Genetic Diversity of Kedu Chicken Based on Phenotypic Characteristics and Microsatellite Loci (original) (raw)
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The genetic variability of three varieties of indigenous Kadaknath breed of poultry was evaluated using 25 microsatellite markers. All the 25 microsatellite markers were found to be polymorphic in all the three varieties. Number of alleles observed for all the markers varied from 3 to 10. Allele size of polymorphic loci ranged from 98-356 bp and showed very large variation across loci. Average heterozygosity values were found to be 0.721, 0.694 and 0.689 in Jet black, Golden and Pencilled varieties, respectively. Overall heterozygosity value for all the microsatellite loci among all the three varieties was found to be 0.701. Average polymorphic information content (PIC) values were found to be 0.671, 0.699, and 0.617 in Jet black, Golden and Pencilled varieties, respectively. Overall PIC values for all the microsatellite loci among all the three varieties were found to be 0.662. The Nei's standard genetic distance (Ds) values between Jet black and Golden, Jet black and Pencilled, and Golden and Pencilled varieties were found to be 0.1678, 0.0951 and 0.1943 respectively. Phylogenetic consensus tree constructed using the boostrapped data and neighbour-joining method grouped all the three varieties into one cluster. Therefore, it is concluded that all the three varieties of Kadaknath breed had negligible genetic distance between each other.
2011
The genetic variability of three native chicken populations (Dashtiari, Khazak and Zabol) derived from Sistan and Baluchistan province in Iran was evaluated with 10 microsatellites markers (MCW5, MCW16, MCW18, MCW34, MCW39, ADL225, ADL262, ADL185, ADL136, ADL210). The mean heterozygosity was 0.77, 0.79 and 0.52 for Khazak, Dashtiari and Zabol chickens, respectively. The highest PIC was 0.81 in ADL225 and ADL136 at Dashtiari and Khazak chickens. The results of the heterozygosity were consistent with polymorphism information content (PIC). The genetic information in the current investigation will be used in conservation and improvement program of three native chickens.
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.
Asian Australasian Journal of Animal Sciences, 2008
The genetic structure and diversity of 15 Chinese indigenous chicken breeds was investigated using 29 microsatellite markers. The total number of birds examined was 542, on average 36 birds per breed. A total of 277 alleles (mean number 9.55 alleles per locus, ranging from 2 to 25) was observed. All populations showed high levels of heterozygosity with the lowest estimate of 0.440 for the Gushi chickens, and the highest one of 0.644 observed for Wannan Three-yellow chickens. The global heterozygote deficit across all populations (F IT ) amounted to 0.180 (p<0.001). About 16% of the total genetic variability originated from differences between breeds, with all loci contributing significantly to this differentiation. An unrooted consensus tree was constructed using the Neighbour-Joining method and pair-wise distances based on marker estimated kinships. Two main groups were found. The heavy-body type populations grouped together in one cluster while the light-body type populations formed the second cluster. The STRUCTURE software was used to assess genetic clustering of these chicken breeds. Similar to the phylogenetic analysis, the heavy-body type and light-body type populations separated first. Clustering analysis provided an accurate representation of the current genetic relations among the breeds. Remarkably similar breed rankings were obtained with all methods. (
Evaluation of genetic diversity in Chinese indigenous chicken breeds using microsatellite markers
Science China-life Sciences, 2006
China is rich in chicken genetic resources, and many indigenous breeds can be found throughout the country. Due to poor productive ability, some of them are threatened by the commercial varieties from domestic and foreign breeding companies. In a large-scale investigation into the current status of Chinese poultry genetic resources, 78 indigenous chicken breeds were surveyed and their blood samples collected. The genomes of these chickens were screened using microsatellite analysis. A total of 2740 individuals were genotyped for 27 microsatellite markers on 13 chromosomes. The number of alleles of the 27 markers ranged from 6 to 51 per locus with a mean of 18.74. Heterozygosity (H) values of the 78 chicken breeds were all more than 0.5. The average H value (0.622) and polymorphism information content (PIC, 0.573) of these breeds suggested that the Chinese indigenous chickens possessed more genetic diversity than that reported in many other countries. The fixation coefficients of subpopulations within the total population (F ST) for the 27 loci varied from 0.065 (LEI0166) to 0.209 (MCW0078), with a mean of 0.106. For all detected microsatellite loci, only one (LEI0194) deviated from Hardy-Weinberg equilibrium (HWE) across all the populations. As genetic drift or non-random mating can occur in small populations, breeds kept on conservation farms such as Langshan chicken generally had lower H values, while those kept on large populations within conservation regions possessed higher polymorphisms. The high genetic diversity in Chinese indigenous breeds is in agreement with great phenotypic variation of these breeds. Using Nei’s genetic distance and the Neighbor-Joining method, the indigenous Chinese chickens were classified into six categories that were generally consistent with their geographic distributions. The molecular information of genetic diversity will play an important role in conservation, supervision, and utilization of the chicken resources.
