1
|
Kambal S, Tijjani A, Ibrahim SAE, Ahmed MKA, Mwacharo JM, Hanotte O. Candidate signatures of positive selection for environmental adaptation in indigenous African cattle: A review. Anim Genet 2023; 54:689-708. [PMID: 37697736 DOI: 10.1111/age.13353] [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: 07/28/2023] [Revised: 07/28/2023] [Accepted: 08/19/2023] [Indexed: 09/13/2023]
Abstract
Environmental adaptation traits of indigenous African cattle are increasingly being investigated to respond to the need for sustainable livestock production in the context of unpredictable climatic changes. Several studies have highlighted genomic regions under positive selection probably associated with adaptation to environmental challenges (e.g. heat stress, trypanosomiasis, tick and tick-borne diseases). However, little attention has focused on pinpointing the candidate causative variant(s) controlling the traits. This review compiled information from 22 studies on signatures of positive selection in indigenous African cattle breeds to identify regions under positive selection. We highlight some key candidate genome regions and genes of relevance to the challenges of living in extreme environments (high temperature, high altitude, high infectious disease prevalence). They include candidate genes involved in biological pathways relating to innate and adaptive immunity (e.g. BoLAs, SPAG11, IL1RL2 and GFI1B), heat stress (e.g. HSPs, SOD1 and PRLH) and hypoxia responses (e.g. BDNF and INPP4A). Notably, the highest numbers of candidate regions are found on BTA3, BTA5 and BTA7. They overlap with genes playing roles in several biological functions and pathways. These include but are not limited to growth and feed intake, cell stability, protein stability and sweat gland development. This review may further guide targeted genome studies aiming to assess the importance of candidate causative mutations, within regulatory and protein-coding genome regions, to further understand the biological mechanisms underlying African cattle's unique adaption.
Collapse
Affiliation(s)
- Sumaya Kambal
- Livestock Genetics, International Livestock Research Institute, Addis Ababa, Ethiopia
- Department of Genetics and Animal Breeding, Faculty of Animal Production, University of Khartoum, Khartoum, Sudan
- Department of Bioinformatics and Biostatistics, National University, Khartoum, Sudan
| | - Abdulfatai Tijjani
- Centre for Tropical Livestock Genetics and Health, International Livestock Research Institute, Addis Ababa, Ethiopia
- The Jackson Laboratory, Bar Harbor, Maine, USA
| | - Sabah A E Ibrahim
- Department of Bioinformatics and Biostatistics, National University, Khartoum, Sudan
| | - Mohamed-Khair A Ahmed
- Department of Genetics and Animal Breeding, Faculty of Animal Production, University of Khartoum, Khartoum, Sudan
| | - Joram M Mwacharo
- Scotland's Rural College and Centre for Tropical Livestock Genetics and Health, Edinburgh, UK
- Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas, Addis Ababa, Ethiopia
| | - Olivier Hanotte
- Livestock Genetics, International Livestock Research Institute, Addis Ababa, Ethiopia
- Centre for Tropical Livestock Genetics and Health, International Livestock Research Institute, Addis Ababa, Ethiopia
- School of Life Sciences, University of Nottingham, Nottingham, UK
| |
Collapse
|
2
|
Riggio V, Madder M, Labuschagne M, Callaby R, Zhao R, Djikeng A, Fourie J, Prendergast JGD, Morrison LJ. Meta-analysis of heritability estimates and genome-wide association for tick-borne haemoparasites in African cattle. Front Genet 2023; 14:1197160. [PMID: 37576560 PMCID: PMC10417722 DOI: 10.3389/fgene.2023.1197160] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 07/05/2023] [Indexed: 08/15/2023] Open
Abstract
The control of tick-borne haemoparasites in cattle largely relies on the use of acaricide drugs against the tick vectors, with some vaccination also being used against selected pathogens. These interventions can be difficult in Africa, where accessibility and cost of vaccines can be issues, and the increasing resistance of tick vectors to the widely used acaricides is a complication to disease control. A potential complementary control strategy could be the exploitation of any natural host genetic resistance to the pathogens. However, there are currently very few estimates of the extent of host resistance to tick-borne haemoparasites, and a significant contributing factor to this knowledge gap is likely to be the difficulty of collecting appropriate samples and data in the smallholder systems that predominate livestock production in low- and middle-income countries, particularly at scale. In this study, we have estimated the heritability for the presence/absence of several important haemoparasite species (including Anaplasma marginale, Babesia bigemina, Babesia bovis, and Ehrlichia ruminantium), as well as for relevant traits such as body weight and body condition score (BCS), in 1,694 cattle from four African countries (Burkina Faso, Ghana, Nigeria, and Tanzania). Heritability estimates within countries were mostly not significant, ranging from 0.05 to 0.84 across traits and countries, with standard errors between 0.07 and 0.91. However, the weighted mean of heritability estimates was moderate and significant for body weight and BCS (0.40 and 0.49, respectively), with significant heritabilities also observed for the presence of A. marginale (0.16) and E. ruminantium (0.19). In a meta-analysis of genome-wide association studies (GWAS) for these traits, two peaks were identified as reaching the suggestive significance threshold (p < 1.91 × 10-7 and p < 1.89 × 10-7, respectively): one on chromosome 24 for BCS and one on chromosome 8 for the E. ruminantium infection status. These findings indicate that there is likely to be a genetic basis that contributes to pathogen presence/absence for tick-borne haemoparasite species, which could potentially be exploited to improve cattle resistance in Africa to the economically important diseases caused by these pathogens.
Collapse
Affiliation(s)
- Valentina Riggio
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | | | | | - Rebecca Callaby
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Rongrong Zhao
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Appolinaire Djikeng
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | | | - James G. D. Prendergast
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Liam J. Morrison
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| |
Collapse
|
3
|
Duhan N, Kaur S, Kaundal R. ranchSATdb: A Genome-Wide Simple Sequence Repeat (SSR) Markers Database of Livestock Species for Mutant Germplasm Characterization and Improving Farm Animal Health. Genes (Basel) 2023; 14:1481. [PMID: 37510385 PMCID: PMC10378808 DOI: 10.3390/genes14071481] [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: 05/26/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Microsatellites, also known as simple sequence repeats (SSRs), are polymorphic loci that play an important role in genome research, animal breeding, and disease control. Ranch animals are important components of agricultural landscape. The ranch animal SSR database, ranchSATdb, is a web resource which contains 15,520,263 putative SSR markers. This database provides a comprehensive tool for performing end-to-end marker selection, from SSRs prediction to generating marker primers and their cross-species feasibility, visualization of the resulting markers, and finding similarities between the genomic repeat sequences all in one place without the need to switch between other resources. The user-friendly online interface allows users to browse SSRs by genomic coordinates, repeat motif sequence, chromosome, motif type, motif frequency, and functional annotation. Users may enter their preferred flanking area around the repeat to retrieve the nucleotide sequence, they can investigate SSRs present in the genic or the genes between SSRs, they can generate custom primers, and they can also execute in silico validation of primers using electronic PCR. For customized sequences, an SSR prediction pipeline called miSATminer is also built. New species will be added to this website's database on a regular basis throughout time. To improve animal health via genomic selection, we hope that ranchSATdb will be a useful tool for mapping quantitative trait loci (QTLs) and marker-assisted selection. The web-resource is freely accessible at https://bioinfo.usu.edu/ranchSATdb/.
Collapse
Affiliation(s)
- Naveen Duhan
- Department of Plants, Soils, and Climate/Center for Integrated BioSystems, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322, USA
- Bioinformatics Facility, Center for Integrated BioSystems, Utah State University, Logan, UT 84322, USA
| | - Simardeep Kaur
- Department of Plants, Soils, and Climate/Center for Integrated BioSystems, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322, USA
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
- ICAR-Research Complex for North Eastern Hill Region (NEH), Umiam 793103, India
| | - Rakesh Kaundal
- Department of Plants, Soils, and Climate/Center for Integrated BioSystems, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322, USA
- Bioinformatics Facility, Center for Integrated BioSystems, Utah State University, Logan, UT 84322, USA
| |
Collapse
|
4
|
Vinkler M, Fiddaman SR, Těšický M, O'Connor EA, Savage AE, Lenz TL, Smith AL, Kaufman J, Bolnick DI, Davies CS, Dedić N, Flies AS, Samblás MMG, Henschen AE, Novák K, Palomar G, Raven N, Samaké K, Slade J, Veetil NK, Voukali E, Höglund J, Richardson DS, Westerdahl H. Understanding the evolution of immune genes in jawed vertebrates. J Evol Biol 2023; 36:847-873. [PMID: 37255207 PMCID: PMC10247546 DOI: 10.1111/jeb.14181] [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: 09/23/2022] [Revised: 04/23/2023] [Accepted: 04/26/2023] [Indexed: 06/01/2023]
Abstract
Driven by co-evolution with pathogens, host immunity continuously adapts to optimize defence against pathogens within a given environment. Recent advances in genetics, genomics and transcriptomics have enabled a more detailed investigation into how immunogenetic variation shapes the diversity of immune responses seen across domestic and wild animal species. However, a deeper understanding of the diverse molecular mechanisms that shape immunity within and among species is still needed to gain insight into-and generate evolutionary hypotheses on-the ultimate drivers of immunological differences. Here, we discuss current advances in our understanding of molecular evolution underpinning jawed vertebrate immunity. First, we introduce the immunome concept, a framework for characterizing genes involved in immune defence from a comparative perspective, then we outline how immune genes of interest can be identified. Second, we focus on how different selection modes are observed acting across groups of immune genes and propose hypotheses to explain these differences. We then provide an overview of the approaches used so far to study the evolutionary heterogeneity of immune genes on macro and microevolutionary scales. Finally, we discuss some of the current evidence as to how specific pathogens affect the evolution of different groups of immune genes. This review results from the collective discussion on the current key challenges in evolutionary immunology conducted at the ESEB 2021 Online Satellite Symposium: Molecular evolution of the vertebrate immune system, from the lab to natural populations.
Collapse
Affiliation(s)
- Michal Vinkler
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | | | - Martin Těšický
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | | | - Anna E. Savage
- Department of BiologyUniversity of Central FloridaFloridaOrlandoUSA
| | - Tobias L. Lenz
- Research Unit for Evolutionary ImmunogenomicsDepartment of BiologyUniversity of HamburgHamburgGermany
| | | | - Jim Kaufman
- Institute for Immunology and Infection ResearchUniversity of EdinburghEdinburghUK
- Department of Veterinary MedicineUniversity of CambridgeCambridgeUK
| | - Daniel I. Bolnick
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticutUSA
| | | | - Neira Dedić
- Department of Botany and ZoologyMasaryk UniversityBrnoCzech Republic
| | - Andrew S. Flies
- Menzies Institute for Medical ResearchUniversity of TasmaniaHobartTasmaniaAustralia
| | - M. Mercedes Gómez Samblás
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
- Department of ParasitologyUniversity of GranadaGranadaSpain
| | | | - Karel Novák
- Department of Genetics and BreedingInstitute of Animal SciencePragueUhříněvesCzech Republic
| | - Gemma Palomar
- Faculty of BiologyInstitute of Environmental SciencesJagiellonian UniversityKrakówPoland
| | - Nynke Raven
- Department of ScienceEngineering and Build EnvironmentDeakin UniversityVictoriaWaurn PondsAustralia
| | - Kalifa Samaké
- Department of Genetics and MicrobiologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | - Joel Slade
- Department of BiologyCalifornia State UniversityFresnoCaliforniaUSA
| | | | - Eleni Voukali
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | - Jacob Höglund
- Department of Ecology and GeneticsUppsala UniversitetUppsalaSweden
| | | | | |
Collapse
|
5
|
Anyogu DC, Shoyinka SVO, Ihedioha JI. Infection of West African dwarf rams with Trypanosoma brucei brucei and Trypanosoma congolense significantly alter serum electrolytes, redox balance, sperm parameters, and gonadal morphology. Vet Res Commun 2023; 47:17-27. [PMID: 35389159 DOI: 10.1007/s11259-022-09921-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 03/23/2022] [Indexed: 01/27/2023]
Abstract
Trypanotolerance of the West African dwarf (WAD) breeds may not rule out significant pathophysiological changes that may affect productivity. In this study, the effects of infection of WAD rams with Trypanosoma brucei brucei (Tbb) and Trypanosoma congolense (Tc) on their serum levels of electrolytes [calcium, phosphorus, sodium, potassium]; oxidative stress markers [superoxide dismutase (SOD), malondialdehyde (MDA)]; and sperm parameters [sperm count, motility, vitality, and morphology] were investigated. Fifteen WAD rams, assigned to 3 groups (A, B & C) of 5 rams each, were used for the study. Group A rams were infected with Tbb, while Group B rams were infected with Tc, both intraperitoneally, at the dose of 106 trypanosomes/animal. Group C rams served as the uninfected control. The infections were monitored for 70 days. Serum calcium levels were significantly (p < 0.05) lower in Tbb and Tc infected rams compared to the control throughout the study. Serum sodium was significantly (p < 0.05) higher in the Tb infected rams compared to the Tc infected and control rams on days 14 and 28 PI. Serum SOD activity decreased while MDA levels increased in both infected groups of rams. Tbb infected rams were azoospermic, while Tc infected rams had lower sperm motility, vitality and concentration, and higher number of abnormal sperm cells compared to the control. Necrotic and inflammatory lesions occurred in the testis and epididymis of both infected rams. These results suggest that despite trypanotolerance, trypanosome infections in the WAD rams significantly impact on health and reproduction.
