Genetic diversity of indigenous chickens from selected areas in Kenya using microsatellite markers (original) (raw)
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Study on the genetic diversity of native chickens in northwest Ethiopia using microsatellite markers
In this study, indigenous chicken populations representing seven different areas of northwest Ethiopia were studied using microsatellite markers to determine genetic diversity and variation. Three local lines of South African chicken and two commercial chicken strains were included for comparison. The Ethiopian chicken population Gassay/Farta had the highest number of alleles per locus (10) for microsatellite marker MCW 158. MCW 154 was the most polymorphic marker across all populations with an average of seven different alleles. A high genetic diversity was observed in overall loci for all populations with heterozygosity (Ho) value of 0.77. The highest heterozygosity (0.93) across all markers was observed in the Mecha chicken population, while the lowest heterozygosity across all loci (0.66) was observed in the White Leghorn breed. The RIR commercial chicken breed showed higher genetic distance (lower genetic similarity) with the Ethiopian chicken populations than the South African...
Agriculturae Conspectus Scientificus, 2022
Knowledge of genetic diversity is a prerequisite for better utilization of any genetic resource. However, such information is insufficient for Nigerian indigenous chicken (NIC). Deoxyribonucleic acid (DNA) of NIC was extracted from FTA® paper and amplified with predefined microsatellite primer sets. A total of 180 chickens: northeast (NE; n=44), northwest (NW; n=25), north-central (NC; n=42) and southwest (SW; n=69) were genotyped along with 15 microsatellite markers to assess genetic diversity, demographic and population stratification. All microsatellites typed were found to be polymorphic (mean PIC = 0.53), and a total of 44 distinct alleles were detected. For all the loci, average inbreeding values (FIS) were ranged from-0.01 (NW chickens) to 0.17 (SW chickens), with an average value of 0.12, thus suggesting heterozygote excess. Most of the microsatellites deviated from Hardy-Weinberg equilibrium. SW and NC chickens related more closely having a genetic distance value of 0.02. The cluster analyses using STRUCTURE program indicated there were three primary populations, which provided evidence of extensive sharing of genetic variability, revealing varying levels of admixture among the studied population. The AMOVA analysis result indicated the proportion of genetic variation due to differences among populations and within populations was 5.46% and 96.56% respectively. Our results revealed multiple waves of introduction of diverse gene pools, and high panmixia has created and maintained a unique set of Gallus biodiversity in Nigeria.
Agriculturae Conspectus Scientificus, 2021
To understand the level of genetic diversity among and within three improved locally adapted chicken populations in Nigeria, six microsatellite markers were used with 100 genomic DNA from Shika Brown (SB = 34), FUNAAB Alpha (FA = 33), and Noiler (NL = 33). The allelic and genotypic profiles of each representative from each population were determined through polymerase chain reaction amplification of the repeat region. Genetic diversity, genetic distance, level of inbreeding, polymorphism information content, and combined exclusion probabilities of markers (CPE/CPF) were analyzed using Microsoft Excel microsatellite toolkit, GenAlex, Microsatellite Analyser, FSTAT, and Poptree2. 416 alleles with 18.99% rare and 81.01% fixed alleles were observed across populations. The mean number of alleles was 23.111 ± 0.43, mean effective number of alleles was 16.975 ± 0.75, the expected heterozygosity was 0.940 ± 0.00, observed heterozygosity was 0.396 ± 0.02, mean PIC value was 0.937, and mean gene flow rate was 10.874 ± 0.817. The mean FIS was 0.579 ± 0.037 and the global FST was 0.023 ± 0.002. Nei's genetic distance revealed that Shika Brown and the Noiler chicken populations were related (0.6985). The combined exclusion probability (CPE) across markers and populations was 0.999 (excluding a parent) and CPF was 1.000 (excluding both parents). The PIC/marker values across populations were greater than the minimum value of 0.5. High FIS and low FST value indicated a high inbreeding level within and low degree of genetic differentiation among the chicken populations. In conclusion, the microsatellite markers used are highly polymorphic and suitable for parentage analysis, control inbreeding, and could be used as baseline genetic information in conservation programs.
