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Belay S, Belay G, Nigussie H, Jian-Lin H, Tijjani A, Ahbara AM, Tarekegn GM, Woldekiros HS, Mor S, Dobney K, Lebrasseur O, Hanotte O, Mwacharo JM. Whole-genome resource sequences of 57 indigenous Ethiopian goats. Sci Data 2024; 11:139. [PMID: 38287052 PMCID: PMC10825132 DOI: 10.1038/s41597-024-02973-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 01/16/2024] [Indexed: 01/31/2024] Open
Abstract
Domestic goats are distributed worldwide, with approximately 35% of the one billion world goat population occurring in Africa. Ethiopia has 52.5 million goats, ~99.9% of which are considered indigenous landraces deriving from animals introduced to the Horn of Africa in the distant past by nomadic herders. They have continued to be managed by smallholder farmers and semi-mobile pastoralists throughout the region. We report here 57 goat genomes from 12 Ethiopian goat populations sampled from different agro-climates. The data were generated through sequencing DNA samples on the Illumina NovaSeq 6000 platform at a mean depth of 9.71x and 150 bp pair-end reads. In total, ~2 terabytes of raw data were generated, and 99.8% of the clean reads mapped successfully against the goat reference genome assembly at a coverage of 99.6%. About 24.76 million SNPs were generated. These SNPs can be used to study the population structure and genome dynamics of goats at the country, regional, and global levels to shed light on the species' evolutionary trajectory.
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Affiliation(s)
- Shumuye Belay
- Tigray Agricultural Research Institute, Mekelle, Tigray, Ethiopia.
- Addis Ababa University, Department of Microbial, Cellular and Molecular Biology, Addis Ababa, Ethiopia.
- LiveGene Program, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia.
| | - Gurja Belay
- Addis Ababa University, Department of Microbial, Cellular and Molecular Biology, Addis Ababa, Ethiopia.
| | - Helen Nigussie
- Addis Ababa University, Department of Microbial, Cellular and Molecular Biology, Addis Ababa, Ethiopia
| | - Han Jian-Lin
- ILRI-CAAS Joint Laboratory on Livestock and Forage Genetic Resources, Beijing, China
| | - Abdulfatai Tijjani
- LiveGene Program, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | - Abulgasim M Ahbara
- Animal and Veterinary Sciences, Scotland's Rural College (SRUC), Roslin Institute Building, Midlothian, UK
- Department of Zoology, Misurata University, Misurata, Libya
| | - Getinet M Tarekegn
- Animal and Veterinary Sciences, Scotland's Rural College (SRUC), Roslin Institute Building, Midlothian, UK
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Helina S Woldekiros
- Department of Anthropology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Siobhan Mor
- LiveGene Program, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Keith Dobney
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool, UK
- School of Philosophical and Historical Inquiry, University of Sydney, Sydney, Australia
| | - Ophelie Lebrasseur
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool, UK
| | - Olivier Hanotte
- LiveGene Program, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Joram M Mwacharo
- Animal and Veterinary Sciences, Scotland's Rural College (SRUC), Roslin Institute Building, Midlothian, UK.
- Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia.
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Onzima RB, Upadhyay MR, Mukiibi R, Kanis E, Groenen MAM, Crooijmans RPMA. Genome-wide population structure and admixture analysis reveals weak differentiation among Ugandan goat breeds. Anim Genet 2018; 49:59-70. [PMID: 29344947 PMCID: PMC5838551 DOI: 10.1111/age.12631] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/18/2017] [Indexed: 12/18/2022]
Abstract
Uganda has a large population of goats, predominantly from indigenous breeds reared in diverse production systems, whose existence is threatened by crossbreeding with exotic Boer goats. Knowledge about the genetic characteristics and relationships among these Ugandan goat breeds and the potential admixture with Boer goats is still limited. Using a medium‐density single nucleotide polymorphism (SNP) panel, we assessed the genetic diversity, population structure and admixture in six goat breeds in Uganda: Boer, Karamojong, Kigezi, Mubende, Small East African and Sebei. All the animals had genotypes for about 46 105 SNPs after quality control. We found high proportions of polymorphic SNPs ranging from 0.885 (Kigezi) to 0.928 (Sebei). The overall mean observed (HO) and expected (HE) heterozygosity across breeds was 0.355 ± 0.147 and 0.384 ± 0.143 respectively. Principal components, genetic distances and admixture analyses revealed weak population sub‐structuring among the breeds. Principal components separated Kigezi and weakly Small East African from other indigenous goats. Sebei and Karamojong were tightly entangled together, whereas Mubende occupied a more central position with high admixture from all other local breeds. The Boer breed showed a unique cluster from the Ugandan indigenous goat breeds. The results reflect common ancestry but also some level of geographical differentiation. admixture and f4 statistics revealed gene flow from Boer and varying levels of genetic admixture among the breeds. Generally, moderate to high levels of genetic variability were observed. Our findings provide useful insights into maintaining genetic diversity and designing appropriate breeding programs to exploit within‐breed diversity and heterozygote advantage in crossbreeding schemes.
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Affiliation(s)
- R B Onzima
- Wageningen University & Research, Animal Breeding and Genomics, P O Box 338, 6700AH, Wageningen, The Netherlands.,National Agricultural Research Organization (NARO), P O Box 295, Entebbe, Uganda
| | - M R Upadhyay
- Wageningen University & Research, Animal Breeding and Genomics, P O Box 338, 6700AH, Wageningen, The Netherlands.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - R Mukiibi
- Department of Agriculture, Food and Nutritional Sciences (AFNS), Faculty of Agriculture, Life and Environmental Sciences, University of Alberta, 1416 College Plaza Edmonton, T6G 2C8, Alberta, Canada
| | - E Kanis
- Wageningen University & Research, Animal Breeding and Genomics, P O Box 338, 6700AH, Wageningen, The Netherlands
| | - M A M Groenen
- Wageningen University & Research, Animal Breeding and Genomics, P O Box 338, 6700AH, Wageningen, The Netherlands
| | - R P M A Crooijmans
- Wageningen University & Research, Animal Breeding and Genomics, P O Box 338, 6700AH, Wageningen, The Netherlands
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Yakubu A, Salako A, Donato M, Takeet M, Peters S, Wheto M, Okpeku M, Imumorin I. Interleukin-2 ((IL-2) gene polymorphism and association with heat tolerance in Nigerian goats. Small Rumin Res 2016. [DOI: 10.1016/j.smallrumres.2016.07.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Awotunde EO, Bemji MN, Olowofeso O, James IJ, Ajayi OO, Adebambo AO. Mitochondrial DNA Sequence Analyses and Phylogenetic Relationships Among Two Nigerian Goat Breeds and the South African Kalahari Red. Anim Biotechnol 2015; 26:180-7. [DOI: 10.1080/10495398.2014.977907] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Yakubu A, Salako AE, De Donato M, Takeet MI, Peters SO, Adefenwa MA, Okpeku M, Wheto M, Agaviezor BO, Sanni TM, Ajayi OO, Onasanya GO, Ekundayo OJ, Ilori BM, Amusan SA, Imumorin IG. Genetic Diversity in Exon 2 of the Major Histocompatibility Complex Class II DQB1 Locus in Nigerian Goats. Biochem Genet 2013; 51:954-66. [DOI: 10.1007/s10528-013-9620-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Accepted: 02/13/2013] [Indexed: 10/26/2022]
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