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Maki Mateso JC, Dewitte O, Bielders CL. Living with landslides: Land use on unstable hillslopes in a rural tropical mountainous environment in DR Congo. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 925:171624. [PMID: 38471586 DOI: 10.1016/j.scitotenv.2024.171624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 02/28/2024] [Accepted: 03/08/2024] [Indexed: 03/14/2024]
Abstract
Landslides are processes that naturally occur on numerous hillslopes across the world. In inhabited regions, landslides are commonly seen as a threat and a land degradation process. Yet, in densely-populated rural mountainous regions in the tropics, local communities have often no choice but to live on steep terrains naturally impacted by landslides. Besides, landslides may also be a source of opportunities for these communities. However, little is known on the rationale underlying land use in landslides. The aim of this study was to assess the extent, modes of valorization and degree of satisfaction of famers exploiting landslides in a populated rural mountainous environment of DR Congo (territory of Kalehe). We interviewed 82 farmers living on 57 representative landslides, these mass movements having been selected according to their characteristics (size, type) and position along the hillslopes and taking into account accessibility or safety constraints. We show that almost all landslides are being exploited by farmers and that they adapt their land use to the type of landslide. Indeed, significant contrasts are observed between landslides and the surrounding hillslopes for subsistence crops, forests, eucalyptus plantations and pasture. Farmers also adapt land use according to local variations in slope or wetness within a given landslide. Nearly half of the farmers reported that their land was more valuable inside than outside landslides. Better soil fertility, higher soil moisture, lower sand or stone content, lower slopes are some of the main factors that increase the land value, offering more favorable conditions for cropping than on land outside landslides. Despite the perceived risk of landsliding, famers settlement on unstable slopes appears justified by the immediacy of the benefits that outweigh the potential dangers. Better understanding the reasons for the settlement of populations on unstable slopes may help devise better risk reduction strategies.
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Affiliation(s)
- Jean-Claude Maki Mateso
- Centre de Recherche en Sciences Naturelles, Department of Geophysics, D.S Bukavu, Lwiro, Democratic Republic of the Congo; Université catholique de Louvain, Earth and Life Institute - Environmental Sciences, Croix du Sud 2, 1348 Louvain-La-Neuve, Belgium.
| | - Olivier Dewitte
- Royal Museum for Central Africa, Department of Earth Sciences, Leuvensesteenweg 13, 3080 Tervuren, Belgium.
| | - Charles L Bielders
- Université catholique de Louvain, Earth and Life Institute - Environmental Sciences, Croix du Sud 2, 1348 Louvain-La-Neuve, Belgium.
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Ndihokubwayo F, Koç A. Breeding pure and crossbreeds of European cattle breeds for milk production improvement under tropical climate conditions—a review. Trop Anim Health Prod 2024; 56:23. [DOI: https:/doi.org/10.1007/s11250-023-03868-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023]
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Ndihokubwayo F, Koç A. Breeding pure and crossbreeds of European cattle breeds for milk production improvement under tropical climate conditions-a review. Trop Anim Health Prod 2023; 56:23. [PMID: 38127200 DOI: 10.1007/s11250-023-03868-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023]
Abstract
The aim of this review was to present the breeding status of pure or crossbreeds of European cattle with African indigenous cattle in order to improve milk yield in African tropical conditions. As the African indigenous breeds are characterized by small size, low body weight (300-450 kg) and low production performances (less than 1000 kg per lactation), short lactation length (205-240 days), etc., the crossbreeding with pure European cattle was done in order to ameliorate production performances especially milk and beef production. As results, it was seen that F1 offspring improved output productions than their parents of tropical origin. Also, it was seen that F1 offspring showed disease and heat resistance than their parents of temperate climate origin. However, at different degrees of crossbreeding, it was seen that the offspring can demonstrate bad production performances than their parents and therefore, the crossbreeding has to respect a certain degree. Other consequences are that the crossbreeding of local and pure European cattle breeds has resulted in calving complications in African local cattle. In African indigenous cattle, the selection as an improvement tool was given less emphasis as a solution to improve output production. That is why, the implementation of a well-prepared selection programs could be practiced in African indigenous cattle in order to preserve African cattle genotypes, as they are endangered of extinction due to various crossbreeding with exotic cattle breeds.
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Affiliation(s)
- Frederic Ndihokubwayo
- Faculty of Agriculture, Department of Animal Science, Aydın Adnan Menderes University, 09100, Aydın, Turkey.
| | - Atakan Koç
- Faculty of Agriculture, Department of Animal Science, Aydın Adnan Menderes University, 09100, Aydın, Turkey
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Friedrich J, Bailey RI, Talenti A, Chaudhry U, Ali Q, Obishakin EF, Ezeasor C, Powell J, Hanotte O, Tijjani A, Marshall K, Prendergast J, Wiener P. Mapping restricted introgression across the genomes of admixed indigenous African cattle breeds. Genet Sel Evol 2023; 55:91. [PMID: 38097935 PMCID: PMC10722721 DOI: 10.1186/s12711-023-00861-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 11/24/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND The genomes of indigenous African cattle are composed of components with Middle Eastern (taurine) and South Asian (indicine) origins, providing a valuable model to study hybridization and to identify genetic barriers to gene flow. In this study, we analysed indigenous African cattle breeds as models of hybrid zones, considering taurine and indicine samples as ancestors. In a genomic cline analysis of whole-genome sequence data, we considered over 8 million variants from 144 animals, which allows for fine-mapping of potential genomic incompatibilities at high resolution across the genome. RESULTS We identified several thousand variants that had significantly steep clines ('SCV') across the whole genome, indicating restricted introgression. Some of the SCV were clustered into extended regions, with the longest on chromosome 7, spanning 725 kb and including 27 genes. We found that variants with a high phenotypic impact (e.g. indels, intra-genic and missense variants) likely represent greater genetic barriers to gene flow. Furthermore, our findings provide evidence that a large proportion of breed differentiation in African cattle could be linked to genomic incompatibilities and reproductive isolation. Functional evaluation of genes with SCV suggest that mitonuclear incompatibilities and genes associated with fitness (e.g. resistance to paratuberculosis) could account for restricted gene flow in indigenous African cattle. CONCLUSIONS To our knowledge, this is the first time genomic cline analysis has been applied to identify restricted introgression in the genomes of indigenous African cattle and the results provide extended insights into mechanisms (e.g. genomic incompatibilities) contributing to hybrid differentiation. These results have important implications for our understanding of genetic incompatibilities and reproductive isolation and provide important insights into the impact of cross-breeding cattle with the aim of producing offspring that are both hardy and productive.
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Affiliation(s)
- Juliane Friedrich
- Division of Genetics and Genomics, The Roslin Institute and Royal (Dick), School of Veterinary Studies, University of Edinburgh, Midlothian, UK.
| | - Richard I Bailey
- Department of Ecology and Vertebrate Zoology, University of Łódź, Łódź, Poland
| | - Andrea Talenti
- Division of Genetics and Genomics, The Roslin Institute and Royal (Dick), School of Veterinary Studies, University of Edinburgh, Midlothian, UK
| | - Umer Chaudhry
- School of Veterinary Medicine, St. George's University, St. George's, Caribbean, Grenada
| | - Qasim Ali
- Department of Parasitology, The University of Agriculture Dera Ismail Khan, Khyber Pakhtunkhwa, Pakistan
| | - Emmanuel F Obishakin
- Biotechnology Division, National Veterinary Research Institute, Vom, Plateau State, Nigeria
| | - Chukwunonso Ezeasor
- Department of Veterinary Pathology and Microbiology, University of Nigeria, Nsukka, Enugu State, Nigeria
| | - Jessica Powell
- Division of Infection and Immunity, The Roslin Institute and Royal (Dick), School of Veterinary Studies, University of Edinburgh, Midlothian, UK
| | - Olivier Hanotte
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
- School of Life Sciences, University of Nottingham, Nottingham, UK
- Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, University of Edinburgh, Midlothian, UK
| | | | - Karen Marshall
- Centre for Tropical Livestock Genetics and Health (CTLGH), ILRI Kenya, Nairobi, Kenya
| | - James Prendergast
- Division of Genetics and Genomics, The Roslin Institute and Royal (Dick), School of Veterinary Studies, University of Edinburgh, Midlothian, UK
| | - Pamela Wiener
- Division of Genetics and Genomics, The Roslin Institute and Royal (Dick), School of Veterinary Studies, University of Edinburgh, Midlothian, UK.
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Sambe BS, Diouf MN, Ndiaye B, Houaga I, Badji MN, Diop M, Sembene M. Genetic differentiation and structuration of the Gobra zebu cattle breeds reared in Senegal. Trop Anim Health Prod 2023; 55:389. [PMID: 37917217 DOI: 10.1007/s11250-023-03803-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 10/17/2023] [Indexed: 11/04/2023]
Abstract
The Gobra zebu genetic breeding program has resulted in the genetic improvement of a new population. This population gained genetic characteristics that set them apart from the other cattle populations reared in Senegal. The cause of these differences might be the reproductive isolation and selection to which this population of the "Centre de Recherches Zootechniques" of Dahra has been subjected since the 1950s. This study aimed to assess the genetic differentiation and structuration of this population compared to the main cattle breeds used in Senegal. A total of 180 individuals, selected from the Gobra selection nucleus and bovine populations from four main breeds in Senegal, were included in this study. We used a panel of 21 microsatellite markers among those recommended by the Food Agriculture Organization, to conduct the molecular genotyping of our sampled populations. The basic genetic parameters of differentiation and structuration were calculated using various bioinformatics software. The results of this study, particularly the degrees of genetic differentiation (Fst), the coefficient of genetic homogeneity (Gst), and the gene flow (Nm), show a significant genetic differentiation of the Gobra from the station compared to the other populations studied. Structuring and phylogeny analyses reveal a micro-structuring within the Gobra population as a novelty. This micro-structuring clearly identifies the Gobra individuals from Dahra's station among the other Gobra populations studied. The main causes of these observations would be reproductive isolation and the selection pressure exerted on this population for several decades.
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Affiliation(s)
- Babacar Souleymane Sambe
- Laboratoire National de L'Elevage Et de Recherches Vétérinaires (LNERV), Dakar, Sénégal.
- Département de Biologie Animale, Université Cheikh Anta Diop (UCAD), Dakar, Sénégal.
- Pôle Immunophysiopathologie Et Maladies Infectieuses (IPD/IMI), Institut Pasteur de Dakar, Dakar, Sénégal.
| | - Mame Nahé Diouf
- Laboratoire National de L'Elevage Et de Recherches Vétérinaires (LNERV), Dakar, Sénégal
| | - Bakary Ndiaye
- Laboratoire National de L'Elevage Et de Recherches Vétérinaires (LNERV), Dakar, Sénégal
- Département de Biologie Animale, Université Cheikh Anta Diop (UCAD), Dakar, Sénégal
| | - Isidore Houaga
- Centre International de Recherche-Développement Sur L'Elevage en Zone Subhumide (CIRDES), Bobo-Dioulasso, Burkina Faso
- Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Midlothian, UK
| | - Marc Noël Badji
- Laboratoire National de L'Elevage Et de Recherches Vétérinaires (LNERV), Dakar, Sénégal
- Département de Biologie Animale, Université Cheikh Anta Diop (UCAD), Dakar, Sénégal
| | - Mamadou Diop
- Laboratoire National de L'Elevage Et de Recherches Vétérinaires (LNERV), Dakar, Sénégal
| | - Mbacké Sembene
- Département de Biologie Animale, Université Cheikh Anta Diop (UCAD), Dakar, Sénégal
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Ginja C, Guimarães S, da Fonseca RR, Rasteiro R, Rodríguez-Varela R, Simões LG, Sarmento C, Belarte MC, Kallala N, Torres JR, Sanmartí J, Arruda AM, Detry C, Davis S, Matos J, Götherström A, Pires AE, Valenzuela-Lamas S. Iron age genomic data from Althiburos - Tunisia renew the debate on the origins of African taurine cattle. iScience 2023; 26:107196. [PMID: 37485357 PMCID: PMC10359934 DOI: 10.1016/j.isci.2023.107196] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 12/22/2022] [Accepted: 06/20/2023] [Indexed: 07/25/2023] Open
Abstract
The Maghreb is a key region for understanding the dynamics of cattle dispersal and admixture with local aurochs following their earliest domestication in the Fertile Crescent more than 10,000 years ago. Here, we present data on autosomal genomes and mitogenomes obtained for four archaeological specimens of Iron Age (∼2,800 cal BP-2,000 cal BP) domestic cattle from the Eastern Maghreb, i.e. Althiburos (El Kef, Tunisia). D-loop sequences were obtained for an additional eight cattle specimens from this site. Maternal lineages were assigned to the elusive R and ubiquitous African-T1 haplogroups found in two and ten Althiburos specimens, respectively. Our results can be explained by post-domestication hybridization of Althiburos cattle with local aurochs. However, we cannot rule out an independent domestication in North Africa considering the shared ancestry of Althiburos cattle with the pre-domestic Moroccan aurochs and present-day African taurine cattle.