Genetic structure among the local chicken ecotypes of Tanzania based on microsatellite DNA typing
A study was conducted to evaluate the genetic structure of local chicken ecotypes of Tanzania using 20 polymorphic microsatellite DNA markers. A standard PCR was followed by manual genotyping (6% native polyacrylamide gel visualized by silver staining). Phylogenetic analysis of 13 individuals from each of the nine ecotypes named Ching'wekwe, Kuchi, Mbeya, Morogoro-medium, N'zenzegere, Pemba, Singamagazi, Unguja and a White Leghorn breed was performed. The ten populations assorted into nine clusters with chickens from the same ecotype often clustering together. It is concluded that there is high genetic relatedness within indigenous chicken ecotype than between ecotypes. This offers a basic step towards rational decision-making on the modalities of selective breeding without compromising the existence of each unique genetic resource.
Animal Science Journal, 2010
The characterization of indigenous animal genetic resources is a requisite step in providing needed information for the conservation of useful genotypes against future needs. Thus, in this study, 22 microsatellite markers were used to genotype 114 local chickens from the Forest (n = 59) and Savannah (n = 55) eco-zones of Ghana and the results compared to those of the ancestral red junglefowl (n = 15) and two European commercial chicken populations -a broiler (n = 25) and white leghorn (n = 25). A total of 171 alleles were observed, with an average of 7.8 alleles per locus. The local Ghanaian chickens showed higher diversity in terms of the observed number of alleles per locus (6.6) and observed heterozygosity (0.568) compared with the combined control populations (6.0 and 0.458, respectively). However, Wright's F-statistics revealed negligible genetic differentiation (FST) in local Ghanaian chicken populations. In addition, 65% of the Savannah chickens were inferred to be more likely from the Forest, suggesting a south-north dispersal of chickens from their probable original location in the Forest zone to the Savannah areas. It is concluded that the Forest and Savannah chickens of Ghana are a single, randomly mating unselected population, characterized by high genetic diversity and constitute a valuable resource for conservation and improvement.
Genetic Diversity of Kedu Chicken Based on Phenotypic Characteristics and Microsatellite Loci
International Journal of Poultry Science, 2012
This study was aimed to evaluate the genetic diversity based on phenotype and the genetic relationship between four kinds of Kedu chicken, using 4 microsatellite markers. The result from the phenotype observations showed that the four chicken breeds have qualitatively different plumage, skin, comb and shank colours. Cemani chickens' have lower egg production than others. The results from the isolation and identification of DNA using microsatellite primers showed that the 4 primers were polymorphics. The highest polymorphic information contain values based on locus derived from the entire population was LEI 0147 (0.643), while the average polymorphic information contain value on each population were 0.362, 0.531, 0.482 and 0.568 for Cemani, white Kedu, red Kedu and black Kedu chickens, respectively. Estimation of the heterozygosity value on loci of different populations of Kedu chickens showed a large variation (0.618-0.743). Genetic distance analysis showed that among Kedu chickens had a genetic relationship ranging from 0.018 to 0.236. The conclusion was that the genetic diversity based on chicken phenotypes and based on microsatellite markers in the population of Kedu chickens indicated a high diversity and had a relatively distant genetic relationship.
The Investigation of Genetic Variation at Microsatellite Loci in Mazandaran Native Chickens
International Journal of Poultry Science, 2007
Blood samples of Mazandaran native chickens were collected. A total of 90 genomic DNAs were isolated through optimized and modified salting-out procedure. The samples were used in Polymerase Chain Reaction (PCR) with 20 micro satellite markers. Amplified PCR-products with the markers were separated on 8% denaturing polyacrylamide gel. One locus (MCW216) was monomorphic. According to allele frequencies of 20 micro satellite sites, mean heterozygosity (H) and Polymorphism Information Content (PIC) were calculated. The number of alleles varying from 1 to 6 and an estimate of average heterozygosity excluding the monomorphic data was calculated as 0.5872. The average heterozygosity and PIC value calculated from data on polymorphic and monomorphic loci was 0.5579 and 0.4939, respectively. The results of the heterozygosity were consistent with that of PIC. Diversity estimates in this study are lower than the observed frequencies of heterozygotes reported in other species using micro satellite markers. Other parameters for intrapopulation variation and Hardy-Weinberg proportions were also considered. All the loci except MCW222 and MCW165 showed deviations from Hardy-Weinberg equilibrium (p<0.005). Some of micro satellite sites were highly polymorphic, so they were effective markers for genetic diversity analysis. These results could provide basic molecular data for the research on the germplasm characteristics of Mazandaran native chickens.