Collapse
Affiliation(s)
- Davinson C Anyogu
- Department of Veterinary Pathology and Microbiology, University of Nigeria, Nsukka, Enugu, 410002, Nigeria.
| | - Shodeinde V O Shoyinka
- Department of Veterinary Pathology and Microbiology, University of Nigeria, Nsukka, Enugu, 410002, Nigeria
| | - John I Ihedioha
- Department of Veterinary Pathology and Microbiology, University of Nigeria, Nsukka, Enugu, 410002, Nigeria
| |
Collapse
|
6
|
Identification and Characterization of Copy Number Variations Regions in West African Taurine Cattle. Animals (Basel) 2022; 12:ani12162130. [PMID: 36009719 PMCID: PMC9405125 DOI: 10.3390/ani12162130] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/29/2022] [Accepted: 08/16/2022] [Indexed: 11/17/2022] Open
Abstract
A total of 106 West African taurine cattle belonging to the Lagunaire breed of Benin (33), the N’Dama population of Burkina Faso (48), and N’Dama cattle sampled in Congo (25) were analyzed for Copy Number Variations (CNVs) using the BovineHDBeadChip of Illumina and two different CNV calling programs: PennCNV and QuantiSNP. Furthermore, 89 West African zebu samples (Bororo cattle of Mali and Zebu Peul sampled in Benin and Burkina Faso) were used as an outgroup to ensure that analyses reflect the taurine cattle genomic background. Analyses identified 307 taurine-specific CNV regions (CNVRs), covering about 56 Mb on all bovine autosomes. Gene annotation enrichment analysis identified a total of 840 candidate genes on 168 taurine-specific CNVRs. Three different statistically significant functional term annotation clusters (from ACt1 to ACt3) involved in the immune function were identified: ACt1 includes genes encoding lipocalins, proteins involved in the modulation of immune response and allergy; ACt2 includes genes encoding coding B-box-type zinc finger proteins and butyrophilins, involved in innate immune processes; and Act3 includes genes encoding lectin receptors, involved in the inflammatory responses to pathogens and B- and T-cell differentiation. The overlap between taurine-specific CNVRs and QTL regions associated with trypanotolerant response and tick-resistance was relatively low, suggesting that the mechanisms underlying such traits may not be determined by CNV alterations. However, four taurine-specific CNVRs overlapped with QTL regions associated with both traits on BTA23, therefore suggesting that CNV alterations in major histocompatibility complex (MHC) genes can partially explain the existence of genetic mechanisms shared between trypanotolerance and tick resistance in cattle. This research contributes to the understanding of the genomic features of West African taurine cattle.
Collapse
|
7
|
Boulangé A, Lejon V, Berthier D, Thévenon S, Gimonneau G, Desquesnes M, Abah S, Agboho P, Chilongo K, Gebre T, Fall AG, Kaba D, Magez S, Masiga D, Matovu E, Moukhtar A, Neves L, Olet PA, Pagabeleguem S, Shereni W, Sorli B, Taioe MO, Tejedor Junco MT, Yagi R, Solano P, Cecchi G. The COMBAT project: controlling and progressively minimizing the burden of vector-borne animal trypanosomosis in Africa. OPEN RESEARCH EUROPE 2022; 2:67. [PMID: 37645305 PMCID: PMC10445831 DOI: 10.12688/openreseurope.14759.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/02/2022] [Indexed: 11/23/2023]
Abstract
Vector-borne diseases affecting livestock have serious impacts in Africa. Trypanosomosis is caused by parasites transmitted by tsetse flies and other blood-sucking Diptera. The animal form of the disease is a scourge for African livestock keepers, is already present in Latin America and Asia, and has the potential to spread further. A human form of the disease also exists, known as human African trypanosomosis or sleeping sickness. Controlling and progressively minimizing the burden of animal trypanosomosis (COMBAT) is a four-year research and innovation project funded by the European Commission, whose ultimate goal is to reduce the burden of animal trypanosomosis (AT) in Africa. The project builds on the progressive control pathway (PCP), a risk-based, step-wise approach to disease reduction or elimination. COMBAT will strengthen AT control and prevention by improving basic knowledge of AT, developing innovative control tools, reinforcing surveillance, rationalizing control strategies, building capacity, and raising awareness. Knowledge gaps on disease epidemiology, vector ecology and competence, and biological aspects of trypanotolerant livestock will be addressed. Environmentally friendly vector control technologies and more effective and adapted diagnostic tools will be developed. Surveillance will be enhanced by developing information systems, strengthening reporting, and mapping and modelling disease risk in Africa and beyond. The socio-economic burden of AT will be assessed at a range of geographical scales. Guidelines for the PCP and harmonized national control strategies and roadmaps will be developed. Gender equality and ethics will be pivotal in all project activities. The COMBAT project benefits from the expertise of African and European research institutions, national veterinary authorities, and international organizations. The project consortium comprises 21 participants, including a geographically balanced representation from 13 African countries, and it will engage a larger number of AT-affected countries through regional initiatives.
Collapse
Affiliation(s)
- Alain Boulangé
- CIRAD, UMR INTERTRYP, Bouaké, 01 BP 1500, Cote d'Ivoire
- CIRAD, IRD, INTERTRYP, Univ of Montpellier, Montpellier, F-34398, France
| | - Veerle Lejon
- CIRAD, IRD, UMR INTERTRYP, Univ of Montpellier, Montpellier, F-34398, France
| | - David Berthier
- CIRAD, IRD, INTERTRYP, Univ of Montpellier, Montpellier, F-34398, France
- CIRAD, UMR INTERTRYP, Montpellier, F-34398, France
| | - Sophie Thévenon
- CIRAD, IRD, INTERTRYP, Univ of Montpellier, Montpellier, F-34398, France
- CIRAD, UMR INTERTRYP, Montpellier, F-34398, France
| | - Geoffrey Gimonneau
- CIRAD, IRD, INTERTRYP, Univ of Montpellier, Montpellier, F-34398, France
- CIRAD, UMR INTERTRYP, Dakar-Hann, BP 2057, Senegal
| | - Marc Desquesnes
- CIRAD, IRD, INTERTRYP, Univ of Montpellier, Montpellier, F-34398, France
- CIRAD, UMR INTERTRYP, Toulouse, F-31076, France
| | - Samuel Abah
- Mission Spéciale D'Eradication des Glossines (MSEG), Ministère de l'Elevage, des Pêches et des Industries Animales, Ngaoundéré, BP 263, Cameroon
| | - Prudenciène Agboho
- Centre International de Recherche-Développement sur l’Elevage en zone Subhumide (CIRDES), Bobo-Dioulasso, 01 BP 454, Burkina Faso
| | - Kalinga Chilongo
- Tsetse and Trypanosomosis Control Unit (TTCU), Ministry of Fisheries and Livestock, P.O Box 50197, Lusaka, 10101, Zambia
| | - Tsegaye Gebre
- National Institute for Control and Eradication of Tsetse and Trypanosomosis (NICETT), P.O Box 19917, Addis Ababa, Ethiopia
| | - Assane Gueye Fall
- Institut Sénégalais de Recherches Agricoles (ISRA), Dakar-Hann, BP 2057, Senegal
| | - Dramane Kaba
- Institut Pierre Richet (IPR), Institut National de Santé Publique, Bouaké, 01 BP 1500, Cote d'Ivoire
| | - Stefan Magez
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel (VUB), Brussels, B-1050, Belgium
| | - Daniel Masiga
- International Centre of Insect Physiology and Ecology (ICIPE), Nairobi, 00100, Kenya
| | | | - Aldjibert Moukhtar
- Institut de Recherche en Elevage pour le Développement (IRED), N'Djamena, Route de Farcha, BP 433, Chad
| | - Luis Neves
- Centro de Biotecnologia, Universidade Eduardo Mondlane, Maputo, 00200, Mozambique
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Sciences, University of Pretoria, Onderstepoort, 0110, South Africa
| | - Pamela A. Olet
- Kenya Tsetse and Trypanosomosis Eradication Council (KENTTEC), Nairobi, 00800, Kenya
| | - Soumaïla Pagabeleguem
- Insectarium de Bobo-Dioulasso – Campagne d'Eradication de la mouche Tsé-tsé et de la Trypanosomose (IBD-CETT), Ministère des ressources animales et halieutiques, Bobo-Dioulasso, 01 BP 1087, Burkina Faso
| | - William Shereni
- Division of Tsetse Control Services (TCD), Ministry of Lands, Agriculture, Fisheries, Water and Rural Development, P.O Box CY52, Harare, Zimbabwe
| | - Brice Sorli
- Institut d'Electronique et des Systèmes (IES), Université de Montpellier, Montpellier, F-34090, France
| | - Moeti O. Taioe
- Onderstepoort Veterinary Research, Agricultural Research Council (ARC), Pretoria, 0110, South Africa
| | | | - Rehab Yagi
- Central Veterinary Research Laboratory (CVRL), Animal Resources Research Corporation, Khartoum, 12217, Sudan
| | - Philippe Solano
- CIRAD, IRD, UMR INTERTRYP, Univ of Montpellier, Montpellier, F-34398, France
| | - Giuliano Cecchi
- Animal Production and Health Division, Food and Agriculture Organization of the United Nations (FAO), Rome, 00153, Italy
| |
Collapse
|
8
|
Boulangé A, Lejon V, Berthier D, Thévenon S, Gimonneau G, Desquesnes M, Abah S, Agboho P, Chilongo K, Gebre T, Fall AG, Kaba D, Magez S, Masiga D, Matovu E, Moukhtar A, Neves L, Olet PA, Pagabeleguem S, Shereni W, Sorli B, Taioe MO, Tejedor Junco MT, Yagi R, Solano P, Cecchi G. The COMBAT project: controlling and progressively minimizing the burden of vector-borne animal trypanosomosis in Africa. OPEN RESEARCH EUROPE 2022; 2:67. [PMID: 37645305 PMCID: PMC10445831 DOI: 10.12688/openreseurope.14759.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/02/2022] [Indexed: 08/31/2023]
Abstract
Vector-borne diseases affecting livestock have serious impacts in Africa. Trypanosomosis is caused by parasites transmitted by tsetse flies and other blood-sucking Diptera. The animal form of the disease is a scourge for African livestock keepers, is already present in Latin America and Asia, and has the potential to spread further. A human form of the disease also exists, known as human African trypanosomosis or sleeping sickness. Controlling and progressively minimizing the burden of animal trypanosomosis (COMBAT) is a four-year research and innovation project funded by the European Commission, whose ultimate goal is to reduce the burden of animal trypanosomosis (AT) in Africa. The project builds on the progressive control pathway (PCP), a risk-based, step-wise approach to disease reduction or elimination. COMBAT will strengthen AT control and prevention by improving basic knowledge of AT, developing innovative control tools, reinforcing surveillance, rationalizing control strategies, building capacity, and raising awareness. Knowledge gaps on disease epidemiology, vector ecology and competence, and biological aspects of trypanotolerant livestock will be addressed. Environmentally friendly vector control technologies and more effective and adapted diagnostic tools will be developed. Surveillance will be enhanced by developing information systems, strengthening reporting, and mapping and modelling disease risk in Africa and beyond. The socio-economic burden of AT will be assessed at a range of geographical scales. Guidelines for the PCP and harmonized national control strategies and roadmaps will be developed. Gender equality and ethics will be pivotal in all project activities. The COMBAT project benefits from the expertise of African and European research institutions, national veterinary authorities, and international organizations. The project consortium comprises 21 participants, including a geographically balanced representation from 13 African countries, and it will engage a larger number of AT-affected countries through regional initiatives.