Study of genetic polymorphism of various chicken breeds using microsatellite markers
Indian Journal of Animal Research, 2015
A total number of 76 randomly selected birds i.e. 20 of Hill fowl (HF), 14 of Rhode Island Red (RIR), 14 of Kadaknath (KN), 14 of White LeghWDDorn (WLH) and 14 of White Cornish (WC) were genotyped using 25 microsatellite markers in the present study. Out of 25 microsatellite loci, 17 (~70%) were found to be polymorphic among these breeds. Across the breeds, total number of alleles ranged from 2 to 3 at polymorphic locus and average number of alleles per locus was 2.41. The allele size ranged between 98 bp and 340 bp. Among all the polymorphic microsatellite loci, observed heterozygosity were 0.441, 0.415, 0.287, 0.296 and 0.376 and expected heterozygosity were 0.435, 0.443, 0.387, 0.384 and 0.442 in HF, RIR, KN, WLH and WC, respectively. Polymorphic Information Content (PIC) estimates, across all the polymorphic loci were 0.346, 0.342, 0.305, 0.297 and 0.330 in HF, RIR, KN, WLH and WC, respectively.
Microsatellite marker based genetic diversity among four varieties of Pakistani Aseel chicken
2012
Indian Aseel chicken (Gallus gallus) is traditionally used as a favorite game bird all over the world. Bird fighting communities of Pakistan are the major source of its conservation and there are at least four distinctively recognized varieties of Aseel chicken based upon selective breeding, geographical location and color patterns. A pioneering study on genetic diversity of these varieties namely Lakha (n=17), Mushki (n=19), Mianwali (n=19) and Peshawari (n=13) was undertaken using FAO recommended 10 microsatellite loci. A total of 91 alleles were observed in 4 varieties of Aseel chicken with an average of 9.1 alleles per locus. Number of alleles varied between 4 to 8 in Lakha, 4 to 9 in Mushki, 3 to 10 in Mianwali and 3 to 7 in Pashawari. Mean polymorphic information content values were 0.67, 0.69, 0.71 and 0.65 in individual varieties, respectively. Mean observed and expected heterozygosity index values of 0.3941 and 0.7376 were recorded in Lakha, 0.4105 and 0.7468 for Mushki, 0....
Tow avian species; Japanese quail and Sinai chickens were examined genetically using 3 microsatellite markers to detect genetic variation. The studied loci on average produced 5.666 alleles per locus (range: 4-8). The mean observed heterozygosity (H o ) was 0.568 and ranged across loci from 0.125 to 0.900, whereas the mean expected heterozygosity (H e ) was 0.697 and ranged between 0.611 and 0.843. The polymorphic information content (PIC) values varied among loci and ranged between 0.519 for locus GUJ0063 and 0.806 for locus GUJ0087 with overall mean 0.637. Differentiation among populations was high (F ST = 0.311; R ST = -0.042). Sinai chickens showed no departure from Hardy-Weinberg equilibrium, while Japanese quails were not in Hardy-Weinberg equilibrium. These results reflect that, the set of studied markers can be used effectively to capture the magnitude of genetic variability in both of Sinai chicken and Japanese quail populations.
Genetic diversity of indigenous chickens from selected areas in Kenya using microsatellite markers
In this study, indigenous chickens were collected from eight different regions in Kenya and kept at InCIP-Egerton University. These were studied using eighteen microsatellite markers to determine genetic variation. Statistics related to genetic variation were estimated using GenA-LEx6. Mean percentage polymorphic loci (PPL) was 96.71% and 4% genetic variance (p ! 0.003) was seen between the eight populations. MCW0123 marker had the highest genetic variance of 13% among populations (p ! 0.003) at 95% CI. Mean He ranged from 0.351 ± 0.031 (SIB) to 0.434 ± 0.022 (BM) with a grand mean He of 0.399 ± 0.011 across the populations using the microsatellite markers. Nei's genetic distance ranged from 0.016 (SIB and WP) to 0.126 (NR and SIB). DARwin6.501 analysis software was used to draw the population dendrogram and two major population clusters were observed, also seen with PCoA. This study found a lot of genetic variation and relatedness within and among populations. Based on the phylogenetic tree result, it is concluded that the clustering of the chicken populations in the present study is not based on geographical proximity. The microsatellite markers used in this study were suitable for the measurement of the genetic biodiversity and relationship of Kenyan chicken populations. These results can therefore serve as an initial step to plan the conservation of indigenous chickens in Kenya.
Genetic Diversity of Eight Native Indonesian Chicken Breeds on Microsatellite Markers
HAYATI Journal of Biosciences
Indonesia has diversity in native chickens based on phenotypes. This diversity is utilized for economic purposes such as meat, eggs, fancy, crowing, and fighting. This study aimed to determine the genetic structure of eight native Indonesian chicken breeds with microsatellite markers, the genetic distance, and inbreeding coefficient of each breed of chicken used for crossbreeding programs to obtain a positive heterosis effect for selection programs. The samples used were Arab, Merawang, Pelung, Sentul, Cemani, KUB, Black Kedu and White Kedu. Broiler chickens (Cobb) were used as the outgroup in this study. A total of 192 DNA samples from eight breeds were used in this study. A total of 24 microsatellite markers were used in this study to observe the genetic diversity of 8 native breeds. The POPGENE, Cervus, and FSTAT were used to generate the observed number of alleles, the effective number of alleles, observed heterozygosity value, expected heterozygosity value, the heterozygote def...