Genetic diversity, population structure and ancestral origin of KwaZulu-Natal native chicken ecotypes using microsatellite and mitochondrial DNA markers (original) (raw)
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Genetic diversity and conservation of South African indigenous chicken populations
Journal of Animal Breeding and Genetics, 2011
Village chickens kept under smallholder-low input systems are considered important genetic resources that should be conserved against production threats and replacement with commercial hybrids (Muchadeyi et al. 2005, 2007a). In South Africa and most African countries, indigenous chickens are raised by smallholder farmers with little resources. Characterization of these genetic resources will serve as an
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...
Diversity and origin of South African chickens
Poultry Science, 2011
South African domestic chickens are important bird genetic resources, and more conservation efforts are being made to save these unique genotypes. Survey findings on South African chickens have illustrated that village chickens play very important socioeconomic roles in poor rural communities in that they can convert available feed around a house or village into highly nutritious, well-appreciated products (Mtileni et al., 2009). The animal protein consumed in rural areas frequently comes from village chicken meat and eggs. Chickens also have roles in traditional ceremonies and other customs as gift payments (Mtileni et al., 2009). These highly valuable genetic resources should be conserved for their adaptive features, traits of scientific and economic interest, cultural-historical value, strong links to regional traditions, and the ability to generate income for poor rural communities. Recent findings by Mtileni et al. (2011) using microsatellites shows that South African chicken populations added diversity to the existing diversity of both other African chickens as well as to purebred commercial lines, further justifying efforts to conserve these valuable genetic resources. Several hypotheses have been proposed regarding the maternal lineages of South African chickens. On the basis of microsatellite work, South African chickens could be a product of multiple domestication events,
Tropical Animal Health and Production, 2016
Conservation of locally adapted indigenous livestock breeds has become an important objective in sustainable animal breeding, as these breeds represent a unique genetic resource. Therefore, the Agricultural Research Council of South Africa initiated a conservation programme for four South African indigenous chicken breeds. The evaluation and monitoring of the genetic constitution of these conservation flocks is important for proper management of the conservation programme. Using molecular genetic analyses, the effective population sizes and relatedness of these conservation flocks were compared to village (field) chicken populations from which they were derived. Genetic diversity within and between these populations are further discussed within the context of population size. The conservation flocks for the respective breeds had relatively small effective population sizes (point estimate range 38.6-78.6) in comparison to the field populations (point estimate range 118.9-580.0). Furthermore, evidence supports a transient heterozygous excess, generally associated with the occurrence of a recent population bottleneck. Genetic diversity, as measured by the number of alleles, heterozygosity and information index, was also significantly reduced in the conservation flocks. The average relatedness amongst the conservation flocks was high, whilst it remained low for the field populations. There was also significant evidence for population differentiation between field and conservation populations. F st estimates for conservation flocks were moderate to high with a maximum reached between VD_C and VD_F (0.285). However, F st estimates for field population were excessively low between the NN_C and EC_F (0.007) and between EC_F and OV_F (0.009). The significant population differentiation of the conservation flocks from their geographically correlated field populations of origin is further supported by the analysis of molecular variance (AMOVA), with 10.51 % of genetic diversity ascribed to population differences within groups (F SC = 0.106). The results suggest that significant genetic erosion has occurred within the conservation flocks due to inbreeding, pronounced effects of random drift and selection. It might be necessary to introduce new breeding individuals from the respective field populations in order to increase the effective population sizes of the conservation flocks and counter the effects of genetic erosion.
Genetic distinctness of African, Asian and South American local chickens
Animal Genetics, 2000
The genetic variability of various local chicken populations derived from Bolivia, India, Nigeria and Tanzania was evaluated with 22 microsatellites. Between two and 11 alleles per locus were detected. All populations showed high levels of heterozygosity with the lowest value of 45% for the population named Aseel from India and the highest value of 67% for Arusha from Tanzania. A dendrogram was constructed based on CHORD distance by upgma analysis. Within this tree the populations were assorted according to their geographical origin. Bootstrapping values within the dendrogram were between 37 and 99%. The contribution of the determination of genetic variability with genetic markers to the decision on conservation and/or further use of the populations in crossbreeding programs designed to create genetic stocks with improved adaptability and productivity in tropical countries is discussed.
The amount of linkage disequilibrium (LD) is an important source of information about historical events of recombination and allows inferences about genetic diversity and genomic regions that have undergone selection. Linkage disequilibrium is equally important in studying effective population size and rate of inbreeding particularly in extensively raised and wild animal populations where pedigree records are scarce. The objective of this study was to investigate LD in village chicken populations of Southern Africa. These chickens are raised under scavenging systems of production characterized by uncontrolled breeding and frequent population bottlenecks due to disease outbreaks and fluctuations in feed supplies. DNA samples from 312 extensively raised chickens from South Africa, Malawi and Zimbabwe were genotyped using the Illumina iSelect chicken SNP60K BeadChip. A panel of 43,157 out of the total 57,636 (74.8%) SNPs was used in the final analysis after screening for those that had a minor allele frequency of less than 5%, were out of Hardy-Weinberg equilibrium (P<0.01) and had a call rate of less that 95%. Results indicated that LD averaged between 0.45 and 0.58 for SNPs that had a pairwise distance of less than 20 kb. LD dropped to 0.34 for SNPs between 20 and 100 kb after which it remained constant. LD was further analyzed for its decay over marker distance and differences between populations from different geographic locations. Results are discussed in terms of historical changes in effective population size and resultant recombination rates. The utility of the iSelect chicken SNP60K beadchip in investigating free-range chicken population genetics is demonstrated.
