequence Type C were more frequent in RDT-/PCR+ samples (1.9% vs 1.5%) and (13% vs 8%), P<0.05 respectively. Genetic relatedness analysis revealed small clusters of gene deleted parasites in Uganda, but no clustering with Eritrean parasites. Conclusion: We observed a high level of genetic diversity of P. falciparum parasites reflected in the frequency of multiclonal infections, multiplicity of infection and variability of the pfhrp2 gene in these samples. These findings are consistent with the high malaria transmission intensity and endemicity in these settings despite the scaling up of malaria interventions. Findings highlight the need for selection of appropriate molecular tools for detection of drug resistance and pfhrp2 gene deletions in multiclonal infections. Genetic analysis suggested spontaneous emergence and clonal expansion of pfhrp2 deleted parasites that require close monitoring to inform national malaria diagnosis and case management policies. We recommend future molecular epidemiological surveys on parasite genomics that are more representative with wider coverage.

scholarly journals De novo developed microsatellite markers in gill parasites of the genus Dactylogyrus (Monogenea): revealing the phylogeographic pattern of population structure in the generalist parasite Dactylogyrus vistulae

2021 ◽  
Author(s):  
Michal Benovics ◽  
Lenka Gettová ◽  
Andrea Simková
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Microsatellite Markers ◽  
Parasite Species ◽  
De Novo ◽  
High Genetic Diversity ◽  
Genetic Studies ◽  
The North ◽  
Gill Parasites ◽  
Modern Population

Approaches using microsatellite markers are considered the gold standard for modern population-genetic studies. However, though they have found application in research into various platyhelminth taxa, they remained substantially underutilized in the study of monogeneans. In the present study, a newly-developed set of 24 microsatellite markers was used to investigate the genetic diversity of the generalist monogenean species D. vistulae. The analyzed parasite specimens were collected from 13 cyprinoid species from 11 sites in the Apennine and Balkan peninsulas. A total of 159 specimens were genotyped at each of the loci and the number of alleles per locus ranged from 2 to 16, with a mean number of 6.958 alleles per locus. Exceptionally high genetic diversity was observed among D. vistulae individuals in the southern Balkans, suggesting that this region might represent the center of diversification of the genus in Europe, from where Dactylogyrus parasites expanded into the north. The initial clustering analysis divided all investigated specimens into three major clusters; however, the results of the subsequent analyses revealed the existence of various subpopulations, suggesting that the population structure of D. vistulae is associated with the diversification of their cyprinoid hosts. In addition, partition of the parasite population was observed in regions of the sympatric occurrence of two host species, indicating that these hosts may represent a barrier to gene flow, even for generalist parasite species.

scholarly journals Analysis of Genetic Diversity and Population Structure of Orobanche foetida Populations From Tunisia Using RADseq

2021 ◽  
Vol 12 ◽  
Author(s):  
Amal Boukteb ◽  
Shota Sakaguchi ◽  
Yasunori Ichihashi ◽  
Mohamed Kharrat ◽  
Atsushi J. Nagano ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Faba Bean ◽  
Isolation By Distance ◽  
Distance Effect ◽  
Wild Plant ◽  
Clustering Methods ◽  
North West ◽  
North East ◽  
The North

Orobanche foetida Poiret is a holoparasitic plant that lacks chlorophyll and totally depending on its host for its growth. Orobanche foetida parasitizes host plant roots and extract nutrient and water via a haustorium. Although O. foetida distributes in the Mediterranean region as a wild plant parasite, it parasitizes faba bean causing serious damages which may reach 90% yield losses in Tunisia. Analysis of genetic diversity of the parasite is important to better understand its evolution and spread, remained largely unknown. In this work, we present the first study on genetic diversity and population structure using the robust technique Restriction-site-Associated DNA sequencing (RADseq) for Orobanche spp. We collected 244 samples of O. foetida from 18 faba bean fields in the north of Tunisia including 17 populations from the north-west and one population form the north-east. To overcome the difficulty of SNP discovery in O. foetida genome as a non-model and tetraploid plant, we utilized three different informatics pipelines, namely UNEAK, pyRAD and Stacks. This study showed that genetic differentiation occurred in the Tunisian O. foetida emphasizing the isolation by distance effect. However, no strong population clustering was detected in this work basing on the three data sets and clustering methods used. The present study shed the light on the current distribution and the genetic variation situation of the fetid broomrape in Tunisia, highlighting the importance of understanding the evolution of this parasite and its genetic background. This will aid in developing efficient strategies to control this parasite and its expansion in Tunisia and worldwide.

Sign in / Sign up

Export Citation Format

Share Document