Collapse
Affiliation(s)
- Alain Boulangé
- CIRAD, UMR INTERTRYP, Bouaké, 01 BP 1500, Cote d'Ivoire
- CIRAD, IRD, INTERTRYP, Univ of Montpellier, Montpellier, F-34398, France
| | - Veerle Lejon
- CIRAD, IRD, UMR INTERTRYP, Univ of Montpellier, Montpellier, F-34398, France
| | - David Berthier
- CIRAD, IRD, INTERTRYP, Univ of Montpellier, Montpellier, F-34398, France
- CIRAD, UMR INTERTRYP, Montpellier, F-34398, France
| | - Sophie Thévenon
- CIRAD, IRD, INTERTRYP, Univ of Montpellier, Montpellier, F-34398, France
- CIRAD, UMR INTERTRYP, Montpellier, F-34398, France
| | - Geoffrey Gimonneau
- CIRAD, IRD, INTERTRYP, Univ of Montpellier, Montpellier, F-34398, France
- CIRAD, UMR INTERTRYP, Dakar-Hann, BP 2057, Senegal
| | - Marc Desquesnes
- CIRAD, IRD, INTERTRYP, Univ of Montpellier, Montpellier, F-34398, France
- CIRAD, UMR INTERTRYP, Toulouse, F-31076, France
| | - Samuel Abah
- Mission Spéciale D'Eradication des Glossines (MSEG), Ministère de l'Elevage, des Pêches et des Industries Animales, Ngaoundéré, BP 263, Cameroon
| | - Prudenciène Agboho
- Centre International de Recherche-Développement sur l’Elevage en zone Subhumide (CIRDES), Bobo-Dioulasso, 01 BP 454, Burkina Faso
| | - Kalinga Chilongo
- Tsetse and Trypanosomosis Control Unit (TTCU), Ministry of Fisheries and Livestock, P.O Box 50197, Lusaka, 10101, Zambia
| | - Tsegaye Gebre
- National Institute for Control and Eradication of Tsetse and Trypanosomosis (NICETT), P.O Box 19917, Addis Ababa, Ethiopia
| | - Assane Gueye Fall
- Institut Sénégalais de Recherches Agricoles (ISRA), Dakar-Hann, BP 2057, Senegal
| | - Dramane Kaba
- Institut Pierre Richet (IPR), Institut National de Santé Publique, Bouaké, 01 BP 1500, Cote d'Ivoire
| | - Stefan Magez
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel (VUB), Brussels, B-1050, Belgium
| | - Daniel Masiga
- International Centre of Insect Physiology and Ecology (ICIPE), Nairobi, 00100, Kenya
| | | | - Aldjibert Moukhtar
- Institut de Recherche en Elevage pour le Développement (IRED), N'Djamena, Route de Farcha, BP 433, Chad
| | - Luis Neves
- Centro de Biotecnologia, Universidade Eduardo Mondlane, Maputo, 00200, Mozambique
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Sciences, University of Pretoria, Onderstepoort, 0110, South Africa
| | - Pamela A. Olet
- Kenya Tsetse and Trypanosomosis Eradication Council (KENTTEC), Nairobi, 00800, Kenya
| | - Soumaïla Pagabeleguem
- Insectarium de Bobo-Dioulasso – Campagne d'Eradication de la mouche Tsé-tsé et de la Trypanosomose (IBD-CETT), Ministère des ressources animales et halieutiques, Bobo-Dioulasso, 01 BP 1087, Burkina Faso
| | - William Shereni
- Division of Tsetse Control Services (TCD), Ministry of Lands, Agriculture, Fisheries, Water and Rural Development, P.O Box CY52, Harare, Zimbabwe
| | - Brice Sorli
- Institut d'Electronique et des Systèmes (IES), Université de Montpellier, Montpellier, F-34090, France
| | - Moeti O. Taioe
- Onderstepoort Veterinary Research, Agricultural Research Council (ARC), Pretoria, 0110, South Africa
| | | | - Rehab Yagi
- Central Veterinary Research Laboratory (CVRL), Animal Resources Research Corporation, Khartoum, 12217, Sudan
| | - Philippe Solano
- CIRAD, IRD, UMR INTERTRYP, Univ of Montpellier, Montpellier, F-34398, France
| | - Giuliano Cecchi
- Animal Production and Health Division, Food and Agriculture Organization of the United Nations (FAO), Rome, 00153, Italy
| |
Collapse
|
9
|
Rajavel A, Klees S, Hui Y, Schmitt AO, Gültas M. Deciphering the Molecular Mechanism Underlying African Animal Trypanosomiasis by Means of the 1000 Bull Genomes Project Genomic Dataset. BIOLOGY 2022; 11:biology11050742. [PMID: 35625470 PMCID: PMC9138820 DOI: 10.3390/biology11050742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 05/05/2022] [Accepted: 05/10/2022] [Indexed: 11/16/2022]
Abstract
Simple Summary Climate change is increasing the risk of spreading vector-borne diseases such as African Animal Trypanosomiasis (AAT), which is causing major economic losses, especially in sub-Saharan African countries. Mainly considering this disease, we have investigated transcriptomic and genomic data from two cattle breeds, namely Boran and N‘Dama, where the former is known for its susceptibility and the latter one for its tolerance to the AAT. Despite the rich literature on this disease, there is still a need to investigate underlying genetic mechanisms to decipher the complex interplay of regulatory SNPs (rSNPs), their corresponding gene expression profiles and the downstream effectors associated with the AAT disease. The findings of this study complement our previous results, which mainly involve the upstream events, including transcription factors (TFs) and their co-operations as well as master regulators. Moreover, our investigation of significant rSNPs and effectors found in the liver, spleen and lymph node tissues of both cattle breeds could enhance the understanding of distinct mechanisms leading to either resistance or susceptibility of cattle breeds. Abstract African Animal Trypanosomiasis (AAT) is a neglected tropical disease and spreads by the vector tsetse fly, which carries the infectious Trypanosoma sp. in their saliva. Particularly, this parasitic disease affects the health of livestock, thereby imposing economic constraints on farmers, costing billions of dollars every year, especially in sub-Saharan African countries. Mainly considering the AAT disease as a multistage progression process, we previously performed upstream analysis to identify transcription factors (TFs), their co-operations, over-represented pathways and master regulators. However, downstream analysis, including effectors, corresponding gene expression profiles and their association with the regulatory SNPs (rSNPs), has not yet been established. Therefore, in this study, we aim to investigate the complex interplay of rSNPs, corresponding gene expression and downstream effectors with regard to the AAT disease progression based on two cattle breeds: trypanosusceptible Boran and trypanotolerant N’Dama. Our findings provide mechanistic insights into the effectors involved in the regulation of several signal transduction pathways, thereby differentiating the molecular mechanism with regard to the immune responses of the cattle breeds. The effectors and their associated genes (especially MAPKAPK5, CSK, DOK2, RAC1 and DNMT1) could be promising drug candidates as they orchestrate various downstream regulatory cascades in both cattle breeds.
Collapse
Affiliation(s)
- Abirami Rajavel
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany; (S.K.); (Y.H.); (A.O.S.)
- Center for Integrated Breeding Research (CiBreed), Georg-August University, Carl-Sprengel-Weg 1, 37075 Göttingen, Germany
- Correspondence: (A.R.); (M.G.)
| | - Selina Klees
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany; (S.K.); (Y.H.); (A.O.S.)
- Center for Integrated Breeding Research (CiBreed), Georg-August University, Carl-Sprengel-Weg 1, 37075 Göttingen, Germany
| | - Yuehan Hui
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany; (S.K.); (Y.H.); (A.O.S.)
| | - Armin Otto Schmitt
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany; (S.K.); (Y.H.); (A.O.S.)
- Center for Integrated Breeding Research (CiBreed), Georg-August University, Carl-Sprengel-Weg 1, 37075 Göttingen, Germany
| | - Mehmet Gültas
- Center for Integrated Breeding Research (CiBreed), Georg-August University, Carl-Sprengel-Weg 1, 37075 Göttingen, Germany
- Faculty of Agriculture, South Westphalia University of Applied Sciences, Lübecker Ring 2, 59494 Soest, Germany
- Correspondence: (A.R.); (M.G.)
| |
Collapse
|
10
|
Malatji DP. Breeding of African sheep reared under low-input/output smallholder production systems for trypanotolerance. Vet World 2022; 15:1031-1043. [PMID: 35698514 PMCID: PMC9178589 DOI: 10.14202/vetworld.2022.1031-1043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 03/11/2022] [Indexed: 11/30/2022] Open
Abstract
Trypanosomiasis is a disease caused by unicellular protozoan parasites. Small ruminants succumb to trypanosomiasis in areas of high tsetse fly challenge, resulting in serious economic loss often to farmers in low-input smallholder systems. At present, trypanosomiasis is treated with trypanocidal drugs, but access to these can be limited, and increasing parasite resistance raises questions about their efficacy. The development of trypanotolerance in small ruminant flocks through targeted breeding strategies is considered a sustainable and economical option for controlling African trypanosomiasis. Recently, quantitative trait loci (QTLs) associated with trypanotolerance traits in sheep have been reported. The results of these studies form the basis for more studies to identify QTLs associated with trypanosomiasis resistance, particularly in African livestock species. For example, signatures of positive selection for trypanotolerance have been identified using genome-wide single-nucleotide polymorphism data. However, there are several challenges in performing genetic analyses using data from low-input smallholder systems, including a lack of recorded pedigree and production records and the need for large sample sizes when flock sizes are often fewer than 50 animals. Breeding strategies to improve trypanotolerance should also preserve existing genetic diversity as well as minimize excessive genetic introgression by trypanosusceptible breeds. This review discusses the possibilities of breeding for trypanosome tolerance/resistance in low-input/low-output small ruminant production systems. Potential challenges are outlined, and potential available genetic resources are described as a foundation for future work.
Collapse
Affiliation(s)
- Dikeledi P. Malatji
- Department of Agriculture and Animal Health, College of Agriculture and Environmental Sciences, University of South Africa, Johannesburg, Gauteng Province, South Africa
| |
Collapse
|
11
|
Crum TE, Schnabel RD, Decker JE, Taylor JF. Taurine and Indicine Haplotype Representation in Advanced Generation Individuals From Three American Breeds. Front Genet 2021; 12:758394. [PMID: 34733318 PMCID: PMC8558500 DOI: 10.3389/fgene.2021.758394] [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: 08/13/2021] [Accepted: 09/27/2021] [Indexed: 11/14/2022] Open
Abstract
Development of the American Breeds of beef cattle began in the 1920s as breeders and U. S. Experiment Station researchers began to create Bos taurus taurus × Bos taurus indicus hybrids using Brahman as the B. t. indicus source. By 1954, U.S. Breed Associations had been formed for Brangus (5/8 Angus × 3/8 Brahman), Beefmaster (½ Brahman × ¼ Shorthorn × ¼ Hereford), and Santa Gertrudis (5/8 Shorthorn × 3/8 Brahman). While these breeds were developed using mating designs expected to create base generation animals with the required genome contributions from progenitor breeds, each association has now registered advanced generation animals in which selection or drift may have caused the realized genome compositions to differ from initial expected proportions. The availability of high-density SNP genotypes for 9,161 Brangus, 3,762 Beefmaster, and 1,942 Santa Gertrudis animals allowed us to compare the realized genomic architectures of breed members to the base generation expectations. We used RFMix to estimate local ancestry and identify genomic regions in which the proportion of Brahman ancestry differed significantly from a priori expectations. For all three breeds, lower than expected levels of Brahman composition were found genome-wide, particularly in early-generation animals where we demonstrate that selection on beef production traits was likely responsible for the taurine enrichment. Using a proxy for generation number, we also contrasted the genomes of early- and advanced-generation animals and found that the indicine composition of the genome has increased with generation number likely due to selection on adaptive traits. Many of the most-highly differentiated genomic regions were breed specific, suggesting that differences in breeding objectives and selection intensities exist between the breeds. Global ancestry estimation is commonly performed in admixed animals to control for stratification in association studies. However, local ancestry estimation provides the opportunity to investigate the evolution of specific chromosomal segments and estimate haplotype effects on trait variation in admixed individuals. Investigating the genomic architecture of the American Breeds not only allows the estimation of indicine and taurine genome proportions genome-wide, but also the locations within the genome where either taurine or indicine alleles confer a selective advantage.
Collapse
Affiliation(s)
- Tamar E Crum
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States
| | - Robert D Schnabel
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States.,Informatics Institute, University of Missouri, Columbia, MO, United States
| | - Jared E Decker
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States.,Informatics Institute, University of Missouri, Columbia, MO, United States
| | - Jeremy F Taylor
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States
| |
Collapse
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
Genome-wide association study of trypanosome prevalence and morphometric traits in purebred and crossbred Baoulé cattle of Burkina Faso. PLoS One 2021; 16:e0255089. [PMID: 34351956 PMCID: PMC8341487 DOI: 10.1371/journal.pone.0255089] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 07/09/2021] [Indexed: 11/27/2022] Open
Abstract
In this study, single-SNP GWAS analyses were conducted to find regions affecting tolerance against trypanosomosis and morphometrics traits in purebred and crossbred Baoulé cattle of Burkina Faso. The trypanosomosis status (positive and negative) and a wide set of morphological traits were recorded for purebred Baoulé and crossbred Zebu x Baoulé cattle, and genotyped with the Illumina Bovine SNP50 BeadChip. After quality control, 36,203 SNPs and 619 animals including 343 purebred Baoulé and 279 crossbreds were used for the GWAS analyses. Several important genes were found that can influence morphological parameters. Although there were no genes identified with a reported strong connection to size traits, many of them were previously identified in various growth-related studies. A re-occurring theme for the genes residing in the regions identified by the most significant SNPs was pleiotropic effect on growth of the body and the cardiovascular system. Regarding trypanosomosis tolerance, two potentially important regions were identified in purebred Baoulé on chromosomes 16 and 24, containing the CFH, CRBN, TRNT1 and, IL5RA genes, and one additional genomic region in Baoulé, x Zebu crossbreds on chromosome 5, containing MGAT4C and NTS. Almost all of these regions and genes were previously related to the trait of interest, while the CRBN gene was to our knowledge presented in the context of trypanosomiasis tolerance for the first time.
