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Sheriff O, Ahbara AM, Haile A, Alemayehu K, Han JL, Mwacharo JM. Whole-genome resequencing reveals genomic variation and dynamics in Ethiopian indigenous goats. Front Genet 2024; 15:1353026. [PMID: 38854428 PMCID: PMC11156998 DOI: 10.3389/fgene.2024.1353026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 04/16/2024] [Indexed: 06/11/2024] Open
Abstract
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.
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Affiliation(s)
- Oumer Sheriff
- Department of Animal Science, Assosa University, Assosa, Ethiopia
- Department of Animal Production and Technology, Bahir Dar University, Bahir Dar, Ethiopia
- Biotechnology Research Institute, Bahir Dar University, Bahir Dar, Ethiopia
| | - Abulgasim M. Ahbara
- Department of Zoology, Faculty of Sciences, Misurata University, Misurata, Libya
- Animal and Veterinary Sciences Scotland's Rural College (SRUC) and The Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute Building, Edinburgh, United Kingdom
| | - Aynalem Haile
- Resilient Agricultural Livelihood Systems Program (RALSP), International Center for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia
| | - Kefyalew Alemayehu
- Department of Animal Production and Technology, Bahir Dar University, Bahir Dar, Ethiopia
- Biotechnology Research Institute, Bahir Dar University, Bahir Dar, Ethiopia
- Ethiopian Agricultural Transformation Institute, Amhara Agricultural Transformation Center, Bahir Dar, Ethiopia
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Livestock Genetics Program, International Livestock Research Institute, Nairobi, Kenya
| | - Joram M. Mwacharo
- Animal and Veterinary Sciences Scotland's Rural College (SRUC) and The Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute Building, Edinburgh, United Kingdom
- Resilient Agricultural Livelihood Systems Program (RALSP), International Center for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia
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Lee YL, Takeda H, Costa Monteiro Moreira G, Karim L, Mullaart E, Coppieters W, Appeltant R, Veerkamp RF, Groenen MAM, Georges M, Bosse M, Druet T, Bouwman AC, Charlier C. A 12 kb multi-allelic copy number variation encompassing a GC gene enhancer is associated with mastitis resistance in dairy cattle. PLoS Genet 2021; 17:e1009331. [PMID: 34288907 PMCID: PMC8328317 DOI: 10.1371/journal.pgen.1009331] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 08/02/2021] [Accepted: 06/08/2021] [Indexed: 12/24/2022] Open
Abstract
Clinical mastitis (CM) is an inflammatory disease occurring in the mammary glands of lactating cows. CM is under genetic control, and a prominent CM resistance QTL located on chromosome 6 was reported in various dairy cattle breeds. Nevertheless, the biological mechanism underpinning this QTL has been lacking. Herein, we mapped, fine-mapped, and discovered the putative causal variant underlying this CM resistance QTL in the Dutch dairy cattle population. We identified a ~12 kb multi-allelic copy number variant (CNV), that is in perfect linkage disequilibrium with a lead SNP, as a promising candidate variant. By implementing a fine-mapping and through expression QTL mapping, we showed that the group-specific component gene (GC), a gene encoding a vitamin D binding protein, is an excellent candidate causal gene for the QTL. The multiplicated alleles are associated with increased GC expression and low CM resistance. Ample evidence from functional genomics data supports the presence of an enhancer within this CNV, which would exert cis-regulatory effect on GC. We observed that strong positive selection swept the region near the CNV, and haplotypes associated with the multiplicated allele were strongly selected for. Moreover, the multiplicated allele showed pleiotropic effects for increased milk yield and reduced fertility, hinting that a shared underlying biology for these effects may revolve around the vitamin D pathway. These findings together suggest a putative causal variant of a CM resistance QTL, where a cis-regulatory element located within a CNV can alter gene expression and affect multiple economically important traits.