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Affiliation(s)
- Catarina Ginja
- BIOPOLIS-CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos - ArchGen group, Universidade do Porto, Vairão, Portugal
| | - Silvia Guimarães
- BIOPOLIS-CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos - ArchGen group, Universidade do Porto, Vairão, Portugal
| | - Rute R. da Fonseca
- Center for Global Mountain Biodiversity, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Rita Rasteiro
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | | | - Luciana G. Simões
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Cindy Sarmento
- BIOPOLIS-CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos - ArchGen group, Universidade do Porto, Vairão, Portugal
| | - Maria Carme Belarte
- ICREA, Institut Català de Recerca i Estudis Avançats, Barcelona, Spain
- ICAC, Institut Català d'Arqueologia Clàssica, Tarragona, Spain
| | - Nabil Kallala
- INP, Institut National du Patrimoine, Tunis, Tunisia
- Faculté des Sciences Humaines et Sociales, Université de Tunis, Tunis, Tunisia
| | | | - Joan Sanmartí
- In memoriam, Departament de Prehistòria, Història Antiga i Arqueologia, Universitat de Barcelona, Barcelona, Spain
| | - Ana Margarida Arruda
- UNIARQ, Centro de Arqueologia da Universidade de Lisboa, Faculdade de Letras da Universidade de Lisboa, Lisboa, Portugal
| | - Cleia Detry
- UNIARQ, Centro de Arqueologia da Universidade de Lisboa, Faculdade de Letras da Universidade de Lisboa, Lisboa, Portugal
| | - Simon Davis
- BIOPOLIS-CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos - ArchGen group, Universidade do Porto, Vairão, Portugal
- LARC/DGPC, Laboratório de Arqueociências, Direcção Geral do Património Cultural, Lisboa, Portugal
| | - José Matos
- Unidade Estratégica de Investigação e Serviços de Biotecnologia e Recursos Genéticos, Instituto Nacional de Investigação Agrária e Veterinária, I.P, Oeiras, Portugal
- CE3C, Centro de Ecologia, Evolução e Alterações Ambientais, Universidade de Lisboa, Lisboa, Portugal
| | | | - Ana Elisabete Pires
- BIOPOLIS-CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos - ArchGen group, Universidade do Porto, Vairão, Portugal
- Faculdade de Medicina Veterinária, Universidade Lusófona, Lisboa, Portugal
| | - Silvia Valenzuela-Lamas
- UNIARQ, Centro de Arqueologia da Universidade de Lisboa, Faculdade de Letras da Universidade de Lisboa, Lisboa, Portugal
- Archaeology of Social Dynamics, Consejo Superior de Investigaciones Científicas-Institució Milà i Fontanals d'Humanitats (CSIC-IMF), Barcelona, Spain
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Solodneva E, Svishcheva G, Smolnikov R, Bazhenov S, Konorov E, Mukhina V, Stolpovsky Y. Genetic Structure Analysis of 155 Transboundary and Local Populations of Cattle ( Bos taurus, Bos indicus and Bos grunniens) Based on STR Markers. Int J Mol Sci 2023; 24:5061. [PMID: 36902492 PMCID: PMC10003406 DOI: 10.3390/ijms24055061] [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: 11/30/2022] [Revised: 01/31/2023] [Accepted: 02/01/2023] [Indexed: 03/09/2023] Open
Abstract
Every week, 1-2 breeds of farm animals, including local cattle, disappear in the world. As the keepers of rare allelic variants, native breeds potentially expand the range of genetic solutions to possible problems of the future, which means that the study of the genetic structure of these breeds is an urgent task. Providing nomadic herders with valuable resources necessary for life, domestic yaks have also become an important object of study. In order to determine the population genetic characteristics, and clarify the phylogenetic relationships of modern representatives of 155 cattle populations from different regions of the world, we collected a large set of STR data (10,250 individuals), including unique native cattle, 12 yak populations from Russia, Mongolia and Kyrgyzstan, as well as zebu breeds. Estimation of main population genetic parameters, phylogenetic analysis, principal component analysis and Bayesian cluster analysis allowed us to refine genetic structure and provided insights in relationships of native populations, transboundary breeds and populations of domestic yak. Our results can find practical application in conservation programs of endangered breeds, as well as become the basis for future fundamental research.
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Affiliation(s)
- Evgenia Solodneva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia
| | - Gulnara Svishcheva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Rodion Smolnikov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia
| | - Sergey Bazhenov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia
| | - Evgenii Konorov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia
- Gorbatov Federal Research Center for Food Systems, Russian Academy of Sciences, 109316 Moscow, Russia
| | - Vera Mukhina
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia
| | - Yurii Stolpovsky
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia
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Tenagne A, Taye M, Dessie T, Muluneh B, Kebede D, Tarekegn GM. Quantifying morphometric and adaptive characteristics of indigenous cattle genetic resources in northwest Ethiopia. PLoS One 2023; 18:e0280640. [PMID: 36940195 PMCID: PMC10027228 DOI: 10.1371/journal.pone.0280640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 01/04/2023] [Indexed: 03/21/2023] Open
Abstract
Ethiopia is the gateway of livestock genetic resources to Africa and has a wide range of altitude. It is endowed with huge diverse cattle genetic resources. The aim of this research was to determine the morphometric and potentioally adaptive characteristics of cattle populations. Multi-stage purposive and random sampling methods were employed to select the study areas, households and animals. A total of 1200 adult cattle were sampled and characterized for 14 qualitative and eight morphometric variables. The comparison of marginal means, chi-square tests, canonical discriminant analysis, and clustering analysis were employed using SAS and SPSS statistical software. The sex of the animal, location and agro-ecology were fitted as fixed effects in the model and had highly significant (p<0.001) effects for most body measurements. The chi-square test values of all categorical variables were significantly different (p<0.001) and potentioally adaptive characteristics such as coat colour type, navel flap, and tail length had higher association (> 0.45) values. White with red, light red, black and dark red were the most predominant coat colour types of cattle. The maximum hit rates were recorded in Enebsie and Sinan cattle. From five extracted canonical variate, (can1 and can2) accounted 75.4% and 78.8% in the female and male cattle populations, respectively. The canonical class has separated cattle populations of Sinan from Banja at can1 and Mecha from Sinan populations at can2. The square Mahalanobis distances between sites were significant (p<0.001) and the largest distance was found between Banja and Sinan locations. Cluster analysis result classified the study populations into four major cattle groups. The cumulative analysis results showed that the cattle populations of the study area can be categorized into four breed types as Jawi Sanga, Gojjam Zenga, Banja cattle, and Sinan cattle. However, this morphology based grouping need to be confirmed by molecular data.
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Affiliation(s)
- Andualem Tenagne
- Department of Animal Science, College of Agriculture and Environmental Sciences, Bahir Dar University, Bahir Dar, Ethiopia
- Department of Animal Sciences, Assosa University, Assosa, Ethiopia
| | - Mengistie Taye
- Department of Animal Science, College of Agriculture and Environmental Sciences, Bahir Dar University, Bahir Dar, Ethiopia
- Institute of Biotechnology, Bahir Dar University, Bahir Dar, Ethiopia
| | - Tadelle Dessie
- Department of Animal Science, College of Agriculture and Environmental Sciences, Bahir Dar University, Bahir Dar, Ethiopia
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | - Bekalu Muluneh
- Department of Animal Science, College of Agriculture and Environmental Sciences, Bahir Dar University, Bahir Dar, Ethiopia
- Department of Animal and Range Sciences, Wolaita Sodo University, Dawuro Tarcha Campus, Tarcha, Ethiopia
| | - Damitie Kebede
- Department of Animal Science, College of Agriculture and Environmental Sciences, Bahir Dar University, Bahir Dar, Ethiopia
- Institute of Biotechnology, Bahir Dar University, Bahir Dar, Ethiopia
| | - Getinet Mekuriaw Tarekegn
- Department of Animal Science, College of Agriculture and Environmental Sciences, Bahir Dar University, Bahir Dar, Ethiopia
- Institute of Biotechnology, Bahir Dar University, Bahir Dar, Ethiopia
- Animal and Veterinary Science, Scotland's Rural College (SRUC), Roslin Institute Building, Easter Bush, Roslin, United Kingdom
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9
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Genome-wide local ancestry and evidence for mitonuclear coadaptation in African hybrid cattle populations (Bos taurus/indicus). iScience 2022; 25:104672. [PMID: 35832892 PMCID: PMC9272374 DOI: 10.1016/j.isci.2022.104672] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/11/2022] [Accepted: 06/21/2022] [Indexed: 11/21/2022] Open
Abstract
The phenotypic diversity of African cattle reflects adaptation to a wide range of agroecological conditions, human-mediated selection preferences, and complex patterns of admixture between the humpless Bos taurus (taurine) and humped Bos indicus (zebu) subspecies, which diverged 150-500 thousand years ago. Despite extensive admixture, all African cattle possess taurine mitochondrial haplotypes, even populations with significant zebu biparental and male uniparental nuclear ancestry. This has been interpreted as the result of human-mediated dispersal ultimately stemming from zebu bulls imported from South Asia during the last three millennia. Here, we assess whether ancestry at mitochondrially targeted nuclear genes in African admixed cattle is impacted by mitonuclear functional interactions. Using high-density SNP data, we find evidence for mitonuclear coevolution across hybrid African cattle populations with a significant increase of taurine ancestry at mitochondrially targeted nuclear genes. Our results, therefore, support the hypothesis of incompatibility between the taurine mitochondrial genome and the zebu nuclear genome.
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Mauki DH, Tijjani A, Ma C, Ng’ang’a SI, Mark AI, Sanke OJ, Abdussamad AM, Olaogun SC, Ibrahim J, Dawuda PM, Mangbon GF, Kazwala RR, Gwakisa PS, Yin TT, Li Y, Peng MS, Adeola AC, Zhang YP. Genome-wide investigations reveal the population structure and selection signatures of Nigerian cattle adaptation in the sub-Saharan tropics. BMC Genomics 2022; 23:306. [PMID: 35428239 PMCID: PMC9012019 DOI: 10.1186/s12864-022-08512-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 03/29/2022] [Indexed: 11/11/2022] Open
Abstract
Background Cattle are considered to be the most desirable livestock by small scale farmers. In Africa, although comprehensive genomic studies have been carried out on cattle, the genetic variations in indigenous cattle from Nigeria have not been fully explored. In this study, genome-wide analysis based on genotyping-by-sequencing (GBS) of 193 Nigerian cattle was used to reveal new insights on the history of West African cattle and their adaptation to the tropical African environment, particularly in sub-Saharan region. Results The GBS data were evaluated against whole-genome sequencing (WGS) data and high rate of variant concordance between the two platforms was evident with high correlated genetic distance matrices genotyped by both methods suggestive of the reliability of GBS applicability in population genetics. The genetic structure of Nigerian cattle was observed to be homogenous and unique from other African cattle populations. Selection analysis for the genomic regions harboring imprints of adaptation revealed genes associated with immune responses, growth and reproduction, efficiency of feeds utilization, and heat tolerance. Our findings depict potential convergent adaptation between African cattle, dogs and humans with adaptive genes SPRY2 and ITGB1BP1 possibly involved in common physiological activities. Conclusion The study presents unique genetic patterns of Nigerian cattle which provide new insights on the history of cattle in West Africa based on their population structure and the possibility of parallel adaptation between African cattle, dogs and humans in Africa which require further investigations. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08512-w.
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Kwon T, Kim K, Caetano-Anolles K, Sung S, Cho S, Jeong C, Hanotte O, Kim H. Mitonuclear incompatibility as a hidden driver behind the genome ancestry of African admixed cattle. BMC Biol 2022; 20:20. [PMID: 35039029 PMCID: PMC8764764 DOI: 10.1186/s12915-021-01206-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 12/03/2021] [Indexed: 11/10/2022] Open
Abstract
Background Africa is an important watershed in the genetic history of domestic cattle, as two lineages of modern cattle, Bos taurus and B. indicus, form distinct admixed cattle populations. Despite the predominant B. indicus nuclear ancestry of African admixed cattle, B. indicus mitochondria have not been found on the continent. This discrepancy between the mitochondrial and nuclear genomes has been previously hypothesized to be driven by male-biased introgression of Asian B. indicus into ancestral African B. taurus. Given that this hypothesis mandates extreme demographic assumptions relying on random genetic drift, we propose a novel hypothesis of selection induced by mitonuclear incompatibility and assess these hypotheses with regard to the current genomic status of African admixed cattle. Results By analyzing 494 mitochondrial and 235 nuclear genome sequences, we first confirmed the genotype discrepancy between mitochondrial and nuclear genome in African admixed cattle: the absence of B. indicus mitochondria and the predominant B. indicus autosomal ancestry. We applied approximate Bayesian computation (ABC) to assess the posterior probabilities of two selection hypotheses given this observation. The results of ABC indicated that the model assuming both male-biased B. indicus introgression and selection induced by mitonuclear incompatibility explains the current genomic discrepancy most accurately. Subsequently, we identified selection signatures at autosomal loci interacting with mitochondria that are responsible for integrity of the cellular respiration system. By contrast with B. indicus-enriched genome ancestry of African admixed cattle, local ancestries at these selection signatures were enriched with B. taurus alleles, concurring with the key expectation of selection induced by mitonuclear incompatibility. Conclusions Our findings support the current genome status of African admixed cattle as a potential outcome of male-biased B. indicus introgression, where mitonuclear incompatibility exerted selection pressure against B. indicus mitochondria. This study provides a novel perspective on African cattle demography and supports the role of mitonuclear incompatibility in the hybridization of mammalian species. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01206-x.
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Affiliation(s)
- Taehyung Kwon
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Kwondo Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea.,eGnome, Inc, Seoul, South Korea
| | | | | | | | - Choongwon Jeong
- School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Olivier Hanotte
- School of Life Sciences, University of Nottingham, Nottingham, UK. .,LiveGene, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia. .,The Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, The University of Edinburgh, Edinburgh, UK.
| | - Heebal Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea. .,eGnome, Inc, Seoul, South Korea. .,Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, South Korea.