Collapse
|
14
|
Serranito B, Taurisson-Mouret D, Harkat S, Laoun A, Ouchene-Khelifi NA, Pompanon F, Benjelloun B, Cecchi G, Thevenon S, Lenstra JA, Da Silva A. Search for Selection Signatures Related to Trypanosomosis Tolerance in African Goats. Front Genet 2021; 12:715732. [PMID: 34413881 PMCID: PMC8369930 DOI: 10.3389/fgene.2021.715732] [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: 05/27/2021] [Accepted: 06/28/2021] [Indexed: 12/13/2022] Open
Abstract
Livestock is heavily affected by trypanosomosis in Africa. Through strong selective pressure, several African indigenous breeds of cattle and small ruminants have acquired varying degrees of tolerance against this disease. In this study, we combined LFMM and PCAdapt for analyzing two datasets of goats from West-Central Africa and East Africa, respectively, both comprising breeds with different assumed levels of trypanotolerance. The objectives were (i) to identify molecular signatures of selection related to trypanotolerance; and (ii) to guide an optimal sampling for subsequent studies. From 33 identified signatures, 18 had been detected previously in the literature as being mainly associated with climatic adaptations. The most plausible signatures of trypanotolerance indicate the genes DIS3L2, COPS7B, PD5A, UBE2K, and UBR1. The last gene is of particular interest since previous literature has already identified E3-ubiquitin ligases as playing a decisive role in the immune response. For following-up on these findings, the West-Central African area appears particularly relevant because of (i) a clear parasitic load gradient related to a humidity gradient, and (ii) still restricted admixture levels between goat breeds. This study illustrates the importance of protecting local breeds, which have retained unique allelic combinations conferring their remarkable adaptations.
Collapse
Affiliation(s)
- Bruno Serranito
- Museum National d’Histoire Naturelle, CRESCO, Dinard, France
- University of Limoges, PEREINE, E2LIM, Limoges, France
| | | | - Sahraoui Harkat
- Science Veterinary Institute, University of Blida, Blida, Algeria
| | | | | | - François Pompanon
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Badr Benjelloun
- National Institute of Agronomic Research, Regional Centre of Agronomic Research, Beni-Mellal, Morocco
| | - Giuliano Cecchi
- Food and Agriculture Organization of the United Nations, Animal Production and Health Division, Rome, Italy
| | - Sophie Thevenon
- CIRAD, UMR INTERTRYP, Montpellier, France
- INTERTRYP, University of Montpellier, CIRAD, IRD, Montpellier, France
| | | | - Anne Da Silva
- University of Limoges, PEREINE, E2LIM, Limoges, France
| |
Collapse
|
15
|
Jaimes-Dueñez J, Mogollón-Waltero E, Árias-Landazabal N, Rangel-Pachon D, Jimenez-Leaño A, Mejia-Jaramillo A, Triana-Chávez O. Molecular surveillance of Trypanosoma spp. reveals different clinical and epidemiological characteristics associated with the infection in three creole cattle breeds from Colombia. Prev Vet Med 2021; 193:105414. [PMID: 34175568 DOI: 10.1016/j.prevetmed.2021.105414] [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: 02/16/2021] [Revised: 05/17/2021] [Accepted: 06/17/2021] [Indexed: 10/21/2022]
Abstract
In South America, Colombia is the third-largest livestock producer with approximately 28.8 million cattle, of which Colombian Creole cattle represent around 1% of the livestock population. Animal Trypanosomiasis (AT) is one of the most critical problems in the livestock industry, reducing its production by about 30 %. Considering the paucity of information to understand the epidemiological features of AT in Colombian Creole cattle, the present study reports the molecular prevalence and clinical traits associated with the infection of Trypanosoma spp. in three Colombian Creole breeds. From 2019 to 2020, cross-sectional surveillance in farms of central and west of Colombia was designed to evaluate the mentioned characteristics in Casanareño, Chino Santandereano, and Sanmartinero Creole breeds. Molecular analysis showed an AT prevalence of 60.2 % (95 % CI = 54.2 % - 66.2 %). The Chino Santandereano population presented the highest value (Trypanosoma spp., 75.2 %, T. theileri 59.6 % and T. evansi 15.6 %), followed by Casanareño (Trypanosoma spp., 65.3 %, T. theileri 38.6 %, T. evansi 24.0 %, and T. vivax 5.3 %) and Sanmartinero (Trypanosoma spp., 33.3 %, T. theileri 24.0 % and T. evansi 9.3 %). Features such as breeds, age, and feeding system were significantly associated with AT prevalence (P < 0.05). Additionally, a low level of serum total proteins was observed during T. evansi infection in Sanmartinero (P < 0.05). To our knowledge, this is the first cross-sectional survey that evaluates using molecular methods the infection of Trypanosoma spp. in Colombian Creole breeds, showing significant variations in the prevalence and clinical signs associated with the infection. These results suggest different degrees of trypanotolerance in these breeds, as well as a possible effect of environmental variables on the prevalence and clinical characteristics associated with the infection. The epidemiological and economic implications of these findings are discussed here.
Collapse
Affiliation(s)
- Jeiczon Jaimes-Dueñez
- Grupo de Investigación en Ciencias Animales - GRICA, Facultad de Medicina Veterinaria y Zootecnia, Universidad Cooperativa de Colombia UCC, Bucaramanga, Colombia; Grupo Biología y Control de Enfermedades Infecciosas - BCEI, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia, Medellín, Colombia.
| | - Edgar Mogollón-Waltero
- Grupo de Investigación en Ciencias Animales - GRICA, Facultad de Medicina Veterinaria y Zootecnia, Universidad Cooperativa de Colombia UCC, Bucaramanga, Colombia
| | - Norberto Árias-Landazabal
- Grupo de Investigación en Ciencias Animales - GRICA, Facultad de Medicina Veterinaria y Zootecnia, Universidad Cooperativa de Colombia UCC, Bucaramanga, Colombia
| | - David Rangel-Pachon
- Grupo de Investigación en Ciencias Animales - GRICA, Facultad de Medicina Veterinaria y Zootecnia, Universidad Cooperativa de Colombia UCC, Bucaramanga, Colombia
| | - Angela Jimenez-Leaño
- Grupo de Investigación en Ciencias Animales - GRICA, Facultad de Medicina Veterinaria y Zootecnia, Universidad Cooperativa de Colombia UCC, Bucaramanga, Colombia
| | - Ana Mejia-Jaramillo
- Grupo Biología y Control de Enfermedades Infecciosas - BCEI, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia, Medellín, Colombia
| | - Omar Triana-Chávez
- Grupo Biología y Control de Enfermedades Infecciosas - BCEI, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia, Medellín, Colombia
| |
Collapse
|
16
|
Bayssa M, Yigrem S, Betsha S, Tolera A. Production, reproduction and some adaptation characteristics of Boran cattle breed under changing climate: A systematic review and meta-analysis. PLoS One 2021; 16:e0244836. [PMID: 34048433 PMCID: PMC8162631 DOI: 10.1371/journal.pone.0244836] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 05/12/2021] [Indexed: 12/05/2022] Open
Abstract
Introduction Climate change affects livestock production and productivity, which could threaten livestock-based food security in pastoral and agro-pastoral production systems of the tropics and sub-tropics. Boran cattle breed is one of the hardiest Zebu cattle reared by Borana Oromo pastoralists for milk and meat production. However, there is limited comprensive information on production, reproduction and adaption traits of the Boran cattle in Ethiopia. Thus, this paper aims to compile the main production, reproduction and some adaptation traits of Boran cattle based on systematic review and meta-analysis of peer reviewed published and unpublished literature. Methodology A combination of systematic review and meta-analysis based on PRISMA guideline was employed. Accordingly, out of 646 recorded articles identified through database searching, 64 were found to be eligible for production, reproduction and adaptation characteristics of the Boran cattle, 28 articles were included in qualitative systematic review while 36 articles were used for quantitative meta-analysis. Result The Boran cattle breed has the ability to survive, produce and reproduce under high ambient temperature, utilize low quality forage resources, and resist water shortage or long watering intervals and tick infestations. The review revealed that the breed employs various adaptation responses (morphological, physiological, biochemical, metabolic, cellular and molecular responses) to cope with harsh environmental conditions including climate change, rangeland degradation, seasonal feed and water shortages and high incidences of tick infestations. The meta-analysis using a random-effects model allowed provision of pooled estimates of heritability and genetic correlations for reproduction and production traits, which could be used to solve genetic prediction equations under a population level in purebred Boran cattle. In addition, heritability and genetic-correlation estimates found in the present study suggest that there is high genetic variability for most traits in Boran cattle, and that genetic progress is possible for all studied traits in this breed. Conclusion The Boran cattle breed has the ability to survive, produce and reproduce under high ambient temperature, utilize low quality forage resources, and resist water shortage or long watering intervals and tick infestations. However, currently there are several challenges such as recurrent droughts, pasture deterioration and lack of systematic selection and breeding programs that play to undermine the realization of the potential of the breed. Thus, we recommend systematic selection for enhancing the reproductive and production performances without compromising the adaptation traits of the breed coupled with improved management of rangelands.
Collapse
Affiliation(s)
- Merga Bayssa
- College of Agriculture, Hawassa University, Hawassa, Ethiopia
- * E-mail:
| | | | - Simret Betsha
- College of Agriculture, Hawassa University, Hawassa, Ethiopia
| | - Adugna Tolera
- College of Agriculture, Hawassa University, Hawassa, Ethiopia
| |
Collapse
|
17
|
Rajavel A, Schmitt AO, Gültas M. Computational Identification of Master Regulators Influencing Trypanotolerance in Cattle. Int J Mol Sci 2021; 22:ijms22020562. [PMID: 33429951 PMCID: PMC7827104 DOI: 10.3390/ijms22020562] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/31/2020] [Accepted: 01/05/2021] [Indexed: 12/15/2022] Open
Abstract
African Animal Trypanosomiasis (AAT) is transmitted by the tsetse fly which carries pathogenic trypanosomes in its saliva, thus causing debilitating infection to livestock health. As the disease advances, a multistage progression process is observed based on the progressive clinical signs displayed in the host’s body. Investigation of genes expressed with regular monotonic patterns (known as Monotonically Expressed Genes (MEGs)) and of their master regulators can provide important clue for the understanding of the molecular mechanisms underlying the AAT disease. For this purpose, we analysed MEGs for three tissues (liver, spleen and lymph node) of two cattle breeds, namely trypanosusceptible Boran and trypanotolerant N’Dama. Our analysis revealed cattle breed-specific master regulators which are highly related to distinguish the genetic programs in both cattle breeds. Especially the master regulators MYC and DBP found in this study, seem to influence the immune responses strongly, thereby susceptibility and trypanotolerance of Boran and N’Dama respectively. Furthermore, our pathway analysis also bolsters the crucial roles of these master regulators. Taken together, our findings provide novel insights into breed-specific master regulators which orchestrate the regulatory cascades influencing the level of trypanotolerance in cattle breeds and thus could be promising drug targets for future therapeutic interventions.
Collapse
Affiliation(s)
- Abirami Rajavel
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany; (A.R.); (A.O.S.)
| | - Armin Otto Schmitt
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany; (A.R.); (A.O.S.)
- Center for Integrated Breeding Research (CiBreed), Albrecht-Thaer-Weg 3, Georg-August University, 37075 Göttingen, Germany
| | - Mehmet Gültas
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany; (A.R.); (A.O.S.)
- Center for Integrated Breeding Research (CiBreed), Albrecht-Thaer-Weg 3, Georg-August University, 37075 Göttingen, Germany
- Correspondence:
| |
Collapse
|
18
|
Abstract
Genomic variation exists in cattle that affects their susceptibility to the complex of pathogens responsible for bovine respiratory disease (BRD). Heritability estimates and genome-wide association analyses (GWAA) support the role of host genomic variation in BRD susceptibility. Heritability estimates for BRD susceptibility range from 0.02 to 0.29 depending on the population, the definition of the disease, and the accuracy of diagnosis. GWAA have identified genomic regions (loci) associated with BRD in beef and dairy cattle based on a variety of BRD diagnostic criteria. National standards need to be developed for BRD diagnostics and reporting to facilitate selection. Commercial genotyping is available to predict BRD susceptibility in dairy cattle and for the selection of replacement animals. Disease pathogen profiles vary by region and can result in genetic heterogeneity where different loci are important for susceptibility to different BRD pathogens. Although the identification of the BRD pathogens may not be critical for treatment, it is of paramount importance in identifying loci that render cattle susceptible to the disease. Identification of loci associated with host susceptibility to BRD provides a foundation for genomic selection to reduce disease and opens the possibilities to a better understanding of how the host defends itself.