2012
The study aimed to evaluate the genetic diversity of Tanzanian chicken populations through phylogenetic relationship, and to trace the history of Tanzanian indigenous chickens. Five ecotypes of Tanzanian local chickens (Ching'wekwe, Kuchi, Morogoro-medium, Pemba and Unguja) from eight regions were studied. Diversity was assessed based on morphological measurements and 29 microsatellite markers recommended by ISAG/FAO advisory group on animal genetic diversity. A principal component analysis (PCA) of morphological measures distinguished individuals most by body sizes and body weight. Morogoro Medium, Pemba and Unguja were grouped together, while Ching'wekwe stood out because of their disproportionate short shanks and ulna bones. Kuchi formed an independent group owing to their comparably long body sizes. Microsatellite analysis revealed three clusters of Tanzanian chicken populations. These clusters encompassed i) Morogoro-medium and Ching'wekwe from Eastern and Central Zones ii) Unguja and Pemba from Zanzibar Islands and iii) Kuchi from Lake Zone regions, which formed an independent cluster. Sequence polymorphism of D-loop region was analysed to disclose the likely maternal origin of Tanzanian chickens. According to reference mtDNA haplotypes, the Tanzanian chickens that were sampled encompass two haplogroups of different genealogical origin. From haplotype network analysis, Tanzanian chickens probably originated on the Indian subcontinent and in Southeast Asia. The majority of Kuchi chickens clustered in a single haplogroup, which was previously found in Shamo game birds sampled from Shikoku Island of Japan in the Kōchi Prefecture. Analysis of phenotypic and molecular data, as well as the linguistic similarity of the breed names, suggests a recent introduction of the Kuchi breed to Tanzania.
South African Journal Of Animal Science
The objective of the study was to determine genetic diversity within South African indigenous chicken populations and the effectiveness of the current conservation flocks in capturing the available diversity in the founder populations. Two chicken populations, Venda (VD_C) and Ovambo (OV_C) conservation flocks (n = 56) from the Animal Production Institute in Irene and two founder population from which these conservation flocks were sampled; Venda (VD_F) and Ovambo (OV_F) field populations (n = 72) were genotyped for 29 autosomal microsatellite markers. All microsatellites typed were found to be polymorphic. A total of 213 alleles were observed for all four populations. The mean number of alleles per population ranged from 3.52 ± 1.09 (VD_C) to 6.62 ± 3.38 (OV_F). Mean observed (H O) and expected (H E) heterozygosity in the conservation flocks were 0.55 and 0.57 respectively. The corresponding values for the founder population were 0.62 and 0.68. The observed within population divers...
Italian Journal of Animal Science
South African native chicken breeds are no exception to the declining of local domestic breeds that has long been recognised and found associated with the commercialisation of breeding in domestic animals. The aims of the study were: (i) to provide a comprehensive view of genetic variation in four KwaZulu-Natal indigenous chicken populations (Jozini, Newcastle, Pietermaritzburg, and Port Shepstone), and (ii) to estimate the extent of differentiation of the village populations from three conserved South African indigenous pure breeds (Potchefstroom koekoek, Ovambo, and Venda) by genotyping individuals at 19 autosomal microsatellite loci. Finally, (iii) new information to the history of KwaZulu-Natal indigenous chicken populations was made available by exploring their phylogenetic relationship and their possible maternal origin through the mitochondrial DNA. The results suggested noticeable genetic diversity within and between ecotypes with clear sub-structuring between them. The indigenous populations had high genetic diversity (observed heterozygosity ranging from 0.61 in Pietermaritzburg to 0.70 in Jozini) while conserved populations showed considerable within population inbreeding coefficient (from 0.01 in Potchefstroom koekoek to 0.18 in Ovambo). Median-joining network analyses indicated the dominance of haplogroup E suggesting a likely Southeast Asia and/or Indian subcontinent origin. The presence of haplogroup B and C not only emphasises multiple maternal origin but also highlights genetic introgression of local chickens with commercial genotypes. These results highlighted the importance of local breeds as a genetic reservoir; moreover, the conservation of local breeds may play an important role in the local economy as a source of high-quality products for consumers. HIGHLIGHTS The genetic variation and differentiation of KwaZulu-Natal indigenous chicken populations and pure South African chicken breeds is investigated. The village populations showed a noticeable genetic variability with clear sub-structuring between them. The results can be used to improve a sustainable breeding and conservation programs to control possible genetic dilution with commercial genotypes.