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12
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Bartens MC, Gibson AJ, Etherington GJ, Di Palma F, Holder A, Werling D, Willcocks S. Single Nucleotide Polymorphisms in the Bovine TLR2 Extracellular Domain Contribute to Breed and Species-Specific Innate Immune Functionality. Front Immunol 2022; 12:764390. [PMID: 35003078 PMCID: PMC8732954 DOI: 10.3389/fimmu.2021.764390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 11/26/2021] [Indexed: 11/13/2022] Open
Abstract
Recent evidence suggests that several cattle breeds may be more resistant to infection with the zoonotic pathogen Mycobacterium bovis. Our data presented here suggests that the response to mycobacterial antigens varies in macrophages generated from Brown Swiss (BS) and Holstein Friesian (HF) cattle, two breeds belonging to the Bos taurus family. Whole genome sequencing of the Brown Swiss genome identified several potential candidate genes, in particular Toll-like Receptor-2 (TLR2), a pattern recognition receptor (PRR) that has previously been described to be involved in mycobacterial recognition. Further investigation revealed single nucleotide polymorphisms (SNP) in TLR2 that were identified between DNA isolated from cells of BS and HF cows. Interestingly, one specific SNP, H326Q, showed a different genotype frequency in two cattle subspecies, Bos (B.) taurus and Bos indicus. Cloning of the TLR2 gene and subsequent gene-reporter and chemokine assays revealed that this SNP, present in BS and Bos indicus breeds, resulted in a significantly higher response to mycobacterial antigens as well as tri-acylated lipopeptide ligands in general. Comparing wild-type and H326Q containing TLR2 responses, wild-type bovine TLR2 response showed clear, diminished mycobacterial antigen responses compared to human TLR2, however bovine TLR2 responses containing H326Q were found to be partially recovered compared to human TLR2. The creation of human:bovine TLR2 chimeras increased the response to mycobacterial antigens compared to the full-length bovine TLR2, but significantly reduced the response compared to the full-length human TLR2. Thus, our data, not only present evidence that TLR2 is a major PRR in the mammalian species-specific response to mycobacterial antigens, but furthermore, that there are clear differences between the response seen in different cattle breeds, which may contribute to their enhanced or reduced susceptibility to mycobacterial infection.
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Affiliation(s)
- Marie-Christine Bartens
- Molecular Immunology Group, Centre for Vaccinology and Regenerative Medicine, Department of Pathobiology and Population Science, Royal Veterinary College, Hatfield, United Kingdom.,Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Amanda J Gibson
- Molecular Immunology Group, Centre for Vaccinology and Regenerative Medicine, Department of Pathobiology and Population Science, Royal Veterinary College, Hatfield, United Kingdom
| | | | - Federica Di Palma
- Genome British Columbia, Vancouver, BC, Canada.,Department of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Angela Holder
- Molecular Immunology Group, Centre for Vaccinology and Regenerative Medicine, Department of Pathobiology and Population Science, Royal Veterinary College, Hatfield, United Kingdom
| | - Dirk Werling
- Molecular Immunology Group, Centre for Vaccinology and Regenerative Medicine, Department of Pathobiology and Population Science, Royal Veterinary College, Hatfield, United Kingdom
| | - Sam Willcocks
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
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13
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Goyache F, Pérez-Pardal L, Fernández I, Traoré A, Menéndez-Arias NA, Álvarez I. Ancient autozygous segments subject to positive selection suggest adaptive immune responses in West African cattle. Gene 2021; 803:145899. [PMID: 34400278 DOI: 10.1016/j.gene.2021.145899] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/05/2021] [Accepted: 08/10/2021] [Indexed: 11/19/2022]
Abstract
Small-sized and trypanotolerant West African taurine (Bos taurus) cattle are a unique case of human-mediated process of adaptation to a challenging environment. Extensive gene flow with Sahelian zebu (B. indicus), bigger and with some resistance to tick attack, occurred for centuries and allowed the apparition of stable crossbred populations (sanga) having intermediate characteristics. Up to 237 individuals belonging to 10 different taurine, zebu and sanga cattle populations sampled in Benin, Burkina Faso and Niger were typed using the BovineHD BeadChip of Illumina to identify signatures of selection, assessed using three different Extended-Haplotype-Homozygosity-based statistics, overlapping with ancient, originated 1024 or 2048 generations ago, Homozygosity-By-Descent segments in the cattle genome. Candidate genomic regions were defined ensuring their importance within cattle type and using zebu as reference. Functional annotation analysis identified four statistically significant Annotation Clusters in taurine cattle (from ACt1 to ACt4), one (ACs1) in sanga, and another (ACz1) in zebu cattle, fitting well with expectations. ACt1 included genes primarily associated with innate immunity; ACt2 involved bitter taste receptor genes of importance to adaptation to changing environments; ACt3 included 68 genes coding ATP-binding proteins, some of them located on trypanotolerance-related QTL regions, that can partially underlie immune response and the additive mechanism of trypanotolerance; ACt4 was associated with growth and small size (NPPC gene); ACs1 included genes involved in immune response; and ACz1 is related with ectoparasite resistance. Our results provide a new set of genomic areas and candidate genes giving new insights on the genomic impact of adaptation in West African cattle.
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Affiliation(s)
- Félix Goyache
- SERIDA-Deva, Camino de Rioseco 1225, E-33394-Gijón, Spain.
| | | | - Iván Fernández
- SERIDA-Deva, Camino de Rioseco 1225, E-33394-Gijón, Spain
| | - Amadou Traoré
- Institut de l'Environnement et des Recherches Agricoles (INERA), Ouagadougou 04 BP 8645, Burkina Faso
| | | | - Isabel Álvarez
- SERIDA-Deva, Camino de Rioseco 1225, E-33394-Gijón, Spain
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14
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Alfonzo E, McManus C, Campos G, Portes J, Padilha A, Peripolli V, Braccini Neto J. Spatial distribution of Brazilian bovine taurine breeds associated with climatic, physical and socioeconomic variables. ARQ BRAS MED VET ZOO 2021. [DOI: 10.1590/1678-4162-12206] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
ABSTRACT The objective of this study was to evaluate the spatial distribution of purebred Bos taurus taurus bovine breeds raised in Brazil in association with climatic, physical and socioeconomic variables. The breeds Aberdeen Angus, Ayrshire, Braford, Brangus, Charolais, Devon, Flemish, Hereford, Pinzgauer, Shorthorn and Simental were classified according to their aptitude (milk, meat or dual-purpose). They were spatialized according to their aptitude using state and municipal information. The milk breeds were found in the states of Rio Grande do Sul and Santa Catarina, while the dual-purpose breeds were found in Minas Gerais and Rio Grande do Sul states and the beef breeds were concentrated in the southern region. Only the Aberdeen Angus meat breed showed higher dispersion in other regions. Meat and dual-purpose breeds tended to be raised in regions with lower maximum temperature, average temperature, thermal amplitude and temperature-humidity index. Dual-purpose breeds were found in municipalities with high humidity and altitude, but with a low gross domestic product, little technical guidance received from cooperatives and the government, low control of diseases and parasites, as well as low use of pasture rotation systems. The spatial distribution of Brazilian bovine taurine breeds, regardless of aptitude, was related to climatic, physical and socioeconomic factors.
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Affiliation(s)
| | | | - G.S. Campos
- Universidade Federal do Rio Grande do Sul, Brazil
| | - J.V. Portes
- Universidade Federal do Rio Grande do Sul, Brazil
| | - A.H. Padilha
- Universidade Federal do Rio Grande do Sul, Brazil
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15
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Mauki DH, Adeola AC, Ng’ang’a SI, Tijjani A, Akanbi IM, Sanke OJ, Abdussamad AM, Olaogun SC, Ibrahim J, Dawuda PM, Mangbon GF, Gwakisa PS, Yin TT, Peng MS, Zhang YP. Genetic variation of Nigerian cattle inferred from maternal and paternal genetic markers. PeerJ 2021; 9:e10607. [PMID: 33717663 PMCID: PMC7938780 DOI: 10.7717/peerj.10607] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 11/29/2020] [Indexed: 01/29/2023] Open
Abstract
The African cattle provide unique genetic resources shaped up by both diverse tropical environmental conditions and human activities, the assessment of their genetic diversity will shade light on the mechanism of their remarkable adaptive capacities. We therefore analyzed the genetic diversity of cattle samples from Nigeria using both maternal and paternal DNA markers. Nigerian cattle can be assigned to 80 haplotypes based on the mitochondrial DNA (mtDNA) D-loop sequences and haplotype diversity was 0.985 + 0.005. The network showed two major matrilineal clustering: the dominant cluster constituting the Nigerian cattle together with other African cattle while the other clustered Eurasian cattle. Paternal analysis indicates only zebu haplogroup in Nigerian cattle with high genetic diversity 1.000 ± 0.016 compared to other cattle. There was no signal of maternal genetic structure in Nigerian cattle population, which may suggest an extensive genetic intermixing within the country. The absence of Bos indicus maternal signal in Nigerian cattle is attributable to vulnerability bottleneck of mtDNA lineages and concordance with the view of male zebu genetic introgression in African cattle. Our study shades light on the current genetic diversity in Nigerian cattle and population history in West Africa.
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Affiliation(s)
- David H. Mauki
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Chinese Academy of Sciences, Sino-Africa Joint Research Center, Kunming, Yunnan, China
- University of Academy of Sciences, Kunming College of Life Science, Kunming, Yunnan, China
| | - Adeniyi C. Adeola
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Chinese Academy of Sciences, Sino-Africa Joint Research Center, Kunming, Yunnan, China
| | - Said I. Ng’ang’a
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Chinese Academy of Sciences, Sino-Africa Joint Research Center, Kunming, Yunnan, China
- University of Academy of Sciences, Kunming College of Life Science, Kunming, Yunnan, China
| | | | - Ibikunle Mark Akanbi
- Ministry of Agriculture and Rural Development, Secretariat, Ibadan, Oyo, Nigeria
| | - Oscar J. Sanke
- Taraba State Ministry of Agriculture and Natural Resources, Jalingo, Taraba, Nigeria
| | | | - Sunday C. Olaogun
- Department of Veterinary Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Jebi Ibrahim
- College of veterinary medicine, department of theriogenology, University of agriculture, Makurdi, Makurdi, Benue, Nigeria
| | - Philip M. Dawuda
- Department of Veterinary Surgery and Theriogenology, College of Veterinary Medicine, University of Agriculture Makurdi, Makurdi, Benue, Nigeria
| | | | - Paul S. Gwakisa
- Department of Microbiology, Parasitology and Biotechnology/ Genome Science Center, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Ting-Ting Yin
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Chinese Academy of Sciences, Sino-Africa Joint Research Center, Kunming, Yunnan, China
- University of Academy of Sciences, Kunming College of Life Science, Kunming, Yunnan, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Chinese Academy of Sciences, Sino-Africa Joint Research Center, Kunming, Yunnan, China
- University of Academy of Sciences, Kunming College of Life Science, Kunming, Yunnan, China
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan, China
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16
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Gebrehiwot NZ, Strucken EM, Aliloo H, Marshall K, Gibson JP. The patterns of admixture, divergence, and ancestry of African cattle populations determined from genome-wide SNP data. BMC Genomics 2020; 21:869. [PMID: 33287702 PMCID: PMC7720612 DOI: 10.1186/s12864-020-07270-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 11/23/2020] [Indexed: 12/22/2022] Open
Abstract
Background Humpless Bos taurus cattle are one of the earliest domestic cattle in Africa, followed by the arrival of humped Bos indicus cattle. The diverse indigenous cattle breeds of Africa are derived from these migrations, with most appearing to be hybrids between Bos taurus and Bos indicus. The present study examines the patterns of admixture, diversity, and relationships among African cattle breeds. Methods Data for ~ 40 k SNPs was obtained from previous projects for 4089 animals representing 35 African indigenous, 6 European Bos taurus, 4 Bos indicus, and 5 African crossbred cattle populations. Genetic diversity and population structure were assessed using principal component analyses (PCA), admixture analyses, and Wright’s F statistic. The linkage disequilibrium and effective population size (Ne) were estimated for the pure cattle populations. Results The first two principal components differentiated Bos indicus from European Bos taurus, and African Bos taurus from other breeds. PCA and admixture analyses showed that, except for recently admixed cattle, all indigenous breeds are either pure African Bos taurus or admixtures of African Bos taurus and Bos indicus. The African zebu breeds had highest proportions of Bos indicus ancestry ranging from 70 to 90% or 60 to 75%, depending on the admixture model. Other indigenous breeds that were not 100% African Bos taurus, ranged from 42 to 70% or 23 to 61% Bos indicus ancestry. The African Bos taurus populations showed substantial genetic diversity, and other indigenous breeds show evidence of having more than one African taurine ancestor. Ne estimates based on r2 and r2adj showed a decline in Ne from a large population at 2000 generations ago, which is surprising for the indigenous breeds given the expected increase in cattle populations over that period and the lack of structured breeding programs. Conclusion African indigenous cattle breeds have a large genetic diversity and are either pure African Bos taurus or admixtures of African Bos taurus and Bos indicus. This provides a rich resource of potentially valuable genetic variation, particularly for adaptation traits, and to support conservation programs. It also provides challenges for the development of genomic assays and tools for use in African populations. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07270-x.
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Affiliation(s)
- N Z Gebrehiwot
- Centre for Genetic Analysis and Applications, School of Environmental and Rural Science, University of New England, Armidale, NSW, 2351, Australia.
| | - E M Strucken
- Centre for Genetic Analysis and Applications, School of Environmental and Rural Science, University of New England, Armidale, NSW, 2351, Australia
| | - H Aliloo
- Centre for Genetic Analysis and Applications, School of Environmental and Rural Science, University of New England, Armidale, NSW, 2351, Australia
| | - K Marshall
- International Livestock Research Institute and Centre for Tropical Livestock Genetics and Health, Nairobi, Kenya
| | - J P Gibson
- Centre for Genetic Analysis and Applications, School of Environmental and Rural Science, University of New England, Armidale, NSW, 2351, Australia.