Collapse
|
19
|
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: 44] [Impact Index Per Article: 11.0] [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.
Collapse
|
20
|
Hu G, Do DN, Gray J, Miar Y. Selection for Favorable Health Traits: A Potential Approach to Cope with Diseases in Farm Animals. Animals (Basel) 2020; 10:E1717. [PMID: 32971980 PMCID: PMC7552752 DOI: 10.3390/ani10091717] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 09/21/2020] [Indexed: 12/17/2022] Open
Abstract
Disease is a global problem for animal farming industries causing tremendous economic losses (>USD 220 billion over the last decade) and serious animal welfare issues. The limitations and deficiencies of current non-selection disease control methods (e.g., vaccination, treatment, eradication strategy, genome editing, and probiotics) make it difficult to effectively, economically, and permanently eliminate the adverse influences of disease in the farm animals. These limitations and deficiencies drive animal breeders to be more concerned and committed to dealing with health problems in farm animals by selecting animals with favorable health traits. Both genetic selection and genomic selection contribute to improving the health of farm animals by selecting certain health traits (e.g., disease tolerance, disease resistance, and immune response), although both of them face some challenges. The objective of this review was to comprehensively review the potential of selecting health traits in coping with issues caused by diseases in farm animals. Within this review, we highlighted that selecting health traits can be applied as a method of disease control to help animal agriculture industries to cope with the adverse influences caused by diseases in farm animals. Certainly, the genetic/genomic selection solution cannot solve all the disease problems in farm animals. Therefore, management, vaccination, culling, medical treatment, and other measures must accompany selection solution to reduce the adverse impact of farm animal diseases on profitability and animal welfare.
Collapse
Affiliation(s)
| | | | | | - Younes Miar
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS B2N 5E3, Canada; (G.H.); (D.N.D.); (J.G.)
| |
Collapse
|
21
|
Álvarez I, Fernández I, Traoré A, Pérez-Pardal L, Menéndez-Arias NA, Goyache F. Genomic scan of selective sweeps in Djallonké (West African Dwarf) sheep shed light on adaptation to harsh environments. Sci Rep 2020; 10:2824. [PMID: 32071365 PMCID: PMC7028950 DOI: 10.1038/s41598-020-59839-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 12/11/2019] [Indexed: 02/07/2023] Open
Abstract
The Djallonké (West African Dwarf) sheep is a small-sized haired sheep resulting from a costly evolutionary process of natural adaptation to the harsh environment of West Africa including trypanosome challenge. However, genomic studies carried out in this sheep are scant. In this research, genomic data of 184 Djallonké sheep (and 12 Burkina-Sahel sheep as an outgroup) generated using medium-density SNP Chips were analyzed. Three different statistics (iHS, XP-EHH and nSL) were applied to identify candidate selection sweep regions spanning genes putatively associated with adaptation of sheep to the West African environment. A total of 207 candidate selection sweep regions were defined. Gene-annotation enrichment and functional annotation analyses allowed to identify three statistically significant functional clusters involving 12 candidate genes. Genes included in Functional Clusters associated to selection signatures were mainly related to metabolic response to stress, including regulation of oxidative and metabolic stress and thermotolerance. The bovine chromosomal areas carrying QTLs for cattle trypanotolerance were compared with the regions on which the orthologous functional candidate cattle genes were located. The importance of cattle BTA4 for trypanotolerant response might have been conserved between species. The current research provides new insights on the genomic basis for adaptation and highlights the importance of obtaining information from non-cosmopolite livestock populations managed in harsh environments.
Collapse
Affiliation(s)
- Isabel Álvarez
- Servicio Regional de Investigación y Desarrollo Agroalimentario, E-33394, Gijón, Spain
| | - Iván Fernández
- Servicio Regional de Investigación y Desarrollo Agroalimentario, E-33394, Gijón, Spain
| | - Amadou Traoré
- Institut de l'Environnement et des Recherches Agricoles (INERA), Ouagadougou, 04 BP 8645, Burkina Faso
| | | | | | - Félix Goyache
- Servicio Regional de Investigación y Desarrollo Agroalimentario, E-33394, Gijón, Spain.
| |
Collapse
|
22
|
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.
Collapse
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
| |
Collapse
|
23
|
Yaro M, Munyard KA, Morgan E, Allcock RJN, Stear MJ, Groth DM. Analysis of pooled genome sequences from Djallonke and Sahelian sheep of Ghana reveals co-localisation of regions of reduced heterozygosity with candidate genes for disease resistance and adaptation to a tropical environment. BMC Genomics 2019; 20:816. [PMID: 31699027 PMCID: PMC6836352 DOI: 10.1186/s12864-019-6198-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Accepted: 10/16/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The Djallonke sheep is well adapted to harsh environmental conditions, and is relatively resistant to Haemonchosis and resilient to animal trypanosomiasis. The larger Sahelian sheep, which cohabit the same region, is less well adapted to these disease challenges. Haemonchosis and Trypanosomiasis collectively cost the worldwide animal industry billions of dollars in production losses annually. RESULTS Here, we separately sequenced and then pooled according to breed the genomes from five unrelated individuals from each of the Djallonke and Sahelian sheep breeds (sourced from Ghana), at greater than 22-fold combined coverage for each breed. A total of approximately 404 million (97%) and 343 million (97%) sequence reads from the Djallonke and Sahelian breeds respectively, were successfully mapped to the sheep reference genome Oar v3.1. We identified approximately 11.1 million and 10.9 million single nucleotide polymorphisms (SNPs) in the Djallonke and Sahelian breeds, with approximately 15 and 16% respectively of these not previously reported in sheep. Multiple regions of reduced heterozygosity were also found; 70 co-localised within genomic regions harbouring genes that mediate disease resistance, immune response and adaptation in sheep or cattle. Thirty- three of the regions of reduced heterozygosity co-localised with previously reported genes for resistance to haemonchosis and trypanosomiasis. CONCLUSIONS Our analyses suggest that these regions of reduced heterozygosity may be signatures of selection for these economically important diseases.
Collapse
Affiliation(s)
- M. Yaro
- School of Biomedical Sciences, CHIRI Biosciences Research Precinct, Faculty of Health Sciences, Curtin University, GPO Box U1987, Perth, WA 6845 Australia
| | - K. A. Munyard
- School of Biomedical Sciences, CHIRI Biosciences Research Precinct, Faculty of Health Sciences, Curtin University, GPO Box U1987, Perth, WA 6845 Australia
| | - E. Morgan
- School of Biomedical Sciences, CHIRI Biosciences Research Precinct, Faculty of Health Sciences, Curtin University, GPO Box U1987, Perth, WA 6845 Australia
| | - R. J. N. Allcock
- The University of Western Australia, 35 Stirling Highway, Crawley, Perth, WA Australia
- Pathwest Laboratory Medicine WA, QEII Medical Centre, Monash Avenue, Nedlands, 6009 Australia
| | - M. J. Stear
- Agribio centre for Agribioscience, La Trobe University, Melbourne, Australia
- Institute of Biodiversity, Animal Health and Comparative Medicine University of Glasgow, Bearsden Road, Glasgow, G61 1QH UK
| | - D. M. Groth
- School of Biomedical Sciences, CHIRI Biosciences Research Precinct, Faculty of Health Sciences, Curtin University, GPO Box U1987, Perth, WA 6845 Australia
| |
Collapse
|
24
|
May K, Weimann C, Scheper C, Strube C, König S. Allele substitution and dominance effects of CD166/ALCAM gene polymorphisms for endoparasite resistance and test-day traits in a small cattle population using logistic regression analyses. Mamm Genome 2019; 30:301-317. [PMID: 31650268 DOI: 10.1007/s00335-019-09818-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 10/09/2019] [Indexed: 12/13/2022]
Abstract
The study investigated the effects of four single-nucleotide polymorphisms (SNPs) in the activated leukocyte cell adhesion molecule (ALCAM) gene on liver fluke (Fasciola hepatica) infections (FH-INF), gastrointestinal nematode infections (GIN-INF) and disease indicator traits [e.g. somatic cell score (SCS), fat-to-protein ratio (FPR)] in German dual-purpose cattle (DSN). A genome-wide association study inferred the chip SNP ALCAMc.73+32791A>G as a candidate for F. hepatica resistance in DSN. Because of the crucial function of ALCAM in immune responses, SNPs in the gene might influence further resistance and performance traits. Causal mutations were identified in exon 9 (ALCAMc.1017T>C) and intron 9 (ALCAMc.1104+10T>A, ALCAMc.1104+85T>C) in a selective subset of 94 DSN cows. We applied logistic regression analyses for the association between SNP genotypes with residuals for endoparasite traits (rINF-FH, rGIN-INF) and estimated breeding values (EBVs) for test-day traits. The probability of the heterozygous genotype was estimated in dependency of the target trait. Allele substitution effects for rFH-INF were significant for all four loci. The T allele of the SNPs ALCAMc.1017T>C and ALCAMc.1104+85T>C was the favourable allele when improving resistance against FH-INF. Significant allele substitution for rGIN-INF was only found for the chip SNP ALCAMc.73+32791A>G. We identified significant associations between the SNPs with EBVs for milk fat%, protein% and FPR. Dominance effects for the EBVs of test-day traits ranged from 0.00 to 0.47 SD and were in the direction of improved resistance for rFH-INF. We estimated favourable dominance effects from same genotypes for rFH-INF and FPR, but dominance effects were antagonistic between rFH-INF and SCS.
Collapse
Affiliation(s)
- Katharina May
- Institute of Animal Breeding and Genetics, Justus-Liebig-University of Gießen, 35390, Giessen, Germany.
| | - Christina Weimann
- Institute of Animal Breeding and Genetics, Justus-Liebig-University of Gießen, 35390, Giessen, Germany
| | - Carsten Scheper
- Institute of Animal Breeding and Genetics, Justus-Liebig-University of Gießen, 35390, Giessen, Germany
| | - Christina Strube
- Institute for Parasitology, Center for Infection Medicine, University of Veterinary Medicine Hanover, 30559, Hannover, Germany
| | - Sven König
- Institute of Animal Breeding and Genetics, Justus-Liebig-University of Gießen, 35390, Giessen, Germany
| |
Collapse
|
25
|
Marshall K, Gibson JP, Mwai O, Mwacharo JM, Haile A, Getachew T, Mrode R, Kemp SJ. Livestock Genomics for Developing Countries – African Examples in Practice. Front Genet 2019. [DOI: 10.10.3389/fgene.2019.00297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
|
26
|
Marshall K, Gibson JP, Mwai O, Mwacharo JM, Haile A, Getachew T, Mrode R, Kemp SJ. Livestock Genomics for Developing Countries - African Examples in Practice. Front Genet 2019; 10:297. [PMID: 31105735 PMCID: PMC6491883 DOI: 10.3389/fgene.2019.00297] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 03/19/2019] [Indexed: 01/17/2023] Open
Abstract
African livestock breeds are numerous and diverse, and typically well adapted to the harsh environment conditions under which they perform. They have been used over centuries to provide livelihoods as well as food and nutritional security. However, African livestock systems are dynamic, with many small- and medium-scale systems transforming, to varying degrees, to become more profitable. In these systems the women and men livestock keepers are often seeking new livestock breeds or genotypes - typically those that increase household income through having enhanced productivity in comparison to traditional breeds while maintaining adaptedness. In recent years genomic approaches have started to be utilized in the identification and development of such breeds, and in this article we describe a number of examples to this end from sub-Saharan Africa. These comprise case studies on: (a) dairy cattle in Kenya and Senegal, as well as sheep in Ethiopia, where genomic approaches aided the identification of the most appropriate breed-type for the local productions systems; (b) a cross-breeding program for dairy cattle in East Africa incorporating genomic selection as well as other applications of genomics; (c) ongoing work toward creating a new cattle breed for East Africa that is both productive and resistant to trypanosomiasis; and (d) the use of African cattle as resource populations to identify genomic variants of economic or ecological significance, including a specific case where the discovery data was from a community based breeding program for small ruminants in Ethiopia. Lessons learnt from the various case studies are highlighted, and the concluding section of the paper gives recommendations for African livestock systems to increasingly capitalize on genomic technologies.