BMC Genetics, 2012
Background: Chickens represent an important animal genetic resource for improving farmers' income in Africa. The present study provides a comparative analysis of the genetic diversity of village chickens across a subset of African countries. Four hundred seventy-two chickens were sampled in 23 administrative provinces across Cameroon, Benin, Ghana, Côte d'Ivoire, and Morocco. Geographical coordinates were recorded to analyze the relationships between geographic distribution and genetic diversity. Molecular characterization was performed with a set of 22 microsatellite markers. Five commercial lines, broilers and layers, were also genotyped to investigate potential gene flow. A genetic diversity analysis was conducted both within and between populations. Results: High heterozygosity levels, ranging from 0.51 to 0.67, were reported for all local populations, corresponding to the values usually found in scavenging populations worldwide. Allelic richness varied from 2.04 for a commercial line to 4.84 for one population from Côte d'Ivoire. Evidence of gene flow between commercial and local populations was observed in Morocco and in Cameroon, which could be related to long-term improvement programs with the distribution of crossbred chicks. The impact of such introgressions seemed rather limited, probably because of poor adaptation of exotic birds to village conditions, and because of the consumers' preference for local chickens. No such gene flow was observed in Benin, Ghana, and Côte d'Ivoire, where improvement programs are also less developed. The clustering approach revealed an interesting similarity between local populations found in regions sharing high levels of precipitation, from Cameroon to Côte d'Ivoire. Restricting the study to Benin, Ghana, and Côte d'Ivoire, did not result in a typical breed structure but a south-west to north-east gradient was observed. Three genetically differentiated areas (P < 0.01) were identified, matching with Major Farming Systems (namely Tree Crop, Cereal-Root Crop, and Root Crop) described by the FAO.
The objectives of this study were to analyze genetic diversity and population structure of Sudanese native chicken breeds involved in a conservation program. Five Sudanese native chicken breeds were compared with populations studied previously, which included six purebred lines, six African populations and one Sudanese chicken population. Twenty-nine (29) microsatellite markers were genotyped individually in these five populations. Expected and observed heterozygosity, mean number of alleles per locus and inbreeding coefficient were calculated. A model based cluster analysis was carried out and a Neighbor net was constructed based on marker estimated kinships. Two hundred and one alleles were detected in all populations, with a mean number of 6.93 ± 3.52 alleles per locus. The mean observed and expected heterozygosity across 29 loci was 0.524 and 0.552, respectively. Total inbreeding coefficient (FIT ) was 0.069±0.112, while differentiation of subpopulations (FST 0.026±0.049) was low indicating the absence of clear sub-structuring of the Sudanese native chicken populations. The inbreeding coefficient (F IS ) was 0.036±0.076. STRUCTURE software was used to cluster individuals to 2 ≤ k ≤ 7 assumed clusters. Solutions with the highest similarity coefficient were found at K=5 and K=6, in which Malawian, Zimbabwean, and purebred lines split from Sudanese gene pool. The six Sudanese native chicken populations formed one heterogeneous cluster. We concluded that Sudanese native chickens are highly diverse, and are genetically separated from Malawian, Zimbabwean chickens and six purebred lines. Our study reveals the absence of population sub-structuring of the Sudanese indigenous chicken populations.
Animal Genetics, 2007
The objective of this study was to investigate the population structure of village chickens found in the five agro-ecological zones of Zimbabwe. Twenty-nine microsatellites were genotyped for chickens randomly selected from 13 populations, including the five eco-zones of Zimbabwe (n ¼ 238), Malawi (n ¼ 60), Sudan (n ¼ 48) and six purebred lines (n ¼ 180). A total of 280 alleles were observed in the 13 populations. Forty-eight of these alleles were unique to the Zimbabwe chicken ecotypes. The average number (±SD) of alleles/locus was 9.7 ± 5.10. The overall heterozygote deficiency in the Zimbabwe chickens (F IT ± SE) was 0.08 ± 0.01, over 90% of which was due to within-ecotype deficit (F IS ). Small Nei's standard genetic distances ranging from 0.02 to 0.05 were observed between Zimbabwe ecotypes compared with an average of 0.6 between purebred lines. The STRUCTURE software program was used to cluster individuals to 2 £ K £ 7 assumed clusters. The most probable clustering was found at K ¼ 6. Ninety-seven of 100 STRUCTURE runs were identical, in which Malawi, Sudan and purebred lines split out as independent clusters and the five Zimbabwe ecotypes clustered into one population. The within-ecotype marker-estimated kinships (mean ¼ 0.13) differed only slightly from the between-ecotype estimates. Results from this study lead to a rejection of the hypothesis that village chickens are substructured across agro-ecological zones but indicated high genetic diversity within the Zimbabwe chicken population.