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17
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Callaby R, Kelly R, Mazeri S, Egbe F, Benedictus L, Clark E, Doeschl-Wilson A, Bronsvoort B, Salavati M, Muwonge A. Genetic Diversity of Cameroon Cattle and a Putative Genomic Map for Resistance to Bovine Tuberculosis. Front Genet 2020; 11:550215. [PMID: 33281865 PMCID: PMC7705233 DOI: 10.3389/fgene.2020.550215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 10/19/2020] [Indexed: 11/30/2022] Open
Abstract
Bovine Tuberculosis (bTB) caused by Mycobacterium bovis is a livestock disease of global economic and public health importance. There are currently no effective vaccines available for livestock and so control relies on animal level surveillance and pasteurization of dairy products. A new alternative control approach is to exploit the genetic variability of the host; recent studies have demonstrated that breeding European taurine cattle, such as Holsteins for increased resistance to bTB is feasible. The utility of such an approach is still unknown for African cattle populations. This study aims to assess genetic variation in bTB resistance and the underlying genomic architecture of cattle in Cameroon. We conducted a cross-sectional study of 2,346 slaughter cattle in Cameroon. Retropharyngeal lymph node samples were collected and cultured on Lowenstein Jensen media and the BACTEC MGIT 960 system, and M. bovis was identified using the Hain® Genotype kits. A total of 153 cattle were positive for M. bovis and were archived along with a random selection of negative samples. In this study, we genotyped archived samples from 212 cattle. Their genomic diversity was characterized using PCA, hierarchical clustering and admixture analysis. We assessed genetic variation in bTB resistance using heritability analysis and compared quantitative trait loci. Previous research on this study population have shown that Fulani cattle are more susceptible to bTB than mixed breeds. However, here we show that these apparent phenotypic differences in breeds are not reflected by clear genomic differences. At the genetic level, both the Fulani and mixed cattle show similar patterns of admixture with evidence of both taurine and indicine ancestry. There was little European taurine introgression within the studied population. Hierarchical clustering showed clusters of cattle that differed in their susceptibility to bTB. Our findings allude to bTB resistance being polygenic in nature. This study highlights the potential for genetic control of bTB in Africa and the need for further research into the genetics of bTB resistance within African cattle populations.
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Affiliation(s)
- Rebecca Callaby
- Centre for Tropical Livestock Genetics and Health, The Royal (Dick) School of Veterinary Studies, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom.,The Royal (Dick) School of Veterinary Studies, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Robert Kelly
- The Royal (Dick) School of Veterinary Studies, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Stella Mazeri
- The Royal (Dick) School of Veterinary Studies, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Franklyn Egbe
- School of Life Sciences, University of Lincoln, Lincoln, United Kingdom
| | - Lindert Benedictus
- The Royal (Dick) School of Veterinary Studies, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Emily Clark
- Centre for Tropical Livestock Genetics and Health, The Royal (Dick) School of Veterinary Studies, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom.,The Royal (Dick) School of Veterinary Studies, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Andrea Doeschl-Wilson
- The Royal (Dick) School of Veterinary Studies, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Barend Bronsvoort
- Centre for Tropical Livestock Genetics and Health, The Royal (Dick) School of Veterinary Studies, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom.,The Royal (Dick) School of Veterinary Studies, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Mazdak Salavati
- Centre for Tropical Livestock Genetics and Health, The Royal (Dick) School of Veterinary Studies, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom.,The Royal (Dick) School of Veterinary Studies, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Adrian Muwonge
- The Royal (Dick) School of Veterinary Studies, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
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18
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The mosaic genome of indigenous African cattle as a unique genetic resource for African pastoralism. Nat Genet 2020; 52:1099-1110. [PMID: 32989325 DOI: 10.1038/s41588-020-0694-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 08/18/2020] [Indexed: 02/07/2023]
Abstract
Cattle pastoralism plays a central role in human livelihood in Africa. However, the genetic history of its success remains unknown. Here, through whole-genome sequence analysis of 172 indigenous African cattle from 16 breeds representative of the main cattle groups, we identify a major taurine × indicine cattle admixture event dated to circa 750-1,050 yr ago, which has shaped the genome of today's cattle in the Horn of Africa. We identify 16 loci linked to African environmental adaptations across crossbred animals showing an excess of taurine or indicine ancestry. These include immune-, heat-tolerance- and reproduction-related genes. Moreover, we identify one highly divergent locus in African taurine cattle, which is putatively linked to trypanotolerance and present in crossbred cattle living in trypanosomosis-infested areas. Our findings indicate that a combination of past taurine and recent indicine admixture-derived genetic resources is at the root of the present success of African pastoralism.
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19
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Relatively undisturbed African savannas - an important reference for assessing wildlife responses to livestock grazing systems in European rangelands. Glob Ecol Conserv 2020. [DOI: 10.1016/j.gecco.2020.e01124] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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20
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Scheper C, Bohlouli M, Brügemann K, Weimann C, Vanvanhossou SFU, König S, Dossa LH. The role of agro-ecological factors and transboundary transhumance in shaping the genetic diversity in four indigenous cattle populations of Benin. J Anim Breed Genet 2020; 137:622-640. [PMID: 32672901 DOI: 10.1111/jbg.12495] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 05/29/2020] [Accepted: 06/17/2020] [Indexed: 01/03/2023]
Abstract
The indigenous cattle population of Benin is a diverse mix of taurine and hybrid breeds shaped by diverse ecological and climatic conditions with eight agro-ecological zones (AEZ). Presumably, the taurine breeds face current endangerment due to ongoing indicine introgression following climate change and transboundary transhumance. The aim of the study was to investigate the genetic diversity and population structure of the indigenous breeds Lagune, Somba, Pabli and Borgou considering spatial agro-ecological and socio-economic factors (transhumance) based on 50k SNP and microsatellite data. Among the four sampled breeds, six genetic clusters were identified using model-free (discriminant analysis of principal components) and model-based (TESS and ADMIXTURE) methods separating taurine from hybrid breeds. Results based on an extension with publicly available historic SNP data sets from taurine and indicine West African cattle and additional outgroups provided additional insight into changes of genetic structure in the sampled breeds over time. Both taurine breeds, Somba and Lagune, showed a stable foundation but also spatially limited partial indicine introgression associated with transhumance leading to high genetic diversity. In addition, we found evidence for spatial diversity and changes in genetic structure over time in the Borgou breed in comparison of our samples with the historic samples which could be explained by potential continuous indicine introgression into the Borgou breed in two sample regions. Results for the Pabli breed do not conclusively point to full absorbance by the Borgou in comparison with all available Borgou samples. Further research is needed in this regard.
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Affiliation(s)
- Carsten Scheper
- Institute of Animal Breeding and Genetics, Justus-Liebig-University of Gießen, Gießen, Germany
| | - Mehdi Bohlouli
- Institute of Animal Breeding and Genetics, Justus-Liebig-University of Gießen, Gießen, Germany
| | - Kerstin Brügemann
- Institute of Animal Breeding and Genetics, Justus-Liebig-University of Gießen, Gießen, Germany
| | - Christina Weimann
- Institute of Animal Breeding and Genetics, Justus-Liebig-University of Gießen, Gießen, Germany
| | | | - Sven König
- Institute of Animal Breeding and Genetics, Justus-Liebig-University of Gießen, Gießen, Germany
| | - Luc Hippolyte Dossa
- Ecole des Sciences et Techniques de Production Animale, Faculté des Sciences Agronomiques, Université d'Abomey-Calavi, Cotonou, Bénin
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21
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Y-chromosome genetic diversity of Bos indicus cattle in close proximity to the centre of domestication. Sci Rep 2020; 10:9992. [PMID: 32561783 PMCID: PMC7305206 DOI: 10.1038/s41598-020-66133-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 05/11/2020] [Indexed: 02/08/2023] Open
Abstract
Y-chromosome genetic diversity in and around its domestication origin and a better understanding of indicine-specific microsatellite alleles are imperative concerns but less -targeted. We analysed Y-chromosome markers in 301 bulls representing 19 native Indian cattle (Bos indicus) and identified new alleles and haplotypes. Compared to other indicine studies, the high Y-haplotype diversity found in Indian cattle supports the hypothesis of greater genetic variability across the centre of origin decreasing along migratory routes with increasing distance. Hence, a considerable paternal genetic diversity of Indian cattle appears to have been lost in transboundary commercial indicine breeds. The Khillar and Gir are the most diversified populations where the first tends to be the well-differentiated traditional breed carrying strikingly distinct Y-lineages with typical BM861-158 bp allele, characteristics of taurine cattle, while retaining standard indicine lineages for all other markers. Geographical distribution found to be an unreliable predictor of parental variation, and Y-lineages seemed closely related to Indian breed function/utility. The comprehensive Y-chromosome information will be useful to examine the demographic expansion/spread of Bos indicus lineages from close proximity to the domestication centre across different countries worldwide and such diversity should be preserved through effective management and conservation programs.
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Adoligbe MC, Amaveda MA, Adido MS, Djimenou D, Farougou S. Muturu cattle breed management in the smallholder farming area of the Ouémé district in the south of Benin: rearing practices, objectives, and constraints. Trop Anim Health Prod 2020; 52:3015-3025. [PMID: 32556907 DOI: 10.1007/s11250-020-02320-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Accepted: 06/09/2020] [Indexed: 11/30/2022]
Abstract
An exploratory survey was conducted to understand breeding practices and breeding objectives as well as the constraints as a first step towards developing breeding strategies for the conservation of Muturu cattle breed in Ouémé smallholder farming area of South Benin. Data were generated through randomly interviewing 100 selected Muturu cattle keepers in the municipalities of Adjarra, Adjohoun, Akpro-Missérété, and Bonou using an electronic animal genetic resource characterization, inventory, and monitoring tool. Results indicated that the Muturu cattle were mainly kept for their meat. The mean herd sizes of 3, 5, 4, and 33 were obtained in Adjarra, Adjohoun, Akpro-Misserete, and Bonou respectively. Cattle keepers were exclusively male in the various municipalities surveyed except for Adjohoun, where 28.57% of cattle keepers were female. Preference was given to this breed because it is less demanding in terms of inputs and well adapted to the local environment. Mating was generally uncontrolled. The animals were fed on a natural pasture exclusively irrespective of the season. Robustness and vigor were the most frequently reported traits in selecting breeding bulls, while breeding females were kept based on their offspring's growth and conformation. The decline in the number of Muturu cattle in the region was largely attributed to the competition for land used for other purposes such as crop cultivation and animal theft. Considering the devastating threat on the Muturu cattle breed, it is recommended that a participatory management scheme be designed and implemented for in situ conservation of the Muturu cattle breed in Benin.
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Affiliation(s)
- M C Adoligbe
- Polytechnic School of Abomey-Calavi, Unit of Research on Communicable Diseases, University of Abomey-Calavi, P.O. Box 2009, Cotonou, Benin.
| | - M A Amaveda
- Polytechnic School of Abomey-Calavi, Unit of Research on Communicable Diseases, University of Abomey-Calavi, P.O. Box 2009, Cotonou, Benin
| | - M S Adido
- Technology and Innovation, Pan African University Institute for Basic Sciences, P.O. Box 62000-00200, Nairobi, Kenya
| | - D Djimenou
- Polytechnic School of Abomey-Calavi, Unit of Research on Communicable Diseases, University of Abomey-Calavi, P.O. Box 2009, Cotonou, Benin
| | - S Farougou
- Polytechnic School of Abomey-Calavi, Unit of Research on Communicable Diseases, University of Abomey-Calavi, P.O. Box 2009, Cotonou, Benin
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23
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Mkize LS, Zishiri OT. Population genetic structure and maternal lineage of South African crossbred Nguni cattle using the cytochrome b gene in mtDNA. Trop Anim Health Prod 2020; 52:2079-2089. [PMID: 32048149 DOI: 10.1007/s11250-020-02231-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 01/30/2020] [Indexed: 10/25/2022]
Abstract
The Nguni cattle breed predominates South Africa and is endowed with traits favourable against environmental stressors such as heat stress and resistance to diseases. Interventions to improve production have led to the erosion of the genetic integrity of local breeds and the introduction of exotic breeds has proved ineffective as they fail to perform well due to different climatic conditions and production systems. In this study, the genetic structure and genetic lineage of Nguni crossbreds from 6 populations were assessed using the mitochondrial cytochrome b gene. Twelve polymorphic sites were detected resulting in 11 haplotypes with haplotype and nucleotide diversities of 0.550 ± 0.135 and 0.0019 ± 0.0011, respectively. Only 2 of the 6 populations displayed recent population expansion events, whereas the majority adhered to neutral evolution. The basal haplotype contained approximately 60% of the studied populations and there were four unique haplotypes that were revealed. A possible Nguni descript haplotype was uncovered, and this haplotype was found in all populations but was however devoid of individuals from around the world. The genetic structure of the populations was rather low (average pairwise FST = 0.066 and Slatkins FST = 0.094), and approximately 96% of the total genetic variation was accounted for by differences within populations. Phylogenetic analyses supported the clustering of all the samples within the Bos taurus clade and no Bos indicus haplotype was detected. Furthermore, no intermediate haplotype of taurine and indicine was detected. Overall, the maternal lineage of the crossbreds points to a taurine origin and the low genetic diversity depicts the retention of the Nguni genetic pool and possibly its superior adaptive traits.
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Affiliation(s)
| | - Oliver Tendayi Zishiri
- School of Life Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban, 4000, South Africa.
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24
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Cooke RF, Daigle CL, Moriel P, Smith SB, Tedeschi LO, Vendramini JMB. Cattle adapted to tropical and subtropical environments: social, nutritional, and carcass quality considerations. J Anim Sci 2020; 98:skaa014. [PMID: 31955200 PMCID: PMC7023624 DOI: 10.1093/jas/skaa014] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 01/14/2020] [Indexed: 02/07/2023] Open
Abstract
Beef production needs to increase from 60 million to 130 million tons by 2050 to feed a growing world population, and 70% of this production increase is expected from beef industries located in subtropical and tropical regions of the world. Bos indicus-influenced cattle predominate in these regions but are often managed using practices developed for Bos taurus breeds reared in temperate climates. Hence, a fundamental step to meet the increasing global demand for beef is to develop specific management for B. indicus-influenced cattle in tropical or subtropical environments. Bos taurus and B. indicus are different subspecies, and diverge in social and biological functions due to selection pressure caused by complex evolutionary and domestication processes. Bos indicus cattle display different social responses compared with B. taurus counterparts, which must be taken into account by management planning as these traits directly impact cattle performance and welfare. In tropical and subtropical regions, warm-season perennial C4 grasses are the dominant forages, and their availability has a significant influence on the productivity of beef cattle systems. The resilience of C4 grasses under adverse conditions is one of their most important characteristics, even though these forages have reduced nutritive value compared with forages from temperate climates. Accordingly, nutritional planning in tropical and subtropical conditions must include management to optimize the quantity and quality of C4 forages. Nutritional requirements of cattle raised within these conditions also require special attention, including inherent metabolic compromises to cope with environmental constraints and altered energy requirements due to body composition and heat tolerance. Nutritional interventions to enhance beef production need to be specifically tailored and validated in B. indicus-influenced cattle. As an example, supplementation programs during gestation or early life to elicit fetal programming or metabolic imprinting effects, respectively, yield discrepant outcomes between subspecies. Bos indicus-influenced cattle produce carcasses with less marbling than B. taurus cattle, despite recent genetic and management advances. This outcome is mostly related to reduced intramuscular adipocyte volume in B. indicus breeds, suggesting a lesser need for energy stored intramuscularly as a mechanism to improve thermotolerance in tropical and subtropical climates.