Collapse
Affiliation(s)
- Karen Marshall
- Livestock Genetics Program, International Livestock Research Institute, Nairobi, Kenya
- Centre for Tropical Livestock Genetics and Health, Nairobi, Kenya
| | - John P. Gibson
- School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia
| | - Okeyo Mwai
- Livestock Genetics Program, International Livestock Research Institute, Nairobi, Kenya
| | - Joram M. Mwacharo
- Small Ruminant Breeding and Genomics Group, International Center for Agricultural Research in the Dry Areas, Addis Ababa, Ethiopia
| | - Aynalem Haile
- Small Ruminant Breeding and Genomics Group, International Center for Agricultural Research in the Dry Areas, Addis Ababa, Ethiopia
| | - Tesfaye Getachew
- Small Ruminant Breeding and Genomics Group, International Center for Agricultural Research in the Dry Areas, Addis Ababa, Ethiopia
| | - Raphael Mrode
- Livestock Genetics Program, International Livestock Research Institute, Nairobi, Kenya
- Scotland’s Rural College, Edinburgh, United Kingdom
| | - Stephen J. Kemp
- Livestock Genetics Program, International Livestock Research Institute, Nairobi, Kenya
- Centre for Tropical Livestock Genetics and Health, Nairobi, Kenya
| |
Collapse
|
27
|
Burrow HM, Mans BJ, Cardoso FF, Birkett MA, Kotze AC, Hayes BJ, Mapholi N, Dzama K, Marufu MC, Githaka NW, Djikeng A. Towards a new phenotype for tick resistance in beef and dairy cattle: a review. ANIMAL PRODUCTION SCIENCE 2019. [DOI: 10.1071/an18487] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
About 80% of the world’s cattle are affected by ticks and tick-borne diseases, both of which cause significant production losses. Cattle host resistance to ticks is the most important factor affecting the economics of tick control, but it is largely neglected in tick-control programs due to technical difficulties and costs associated with identifying individual-animal variation in resistance. The present paper reviews the scientific literature to identify factors affecting resistance of cattle to ticks and the biological mechanisms of host tick resistance, to develop alternative phenotype(s) for tick resistance. If new cost-effective phenotype(s) can be developed and validated, then tick resistance of cattle could be genetically improved using genomic selection, and incorporated into breeding objectives to simultaneously improve cattle productive attributes and tick resistance. The phenotype(s) could also be used to improve tick control by using cattle management. On the basis of the present review, it is recommended that three possible phenotypes (haemolytic analysis; measures of skin hypersensitivity reactions; simplified artificial tick infestations) be further developed to determine their practical feasibility for consistently, cost-effectively and reliably measuring cattle tick resistance in thousands of individual animals in commercial and smallholder farmer herds in tropical and subtropical areas globally. During evaluation of these potential new phenotypes, additional measurements should be included to determine the possibility of developing a volatile-based resistance phenotype, to simultaneously improve cattle resistance to both ticks and biting flies. Because the current measurements of volatile chemistry do not satisfy the requirements of a simple, cost-effective phenotype for use in commercial cattle herds, consideration should also be given to inclusion of potentially simpler measures to enable indirect genetic selection for volatile-based resistance to ticks.
Collapse
|
28
|
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.
Collapse
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
| |
Collapse
|
29
|
Ropka-Molik K, Stefaniuk-Szmukier M, Piórkowska K, Szmatoła T, Bugno-Poniewierska M. Molecular characterization of the apoptosis-related SH3RF1 and SH3RF2 genes and their association with exercise performance in Arabian horses. BMC Vet Res 2018; 14:237. [PMID: 30107803 PMCID: PMC6092840 DOI: 10.1186/s12917-018-1567-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 08/09/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Apoptosis plays an important role in the regulation of healthy tissue growth and development as well as in controlling the maintenance of homeostasis in exercising muscles. During an intensive physical effort, the regulation of cell death by apoptosis results in the replacement of unaccustomed muscle cells by new cells that are better suited to exercise. The aim of this study was to determine the expression of two genes (SH3FR1 and SH3RF2) that control apoptosis in muscle tissues during training periods characterized by different intensities. The gene expression levels were estimated using real-time PCR method in skeletal muscle biopsies collected from 15 Arabian horses (untrained, after an intense gallop phase, and at the end of the racing season). An association study was performed on 250 Arabian horses to assess the effect of the SH3RF2:c.796 T > C (p.Ser266Pro) variant on race performance traits in flat gallop-racing. RESULTS A gene expression analysis confirmed a significant decrease (p < 0.01) in the anti-apoptotic SH3RF2 (POSHER) gene during training periods that differed in intensity. The highest SH3RF2 expression level was detected in the muscles of untrained horses, whereas the lowest expression was identified at the end of the racing season in horses that were fully adapted to the exercise. A non-significant decrease in SH3RF1 gene expression following the training periods was observed. Moreover, a serine substitution by proline at amino acid position 266 (CC genotype) was negatively associated with the probability of winning races, the number of races in which a horse occurred and the financial value of the prizes. Horses with the TT genotype achieved the highest financial benefits, both for total winnings and for winnings per race in which the horses participated. CONCLUSIONS The present study showed the supposed regulation mechanism of exercise-induced apoptosis in horses at the molecular level. The identified SH3RF2: c.796 T > C missense variant was associated with selected racing performance traits, which is important information during the evaluation of horses' exercise predisposition. The association results and frequencies of the CT and TT genotypes suggest the possibility of using SH3RF2 variant in selection to improve the racing performance of Arabian horses.
Collapse
Affiliation(s)
- K Ropka-Molik
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Kraków, Poland. .,Laboratory of Genomics, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland.
| | - M Stefaniuk-Szmukier
- Department of Horse Breeding, Institute of Animal Science, the University of Agriculture in Cracow, Kraków, Poland
| | - K Piórkowska
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Kraków, Poland
| | - T Szmatoła
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Kraków, Poland
| | - M Bugno-Poniewierska
- Institute of Veterinary Sciences University of Agriculture in Krakow, Kraków, Poland
| |
Collapse
|
30
|
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.
Collapse
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
| |
Collapse
|
31
|
Bahbahani H, Tijjani A, Mukasa C, Wragg D, Almathen F, Nash O, Akpa GN, Mbole-Kariuki M, Malla S, Woolhouse M, Sonstegard T, Van Tassell C, Blythe M, Huson H, Hanotte O. Signatures of Selection for Environmental Adaptation and Zebu × Taurine Hybrid Fitness in East African Shorthorn Zebu. Front Genet 2017. [PMID: 28642786 PMCID: PMC5462927 DOI: 10.3389/fgene.2017.00068] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The East African Shorthorn Zebu (EASZ) cattle are ancient hybrid between Asian zebu × African taurine cattle preferred by local farmers due to their adaptability to the African environment. The genetic controls of these adaptabilities are not clearly understood yet. Here, we genotyped 92 EASZ samples from Kenya (KEASZ) with more than 770,000 SNPs and sequenced the genome of a pool of 10 KEASZ. We observe an even admixed autosomal zebu × taurine genomic structure in the population. A total of 101 and 165 candidate regions of positive selection, based on genome-wide SNP analyses (meta-SS, Rsb, iHS, and ΔAF) and pooled heterozygosity (Hp) full genome sequence analysis, are identified, in which 35 regions are shared between them. A total of 142 functional variants, one novel, have been detected within these regions, in which 30 and 26 were classified as of zebu and African taurine origins, respectively. High density genome-wide SNP analysis of zebu × taurine admixed cattle populations from Uganda and Nigeria show that 25 of these regions are shared between KEASZ and Uganda cattle, and seven regions are shared across the KEASZ, Uganda, and Nigeria cattle. The identification of common candidate regions allows us to fine map 18 regions. These regions intersect with genes and QTL associated with reproduction and environmental stress (e.g., immunity and heat stress) suggesting that the genome of the zebu × taurine admixed cattle has been uniquely selected to maximize hybrid fitness both in terms of reproduction and survivability.
Collapse
Affiliation(s)
- Hussain Bahbahani
- Department of Biological Sciences, Faculty of Science, Kuwait UniversityKuwait, Kuwait
| | - Abdulfatai Tijjani
- School of Life Sciences, University of NottinghamNottingham, United Kingdom.,Centre for Genomics Research and Innovation, National Biotechnology Development AgencyAbuja, Nigeria
| | | | - David Wragg
- Centre for Tropical Livestock Genetics and Health, Roslin InstituteEdinburgh, United Kingdom
| | - Faisal Almathen
- Department of Veterinary Public Health and Animal Husbandry, College of Veterinary Medicine, King Faisal UniversityAl-Hasa, Saudi Arabia
| | - Oyekanmi Nash
- Centre for Genomics Research and Innovation, National Biotechnology Development AgencyAbuja, Nigeria
| | - Gerald N Akpa
- Department of Animal Science, Ahmadu Bello UniversityZaria, Nigeria
| | - Mary Mbole-Kariuki
- School of Life Sciences, University of NottinghamNottingham, United Kingdom
| | - Sunir Malla
- Deep Seq Department, University of NottinghamNottingham, United Kingdom
| | - Mark Woolhouse
- Ashworth Laboratories, Centre for Immunity, Infection and Evolution, University of EdinburghEdinburgh, United Kingdom
| | | | - Curtis Van Tassell
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research ServiceBeltsville, MD, United States
| | - Martin Blythe
- Deep Seq Department, University of NottinghamNottingham, United Kingdom
| | - Heather Huson
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research ServiceBeltsville, MD, United States
| | - Olivier Hanotte
- School of Life Sciences, University of NottinghamNottingham, United Kingdom.,International Livestock Research Institute (ILRI)Addis Ababa, Ethiopia
| |
Collapse
|
32
|
Ilboudo H, Noyes H, Mulindwa J, Kimuda MP, Koffi M, Kaboré JW, Ahouty B, Ngoyi DM, Fataki O, Simo G, Ofon E, Enyaru J, Chisi J, Kamoto K, Simuunza M, Alibu VP, Lejon V, Jamonneau V, Macleod A, Camara M, Bucheton B, Hertz-Fowler C, Sidibe I, Matovu E. Introducing the TrypanoGEN biobank: A valuable resource for the elimination of human African trypanosomiasis. PLoS Negl Trop Dis 2017; 11:e0005438. [PMID: 28570558 PMCID: PMC5453417 DOI: 10.1371/journal.pntd.0005438] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Hamidou Ilboudo
- Centre International de Recherche-Développement sur l’Elevage en zone Subhumide (CIRDES), Bobo-Dioulasso, Burkina Faso
| | - Harry Noyes
- Centre for Genomic Research, University of Liverpool, Liverpool, United Kingdom
| | - Julius Mulindwa
- College of Veterinary Medicine, Animal Resources and Bio-security, Makerere University, Kampala, Uganda
| | - Magambo Phillip Kimuda
- College of Veterinary Medicine, Animal Resources and Bio-security, Makerere University, Kampala, Uganda
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
| | - Mathurin Koffi
- Université Jean Lorougnon Guédé (UJLoG), Daloa, Côte d’Ivoire
| | - Justin Windingoudi Kaboré
- Centre International de Recherche-Développement sur l’Elevage en zone Subhumide (CIRDES), Bobo-Dioulasso, Burkina Faso
| | - Bernadin Ahouty
- Université Jean Lorougnon Guédé (UJLoG), Daloa, Côte d’Ivoire
| | | | - Olivier Fataki
- Institut National de Recherche Biomedicale, Kinshasa, Democratic Republic of Congo
| | - Gustave Simo
- Faculty of Science, University of Dschang, Dschang, Cameroon
| | - Elvis Ofon
- Faculty of Science, University of Dschang, Dschang, Cameroon
| | - John Enyaru
- College of Veterinary Medicine, Animal Resources and Bio-security, Makerere University, Kampala, Uganda
| | - John Chisi
- University of Malawi, College of Medicine, Department of Basic Medical Sciences, Blantyre, Malawi
| | - Kelita Kamoto
- University of Malawi, College of Medicine, Department of Basic Medical Sciences, Blantyre, Malawi
| | - Martin Simuunza
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Vincent P. Alibu
- College of Veterinary Medicine, Animal Resources and Bio-security, Makerere University, Kampala, Uganda
| | - Veerle Lejon
- Institut de Recherche pour le Développement (IRD), Montpellier, France
| | - Vincent Jamonneau
- Institut de Recherche pour le Développement (IRD), Montpellier, France
- Institut Pierre Richet, Bouaké, Côte d’Ivoire
| | - Annette Macleod
- Wellcome Trust Centre for Molecular Parasitology, University Place, Glasgow, United Kingdom
| | - Mamadou Camara
- Programme National de Lutte contre la Trypanosomose Humaine Africaine, Conakry, Guinea
| | - Bruno Bucheton
- Institut de Recherche pour le Développement (IRD), Montpellier, France
- Programme National de Lutte contre la Trypanosomose Humaine Africaine, Conakry, Guinea
| | | | - Issa Sidibe
- Centre International de Recherche-Développement sur l’Elevage en zone Subhumide (CIRDES), Bobo-Dioulasso, Burkina Faso
| | - Enock Matovu
- College of Veterinary Medicine, Animal Resources and Bio-security, Makerere University, Kampala, Uganda
- * E-mail:
| | | |
Collapse
|
33
|
Kim SJ, Ka S, Ha JW, Kim J, Yoo D, Kim K, Lee HK, Lim D, Cho S, Hanotte O, Mwai OA, Dessie T, Kemp S, Oh SJ, Kim H. Cattle genome-wide analysis reveals genetic signatures in trypanotolerant N'Dama. BMC Genomics 2017; 18:371. [PMID: 28499406 PMCID: PMC5427609 DOI: 10.1186/s12864-017-3742-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 04/27/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Indigenous cattle in Africa have adapted to various local environments to acquire superior phenotypes that enhance their survival under harsh conditions. While many studies investigated the adaptation of overall African cattle, genetic characteristics of each breed have been poorly studied. RESULTS We performed the comparative genome-wide analysis to assess evidence for subspeciation within species at the genetic level in trypanotolerant N'Dama cattle. We analysed genetic variation patterns in N'Dama from the genomes of 101 cattle breeds including 48 samples of five indigenous African cattle breeds and 53 samples of various commercial breeds. Analysis of SNP variances between cattle breeds using wMI, XP-CLR, and XP-EHH detected genes containing N'Dama-specific genetic variants and their potential associations. Functional annotation analysis revealed that these genes are associated with ossification, neurological and immune system. Particularly, the genes involved in bone formation indicate that local adaptation of N'Dama may engage in skeletal growth as well as immune systems. CONCLUSIONS Our results imply that N'Dama might have acquired distinct genotypes associated with growth and regulation of regional diseases including trypanosomiasis. Moreover, this study offers significant insights into identifying genetic signatures for natural and artificial selection of diverse African cattle breeds.
