Genetic diversity, population structure and kinship relationships highlight the environmental influence on Uganda’s indigenous goat populations
Knowledge about genetic diversity and population structure among goat populations is essential for understanding environmental adaptation and fostering efficient utilization, development, and conservation of goat breeds. Uganda’s indigenous goats exist in three phenotypic groups: Mubende, Kigezi, an...
| Main Authors: | , , , , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
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Frontiers Media
2024
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/149076 |
| _version_ | 1855520769895825408 |
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| author | Nantongo, Ziwena Birungi, Josephine Opiyo, S.O. Shirima, G. Mugerwa, S. Mutai, Collins Kyalo, Martina Munishi, L. Agaba, M. Mrode, Raphael A. |
| author_browse | Agaba, M. Birungi, Josephine Kyalo, Martina Mrode, Raphael A. Mugerwa, S. Munishi, L. Mutai, Collins Nantongo, Ziwena Opiyo, S.O. Shirima, G. |
| author_facet | Nantongo, Ziwena Birungi, Josephine Opiyo, S.O. Shirima, G. Mugerwa, S. Mutai, Collins Kyalo, Martina Munishi, L. Agaba, M. Mrode, Raphael A. |
| author_sort | Nantongo, Ziwena |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Knowledge about genetic diversity and population structure among goat populations is essential for understanding environmental adaptation and fostering efficient utilization, development, and conservation of goat breeds. Uganda’s indigenous goats exist in three phenotypic groups: Mubende, Kigezi, and Small East African. However, a limited understanding of their genetic attributes and population structure hinders the development and sustainable utilization of the goats. Using the Goat Illumina 60k chip International Goat Genome Consortium V2, the whole-genome data for 1,021 indigenous goats sourced from 10 agroecological zones in Uganda were analyzed for genetic diversity and population structure. A total of 49,337 (82.6%) single-nucleotide polymorphism markers were aligned to the ARS-1 goat genome and used to assess the genetic diversity, population structure, and kinship relationships of Uganda’s indigenous goats. Moderate genetic diversity was observed. The observed and expected heterozygosities were 0.378 and 0.383, the average genetic distance was 0.390, and the average minor allele frequency was 0.30. The average inbreeding coefficient (Fis) was 0.014, and the average fixation index (Fst) was 0.016. Principal component analysis, admixture analysis, and discriminant analysis of principal components grouped the 1,021 goat genotypes into three genetically distinct populations that did not conform to the known phenotypic populations but varied across environmental conditions. Population 1, comprising Mubende (90%) and Kigezi (8.1%) goats, is located in southwest and central Uganda, a warm and humid environment. Population 2, which is 59% Mubende and 49% Small East African goats, is located along the Nile Delta in northwestern Uganda and around the Albertine region, a hot and humid savannah grassland. Population 3, comprising 78.4% Small East African and 21.1% Mubende goats, is found in northeastern to eastern Uganda, a hot and dry Commiphora woodlands. Genetic diversity and population structure information from this study will be a basis for future development, conservation, and sustainable utilization of Uganda’s goat genetic resources. |
| format | Journal Article |
| id | CGSpace149076 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2024 |
| publishDateRange | 2024 |
| publishDateSort | 2024 |
| publisher | Frontiers Media |
| publisherStr | Frontiers Media |
| record_format | dspace |
| spelling | CGSpace1490762025-12-08T10:29:22Z Genetic diversity, population structure and kinship relationships highlight the environmental influence on Uganda’s indigenous goat populations Nantongo, Ziwena Birungi, Josephine Opiyo, S.O. Shirima, G. Mugerwa, S. Mutai, Collins Kyalo, Martina Munishi, L. Agaba, M. Mrode, Raphael A. goats genetics environment landraces Knowledge about genetic diversity and population structure among goat populations is essential for understanding environmental adaptation and fostering efficient utilization, development, and conservation of goat breeds. Uganda’s indigenous goats exist in three phenotypic groups: Mubende, Kigezi, and Small East African. However, a limited understanding of their genetic attributes and population structure hinders the development and sustainable utilization of the goats. Using the Goat Illumina 60k chip International Goat Genome Consortium V2, the whole-genome data for 1,021 indigenous goats sourced from 10 agroecological zones in Uganda were analyzed for genetic diversity and population structure. A total of 49,337 (82.6%) single-nucleotide polymorphism markers were aligned to the ARS-1 goat genome and used to assess the genetic diversity, population structure, and kinship relationships of Uganda’s indigenous goats. Moderate genetic diversity was observed. The observed and expected heterozygosities were 0.378 and 0.383, the average genetic distance was 0.390, and the average minor allele frequency was 0.30. The average inbreeding coefficient (Fis) was 0.014, and the average fixation index (Fst) was 0.016. Principal component analysis, admixture analysis, and discriminant analysis of principal components grouped the 1,021 goat genotypes into three genetically distinct populations that did not conform to the known phenotypic populations but varied across environmental conditions. Population 1, comprising Mubende (90%) and Kigezi (8.1%) goats, is located in southwest and central Uganda, a warm and humid environment. Population 2, which is 59% Mubende and 49% Small East African goats, is located along the Nile Delta in northwestern Uganda and around the Albertine region, a hot and humid savannah grassland. Population 3, comprising 78.4% Small East African and 21.1% Mubende goats, is found in northeastern to eastern Uganda, a hot and dry Commiphora woodlands. Genetic diversity and population structure information from this study will be a basis for future development, conservation, and sustainable utilization of Uganda’s goat genetic resources. 2024-05-30 2024-07-15T11:42:32Z 2024-07-15T11:42:32Z Journal Article https://hdl.handle.net/10568/149076 en Open Access Frontiers Media Nantongo, Z., Birungi, J., Opiyo, S.O., Shirima, G., Mugerwa, S., Mutai, C., Kyalo, M., Munishi, L., Agaba, M. and Mrode, R. 2024. Genetic diversity, population structure and kinship relationships highlight the environmental influence on Uganda’s indigenous goat populations. Frontiers in Genetics 15: 1385611. |
| spellingShingle | goats genetics environment landraces Nantongo, Ziwena Birungi, Josephine Opiyo, S.O. Shirima, G. Mugerwa, S. Mutai, Collins Kyalo, Martina Munishi, L. Agaba, M. Mrode, Raphael A. Genetic diversity, population structure and kinship relationships highlight the environmental influence on Uganda’s indigenous goat populations |
| title | Genetic diversity, population structure and kinship relationships highlight the environmental influence on Uganda’s indigenous goat populations |
| title_full | Genetic diversity, population structure and kinship relationships highlight the environmental influence on Uganda’s indigenous goat populations |
| title_fullStr | Genetic diversity, population structure and kinship relationships highlight the environmental influence on Uganda’s indigenous goat populations |
| title_full_unstemmed | Genetic diversity, population structure and kinship relationships highlight the environmental influence on Uganda’s indigenous goat populations |
| title_short | Genetic diversity, population structure and kinship relationships highlight the environmental influence on Uganda’s indigenous goat populations |
| title_sort | genetic diversity population structure and kinship relationships highlight the environmental influence on uganda s indigenous goat populations |
| topic | goats genetics environment landraces |
| url | https://hdl.handle.net/10568/149076 |
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