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Affiliation(s)
- Reinaldo F Cooke
- Department of Animal Science, Texas A&M University, College Station, TX
| | - Courtney L Daigle
- Department of Animal Science, Texas A&M University, College Station, TX
| | - Philipe Moriel
- Range Cattle Research and Education Center, University of Florida, Ona, FL
| | - Stephen B Smith
- Department of Animal Science, Texas A&M University, College Station, TX
| | - Luis O Tedeschi
- Department of Animal Science, Texas A&M University, College Station, TX
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25
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McHugo GP, Dover MJ, MacHugh DE. Unlocking the origins and biology of domestic animals using ancient DNA and paleogenomics. BMC Biol 2019; 17:98. [PMID: 31791340 PMCID: PMC6889691 DOI: 10.1186/s12915-019-0724-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 11/13/2019] [Indexed: 12/13/2022] Open
Abstract
Animal domestication has fascinated biologists since Charles Darwin first drew the parallel between evolution via natural selection and human-mediated breeding of livestock and companion animals. In this review we show how studies of ancient DNA from domestic animals and their wild progenitors and congeners have shed new light on the genetic origins of domesticates, and on the process of domestication itself. High-resolution paleogenomic data sets now provide unprecedented opportunities to explore the development of animal agriculture across the world. In addition, functional population genomics studies of domestic and wild animals can deliver comparative information useful for understanding recent human evolution.
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Affiliation(s)
- Gillian P McHugo
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, D04 V1W8, Ireland
| | - Michael J Dover
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, D04 V1W8, Ireland
| | - David E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, D04 V1W8, Ireland.
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, D04 V1W8, Ireland.
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26
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Mekonnen YA, Gültas M, Effa K, Hanotte O, Schmitt AO. Identification of Candidate Signature Genes and Key Regulators Associated With Trypanotolerance in the Sheko Breed. Front Genet 2019; 10:1095. [PMID: 31803229 PMCID: PMC6872528 DOI: 10.3389/fgene.2019.01095] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 10/11/2019] [Indexed: 12/23/2022] Open
Abstract
African animal trypanosomiasis (AAT) is caused by a protozoan parasite that affects the health of livestock. Livestock production in Ethiopia is severely hampered by AAT and various controlling measures were not successful to eradicate the disease. AAT affects the indigenous breeds in varying degrees. However, the Sheko breed shows better trypanotolerance than other breeds. The tolerance attributes of Sheko are believed to be associated with its taurine genetic background but the genetic controls of these tolerance attributes of Sheko are not well understood. In order to investigate the level of taurine background in the genome, we compare the genome of Sheko with that of 11 other African breeds. We find that Sheko has an admixed genome composed of taurine and indicine ancestries. We apply three methods: (i) The integrated haplotype score (iHS), (ii) the standardized log ratio of integrated site specific extended haplotype homozygosity between populations (Rsb), and (iii) the composite likelihood ratio (CLR) method to discover selective sweeps in the Sheko genome. We identify 99 genomic regions harboring 364 signature genes in Sheko. Out of the signature genes, 15 genes are selected based on their biological importance described in the literature. We also identify 13 overrepresented pathways and 10 master regulators in Sheko using the TRANSPATH database in the geneXplain platform. Most of the pathways are related with oxidative stress responses indicating a possible selection response against the induction of oxidative stress following trypanosomiasis infection in Sheko. Furthermore, we present for the first time the importance of master regulators involved in trypanotolerance not only for the Sheko breed but also in the context of cattle genomics. Our finding shows that the master regulator Caspase is a key protease which plays a major role for the emergence of adaptive immunity in harmony with the other master regulators. These results suggest that designing and implementing genetic intervention strategies is necessary to improve the performance of susceptible animals. Moreover, the master regulatory analysis suggests potential candidate therapeutic targets for the development of new drugs for trypanosomiasis treatment.
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Affiliation(s)
- Yonatan Ayalew Mekonnen
- Breeding Informatics Group, Department of Animal Sciences, University of Göttingen, Göttingen, Germany
| | - Mehmet Gültas
- Breeding Informatics Group, Department of Animal Sciences, University of Göttingen, Göttingen, Germany.,Center for Integrated Breeding Research (CiBreed), University of Göttingen, Göttingen, Germany
| | - Kefena Effa
- Animal Biosciences, National Program Coordinator for African Dairy Genetic Gain, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | - Olivier Hanotte
- Cells, Organisms amd Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom.,LiveGene, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | - Armin O Schmitt
- Breeding Informatics Group, Department of Animal Sciences, University of Göttingen, Göttingen, Germany.,Center for Integrated Breeding Research (CiBreed), University of Göttingen, Göttingen, Germany
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27
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Utsunomiya YT, Milanesi M, Fortes MRS, Porto-Neto LR, Utsunomiya ATH, Silva MVGB, Garcia JF, Ajmone-Marsan P. Genomic clues of the evolutionary history of Bos indicus cattle. Anim Genet 2019; 50:557-568. [PMID: 31475748 DOI: 10.1111/age.12836] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/19/2019] [Indexed: 01/08/2023]
Abstract
Together with their sister subspecies Bos taurus, zebu cattle (Bos indicus) have contributed to important socioeconomic changes that have shaped modern civilizations. Zebu cattle were domesticated in the Indus Valley 8000 years before present (YBP). From the domestication site, they expanded to Africa, East Asia, southwestern Asia and Europe between 4000 and 1300 YBP, intercrossing with B. taurus to form clinal variations of zebu ancestry across the landmass of Afro-Eurasia. In the past 150 years, zebu cattle reached the Americas and Oceania, where they have contributed to the prosperity of emerging economies. The zebu genome is characterized by two mitochondrial haplogroups (I1 and I2), one Y chromosome haplogroup (Y3) and three major autosomal ancestral groups (Indian-Pakistani, African and Chinese). Phenotypically, zebu animals are recognized by their hump, large ears and excess skin. They are rustic, resilient to parasites and capable of bearing the hot and humid climates of the tropics. Many resources are available to study the zebu genome, including commercial arrays of SNP, reference assemblies and publicly available genotypes and whole-genome sequences. Nevertheless, many of these resources were initially developed to support research and subsidize industrial applications in B. taurus, and therefore they can produce bias in data analysis. The combination of genomics with precision agriculture holds great promise for the identification of genetic variants affecting economically important traits such as tick resistance and heat tolerance, which were naturally selected for millennia and played a major role in the evolution of B. indicus cattle.
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Affiliation(s)
- Y T Utsunomiya
- Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), 16050-680 R. Clovis Pestana 793-Dona Amelia, Araçatuba, SP, Brazil.,International Atomic Energy Agency, Collaborating Centre on Animal Genomics and Bioinformatics, 16050-680 R. Clovis Pestana 793-Dona Amelia, Araçatuba, SP, Brazil
| | - M Milanesi
- Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), 16050-680 R. Clovis Pestana 793-Dona Amelia, Araçatuba, SP, Brazil.,International Atomic Energy Agency, Collaborating Centre on Animal Genomics and Bioinformatics, 16050-680 R. Clovis Pestana 793-Dona Amelia, Araçatuba, SP, Brazil
| | - M R S Fortes
- School of Chemistry and Molecular Biosciences, The University of Queensland, Chemistry Bld, 68 Cooper Rd, Brisbane, 4072, Qld, Australia
| | - L R Porto-Neto
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, 306 Carmody Rd, St Lucia QLD, Brisbane, 4067, Qld, Australia
| | - A T H Utsunomiya
- Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), 16050-680 R. Clovis Pestana 793-Dona Amelia, Araçatuba, SP, Brazil.,International Atomic Energy Agency, Collaborating Centre on Animal Genomics and Bioinformatics, 16050-680 R. Clovis Pestana 793-Dona Amelia, Araçatuba, SP, Brazil
| | - M V G B Silva
- Empresa Brasileira de Pesquisa Agropecuária, Embrapa Gado de Leite, Juiz de Fora, MG, 360381330, Brazil
| | - J F Garcia
- Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), 16050-680 R. Clovis Pestana 793-Dona Amelia, Araçatuba, SP, Brazil.,International Atomic Energy Agency, Collaborating Centre on Animal Genomics and Bioinformatics, 16050-680 R. Clovis Pestana 793-Dona Amelia, Araçatuba, SP, Brazil.,Department of Preventive Veterinary Medicine and Animal Reproduction, School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), 14884-900 Via de Acesso Prof. Paulo Donato Castellane s/n, Jaboticabal, SP, Brazil
| | - P Ajmone-Marsan
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti-DIANA and BioDNA, Centro di Ricerca sulla Biodiversità e sul DNA Antico, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, Piacenza, 29122, Italy
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28
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Ringo AE, Aboge GO, Adjou Moumouni PF, Hun Lee S, Jirapattharasate C, Liu M, Gao Y, Guo H, Zheng W, Efstratiou A, Galon EM, Li J, Thekisoe O, Inoue N, Suzuki H, Xuan X. Molecular detection and genetic characterisation of pathogenic Theileria, Anaplasma and Ehrlichia species among apparently healthy sheep in central and western Kenya. ACTA ACUST UNITED AC 2019; 86:e1-e8. [PMID: 31291731 PMCID: PMC6620505 DOI: 10.4102/ojvr.v86i1.1630] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 01/15/2019] [Accepted: 01/15/2019] [Indexed: 12/15/2022]
Abstract
Tick-borne diseases (TBDs) caused by Theileria, Babesia, Anaplasma and Ehrlichia species are common in tropical and subtropical regions. In this study, we investigated the presence and genetic diversity of Theileria spp., Anaplasma ovis, B. ovis, E. ruminantium and Anaplasma spp. in sheep from the Machakos and Homa Bay counties of Kenya. In order to improve the diagnosis and control of ovine TBDs, a total of 76 blood samples from apparently healthy sheep were screened using a polymerase chain reaction (PCR). The assays were conducted using primers based on Theileria spp. 18S rRNA, Anaplasma ovis Major surface protein-4 (AoMSP4), B. ovis 18S rRNA, E. ruminantium pCS20 and Anaplasma spp. 16S rRNA. The overall infection rates for Theileria spp., A. ovis, E. ruminantium and Anaplasma spp. were 39/76 (51.3%), 26/76 (34.2%), 6/76 (7.9%) and 31/76 (40.8%), respectively. The overall co-infection was 47/76 (61.8%). All Theileria spp. positive samples were confirmed to be of Theileria ovis on sequencing. A phylogenetic analysis of the 18S rRNA gene sequences of T. ovis revealed that all isolates of this study clustered with T. ovis sequences extracted from the GenBank suggesting this gene is highly conserved. E. ruminantium pCS20 sequences were in the same clade on the phylogenetic tree. However, three AoMSP4 sequences from this study appeared in the same clade, while one sequence formed a separate branch revealing genetic divergence. The 16S rRNA sequencing revealed uncharacterised Anaplasma spp. and A. ovis. The phylogenetic analyses of the uncharacterised Anaplasma spp. revealed that the two sequences from this study appear in an independent clade from other sequences extracted from the GenBank. This study provides important information regarding the occurrence of tick-borne pathogens and their degree of genetic diversity among sheep in Kenya, which is useful for the diagnosis and control of TBDs.
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Affiliation(s)
- Aaron E Ringo
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine.
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29
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Zwane AA, Schnabel RD, Hoff J, Choudhury A, Makgahlela ML, Maiwashe A, Van Marle-Koster E, Taylor JF. Genome-Wide SNP Discovery in Indigenous Cattle Breeds of South Africa. Front Genet 2019; 10:273. [PMID: 30988672 PMCID: PMC6452414 DOI: 10.3389/fgene.2019.00273] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 03/12/2019] [Indexed: 01/30/2023] Open
Abstract
Single nucleotide polymorphism arrays have created new possibilities for performing genome-wide studies to detect genomic regions harboring sequence variants that affect complex traits. However, the majority of validated SNPs for which allele frequencies have been estimated are limited primarily to European breeds. The objective of this study was to perform SNP discovery in three South African indigenous breeds (Afrikaner, Drakensberger, and Nguni) using whole genome sequencing. DNA was extracted from blood and hair samples, quantified and prepared at 50 ng/μl concentration for sequencing at the Agricultural Research Council Biotechnology Platform using an Illumina HiSeq 2500. The fastq files were used to call the variants using the Genome Analysis Tool Kit. A total of 1,678,360 were identified as novel using Run 6 of 1000 Bull Genomes Project. Annotation of the identified variants classified them into functional categories. Within the coding regions, about 30% of the SNPs were non-synonymous substitutions that encode for alternate amino acids. The study of distribution of SNP across the genome identified regions showing notable differences in the densities of SNPs among the breeds and highlighted many regions of functional significance. Gene ontology terms identified genes such as MLANA, SYT10, and CDC42EP5 that have been associated with coat color in mouse, and ADAMS3, DNAJC3, and PAG5 genes have been associated with fertility in cattle. Further analysis of the variants detected 688 candidate selective sweeps (ZHp Z-scores ≤ -4) across all three breeds, of which 223 regions were assigned as being putative selective sweeps (ZHp scores ≤-5). We also identified 96 regions with extremely low ZHp Z-scores (≤-6) in Afrikaner and Nguni. Genes such as KIT and MITF that have been associated with skin pigmentation in cattle and CACNA1C, which has been associated with biopolar disorder in human, were identified in these regions. This study provides the first analysis of sequence data to discover SNPs in indigenous South African cattle breeds. The information will play an important role in our efforts to understand the genetic history of our cattle and in designing appropriate breed improvement programmes.