Collapse
Affiliation(s)
- Soo-Jin Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.,C&K Genomics, Seoul National University Research Park, Seoul, 151-919, Republic of Korea
| | - Sojeong Ka
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jung-Woo Ha
- Clova, NAVER Corp., Seongnam, 13561, Republic of Korea
| | - Jaemin Kim
- C&K Genomics, Seoul National University Research Park, Seoul, 151-919, Republic of Korea
| | - DongAhn Yoo
- C&K Genomics, Seoul National University Research Park, Seoul, 151-919, Republic of Korea.,Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Republic of Korea
| | - Kwondo Kim
- C&K Genomics, Seoul National University Research Park, Seoul, 151-919, Republic of Korea.,Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hak-Kyo Lee
- Department of Animal Biotechnology, Chonbuk National University, Jeonju, 66414, Republic of Korea
| | - Dajeong Lim
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, RDA, Jeonju, 55365, Republic of Korea
| | - Seoae Cho
- C&K Genomics, Seoul National University Research Park, Seoul, 151-919, Republic of Korea
| | - Olivier Hanotte
- University of Nottingham, School of Life Sciences, Nottingham, NG7 2RD, UK.,International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Okeyo Ally Mwai
- International Livestock Research Institute, Box 30709-00100, Nairobi, Kenya
| | - Tadelle Dessie
- International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Stephen Kemp
- International Livestock Research Institute, Box 30709-00100, Nairobi, Kenya.,The Centre for Tropical Livestock Genetics and Health, The Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh, Scotland, UK
| | - Sung Jong Oh
- National Institute of Animal Science, RDA, Wanju, 55365, Republic of Korea.
| | - Heebal Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea. .,C&K Genomics, Seoul National University Research Park, Seoul, 151-919, Republic of Korea. .,Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Republic of Korea.
| |
Collapse
|
34
|
Abstract
Infection is one of the leading causes of human mortality and morbidity. Exposure to microbial agents is obviously required. However, also non-microbial environmental and host factors play a key role in the onset, development and outcome of infectious disease, resulting in large of clinical variability between individuals in a population infected with the same microbe. Controlled and standardized investigations of the genetics of susceptibility to infectious disease are almost impossible to perform in humans whereas mouse models allow application of powerful genomic techniques to identify and validate causative genes underlying human diseases with complex etiologies. Most of current animal models used in complex traits diseases genetic mapping have limited genetic diversity. This limitation impedes the ability to create incorporated network using genetic interactions, epigenetics, environmental factors, microbiota, and other phenotypes. A novel mouse genetic reference population for high-resolution mapping and subsequently identifying genes underlying the QTL, namely the Collaborative Cross (CC) mouse genetic reference population (GRP) was recently developed. In this chapter, we discuss a variety of approaches using CC mice for mapping genes underlying quantitative trait loci (QTL) to dissect the host response to polygenic traits, including infectious disease caused by bacterial agents and its toxins.
Collapse
|
35
|
Álvarez I, Pérez-Pardal L, Traoré A, Fernández I, Goyache F. Lack of specific alleles for the bovine chemokine (C-X-C) receptor type 4 (CXCR4) gene in West African cattle questions its role as a candidate for trypanotolerance. INFECTION GENETICS AND EVOLUTION 2016; 42:30-3. [DOI: 10.1016/j.meegid.2016.04.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 04/06/2016] [Accepted: 04/22/2016] [Indexed: 01/11/2023]
|
36
|
Morrison LJ, Vezza L, Rowan T, Hope JC. Animal African Trypanosomiasis: Time to Increase Focus on Clinically Relevant Parasite and Host Species. Trends Parasitol 2016; 32:599-607. [PMID: 27167665 DOI: 10.1016/j.pt.2016.04.012] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 04/19/2016] [Accepted: 04/20/2016] [Indexed: 10/21/2022]
Abstract
Animal African trypanosomiasis (AAT), caused by Trypanosoma congolense and Trypanosoma vivax, remains one of the most important livestock diseases in sub-Saharan Africa, particularly affecting cattle. Despite this, our detailed knowledge largely stems from the human pathogen Trypanosoma brucei and mouse experimental models. In the postgenomic era, the genotypic and phenotypic differences between the AAT-relevant species of parasite or host and their model organism counterparts are increasingly apparent. Here, we outline the timeliness and advantages of increasing the research focus on both the clinically relevant parasite and host species, given that improved tools and resources for both have been developed in recent years. We propose that this shift of emphasis will improve our ability to efficiently develop tools to combat AAT.
Collapse
Affiliation(s)
- Liam J Morrison
- Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.
| | - Laura Vezza
- Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Tim Rowan
- GALVmed, Doherty Building, Pentlands Science Park, Bush Loan, Edinburgh, EH25 0PZ, UK
| | - Jayne C Hope
- Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| |
Collapse
|
37
|
Yaro M, Munyard KA, Stear MJ, Groth DM. Combatting African Animal Trypanosomiasis (AAT) in livestock: The potential role of trypanotolerance. Vet Parasitol 2016; 225:43-52. [PMID: 27369574 DOI: 10.1016/j.vetpar.2016.05.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 04/29/2016] [Accepted: 05/01/2016] [Indexed: 01/09/2023]
Abstract
African Animal Trypanosomiasis (AAT) is endemic in at least 37 of the 54 countries in Africa. It is estimated to cause direct and indirect losses to the livestock production industry in excess of US$ 4.5 billion per annum. A century of intervention has yielded limited success, owing largely to the extraordinary complexity of the host-parasite interaction. Trypanotolerance, which refers to the inherent ability of some African livestock breeds, notably Djallonke sheep, N'Dama cattle and West African Dwarf goats, to withstand a trypanosomiasis challenge and still remain productive without any form of therapy, is an economically sustainable option for combatting this disease. Yet trypanotolerance has not been adequately exploited in the fight against AAT. In this review, we describe new insights into the genetic basis of trypanotolerance and discuss the potential of exploring this phenomenon as an integral part of the solution for AAT, particularly, in the context of African animal production systems.
Collapse
Affiliation(s)
- M Yaro
- School of Biomedical Sciences, Curtin Health Innovation Research Institute, Faculty of Health Sciences, Curtin University, GPO Box U1987, Perth, WA 6845, Australia
| | - K A Munyard
- School of Biomedical Sciences, Curtin Health Innovation Research Institute, Faculty of Health Sciences, Curtin University, GPO Box U1987, Perth, WA 6845, Australia
| | - M J Stear
- Institute of Biodiversity, Animal Health and Comparative Medicine, Glasgow University, Garscube Estate, Bearsden Road, Glasgow G61 1QH, UK
| | - D M Groth
- School of Biomedical Sciences, Curtin Health Innovation Research Institute, Faculty of Health Sciences, Curtin University, GPO Box U1987, Perth, WA 6845, Australia.
| |
Collapse
|
38
|
Lipkin E, Strillacci MG, Eitam H, Yishay M, Schiavini F, Soller M, Bagnato A, Shabtay A. The Use of Kosher Phenotyping for Mapping QTL Affecting Susceptibility to Bovine Respiratory Disease. PLoS One 2016; 11:e0153423. [PMID: 27077383 PMCID: PMC4831767 DOI: 10.1371/journal.pone.0153423] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 03/29/2016] [Indexed: 02/06/2023] Open
Abstract
Bovine respiratory disease (BRD) is the leading cause of morbidity and mortality in feedlot cattle, caused by multiple pathogens that become more virulent in response to stress. As clinical signs often go undetected and various preventive strategies failed, identification of genes affecting BRD is essential for selection for resistance. Selective DNA pooling (SDP) was applied in a genome wide association study (GWAS) to map BRD QTLs in Israeli Holstein male calves. Kosher scoring of lung adhesions was used to allocate 122 and 62 animals to High (Glatt Kosher) and Low (Non-Kosher) resistant groups, respectively. Genotyping was performed using the Illumina BovineHD BeadChip according to the Infinium protocol. Moving average of -logP was used to map QTLs and Log drop was used to define their boundaries (QTLRs). The combined procedure was efficient for high resolution mapping. Nineteen QTLRs distributed over 13 autosomes were found, some overlapping previous studies. The QTLRs contain polymorphic functional and expression candidate genes to affect kosher status, with putative immunological and wound healing activities. Kosher phenotyping was shown to be a reliable means to map QTLs affecting BRD morbidity.
Collapse
Affiliation(s)
- Ehud Lipkin
- Department of Genetics, Hebrew University of Jerusalem, Jerusalem, Israel
| | | | - Harel Eitam
- Department of Ruminant Sciences, Agricultural Research Organization (ARO), Bet-Dagan, Israel
| | - Moran Yishay
- Department of Ruminant Sciences, Agricultural Research Organization (ARO), Bet-Dagan, Israel
| | | | - Morris Soller
- Department of Genetics, Hebrew University of Jerusalem, Jerusalem, Israel
| | | | - Ariel Shabtay
- Department of Ruminant Sciences, Agricultural Research Organization (ARO), Bet-Dagan, Israel
| |
Collapse
|
39
|
Yaro M, Munyard KA, Stear MJ, Groth DM. Molecular identification of livestock breeds: a tool for modern conservation biology. Biol Rev Camb Philos Soc 2016; 92:993-1010. [DOI: 10.1111/brv.12265] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 02/14/2016] [Accepted: 02/18/2016] [Indexed: 12/22/2022]
Affiliation(s)
- Mohammed Yaro
- School of Biomedical Sciences, CHIRI Biosciences Research Precinct, Faculty of Health Sciences; Curtin University; GPO Box U1987 Perth WA 6845 Australia
| | - Kylie A. Munyard
- School of Biomedical Sciences, CHIRI Biosciences Research Precinct, Faculty of Health Sciences; Curtin University; GPO Box U1987 Perth WA 6845 Australia
| | - Michael J. Stear
- Institute of Biodiversity, Animal Health and Comparative Medicine; University of Glasgow; Bearsden Road Glasgow G61 1QH U.K
| | - David M. Groth
- School of Biomedical Sciences, CHIRI Biosciences Research Precinct, Faculty of Health Sciences; Curtin University; GPO Box U1987 Perth WA 6845 Australia
| |
Collapse
|
40
|
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
| |
Collapse
|
41
|
Berthier D, Brenière SF, Bras-Gonçalves R, Lemesre JL, Jamonneau V, Solano P, Lejon V, Thévenon S, Bucheton B. Tolerance to Trypanosomatids: A Threat, or a Key for Disease Elimination? Trends Parasitol 2015; 32:157-168. [PMID: 26643519 DOI: 10.1016/j.pt.2015.11.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 10/20/2015] [Accepted: 11/03/2015] [Indexed: 12/20/2022]
Abstract
So far, research on trypanosomatid infections has been driven by 'disease by disease' approaches, leading to different concepts and control strategies. It is, however, increasingly clear that they share common features such as the ability to generate long-lasting asymptomatic infections in their mammalian hosts. Trypanotolerance, long integrated in animal African trypanosomiasis control, historically refers to the ability of cattle breeds to limit Trypanosoma infection and pathology, but has only recently been recognized in humans. Whilst trypanotolerance is absent from the vocabulary on leishmaniasis and Chagas disease, asymptomatic infections also occur. We review the concept of trypanotolerance across the trypanosomatids and discuss the importance of asymptomatic carriage in the current context of elimination.
