Population genetic structure, linkage disequilibrium and effective population size of conserved and extensively raised village chicken populations of Southern Africa
Extensively raised village chickens are considered a valuable source of biodiversity, with genetic variability developed over thousands of years that ought to be characterised and utilized. Surveys that can reveal a population’s genetic structure and provide an insight into its demographic history w...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2015-02-01
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| Series: | Frontiers in Genetics |
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| Online Access: | http://journal.frontiersin.org/Journal/10.3389/fgene.2015.00013/full |
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| author | Khulekhani Sedwell Khanyile Khulekhani Sedwell Khanyile Edgar Farai Dzomba Farai Catherine Muchadeyi |
| author_facet | Khulekhani Sedwell Khanyile Khulekhani Sedwell Khanyile Edgar Farai Dzomba Farai Catherine Muchadeyi |
| author_sort | Khulekhani Sedwell Khanyile |
| collection | DOAJ |
| description | Extensively raised village chickens are considered a valuable source of biodiversity, with genetic variability developed over thousands of years that ought to be characterised and utilized. Surveys that can reveal a population’s genetic structure and provide an insight into its demographic history will give valuable information to manage and conserve important indigenous animal genetic resources. This study reports population diversity and structure, linkage disequilibrium and effective population sizes of Southern African village chickens and conservation flocks from South Africa. DNA samples from 312 chickens from South African village and conservation flocks (n =146), Malawi (n =30) and Zimbabwe (n =136) were genotyped using the Illumina iSelect chicken SNP60K BeadChip. Population genetic structure analysis distinguished the four conservation flocks from the village chicken populations. Of the four flocks, the Ovambo clustered closer to the village chickens particularly those sampled from South Africa. Clustering of the village chickens followed a geographic gradient whereby South African chickens were closer to those from Zimbabwe than to chickens from Malawi. Different conservation flocks seemed to have maintained different components of the ancestral genomes with a higher proportion of village chicken diversity found in the Ovambo population. Overall population LD averaged over chromosomes ranged from 0.03 ± 0.07 to 0.58 ± 0.41 and averaged 0.15 ± 0.16. Higher LD, ranging from 0.29-0.36, was observed between SNP markers that were less than 10kb apart in the conservation flocks. LD in the conservation flocks steadily decreased to 0.15 (PK) and 0.24 (VD) at SNP marker interval of 500kb. Genomewide LD decay in the village chickens from Malawi, Zimbabwe and South Africa followed a similar trend as the conservation flocks although the mean LD values for the investigated SNP intervals were lower. The results suggest low effective population sizes particularly in the |
| first_indexed | 2024-12-11T13:51:19Z |
| format | Article |
| id | doaj.art-0f1b996cb1804e73aef72bc1f0792232 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-11T13:51:19Z |
| publishDate | 2015-02-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-0f1b996cb1804e73aef72bc1f07922322022-12-22T01:04:16ZengFrontiers Media S.A.Frontiers in Genetics1664-80212015-02-01610.3389/fgene.2015.0001393479Population genetic structure, linkage disequilibrium and effective population size of conserved and extensively raised village chicken populations of Southern AfricaKhulekhani Sedwell Khanyile0Khulekhani Sedwell Khanyile1Edgar Farai Dzomba2Farai Catherine Muchadeyi3Agricultural Research Council, South AfricaUniversity of KwaZulu-NatalUniversity of KwaZulu-NatalAgricultural Research Council, South AfricaExtensively raised village chickens are considered a valuable source of biodiversity, with genetic variability developed over thousands of years that ought to be characterised and utilized. Surveys that can reveal a population’s genetic structure and provide an insight into its demographic history will give valuable information to manage and conserve important indigenous animal genetic resources. This study reports population diversity and structure, linkage disequilibrium and effective population sizes of Southern African village chickens and conservation flocks from South Africa. DNA samples from 312 chickens from South African village and conservation flocks (n =146), Malawi (n =30) and Zimbabwe (n =136) were genotyped using the Illumina iSelect chicken SNP60K BeadChip. Population genetic structure analysis distinguished the four conservation flocks from the village chicken populations. Of the four flocks, the Ovambo clustered closer to the village chickens particularly those sampled from South Africa. Clustering of the village chickens followed a geographic gradient whereby South African chickens were closer to those from Zimbabwe than to chickens from Malawi. Different conservation flocks seemed to have maintained different components of the ancestral genomes with a higher proportion of village chicken diversity found in the Ovambo population. Overall population LD averaged over chromosomes ranged from 0.03 ± 0.07 to 0.58 ± 0.41 and averaged 0.15 ± 0.16. Higher LD, ranging from 0.29-0.36, was observed between SNP markers that were less than 10kb apart in the conservation flocks. LD in the conservation flocks steadily decreased to 0.15 (PK) and 0.24 (VD) at SNP marker interval of 500kb. Genomewide LD decay in the village chickens from Malawi, Zimbabwe and South Africa followed a similar trend as the conservation flocks although the mean LD values for the investigated SNP intervals were lower. The results suggest low effective population sizes particularly in thehttp://journal.frontiersin.org/Journal/10.3389/fgene.2015.00013/fullLinkage Disequilibriumgenetic diversitysnpseffective population sizeVillage chickens |
| spellingShingle | Khulekhani Sedwell Khanyile Khulekhani Sedwell Khanyile Edgar Farai Dzomba Farai Catherine Muchadeyi Population genetic structure, linkage disequilibrium and effective population size of conserved and extensively raised village chicken populations of Southern Africa Frontiers in Genetics Linkage Disequilibrium genetic diversity snps effective population size Village chickens |
| title | Population genetic structure, linkage disequilibrium and effective population size of conserved and extensively raised village chicken populations of Southern Africa |
| title_full | Population genetic structure, linkage disequilibrium and effective population size of conserved and extensively raised village chicken populations of Southern Africa |
| title_fullStr | Population genetic structure, linkage disequilibrium and effective population size of conserved and extensively raised village chicken populations of Southern Africa |
| title_full_unstemmed | Population genetic structure, linkage disequilibrium and effective population size of conserved and extensively raised village chicken populations of Southern Africa |
| title_short | Population genetic structure, linkage disequilibrium and effective population size of conserved and extensively raised village chicken populations of Southern Africa |
| title_sort | population genetic structure linkage disequilibrium and effective population size of conserved and extensively raised village chicken populations of southern africa |
| topic | Linkage Disequilibrium genetic diversity snps effective population size Village chickens |
| url | http://journal.frontiersin.org/Journal/10.3389/fgene.2015.00013/full |
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