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Affiliation(s)
- Young-Lim Lee
- Wageningen University & Research, Animal Breeding and Genomics, Wageningen, the Netherlands
| | - Haruko Takeda
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | | | - Latifa Karim
- GIGA Genomics Platform, GIGA Institute, University of Liège, Liège, Belgium
| | | | - Wouter Coppieters
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
- GIGA Genomics Platform, GIGA Institute, University of Liège, Liège, Belgium
| | | | - Ruth Appeltant
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Roel F. Veerkamp
- Wageningen University & Research, Animal Breeding and Genomics, Wageningen, the Netherlands
| | - Martien A. M. Groenen
- Wageningen University & Research, Animal Breeding and Genomics, Wageningen, the Netherlands
| | - Michel Georges
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Mirte Bosse
- Wageningen University & Research, Animal Breeding and Genomics, Wageningen, the Netherlands
| | - Tom Druet
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Aniek C. Bouwman
- Wageningen University & Research, Animal Breeding and Genomics, Wageningen, the Netherlands
| | - Carole Charlier
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
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Higgins MG, Fitzsimons C, McClure MC, McKenna C, Conroy S, Kenny DA, McGee M, Waters SM, Morris DW. GWAS and eQTL analysis identifies a SNP associated with both residual feed intake and GFRA2 expression in beef cattle. Sci Rep 2018; 8:14301. [PMID: 30250203 PMCID: PMC6155370 DOI: 10.1038/s41598-018-32374-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 09/03/2018] [Indexed: 11/09/2022] Open
Abstract
Residual feed intake (RFI), a measure of feed efficiency, is an important economic and environmental trait in beef production. Selection of low RFI (feed efficient) cattle could maintain levels of production, while decreasing feed costs and methane emissions. However, RFI is a difficult and expensive trait to measure. Identification of single nucleotide polymorphisms (SNPs) associated with RFI may enable rapid, cost effective genomic selection of feed efficient cattle. Genome-wide association studies (GWAS) were conducted in multiple breeds followed by meta-analysis to identify genetic variants associated with RFI and component traits (average daily gain (ADG) and feed intake (FI)) in Irish beef cattle (n = 1492). Expression quantitative trait loci (eQTL) analysis was conducted to identify functional effects of GWAS-identified variants. Twenty-four SNPs were associated (P < 5 × 10-5) with RFI, ADG or FI. The variant rs43555985 exhibited strongest association for RFI (P = 8.28E-06). An eQTL was identified between this variant and GFRA2 (P = 0.0038) where the allele negatively correlated with RFI was associated with increased GFRA2 expression in liver. GFRA2 influences basal metabolic rates, suggesting a mechanism by which genetic variation may contribute to RFI. This study identified SNPs that may be useful both for genomic selection of RFI and for understanding the biology of feed efficiency.
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Affiliation(s)
- Marc G Higgins
- Discipline of Biochemistry, National University of Ireland, Galway, Ireland.,Animal and Bioscience Research Department, Animal & Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, Co. Meath, Ireland
| | - Claire Fitzsimons
- Livestock Systems Research Department, Animal & Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, Co. Meath, Ireland.,Department of Agriculture, Fisheries and the Marine, Celbridge, Co. Kildare, Ireland
| | - Matthew C McClure
- Irish Cattle Breeding Federation, Highfield House, Bandon, Co. Cork, Ireland.,ABS-Global, DeForest, WI, USA
| | - Clare McKenna
- Animal and Bioscience Research Department, Animal & Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, Co. Meath, Ireland
| | - Stephen Conroy
- Irish Cattle Breeding Federation, Highfield House, Bandon, Co. Cork, Ireland
| | - David A Kenny
- Animal and Bioscience Research Department, Animal & Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, Co. Meath, Ireland
| | - Mark McGee
- Livestock Systems Research Department, Animal & Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, Co. Meath, Ireland
| | - Sinéad M Waters
- Animal and Bioscience Research Department, Animal & Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, Co. Meath, Ireland.
| | - Derek W Morris
- Discipline of Biochemistry, National University of Ireland, Galway, Ireland
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Brand B, Scheinhardt MO, Friedrich J, Zimmer D, Reinsch N, Ponsuksili S, Schwerin M, Ziegler A. Erratum to: Adrenal cortex expression quantitative trait loci in a German Holstein × Charolais cross. BMC Genet 2016; 17:148. [PMID: 27903236 PMCID: PMC5129642 DOI: 10.1186/s12863-016-0450-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 10/24/2016] [Indexed: 11/16/2022] Open
Affiliation(s)
- Bodo Brand
- Institute for Genome Biology, Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee, Dummerstorf, Germany.,Current affiliation: Institute for Farm Animal Research and Technology, University of Rostock, Justus-von-Liebig-Weg, 18059, Rostock, Germany
| | - Markus O Scheinhardt
- Institute of Medical Biometry and Statistics, University of Lübeck, Ratzeburger Allee, Lübeck, Germany
| | - Juliane Friedrich
- Institute for Farm Animal Research and Technology, University of Rostock, Justus-von-Liebig-Weg, Rostock, Germany
| | - Daisy Zimmer
- Institute for Farm Animal Research and Technology, University of Rostock, Justus-von-Liebig-Weg, Rostock, Germany
| | - Norbert Reinsch
- Institute for Genetics and Biometry, Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee, Dummerstorf, Germany
| | - Siriluck Ponsuksili
- Institute for Genome Biology, Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee, Dummerstorf, Germany
| | - Manfred Schwerin
- Institute for Genome Biology, Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee, Dummerstorf, Germany.,Institute for Farm Animal Research and Technology, University of Rostock, Justus-von-Liebig-Weg, Rostock, Germany
| | - Andreas Ziegler
- Institute of Medical Biometry and Statistics, University of Lübeck, Ratzeburger Allee, Lübeck, Germany. .,Center for Clinical Trials, University of Lübeck, Ratzeburger Allee, Lübeck, Germany. .,School of Mathematics, Statistics and Computer Science, University of KwaZulu-Natal, Pietermaritzburg, South Africa.
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