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Affiliation(s)
- Avhashoni A. Zwane
- Department of Animal Breeding and Genetics, Agricultural Research Council-Animal Production, Irene, South Africa
- Department of Animal and Wildlife Sciences, University of Pretoria, Pretoria, South Africa
| | - Robert D. Schnabel
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States
- Informatics Institute, University of Missouri, Columbia, MO, United States
| | - Jesse Hoff
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States
| | - Ananyo Choudhury
- Sydney Brenner Institute of Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Mahlako Linah Makgahlela
- Department of Animal Breeding and Genetics, Agricultural Research Council-Animal Production, Irene, South Africa
- Department of Animal, Wildlife and Grassland Sciences, University of the Free State, Bloemfontein, South Africa
| | - Azwihangwisi Maiwashe
- Department of Animal Breeding and Genetics, Agricultural Research Council-Animal Production, Irene, South Africa
- Department of Animal, Wildlife and Grassland Sciences, University of the Free State, Bloemfontein, South Africa
| | - Este Van Marle-Koster
- Department of Animal and Wildlife Sciences, University of Pretoria, Pretoria, South Africa
| | - Jeremy F. Taylor
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States
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30
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Legacies of domestication, trade and herder mobility shape extant male zebu cattle diversity in South Asia and Africa. Sci Rep 2018; 8:18027. [PMID: 30575786 PMCID: PMC6303292 DOI: 10.1038/s41598-018-36444-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 11/22/2018] [Indexed: 11/30/2022] Open
Abstract
All tropically adapted humped cattle (Bos indicus or “zebu”), descend from a domestication process that took place >8,000 years ago in South Asia. Here we present an intercontinental survey of Y-chromosome diversity and a comprehensive reconstruction of male-lineage zebu cattle history and diversity patterns. Phylogenetic analysis revealed that all the zebu Y-chromosome haplotypes in our dataset group within three different lineages: Y3A, the most predominant and cosmopolitan lineage; Y3B, only observed in West Africa; and Y3C, predominant in South and Northeast India. The divergence times estimated for these three Zebu-specific lineages predate domestication. Coalescent demographic models support either de novo domestication of genetically divergent paternal lineages or more complex process including gene flow between wild and domestic animals. Our data suggest export of varied zebu lineages from domestication centres through time. The almost exclusive presence of Y3A haplotypes in East Africa is consistent with recent cattle restocking in this area. The cryptic presence of Y3B haplotypes in West Africa, found nowhere else, suggests that these haplotypes might represent the oldest zebu lineage introduced to Africa ca. 3,000 B.P. and subsequently replaced in most of the world. The informative ability of Interspersed Multilocus Microsatellites and Y-specific microsatellites to identify genetic structuring in cattle populations is confirmed.
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31
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Parada R, Kawka M, Sacharczuk M, Urbański P, Jaszczak K. Cytogenetic and genetic study of a Y-linked microsatellite polymorphism in Polish Black-and-White cattle breed. Saudi J Biol Sci 2018; 25:1406-1410. [PMID: 30505189 PMCID: PMC6251987 DOI: 10.1016/j.sjbs.2017.01.053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 01/09/2017] [Accepted: 01/18/2017] [Indexed: 11/26/2022] Open
Abstract
The aim of the current study was to characterize Polish Black-and-White cattle by morphological study of the Y chromosome. A total of 14 Y-linked microsatellites from UMN and INRA group were genotyped and assessed for polymorphism in a total 22 bulls. Cytogenetic studies in Polish Black-and-White bulls showed the existence of two morphological forms of Y chromosome. Among the 22 karyotypic analyzed bulls, 12 had submetacentric and 10 metacentric Y chromosome. The centromeric index of Y chromosome measured as percentage length of the p arm to total length ratio in the first case was 28 ± 3.97% and in the second 47 ± 7.28%, whereas the relative size of these chromosomes remained within the same range. Morphology and G- and C-banding patterns of both forms of Y chromosome were typical for other cattle breeds originating from Bos taurus. Out of a total of 14 microsatellite loci examined, 13 showed specific alleles for two forms of Y chromosome. In a pool of 62 alleles, 43 (69.3%) were common in the two groups of cattle, 19 (30.7%) can be considered as specific for the group; among them 8 were typical for metacentric group of Y chromosome and 11 for submetacentric.
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Affiliation(s)
- Rafał Parada
- Department of Genomics, Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, Jastrzębiec, ul. Postępu 36A, 05-552 Magdalenka, Poland
| | - Magdalena Kawka
- Department of Genomics, Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, Jastrzębiec, ul. Postępu 36A, 05-552 Magdalenka, Poland
| | - Mariusz Sacharczuk
- Department of Genomics, Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, Jastrzębiec, ul. Postępu 36A, 05-552 Magdalenka, Poland
| | - Paweł Urbański
- Department of Genomics, Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, Jastrzębiec, ul. Postępu 36A, 05-552 Magdalenka, Poland
| | - Kazimierz Jaszczak
- Department of Genomics, Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, Jastrzębiec, ul. Postępu 36A, 05-552 Magdalenka, Poland
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32
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Fonseca PADS, dos Santos FC, Lam S, Suárez-Vega A, Miglior F, Schenkel FS, Diniz LDAF, Id-Lahoucine S, Carvalho MRS, Cánovas A. Genetic mechanisms underlying spermatic and testicular traits within and among cattle breeds: systematic review and prioritization of GWAS results. J Anim Sci 2018; 96:4978-4999. [PMID: 30304443 PMCID: PMC6276581 DOI: 10.1093/jas/sky382] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 09/27/2018] [Indexed: 12/20/2022] Open
Abstract
Reduced bull fertility imposes economic losses in bovine herds. Specifically, testicular and spermatic traits are important indicators of reproductive efficiency. Several genome-wide association studies (GWAS) have identified genomic regions associated with these fertility traits. The aims of this study were as follows: 1) to perform a systematic review of GWAS results for spermatic and testicular traits in cattle and 2) to identify key functional candidate genes for these traits. The identification of functional candidate genes was performed using a systems biology approach, where genes shared between traits and studies were evaluated by a guilt by association gene prioritization (GUILDify and ToppGene software) in order to identify the best functional candidates. These candidate genes were integrated and analyzed in order to identify overlapping patterns among traits and breeds. Results showed that GWAS for testicular-related traits have been developed for beef breeds only, whereas the majority of GWAS for spermatic-related traits were conducted using dairy breeds. When comparing traits measured within the same study, the highest number of genes shared between different traits was observed, indicating a high impact of the population genetic structure and environmental effects. Several chromosomal regions were enriched for functional candidate genes associated with fertility traits. Moreover, multiple functional candidate genes were enriched for markers in a species-specific basis, taurine (Bos taurus) or indicine (Bos indicus). For the different candidate regions identified in the GWAS in the literature, functional candidate genes were detected as follows: B. Taurus chromosome X (BTX) (TEX11, IRAK, CDK16, ATP7A, ATRX, HDAC6, FMR1, L1CAM, MECP2, etc.), BTA17 (TRPV4 and DYNLL1), and BTA14 (MOS, FABP5, ZFPM2). These genes are responsible for regulating important metabolic pathways or biological processes associated with fertility, such as progression of spermatogenesis, control of ciliary activity, development of Sertoli cells, DNA integrity in spermatozoa, and homeostasis of testicular cells. This study represents the first systematic review on male fertility traits in cattle using a system biology approach to identify key candidate genes for these traits.
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Affiliation(s)
- Pablo Augusto de Souza Fonseca
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada
| | | | - Stephanie Lam
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada
| | - Aroa Suárez-Vega
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada
| | - Filippo Miglior
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada
| | - Flavio S Schenkel
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada
| | | | - Samir Id-Lahoucine
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada
| | | | - Angela Cánovas
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada
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Wang S, Xia X, Zhang T, Sun T, Dang R, Huang Y, Lan X, Chen H, Lei C. Y-chromosome haplotype analysis revealing multiple paternal origins in swamp buffaloes of China and Southeast Asia. J Anim Breed Genet 2018; 135:442-449. [DOI: 10.1111/jbg.12364] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Revised: 09/30/2018] [Accepted: 10/02/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Shaoqiang Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi China
| | - Xiaoting Xia
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi China
| | - Tao Zhang
- School of Bioscience and Engineering; Shaanxi University of Technology; Hanzhong Shaanxi China
| | - Ting Sun
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi China
| | - Ruihua Dang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi China
| | - Yongzhen Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi China
| | - Xianyong Lan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi China
| | - Hong Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi China
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Edea Z, Dadi H, Dessie T, Uzzaman MR, Rothschild MF, Kim ES, Sonstegard TS, Kim KS. Genome-wide scan reveals divergent selection among taurine and zebu cattle populations from different regions. Anim Genet 2018; 49:550-563. [PMID: 30246258 DOI: 10.1111/age.12724] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2018] [Indexed: 01/02/2023]
Abstract
In this study, to identify genomic signatures of divergent selection, we genotyped 10 cattle breeds/populations (n = 275), representing eight Ethiopian cattle populations (n = 229) and two zebu populations (n = 46) adapted to tropical and sub-tropical environments, using the high-density single-nucleotide polymorphisms (SNPs) derived mainly from Bos indicus breeds, and using five reference taurine breeds (n = 212). Population genetic differentiation (FST ) values across sliding windows were estimated between zebu and reference combined taurine breeds. The most differentiated regions (FST ≥ 0.53), representing the top 1% smoothed FST values, were considered to represent regions under diversifying selection. In total, 285 and 317 genes were identified in the comparisons of Ethiopian cattle with taurine and Asian zebu with taurine respectively. Some of these genes are involved in stress responses/thermo-tolerance and DNA damage repair (HSPA4, HSF1, CMPK1 and EIF2AK4), pigmentation (ERBB3 and MYO1A), reproduction/fertility (UBE2D3, ID3 and PSPC1), immune response (PIK3CD and AKIRIN2) and body stature and size (MBP2, LYN and NPM1). Additionally, the candidate genes were associated with functional terms (e.g. cellular response to stress, DNA repair, inflammatory response) important for physiological adaptation to environmental stresses. The results of our study may shed light on the influence of artificial and natural selection in shaping the genomic diversity of modern cattle breeds and also may serve as a basis for further genetic investigation of traits of tropical adaptation in cattle.
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Affiliation(s)
- Z Edea
- Department of Animal Science, Chungbuk National University, Cheongju, 28644, Korea
| | - H Dadi
- Department of Biotechnology, Addis Ababa Science and Technology University, P.O. Box 16417, Addis Ababa, Ethiopia
| | - T Dessie
- International Livestock Research Institute (ILRI), P.O. Box 5689, Addis Ababa, Ethiopia
| | - M R Uzzaman
- Department of Animal Science, Chungbuk National University, Cheongju, 28644, Korea.,Animal Genomics & Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365, S. Korea
| | - M F Rothschild
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | - E-S Kim
- Recombinetics, Inc., Saint Paul, MN, 55104, USA
| | | | - K-S Kim
- Department of Animal Science, Chungbuk National University, Cheongju, 28644, Korea
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Bahbahani H, Afana A, Wragg D. Genomic signatures of adaptive introgression and environmental adaptation in the Sheko cattle of southwest Ethiopia. PLoS One 2018; 13:e0202479. [PMID: 30114214 PMCID: PMC6095569 DOI: 10.1371/journal.pone.0202479] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Accepted: 08/04/2018] [Indexed: 11/23/2022] Open
Abstract
Although classified as an African taurine breed, the genomes of Sheko cattle are an admixture of Asian zebu and African taurine ancestries. They populate the humid Bench Maji zone in Sheko and Bench districts in the south-western part of Ethiopia and are considered as a trypanotolerant breed with high potential for dairy production. Here, we investigate the genome of Sheko cattle for candidate signatures of adaptive introgression and positive selection using medium density genome-wide SNP data. Following locus-ancestry deviation analysis, 15 and 72 genome regions show substantial excess and deficiency in Asian zebu ancestry, respectively. Nine and 23 regions show candidate signatures of positive selection following extended haplotype homozygosity (EHH)-based analyses (iHS and Rsb), respectively. The results support natural selection before admixture for one iHS, one Rsb and three zebu ancestry-deficient regions. Genes and/or QTL associated with bovine immunity, fertility, heat tolerance, trypanotolerance and lactation are present within candidate selected regions. The identification of candidate regions under selection in Sheko cattle warrants further investigation of a larger sample size using full genome sequence data to better characterise the underlying haplotypes. The results can then support informative genomic breeding programmes to sustainably enhance livestock productivity in East African trypanosomosis infested areas.
