Whole-genome resequencing reveals genomic variation and dynamics in Ethiopian indigenous goats
Ethiopia has about 52 million indigenous goats with marked phenotypic variability, which is the outcome of natural and artificial selection. Here, we obtained whole-genome sequence data of three Ethiopian indigenous goat populations (Arab, Fellata, and Oromo) from northwestern Ethiopia and analyzed...
| Autores principales: | , , , , , |
|---|---|
| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Frontiers Media
2024
|
| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/169109 |
| _version_ | 1855535505200906240 |
|---|---|
| author | Sheriff, Oumer Ahbara, Abulgasim Haile, Aynalem Alemayehu, Kefyalew Jianlin, Han Mwacharo, Joram |
| author_browse | Ahbara, Abulgasim Alemayehu, Kefyalew Haile, Aynalem Jianlin, Han Mwacharo, Joram Sheriff, Oumer |
| author_facet | Sheriff, Oumer Ahbara, Abulgasim Haile, Aynalem Alemayehu, Kefyalew Jianlin, Han Mwacharo, Joram |
| author_sort | Sheriff, Oumer |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Ethiopia has about 52 million indigenous goats with marked phenotypic variability, which is the outcome of natural and artificial selection. Here, we obtained whole-genome sequence data of three Ethiopian indigenous goat populations (Arab, Fellata, and Oromo) from northwestern Ethiopia and analyzed their genome-wide genetic diversity, population structure, and signatures of selection. We included genotype data from four other Ethiopian goat populations (Abergelle, Keffa, Gumuz, and Woyto-Guji) and goats from Asia; Europe; and eastern, southern, western, and northern Africa to investigate the genetic predisposition of the three Ethiopian populations and performed comparative genomic analysis. Genetic diversity analysis showed that Fellata goats exhibited the lowest heterozygosity values (Ho = 0.288 ± 0.005 and He = 0.334 ± 0.0001). The highest values were observed in Arab goats (Ho = 0.310 ± 0.010 and He = 0.347 ± 4.35e−05). A higher inbreeding coefficient (FROH = 0.137 ± 0.016) was recorded for Fellata goats than the 0.105 ± 0.030 recorded for Arab and the 0.112 ± 0.034 recorded for Oromo goats. This indicates that the Fellata goat population should be prioritized in future conservation activities. The three goat populations showed the majority (∼63%) of runs of homozygosity in the shorter (100–150 Kb) length category, illustrating ancient inbreeding and/or small founder effects. Population relationship and structure analysis separated the Ethiopian indigenous goats into two distinct genetic clusters lacking phylogeographic structure. Arab, Fellata, Oromo, Abergelle, and Keffa represented one genetic cluster. Gumuz and Woyto-Guji formed a separate cluster and shared a common genetic background with the Kenyan Boran goat. Genome-wide selection signature analysis identified nine strongest regions spanning 163 genes influencing adaptation to arid and semi-arid environments (HOXC12, HOXC13, HOXC4, HOXC6, and HOXC9, MAPK8IP2), immune response (IL18, TYK2, ICAM3, ADGRG1, and ADGRG3), and production and reproduction (RARG and DNMT1). Our results provide insights into a thorough understanding of genetic architecture underlying selection signatures in Ethiopian indigenous goats in a semi-arid tropical environment and deliver valuable information for goat genetic improvement, conservation strategy, genome-wide association study, and marker-assisted breeding. |
| format | Journal Article |
| id | CGSpace169109 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2024 |
| publishDateRange | 2024 |
| publishDateSort | 2024 |
| publisher | Frontiers Media |
| publisherStr | Frontiers Media |
| record_format | dspace |
