Signatures of selection in admixed dairy cattle in Tanzania
Multiple studies have investigated selection signatures in domestic cattle and other species. However, there is a dearth of information about the response to selection in genomes of highly admixed crossbred cattle in relation to production and adaptation to tropical environments. In this study, we e...
| Main Authors: | , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
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Frontiers Media
2018
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| Online Access: | https://hdl.handle.net/10568/106434 |
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| author | Cheruiyot, E.K. Bett, R.C. Amimo, Joshua O. Zhang, Y. Mrode, Raphael A. Mujibi, F.D.N. |
| author_browse | Amimo, Joshua O. Bett, R.C. Cheruiyot, E.K. Mrode, Raphael A. Mujibi, F.D.N. Zhang, Y. |
| author_facet | Cheruiyot, E.K. Bett, R.C. Amimo, Joshua O. Zhang, Y. Mrode, Raphael A. Mujibi, F.D.N. |
| author_sort | Cheruiyot, E.K. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Multiple studies have investigated selection signatures in domestic cattle and other species. However, there is a dearth of information about the response to selection in genomes of highly admixed crossbred cattle in relation to production and adaptation to tropical environments. In this study, we evaluated 839 admixed crossbred cows sampled from two major dairy regions in Tanzania namely Rungwe and Lushoto districts, in order to understand their genetic architecture and detect genomic regions showing preferential selection. Animals were genotyped at 150,000 SNP loci using the Geneseek Genomic Profiler (GGP) High Density (HD) SNP array. Population structure analysis showed a large within-population genetic diversity in the study animals with a high degree of variation in admixture ranging between 7% and 100% taurine genes (dairyness) of mostly Holstein and Friesian ancestry. We explored evidence of selection signatures using three statistical methods (iHS, XP-EHH, and pcadapt). Selection signature analysis identified 108 candidate selection regions in the study population. Annotation of these regions yielded interesting genes potentially under strong positive selection including ABCG2, ABCC2, XKR4, LYN, TGS1, TOX, HERC6, KIT, PLAG1, CHCHD7, NCAPG and LCORL that are involved in multiple biological pathways underlying production and adaptation processes. Several candidate selection regions showed an excess of African taurine ancestral allele dosage. Our results provide further useful insight into potential selective sweeps in the genome of admixed cattle with possible adaptive and productive importance. Further investigations will be necessary to better characterize these candidate regions with respect to their functional significance to tropical adaptations for dairy cattle. |
| format | Journal Article |
| id | CGSpace106434 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2018 |
| publishDateRange | 2018 |
| publishDateSort | 2018 |
| publisher | Frontiers Media |
| publisherStr | Frontiers Media |
| record_format | dspace |
| spelling | CGSpace1064342024-10-03T07:40:51Z Signatures of selection in admixed dairy cattle in Tanzania Cheruiyot, E.K. Bett, R.C. Amimo, Joshua O. Zhang, Y. Mrode, Raphael A. Mujibi, F.D.N. livestock cattle dairying genomes research genetics Multiple studies have investigated selection signatures in domestic cattle and other species. However, there is a dearth of information about the response to selection in genomes of highly admixed crossbred cattle in relation to production and adaptation to tropical environments. In this study, we evaluated 839 admixed crossbred cows sampled from two major dairy regions in Tanzania namely Rungwe and Lushoto districts, in order to understand their genetic architecture and detect genomic regions showing preferential selection. Animals were genotyped at 150,000 SNP loci using the Geneseek Genomic Profiler (GGP) High Density (HD) SNP array. Population structure analysis showed a large within-population genetic diversity in the study animals with a high degree of variation in admixture ranging between 7% and 100% taurine genes (dairyness) of mostly Holstein and Friesian ancestry. We explored evidence of selection signatures using three statistical methods (iHS, XP-EHH, and pcadapt). Selection signature analysis identified 108 candidate selection regions in the study population. Annotation of these regions yielded interesting genes potentially under strong positive selection including ABCG2, ABCC2, XKR4, LYN, TGS1, TOX, HERC6, KIT, PLAG1, CHCHD7, NCAPG and LCORL that are involved in multiple biological pathways underlying production and adaptation processes. Several candidate selection regions showed an excess of African taurine ancestral allele dosage. Our results provide further useful insight into potential selective sweeps in the genome of admixed cattle with possible adaptive and productive importance. Further investigations will be necessary to better characterize these candidate regions with respect to their functional significance to tropical adaptations for dairy cattle. 2018-12-19 2020-01-03T13:24:10Z 2020-01-03T13:24:10Z Journal Article https://hdl.handle.net/10568/106434 en Open Access Frontiers Media Cheruiyot, E.K., Bett, R.C., Amimo, J.O., Zhang, Y., Mrode, R. and Mujibi, F.D.N. 2018. Signatures of selection in admixed dairy cattle in Tanzania. Frontiers in Genetics 9:607. |
| spellingShingle | livestock cattle dairying genomes research genetics Cheruiyot, E.K. Bett, R.C. Amimo, Joshua O. Zhang, Y. Mrode, Raphael A. Mujibi, F.D.N. Signatures of selection in admixed dairy cattle in Tanzania |
| title | Signatures of selection in admixed dairy cattle in Tanzania |
| title_full | Signatures of selection in admixed dairy cattle in Tanzania |
| title_fullStr | Signatures of selection in admixed dairy cattle in Tanzania |
| title_full_unstemmed | Signatures of selection in admixed dairy cattle in Tanzania |
| title_short | Signatures of selection in admixed dairy cattle in Tanzania |
| title_sort | signatures of selection in admixed dairy cattle in tanzania |
| topic | livestock cattle dairying genomes research genetics |
| url | https://hdl.handle.net/10568/106434 |
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