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Affiliation(s)
- Hussain Bahbahani
- Department of Biological Sciences, Faculty of Science, Kuwait University, Kuwait City, Kuwait
- * E-mail: ,
| | - Arwa Afana
- Department of Biological Sciences, Faculty of Science, Kuwait University, Kuwait City, Kuwait
| | - David Wragg
- Centre for Tropical Livestock Genetics and Health, The Roslin Institute, Edinburgh, United Kingdom
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Tarekegn GM, Ji XY, Bai X, Liu B, Zhang W, Birungi J, Djikeng A, Tesfaye K. Variations in mitochondrial cytochrome b region among Ethiopian indigenous cattle populations assert Bos taurus maternal origin and historical dynamics. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2018; 31:1393-1400. [PMID: 29642685 PMCID: PMC6127579 DOI: 10.5713/ajas.17.0596] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 03/13/2018] [Indexed: 01/09/2023]
Abstract
Objective This study was carried out to assess the haplotype diversity and population dynamics in cattle populations of Ethiopia. Methods We sequenced the complete mitochondrial cytochrome b gene of 76 animals from five indigenous and one Holstein Friesian×Barka cross bred cattle populations. Results In the sequence analysis, 18 haplotypes were generated from 18 segregating sites and the average haplotype and nucleotide diversities were 0.7540±0.043 and 0.0010±0.000, respectively. The population differentiation analysis shows a weak population structure (4.55%) among the populations studied. Majority of the variation (95.45%) is observed by within populations. The overall average pair-wise distance (FST) was 0.049539 with the highest (FST = 0.1245) and the lowest (FST = 0.011) FST distances observed between Boran and Abigar, and Sheko and Abigar from the indigenous cattle, respectively. The phylogenetic network analysis revealed that all the haplotypes detected clustered together with the Bos taurus cattle and converged to a haplogroup. No haplotype in Ethiopian cattle was observed clustered with the reference Bos indicus group. The mismatch distribution analysis indicates a single population expansion event among the cattle populations. Conclusion Overall, high haplotype variability was observed among Ethiopian cattle populations and they share a common ancestor with Bos taurus.
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Affiliation(s)
- Getinet Mekuriaw Tarekegn
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala P.O. Box 7070, Sweden.,Department of Animal Production and Technology, Bahir Dar University, Bahir Dar P.O. Box 79, Ethiopia
| | - Xiao-Yang Ji
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Xue Bai
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Bin Liu
- Nei Mongol BioNew Technology Co. Ltd, Hohhot 010020, China
| | - Wenguang Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Josephine Birungi
- Biosciences Eastern and Central Africa (BecA) Hub - International Livestock Research Institute, PO Box 30709, Nairobi 00100, Kenya
| | - Appolinaire Djikeng
- Centre for Tropical Livestock Genetics and Health, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland, UK
| | - Kassahun Tesfaye
- Department of Microbial Cellular and Molecular Biology, Addis Ababa University, Addis Ababa P.O. Box, 1176, Ethiopia
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Bahbahani H, Salim B, Almathen F, Al Enezi F, Mwacharo JM, Hanotte O. Signatures of positive selection in African Butana and Kenana dairy zebu cattle. PLoS One 2018; 13:e0190446. [PMID: 29300786 PMCID: PMC5754058 DOI: 10.1371/journal.pone.0190446] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Accepted: 12/14/2017] [Indexed: 02/02/2023] Open
Abstract
Butana and Kenana are two types of zebu cattle found in Sudan. They are unique amongst African indigenous zebu cattle because of their high milk production. Aiming to understand their genome structure, we genotyped 25 individuals from each breed using the Illumina BovineHD Genotyping BeadChip. Genetic structure analysis shows that both breeds have an admixed genome composed of an even proportion of indicine (0.75 ± 0.03 in Butana, 0.76 ± 0.006 in Kenana) and taurine (0.23 ± 0.009 in Butana, 0.24 ± 0.006 in Kenana) ancestries. We also observe a proportion of 0.02 to 0.12 of European taurine ancestry in ten individuals of Butana that were sampled from cattle herds in Tamboul area suggesting local crossbreeding with exotic breeds. Signatures of selection analyses (iHS and Rsb) reveal 87 and 61 candidate positive selection regions in Butana and Kenana, respectively. These regions span genes and quantitative trait loci (QTL) associated with biological pathways that are important for adaptation to marginal environments (e.g., immunity, reproduction and heat tolerance). Trypanotolerance QTL are intersecting candidate regions in Kenana cattle indicating selection pressure acting on them, which might be associated with an unexplored level of trypanotolerance in this cattle breed. Several dairy traits QTL are overlapping the identified candidate regions in these two zebu cattle breeds. Our findings underline the potential to improve dairy production in the semi-arid pastoral areas of Africa through breeding improvement strategy of indigenous local breeds.
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Affiliation(s)
- Hussain Bahbahani
- Department of Biological Sciences, Faculty of Science, Kuwait University, Kuwait city, Kuwait
- * E-mail: ,
| | - Bashir Salim
- Department of Parasitology, Faculty of Veterinary Medicine, University of Khartoum Khartoum North, Sudan
| | - Faisal Almathen
- Department of Veterinary Public Health and Animal Husbandry, College of Veterinary Medicine, King Faisal University, Al-Hasa, Kingdom of Saudi Arabia
| | - Fahad Al Enezi
- Department of Biological Sciences, Faculty of Science, Kuwait University, Kuwait city, Kuwait
| | - Joram M. Mwacharo
- Small Ruminant Genomics Group, International Centre for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia
| | - Olivier Hanotte
- Cells, Organisms and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- LiveGene, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
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Strucken EM, Al-Mamun HA, Esquivelzeta-Rabell C, Gondro C, Mwai OA, Gibson JP. Genetic tests for estimating dairy breed proportion and parentage assignment in East African crossbred cattle. Genet Sel Evol 2017; 49:67. [PMID: 28899355 PMCID: PMC5596489 DOI: 10.1186/s12711-017-0342-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 08/30/2017] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Smallholder dairy farming in much of the developing world is based on the use of crossbred cows that combine local adaptation traits of indigenous breeds with high milk yield potential of exotic dairy breeds. Pedigree recording is rare in such systems which means that it is impossible to make informed breeding decisions. High-density single nucleotide polymorphism (SNP) assays allow accurate estimation of breed composition and parentage assignment but are too expensive for routine application. Our aim was to determine the level of accuracy achieved with low-density SNP assays. METHODS We constructed subsets of 100 to 1500 SNPs from the 735k-SNP Illumina panel by selecting: (a) on high minor allele frequencies (MAF) in a crossbred population; (b) on large differences in allele frequency between ancestral breeds; (c) at random; or (d) with a differential evolution algorithm. These panels were tested on a dataset of 1933 crossbred dairy cattle from Kenya/Uganda and on crossbred populations from Ethiopia (N = 545) and Tanzania (N = 462). Dairy breed proportions were estimated by using the ADMIXTURE program, a regression approach, and SNP-best linear unbiased prediction, and tested against estimates obtained by ADMIXTURE based on the 735k-SNP panel. Performance for parentage assignment was based on opposing homozygotes which were used to calculate the separation value (sv) between true and false assignments. RESULTS Panels of SNPs based on the largest differences in allele frequency between European dairy breeds and a combined Nelore/N'Dama population gave the best predictions of dairy breed proportion (r2 = 0.962 to 0.994 for 100 to 1500 SNPs) with an average absolute bias of 0.026. Panels of SNPs based on the highest MAF in the crossbred population (Kenya/Uganda) gave the most accurate parentage assignments (sv = -1 to 15 for 100 to 1500 SNPs). CONCLUSIONS Due to the different required properties of SNPs, panels that did well for breed composition did poorly for parentage assignment and vice versa. A combined panel of 400 SNPs was not able to assign parentages correctly, thus we recommend the use of 200 SNPs either for breed proportion prediction or parentage assignment, independently.
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Affiliation(s)
- Eva M Strucken
- School of Environmental and Rural Science, University of New England, Armidale, 2350, Australia
| | - Hawlader A Al-Mamun
- School of Environmental and Rural Science, University of New England, Armidale, 2350, Australia
| | | | - Cedric Gondro
- Michigan State University, Animal Science, East Lansing, Michigan, 48824, USA
| | - Okeyo A Mwai
- International Livestock Research Institute, Nairobi, Kenya
| | - John P Gibson
- School of Environmental and Rural Science, University of New England, Armidale, 2350, Australia.
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Claire DH, Donald RK, Tiba M, Jean DR, Aline K, Arsene M, Jean PS, Felicien S, Maximillian M, Theogene S. Management and phenotypic features of indigenous cattle in Rwanda. ACTA ACUST UNITED AC 2017. [DOI: 10.5897/ijlp2017.0362] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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Álvarez I, Pérez-Pardal L, Traoré A, Koudandé DO, Fernández I, Soudré A, Diarra S, Sanou M, Boussini H, Goyache F. Differences in genetic structure assessed using Y-chromosome and mitochondrial DNA markers do not shape the contributions to diversity in African sires. J Anim Breed Genet 2017; 134:393-404. [PMID: 28464302 DOI: 10.1111/jbg.12278] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 03/25/2017] [Indexed: 11/30/2022]
Abstract
Up to 173 African sires belonging to 11 different subpopulations representative of four cattle groups were analysed for six Y-specific microsatellite loci and a mitochondrial DNA fragment. Differences in Y-chromosome and mtDNA haplotype structuring were assessed. In addition, the effect of such structuring on contributions to total genetic diversity was assessed. Thirty-five Y-chromosome and 71 mtDNA haplotypes were identified. Most Y-chromosomes analysed (73.4%) were of zebu origin (11 haplotypes). Twenty-two Y-haplotypes (44 samples) belonged to the African taurine subfamily Y2a. All mtDNA haplotypes belonged to the "African" taurine T1 haplogroup with 16 samples and nine haplotypes belonging to a recently identified subhaplogroup (T1e). Median-joining networks showed that Y-chromosome phylogenies were highly reticulated with clear separation between zebu and taurine clusters. Mitochondrial haplotypes showed a clear star-like shape with small number of mutations separating haplotypes. Mitochondrial-based FST -statistics computed between cattle groups tended to be statistically non-significant (p > .05). Most FST values computed among groups and subpopulations using Y-chromosome markers were statistically significant. AMOVA confirmed that divergence between cattle groups was only significant for Y-chromosome markers (ΦCT = 0.209). At the mitochondrial level, African sires resembled an undifferentiated population with individuals explaining 94.3% of the total variance. Whatever the markers considered, the highest contributions to total Nei's gene diversity and allelic richness were found in West African cattle. Genetic structuring had no effect on patterns of contributions to diversity.
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Affiliation(s)
- I Álvarez
- Área de Genética y Reproducción Animal, SERIDA, Camino de Rioseco, Gijón, Spain
| | - L Pérez-Pardal
- Área de Genética y Reproducción Animal, SERIDA, Camino de Rioseco, Gijón, Spain.,CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
| | - A Traoré
- INERA, Ouagadougou, Burkina Faso
| | | | - I Fernández
- Área de Genética y Reproducción Animal, SERIDA, Camino de Rioseco, Gijón, Spain
| | - A Soudré
- Université de Koudougou, Koudougou, Burkina Faso
| | - S Diarra
- IPR-IFRA Bamako (Mali), Koulikoro, Bamako
| | - M Sanou
- INERA, Ouagadougou, Burkina Faso
| | - H Boussini
- African Union Interafrican Bureau for Animal Resources, Nairobi, Kenya
| | - F Goyache
- Área de Genética y Reproducción Animal, SERIDA, Camino de Rioseco, Gijón, Spain
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Zeller U, Starik N, Göttert T. Biodiversity, land use and ecosystem services—An organismic and comparative approach to different geographical regions. Glob Ecol Conserv 2017. [DOI: 10.1016/j.gecco.2017.03.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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Di Lorenzo P, Lancioni H, Ceccobelli S, Curcio L, Panella F, Lasagna E. Uniparental genetic systems: a male and a female perspective in the domestic cattle origin and evolution. ELECTRON J BIOTECHN 2016. [DOI: 10.1016/j.ejbt.2016.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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Iacolina L, Brajković V, Canu A, Šprem N, Cubric-Curik V, Fontanesi L, Saarma U, Apollonio M, Scandura M. Novel Y-chromosome short tandem repeats in Sus scrofa and their variation in European wild boar and domestic pig populations. Anim Genet 2016; 47:682-690. [PMID: 27558303 DOI: 10.1111/age.12483] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/23/2016] [Indexed: 11/27/2022]
Abstract
Y-chromosome markers are important tools for studying male-specific gene flow within and between populations, hybridization patterns and kinship. However, their use in non-human mammals is often hampered by the lack of Y-specific polymorphic markers. We identified new male-specific short tandem repeats (STRs) in Sus scrofa using the available genome sequence. We selected four polymorphic loci (5-10 alleles per locus), falling in one duplicated and two single-copy regions. A total of 32 haplotypes were found by screening 211 individuals from eight wild boar populations across Europe and five domestic pig populations. European wild boar were characterized by significantly higher levels of haplotype diversity compared to European domestic pigs (HD = 0.904 ± 0.011 and HD = 0.491 ± 0.077 respectively). Relationships among STR haplotypes were investigated by combining them with single nucleotide polymorphisms at two linked genes (AMELY and UTY) in a network analysis. A differentiation between wild and domestic populations was observed (FST = 0.229), with commercial breeds sharing no Y haplotype with the sampled wild boar. Similarly, a certain degree of geographic differentiation was observed across Europe, with a number of local private haplotypes and high diversity in northern populations. The described Y-chromosome markers can be useful to track male inheritance and gene flow in wild and domestic populations, promising to provide insights into evolutionary and population genetics in Sus scrofa.
