Genetic diversity and population structure in South African, French and Argentinian angora goats from genome-wide snp data
The Angora goat populations in Argentina (AR), France (FR) and South Africa (SA) have been kept geographically and genetically distinct. Due to country-specific selection and breeding strategies, there is a need to characterize the populations on a genetic level. In this study we analysed genetic va...
| Main Authors: | , , , , |
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| Format: | Artículo |
| Language: | Inglés |
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2017
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| Online Access: | http://hdl.handle.net/20.500.12123/1093 http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0154353&type=printable https://doi.org/10.1371/journal.pone.0154353 |
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| author | Visser, Carina Lashmar, Simon F. Marle-Koster, Este Van Poli, Mario Andres Allain, Daniel |
| author_browse | Allain, Daniel Lashmar, Simon F. Marle-Koster, Este Van Poli, Mario Andres Visser, Carina |
| author_facet | Visser, Carina Lashmar, Simon F. Marle-Koster, Este Van Poli, Mario Andres Allain, Daniel |
| author_sort | Visser, Carina |
| collection | INTA Digital |
| description | The Angora goat populations in Argentina (AR), France (FR) and South Africa (SA) have been kept geographically and genetically distinct. Due to country-specific selection and breeding strategies, there is a need to characterize the populations on a genetic level. In this study we analysed genetic variability of Angora goats from three distinct geographical regions using the standardized 50k Goat SNP Chip. A total of 104 goats (AR: 30; FR: 26; SA: 48) were genotyped. Heterozygosity values as well as inbreeding coefficients across all autosomes per population were calculated. Diversity, as measured by expected heterozygosity
(HE) ranged from 0.371 in the SA population to 0.397 in the AR population. The SA goats were the only population with a positive average inbreeding coefficient value of 0.009.
After merging the three datasets, standard QC and LD-pruning, 15 105 SNPs remained for further analyses. Principal component and clustering analyses were used to visualize individual relationships within and between populations. All SA Angora goats were separated from the others and formed a well-defined, unique cluster, while outliers were identified in the FR and AR breeds. Apparent admixture between the AR and FR populations was observed, while both these populations showed signs of having some common ancestry with the SA goats. LD averaged over adjacent loci within the three populations per chromosome were calculated. The highest LD values estimated across populations were observed in the shorter intervals across populations. The Ne for the Angora breed was estimated to be 149 animals ten generations ago indicating a declining trend. Results confirmed that geographic isolation and different selection strategies caused genetic distinctiveness between the populations. |
| format | Artículo |
| id | INTA1093 |
| institution | Instituto Nacional de Tecnología Agropecuaria (INTA -Argentina) |
| language | Inglés |
| publishDate | 2017 |
| publishDateRange | 2017 |
| publishDateSort | 2017 |
| record_format | dspace |
| spelling | INTA10932018-02-21T17:50:36Z Genetic diversity and population structure in South African, French and Argentinian angora goats from genome-wide snp data Visser, Carina Lashmar, Simon F. Marle-Koster, Este Van Poli, Mario Andres Allain, Daniel Caprinos Variación Genética Estructura de la Población Genética Goats Genetic Variation Population Structure Genetics Sudáfrica Francia Argentina The Angora goat populations in Argentina (AR), France (FR) and South Africa (SA) have been kept geographically and genetically distinct. Due to country-specific selection and breeding strategies, there is a need to characterize the populations on a genetic level. In this study we analysed genetic variability of Angora goats from three distinct geographical regions using the standardized 50k Goat SNP Chip. A total of 104 goats (AR: 30; FR: 26; SA: 48) were genotyped. Heterozygosity values as well as inbreeding coefficients across all autosomes per population were calculated. Diversity, as measured by expected heterozygosity (HE) ranged from 0.371 in the SA population to 0.397 in the AR population. The SA goats were the only population with a positive average inbreeding coefficient value of 0.009. After merging the three datasets, standard QC and LD-pruning, 15 105 SNPs remained for further analyses. Principal component and clustering analyses were used to visualize individual relationships within and between populations. All SA Angora goats were separated from the others and formed a well-defined, unique cluster, while outliers were identified in the FR and AR breeds. Apparent admixture between the AR and FR populations was observed, while both these populations showed signs of having some common ancestry with the SA goats. LD averaged over adjacent loci within the three populations per chromosome were calculated. The highest LD values estimated across populations were observed in the shorter intervals across populations. The Ne for the Angora breed was estimated to be 149 animals ten generations ago indicating a declining trend. Results confirmed that geographic isolation and different selection strategies caused genetic distinctiveness between the populations. Inst. de Genética "Ewald A. Favret"- IGEAF Fil: Visser, Carina. University of Pretoria. Department of Animal and Wildlife Sciences; Sudáfrica Fil: Lashmar, Simon F. University of Pretoria. Department of Animal and Wildlife Sciences; Sudáfrica Fil: Marle-Koster, Este Van. University of Pretoria. Department of Animal and Wildlife Sciences; Sudáfrica Fil: Poli, Mario Andres. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Genética; Argentina Fil: Allain, Daniel. Institut National de la Recherche Agronomique; Francia 2017-08-31T15:30:07Z 2017-08-31T15:30:07Z 2016 info:eu-repo/semantics/article info:ar-repo/semantics/artículo info:eu-repo/semantics/publishedVersion http://hdl.handle.net/20.500.12123/1093 http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0154353&type=printable Visser C, Lashmar SF, Van Marle-Köster E, Poli MA, Allain D (2016) Genetic Diversity and Population Structure in South African, French and Argentinian Angora Goats from Genome-Wide SNP Data. PLoS ONE 11(5): e0154353. 1932-6203 https://doi.org/10.1371/journal.pone.0154353 eng info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by-nc-sa/4.0/ Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) application/pdf PLoS ONE 11 (5) : e0154353 |
| spellingShingle | Caprinos Variación Genética Estructura de la Población Genética Goats Genetic Variation Population Structure Genetics Sudáfrica Francia Argentina Visser, Carina Lashmar, Simon F. Marle-Koster, Este Van Poli, Mario Andres Allain, Daniel Genetic diversity and population structure in South African, French and Argentinian angora goats from genome-wide snp data |
| title | Genetic diversity and population structure in South African, French and Argentinian angora goats from genome-wide snp data |
| title_full | Genetic diversity and population structure in South African, French and Argentinian angora goats from genome-wide snp data |
| title_fullStr | Genetic diversity and population structure in South African, French and Argentinian angora goats from genome-wide snp data |
| title_full_unstemmed | Genetic diversity and population structure in South African, French and Argentinian angora goats from genome-wide snp data |
| title_short | Genetic diversity and population structure in South African, French and Argentinian angora goats from genome-wide snp data |
| title_sort | genetic diversity and population structure in south african french and argentinian angora goats from genome wide snp data |
| topic | Caprinos Variación Genética Estructura de la Población Genética Goats Genetic Variation Population Structure Genetics Sudáfrica Francia Argentina |
| url | http://hdl.handle.net/20.500.12123/1093 http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0154353&type=printable https://doi.org/10.1371/journal.pone.0154353 |
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