| spelling | CGSpace1691092025-02-28T02:10:57Z Whole-genome resequencing reveals genomic variation and dynamics in Ethiopian indigenous goats Sheriff, Oumer Ahbara, Abulgasim Haile, Aynalem Alemayehu, Kefyalew Jianlin, Han Mwacharo, Joram africa capra hircus whole genome genome dynamics population differentiation pooled heterozygosity Ethiopia has about 52 million indigenous goats with marked phenotypic variability, which is the outcome of natural and artificial selection. Here, we obtained whole-genome sequence data of three Ethiopian indigenous goat populations (Arab, Fellata, and Oromo) from northwestern Ethiopia and analyzed their genome-wide genetic diversity, population structure, and signatures of selection. We included genotype data from four other Ethiopian goat populations (Abergelle, Keffa, Gumuz, and Woyto-Guji) and goats from Asia; Europe; and eastern, southern, western, and northern Africa to investigate the genetic predisposition of the three Ethiopian populations and performed comparative genomic analysis. Genetic diversity analysis showed that Fellata goats exhibited the lowest heterozygosity values (Ho = 0.288 ± 0.005 and He = 0.334 ± 0.0001). The highest values were observed in Arab goats (Ho = 0.310 ± 0.010 and He = 0.347 ± 4.35e−05). A higher inbreeding coefficient (FROH = 0.137 ± 0.016) was recorded for Fellata goats than the 0.105 ± 0.030 recorded for Arab and the 0.112 ± 0.034 recorded for Oromo goats. This indicates that the Fellata goat population should be prioritized in future conservation activities. The three goat populations showed the majority (∼63%) of runs of homozygosity in the shorter (100–150 Kb) length category, illustrating ancient inbreeding and/or small founder effects. Population relationship and structure analysis separated the Ethiopian indigenous goats into two distinct genetic clusters lacking phylogeographic structure. Arab, Fellata, Oromo, Abergelle, and Keffa represented one genetic cluster. Gumuz and Woyto-Guji formed a separate cluster and shared a common genetic background with the Kenyan Boran goat. Genome-wide selection signature analysis identified nine strongest regions spanning 163 genes influencing adaptation to arid and semi-arid environments (HOXC12, HOXC13, HOXC4, HOXC6, and HOXC9, MAPK8IP2), immune response (IL18, TYK2, ICAM3, ADGRG1, and ADGRG3), and production and reproduction (RARG and DNMT1). Our results provide insights into a thorough understanding of genetic architecture underlying selection signatures in Ethiopian indigenous goats in a semi-arid tropical environment and deliver valuable information for goat genetic improvement, conservation strategy, genome-wide association study, and marker-assisted breeding. 2024-05-24 2025-01-15T15:02:23Z 2025-01-15T15:02:23Z Journal Article https://hdl.handle.net/10568/169109 en Open Access application/pdf Frontiers Media Oumer Sheriff, Abulgasim Ahbara, Aynalem Haile, Kefyalew Alemayehu, Han Jianlin, Joram Mwacharo. (24/5/2024). Whole-genome resequencing reveals genomic variation and dynamics in Ethiopian indigenous goats. Frontiers in Genetics, 15. |
| spellingShingle | africa capra hircus whole genome genome dynamics population differentiation pooled heterozygosity Sheriff, Oumer Ahbara, Abulgasim Haile, Aynalem Alemayehu, Kefyalew Jianlin, Han Mwacharo, Joram Whole-genome resequencing reveals genomic variation and dynamics in Ethiopian indigenous goats |
| title | Whole-genome resequencing reveals genomic variation and dynamics in Ethiopian indigenous goats |
| title_full | Whole-genome resequencing reveals genomic variation and dynamics in Ethiopian indigenous goats |
| title_fullStr | Whole-genome resequencing reveals genomic variation and dynamics in Ethiopian indigenous goats |
| title_full_unstemmed | Whole-genome resequencing reveals genomic variation and dynamics in Ethiopian indigenous goats |
| title_short | Whole-genome resequencing reveals genomic variation and dynamics in Ethiopian indigenous goats |
| title_sort | whole genome resequencing reveals genomic variation and dynamics in ethiopian indigenous goats |
| topic | africa capra hircus whole genome genome dynamics population differentiation pooled heterozygosity |
| url | https://hdl.handle.net/10568/169109 |
| work_keys_str_mv | AT sheriffoumer wholegenomeresequencingrevealsgenomicvariationanddynamicsinethiopianindigenousgoats AT ahbaraabulgasim wholegenomeresequencingrevealsgenomicvariationanddynamicsinethiopianindigenousgoats AT haileaynalem wholegenomeresequencingrevealsgenomicvariationanddynamicsinethiopianindigenousgoats AT alemayehukefyalew wholegenomeresequencingrevealsgenomicvariationanddynamicsinethiopianindigenousgoats AT jianlinhan wholegenomeresequencingrevealsgenomicvariationanddynamicsinethiopianindigenousgoats AT mwacharojoram wholegenomeresequencingrevealsgenomicvariationanddynamicsinethiopianindigenousgoats |