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Affiliation(s)
- L Iacolina
- Department of Science for Nature and Environmental Resources, University of Sassari, via Muroni 25, Sassari, I-07100, Italy. .,Department of Chemistry and Bioscience, Aalborg University, Frederik Bajers Vej 7H, Aalborg, 9000, Denmark.
| | - V Brajković
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, Zagreb, 10000, Croatia
| | - A Canu
- Department of Science for Nature and Environmental Resources, University of Sassari, via Muroni 25, Sassari, I-07100, Italy
| | - N Šprem
- Department of Fisheries, Beekeeping, Game Management and Special Zoology, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, Zagreb, 10000, Croatia
| | - V Cubric-Curik
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, Zagreb, 10000, Croatia
| | - L Fontanesi
- Division of Animal Science, Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 46, Bologna, I-40127, Italy
| | - U Saarma
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, Tartu, 51014, Estonia
| | - M Apollonio
- Department of Science for Nature and Environmental Resources, University of Sassari, via Muroni 25, Sassari, I-07100, Italy
| | - M Scandura
- Department of Science for Nature and Environmental Resources, University of Sassari, via Muroni 25, Sassari, I-07100, Italy
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Burger PA. The history of Old World camelids in the light of molecular genetics. Trop Anim Health Prod 2016; 48:905-13. [PMID: 27048619 PMCID: PMC4884201 DOI: 10.1007/s11250-016-1032-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 02/29/2016] [Indexed: 01/19/2023]
Abstract
Old World camels have come into the focus as sustainable livestock species, unique in their morphological and physiological characteristics and capable of providing vital products even under extreme environmental conditions. The evolutionary history of dromedary and Bactrian camels traces back to the middle Eocene (around 40 million years ago, mya), when the ancestors of Camelus emerged on the North American continent. While the genetic status of the two domestic species has long been established, the wild two-humped camel has only recently been recognized as a separate species, Camelus ferus, based on molecular genetic data. The demographic history established from genome drafts of Old World camels shows the independent development of the three species over the last 100,000 years with severe bottlenecks occurring during the last glacial period and in the recent past. Ongoing studies involve the immune system, relevant production traits, and the global population structure and domestication of Old World camels. Based on the now available whole genome drafts, specific metabolic pathways have been described shedding new light on the camels' ability to adapt to desert environments. These new data will also be at the origin for genome-wide association studies to link economically relevant phenotypes to genotypes and to conserve the diverse genetic resources in Old World camelids.
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Affiliation(s)
- Pamela Anna Burger
- Research Institute of Wildlife Ecology, Vetmeduni Vienna, Savoyenstrasse 1, 1160, Vienna, Austria.
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Randhawa IAS, Khatkar MS, Thomson PC, Raadsma HW. A Meta-Assembly of Selection Signatures in Cattle. PLoS One 2016; 11:e0153013. [PMID: 27045296 PMCID: PMC4821596 DOI: 10.1371/journal.pone.0153013] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 03/22/2016] [Indexed: 12/31/2022] Open
Abstract
Since domestication, significant genetic improvement has been achieved for many traits of commercial importance in cattle, including adaptation, appearance and production. In response to such intense selection pressures, the bovine genome has undergone changes at the underlying regions of functional genetic variants, which are termed “selection signatures”. This article reviews 64 recent (2009–2015) investigations testing genomic diversity for departure from neutrality in worldwide cattle populations. In particular, we constructed a meta-assembly of 16,158 selection signatures for individual breeds and their archetype groups (European, African, Zebu and composite) from 56 genome-wide scans representing 70,743 animals of 90 pure and crossbred cattle breeds. Meta-selection-scores (MSS) were computed by combining published results at every given locus, within a sliding window span. MSS were adjusted for common samples across studies and were weighted for significance thresholds across and within studies. Published selection signatures show extensive coverage across the bovine genome, however, the meta-assembly provides a consensus profile of 263 genomic regions of which 141 were unique (113 were breed-specific) and 122 were shared across cattle archetypes. The most prominent peaks of MSS represent regions under selection across multiple populations and harboured genes of known major effects (coat color, polledness and muscle hypertrophy) and genes known to influence polygenic traits (stature, adaptation, feed efficiency, immunity, behaviour, reproduction, beef and dairy production). As the first meta-assembly of selection signatures, it offers novel insights about the hotspots of selective sweeps in the bovine genome, and this method could equally be applied to other species.
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Affiliation(s)
- Imtiaz A. S. Randhawa
- Reprogen - Animal Bioscience Group, Faculty of Veterinary Science, The University of Sydney, 425 Werombi Road, Camden, 2570, NSW, Australia
- * E-mail:
| | - Mehar S. Khatkar
- Reprogen - Animal Bioscience Group, Faculty of Veterinary Science, The University of Sydney, 425 Werombi Road, Camden, 2570, NSW, Australia
| | - Peter C. Thomson
- Reprogen - Animal Bioscience Group, Faculty of Veterinary Science, The University of Sydney, 425 Werombi Road, Camden, 2570, NSW, Australia
| | - Herman W. Raadsma
- Reprogen - Animal Bioscience Group, Faculty of Veterinary Science, The University of Sydney, 425 Werombi Road, Camden, 2570, NSW, Australia
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Tizioto PC, Coutinho LL, Mourão GB, Gasparin G, Malagó-Jr W, Bressani FA, Tullio RR, Nassu RT, Taylor JF, Regitano LCA. Variation inmyogenic differentiation 1mRNA abundance is associated with beef tenderness in Nelore cattle. Anim Genet 2016; 47:491-4. [DOI: 10.1111/age.12434] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/10/2016] [Indexed: 01/12/2023]
Affiliation(s)
| | - L. L. Coutinho
- Department of Animal Science; University of São Paulo/ESALQ; Piracicaba SP Brazil
| | - G. B. Mourão
- Department of Animal Science; University of São Paulo/ESALQ; Piracicaba SP Brazil
| | - G. Gasparin
- Department of Animal Science; University of São Paulo/ESALQ; Piracicaba SP Brazil
| | - W. Malagó-Jr
- Embrapa Southeast Livestock; São Carlos SP Brazil
| | | | - R. R. Tullio
- Embrapa Southeast Livestock; São Carlos SP Brazil
| | - R. T. Nassu
- Embrapa Southeast Livestock; São Carlos SP Brazil
| | - J. F. Taylor
- Division of Animal Sciences; University of Missouri; Columbia MO USA
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Nyamushamba GB, Mapiye C, Tada O, Halimani TE, Muchenje V. Conservation of indigenous cattle genetic resources in Southern Africa's smallholder areas: turning threats into opportunities - A review. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2016; 30:603-621. [PMID: 27004814 PMCID: PMC5411820 DOI: 10.5713/ajas.16.0024] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 02/15/2016] [Accepted: 03/18/2016] [Indexed: 01/14/2023]
Abstract
The current review focuses on characterization and conservation efforts vital for the development of breeding programmes for indigenous beef cattle genetic resources in Southern Africa. Indigenous African cattle breeds were identified and characterized using information from refereed journals, conference papers and research reports. Results of this current review reviewed that smallholder beef cattle production in Southern Africa is extensive and dominated by indigenous beef cattle strains adaptable to the local environment. The breeds include Nguni, Mashona, Tuli, Malawi Zebu, Bovino de Tete, Angoni, Landim, Barotse, Twsana and Ankole. These breeds have important functions ranging from provision of food and income to socio-economic, cultural and ecological roles. They also have adaptive traits ranging from drought tolerant, resistance to ticks and tick borne diseases, heat tolerance and resistance to trypanosomosis. Stakeholders in the conservation of beef cattle were also identified and they included farmers, national government, research institutes and universities as well as breeding companies and societies in Southern Africa. Research efforts made to evaluate threats and opportunities of indigenous beef cattle production systems, assess the contribution of indigenous cattle to household food security and income, genetically and phenotypically characterize and conserve indigenous breeds, and develop breeding programs for smallholder beef production are highlighted. Although smallholder beef cattle production in the smallholder farming systems contributes substantially to household food security and income, their productivity is hindered by several constraints that include high prevalence of diseases and parasites, limited feed availability and poor marketing. The majority of the African cattle populations remain largely uncharacterized although most of the indigenous cattle breeds have been identified.
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Affiliation(s)
- G B Nyamushamba
- Department of Livestock and Pasture Science, University of Fort Hare, Alice 5700, South Africa
| | - C Mapiye
- Department of Animal Sciences, Faculty of AgriSciences, Stellenbosch University, Matieland 7602, South Africa
| | - O Tada
- Department of Animal Production and Technology, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
| | - T E Halimani
- Department of Animal Science, University of Zimbabwe, Harare, Zimbabwe
| | - V Muchenje
- Department of Livestock and Pasture Science, University of Fort Hare, Alice 5700, South Africa
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Wang MD, Dzama K, Rees DJG, Muchadeyi FC. Tropically adapted cattle of Africa: perspectives on potential role of copy number variations. Anim Genet 2015; 47:154-64. [DOI: 10.1111/age.12391] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2015] [Indexed: 12/12/2022]
Affiliation(s)
- M. D. Wang
- Department of Animal Sciences; University of Stellenbosch; Private Bag X1 Matieland 7602 South Africa
- Biotechnology Platform; Agricultural Research Council; Private Bag X5 Onderstepoort 0110 South Africa
| | - K. Dzama
- Department of Animal Sciences; University of Stellenbosch; Private Bag X1 Matieland 7602 South Africa
| | - D. J. G. Rees
- Biotechnology Platform; Agricultural Research Council; Private Bag X5 Onderstepoort 0110 South Africa
| | - F. C. Muchadeyi
- Biotechnology Platform; Agricultural Research Council; Private Bag X5 Onderstepoort 0110 South Africa
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Sanarana Y, Visser C, Bosman L, Nephawe K, Maiwashe A, van Marle-Köster E. Genetic diversity in South African Nguni cattle ecotypes based on microsatellite markers. Trop Anim Health Prod 2015; 48:379-85. [PMID: 26611262 DOI: 10.1007/s11250-015-0962-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 11/13/2015] [Indexed: 10/22/2022]
Abstract
The Nguni cattle breed is a landrace breed adapted to different ecological regions of South Africa. A number of ecotypes are recognised based on phenotype within the breed, but it is not known if they are genetically distinct. In this study, molecular characterisation was performed on Makhathini (MAK), Pedi (PED), Shangaan (SHA) and Venda (VEN) Nguni cattle ecotypes. Two Nguni cattle populations, not kept as separate ecotypes, from the University of Fort Hare (UFH) and Agricultural Research Council Loskop South farm (LOS) were also included. Genotypic data was generated for 189 unrelated Nguni cattle selected based on pedigree records using 22 microsatellite markers. The expected heterozygosity values varied from 69 % (UFH) to 72 % (PED) with a mean number of alleles ranging from 6.0 to 6.9. The F ST estimate demonstrated that 4.8 % of the total genetic variation was due to the genetic differentiation between the populations and 92.2 % accounted for differences within the populations. The genetic distances and structure analysis revealed the closest relationship between MAK, PEDI and SHA ecotypes, followed by SHA and VEN. The UFH population clustered with the MAK ecotype, indicating that they are more genetically similar, while the LOS cattle grouped as a distinct cluster. Results suggest that the genetic differentiation between the PED and SHA ecotypes is low and can be regarded as one ecotype based on limited genetic differences. The results of this study can be applied as a point of reference for further genetic studies towards conservation of Nguni cattle ecotypes.
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Affiliation(s)
- Yandisiwe Sanarana
- Department of Animal and Wildlife Sciences, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa.,Agricultural Research Council, Private Bag X2, Irene, 0062, South Africa
| | - Carina Visser
- Department of Animal and Wildlife Sciences, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa
| | - Lydia Bosman
- Department of Animal and Wildlife Sciences, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa
| | - Khathutshelo Nephawe
- Department of Animal Science, Tshwane University of Technology, Private Bag X680, Pretoria, 0001, South Africa
| | | | - Este van Marle-Köster
- Department of Animal and Wildlife Sciences, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa.
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Ndiaye NP, Sow A, Dayo GK, Ndiaye S, Sawadogo GJ, Sembène M. Genetic diversity and phylogenetic relationships in local cattle breeds of Senegal based on autosomal microsatellite markers. Vet World 2015; 8:994-1005. [PMID: 27047188 PMCID: PMC4774767 DOI: 10.14202/vetworld.2015.994-1005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 07/09/2015] [Accepted: 07/20/2015] [Indexed: 12/04/2022] Open
Abstract
Aim: In Senegal, uncontrolled cross-breeding of cattle breeds and changes in production systems are assumed to lead to an increase of gene flow between populations. This might constitute a relevant threat to livestock improvement. Therewith, this study was carried out to assess the current genetic diversity and the phylogenetic relationships of the four native Senegalese cattle breeds (Gobra zebu, Maure zebu, Djakoré, and N’Dama). Methods: Genomic DNA was isolated from blood samples of 120 unrelated animals collected from three agro-ecological areas of Senegal according to their phenotypic traits. Genotyping was done using 11 specific highly polymorphic microsatellite makers recommended by Food and Agriculture Organization. The basic measures of genetic variation and phylogenetic trees were computed using bioinformatics’ software. Results: A total of 115 alleles were identified with a number of alleles (Na) at one locus ranging from 6 to 16. All loci were polymorphic with a mean polymorphic information content of 0.76. The mean allelic richness (Rs) lay within the narrow range of 5.14 in N’Dama taurine to 6.10 in Gobra zebu. While, the expected heterozygosity (HE) per breed was high in general with an overall mean of 0.76±0.04. Generally, the heterozygote deficiency (FIS) of 0.073±0.026 was relatively due to inbreeding among these cattle breeds or the occurrence of population substructure. The high values of allelic and gene diversity showed that Senegalese native cattle breeds represented an important reservoir of genetic variation. The genetic distances and clustering trees concluded that the N’Dama cattle were most distinct among the investigated cattle populations. So, the principal component analyses showed qualitatively that there was an intensive genetic admixture between the Gobra zebu and Maure zebu breeds. Conclusions: The broad genetic diversity in Senegalese cattle breeds will allow for greater opportunities for improvement of productivity and adaptation relative to global changes. For the development of sustainable breeding and crossbreeding programs of Senegalese local breeds, effective management is needed towards genetic selection and transhumance to ensure their long-term survival.
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Affiliation(s)
- Ndèye Penda Ndiaye
- Department of Animal Biology, FST (UCAD), Dakar Fann-PO 5005, Laboratory of Endocrinology and Radio-immunology, EISMV, Dakar Fann-PO 5077, Senegal
| | - Adama Sow
- Laboratory of Endocrinology and Radio-immunology, EISMV, Dakar Fann-PO 5077, Senegal
| | | | | | | | - Mbacké Sembène
- Department of Animal Biology, FST (UCAD), Dakar Fann-PO 5005, Laboratory CBGP, IRD, Dakar Bel Air- PO 1386, Senegal
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