Collapse
Affiliation(s)
| | | | | | | | - Vincent Jamonneau
- CIRDES Bobo-Dioulasso 01 BP 454, Burkina Faso; IPR, 01 BP 1500 Bouaké 01, Côte d'Ivoire
| | | | - Veerle Lejon
- IRD, UMR INTERTRYP, Montpellier Cedex 5, 34398 France
| | | | - Bruno Bucheton
- IRD, UMR INTERTRYP, Montpellier Cedex 5, 34398 France; PNLTHA, Ministère de la Santé, BP 851 Conakry, République de Guinée
| |
Collapse
|
42
|
Álvarez I, Pérez-Pardal L, Traoré A, Fernández I, Goyache F. African Cattle do not Carry Unique Mutations on the Exon 9 of the ARHGAP15 Gene. Anim Biotechnol 2015; 27:9-12. [DOI: 10.1080/10495398.2015.1053606] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
43
|
Álvarez I, Pérez-Pardal L, Traoré A, Fernández I, Goyache F. Lack of haplotype structuring for two candidate genes for trypanotolerance in cattle. J Anim Breed Genet 2015; 133:105-14. [DOI: 10.1111/jbg.12181] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 06/24/2015] [Indexed: 01/22/2023]
Affiliation(s)
- I. Álvarez
- Área de Genética y Reproducción Animal; SERIDA; Gijón Spain
| | - L. Pérez-Pardal
- CIBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos; Universidade do Porto; Vairão Portugal
| | | | - I. Fernández
- Área de Genética y Reproducción Animal; SERIDA; Gijón Spain
| | - F. Goyache
- Área de Genética y Reproducción Animal; SERIDA; Gijón Spain
| |
Collapse
|
44
|
Mwai O, Hanotte O, Kwon YJ, Cho S. African Indigenous Cattle: Unique Genetic Resources in a Rapidly Changing World. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2015; 28:911-21. [PMID: 26104394 PMCID: PMC4478499 DOI: 10.5713/ajas.15.0002r] [Citation(s) in RCA: 134] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
At least 150 indigenous African cattle breeds have been named, but the majority of African cattle populations remain largely uncharacterized. As cattle breeds and populations in Africa adapted to various local environmental conditions, they acquired unique features. We know now that the history of African cattle was particularly complex and while several of its episodes remain debated, there is no doubt that African cattle population evolved dramatically over time. Today, we find a mosaic of genetically diverse population from the purest Bos taurus to the nearly pure Bos indicus. African cattle are now found all across the continent, with the exception of the Sahara and the river Congo basin. They are found on the rift valley highlands as well as below sea level in the Afar depression. These unique livestock genetic resources are in danger to disappear rapidly following uncontrolled crossbreeding and breed replacements with exotic breeds. Breeding improvement programs of African indigenous livestock remain too few while paradoxically the demand of livestock products is continually increasing. Many African indigenous breeds are endangered now, and their unique adaptive traits may be lost forever. This paper reviews the unique known characteristics of indigenous African cattle populations while describing the opportunities, the necessity and urgency to understand and utilize these resources to respond to the needs of the people of the continent and to the benefit of African farmers.
Collapse
Affiliation(s)
- Okeyo Mwai
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Olivier Hanotte
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Young-Jun Kwon
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-742, Korea
| | - Seoae Cho
- CHO&KIM genomics, Seoul 151-919, Korea
| |
Collapse
|
45
|
Smetko A, Soudre A, Silbermayr K, Müller S, Brem G, Hanotte O, Boettcher PJ, Stella A, Mészáros G, Wurzinger M, Curik I, Müller M, Burgstaller J, Sölkner J. Trypanosomosis: potential driver of selection in African cattle. Front Genet 2015; 6:137. [PMID: 25964796 PMCID: PMC4404968 DOI: 10.3389/fgene.2015.00137] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Accepted: 03/22/2015] [Indexed: 01/21/2023] Open
Abstract
Trypanosomosis is a serious cause of reduction in productivity of cattle in tsetse-fly infested areas. Baoule and other local Taurine cattle breeds in Burkina Faso are trypanotolerant. Zebuine cattle, which are also kept there are susceptible to trypanosomosis but bigger in body size. Farmers have continuously been intercrossing Baoule and Zebu animals to increase production and disease tolerance. The aim of this study was to compare levels of zebuine and taurine admixture in genomic regions potentially involved in trypanotolerance with background admixture of composites to identify differences in allelic frequencies of tolerant and non-tolerant animals. The study was conducted on 214 animals (90 Baoule, 90 Zebu, and 34 composites), genotyped with 25 microsatellites across the genome and with 155 SNPs in 23 candidate regions. Degrees of admixture of composites were analyzed for microsatellite and SNP data separately. Average Baoule admixture based on microsatellites across the genomes of the Baoule- Zebu composites was 0.31, which was smaller than the average Baoule admixture in the trypanosomosis candidate regions of 0.37 (P = 0.15). Fixation index FST measured in the overall genome based on microsatellites or with SNPs from candidate regions indicates strong differentiation between breeds. Nine out of 23 regions had FST ≥ 0.20 calculated from haplotypes or individual SNPs. The levels of admixture were significantly different from background admixture, as revealed by microsatellite data, for six out of the nine regions. Five out of the six regions showed an excess of Baoule ancestry. Information about best levels of breed composition would be useful for future breeding ctivities, aiming at trypanotolerant animals with higher productive capacity.
Collapse
Affiliation(s)
- Anamarija Smetko
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, BOKU-University of Natural Resources and Life Sciences Vienna Vienna, Austria ; Croatian Agricultural Agency Zagreb, Croatia
| | - Albert Soudre
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, BOKU-University of Natural Resources and Life Sciences Vienna Vienna, Austria ; Ecole Normale Supérieure, Université de Koudougou Koudougou, Burkina Faso
| | - Katja Silbermayr
- Institute of Parasitology, University of Veterinary Medicine Vienna, Austria
| | - Simone Müller
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Austria
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Austria
| | - Olivier Hanotte
- School of Life Sciences, University of Nottingham Nottingham, UK
| | - Paul J Boettcher
- Animal Production and Health Division, Agriculture and Consumer Protection Department, Food and Agriculture Organization of the United Nations Rome, Italy ; FAO/IAEA Joint Division on Nuclear Techniques in Food and Agriculture Vienna, Austria
| | | | - Gábor Mészáros
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, BOKU-University of Natural Resources and Life Sciences Vienna Vienna, Austria
| | - Maria Wurzinger
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, BOKU-University of Natural Resources and Life Sciences Vienna Vienna, Austria
| | - Ino Curik
- Faculty of Agriculture, University of Zagreb Zagreb, Croatia
| | - Mathias Müller
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Austria
| | - Jörg Burgstaller
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Austria ; Biotechnology in Animal Production, Department for Agrobiotechnology, IFA Tulln Tulln, Austria
| | - Johann Sölkner
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, BOKU-University of Natural Resources and Life Sciences Vienna Vienna, Austria
| |
Collapse
|
46
|
Abstract
I became enamored of genetics at an early age. The desire to participate in the rebuilding of my people in our ancient homeland led to dairy science at Rutgers University, to Animal Breeding Plans by J.L. Lush, and to the realization that I could combine genetics and dairy science in animal breeding. It is to my mother-in-law that I owe the felicitous phrasing of the titular scientific question that has occupied my professional life: If a bull were a cow, how much milk would he give? Following my PhD (in 1956), I joined the Volcani Institute in Israel and, later (in 1972), the Applied Genetics group at the Hebrew University. The Applied Genetics group had an active marker lab, and this and a paper by Spickett & Thoday led me to explore genetic markers for quantitative trait loci mapping and marker-assisted selection. A chance encounter with Jacques Beckmann in 1980 opened my eyes to the potential of DNA-level markers for these purposes, and the rest followed.
Collapse
Affiliation(s)
- Morris Soller
- Department of Genetics, The Silberman Life Sciences Institute, Edmund Safra Campus, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| |
Collapse
|
47
|
Zavarez LB, Utsunomiya YT, Carmo AS, Neves HHR, Carvalheiro R, Ferenčaković M, Pérez O'Brien AM, Curik I, Cole JB, Van Tassell CP, da Silva MVGB, Sonstegard TS, Sölkner J, Garcia JF. Assessment of autozygosity in Nellore cows (Bos indicus) through high-density SNP genotypes. Front Genet 2015; 6:5. [PMID: 25688258 PMCID: PMC4310349 DOI: 10.3389/fgene.2015.00005] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 01/07/2015] [Indexed: 11/18/2022] Open
Abstract
The use of relatively low numbers of sires in cattle breeding programs, particularly on those for carcass and weight traits in Nellore beef cattle (Bos indicus) in Brazil, has always raised concerns about inbreeding, which affects conservation of genetic resources and sustainability of this breed. Here, we investigated the distribution of autozygosity levels based on runs of homozygosity (ROH) in a sample of 1,278 Nellore cows, genotyped for over 777,000 SNPs. We found ROH segments larger than 10 Mb in over 70% of the samples, representing signatures most likely related to the recent massive use of few sires. However, the average genome coverage by ROH (>1 Mb) was lower than previously reported for other cattle breeds (4.58%). In spite of 99.98% of the SNPs being included within a ROH in at least one individual, only 19.37% of the markers were encompassed by common ROH, suggesting that the ongoing selection for weight, carcass and reproductive traits in this population is too recent to have produced selection signatures in the form of ROH. Three short-range highly prevalent ROH autosomal hotspots (occurring in over 50% of the samples) were observed, indicating candidate regions most likely under selection since before the foundation of Brazilian Nellore cattle. The putative signatures of selection on chromosomes 4, 7, and 12 may be involved in resistance to infectious diseases and fertility, and should be subject of future investigation.
Collapse
Affiliation(s)
- Ludmilla B Zavarez
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista Jaboticabal, São Paulo, Brazil
| | - Yuri T Utsunomiya
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista Jaboticabal, São Paulo, Brazil
| | - Adriana S Carmo
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista Jaboticabal, São Paulo, Brazil
| | - Haroldo H R Neves
- GenSys Consultores Associados Porto Alegre, Rio Grande do Sul, Brazil ; Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista Jaboticabal, São Paulo, Brazil
| | - Roberto Carvalheiro
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista Jaboticabal, São Paulo, Brazil
| | - Maja Ferenčaković
- Department of Animal Science, Faculty of Agriculture, University of Zagreb Zagreb, Croatia
| | - Ana M Pérez O'Brien
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, BOKU - University of Natural Resources and Life Sciences Vienna, Austria
| | - Ino Curik
- Department of Animal Science, Faculty of Agriculture, University of Zagreb Zagreb, Croatia
| | - John B Cole
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research Service Beltsville, MD, USA
| | - Curtis P Van Tassell
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research Service Beltsville, MD, USA
| | - Marcos V G B da Silva
- Bioinformatics and Animal Genomics Laboratory, Embrapa Dairy Cattle Juiz de Fora, Minas Gerais, Brazil
| | - Tad S Sonstegard
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research Service Beltsville, MD, USA
| | - Johann Sölkner
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, BOKU - University of Natural Resources and Life Sciences Vienna, Austria
| | - José F Garcia
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista Jaboticabal, São Paulo, Brazil ; Laboratório de Bioquímica e Biologia Molecular Animal, Departamento de Apoio, Produção e Saúde Animal, Faculdade de Medicina Veterinária de Araçatuba, UNESP - Univ Estadual Paulista Araçatuba, São Paulo, Brazil
| |
Collapse
|
48
|
Ilboudo H, Bras-Gonçalves R, Camara M, Flori L, Camara O, Sakande H, Leno M, Petitdidier E, Jamonneau V, Bucheton B. Unravelling human trypanotolerance: IL8 is associated with infection control whereas IL10 and TNFα are associated with subsequent disease development. PLoS Pathog 2014; 10:e1004469. [PMID: 25375156 PMCID: PMC4223068 DOI: 10.1371/journal.ppat.1004469] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2014] [Accepted: 09/13/2014] [Indexed: 01/20/2023] Open
Abstract
In West Africa, Trypanosoma brucei gambiense, causing human African trypanosomiasis (HAT), is associated with a great diversity of infection outcomes. In addition to patients who can be diagnosed in the early hemolymphatic phase (stage 1) or meningoencephalitic phase (stage 2), a number of individuals can mount long-lasting specific serological responses while the results of microscopic investigations are negative (SERO TL+). Evidence is now increasing to indicate that these are asymptomatic subjects with low-grade parasitemia. The goal of our study was to investigate the type of immune response occurring in these “trypanotolerant” subjects. Cytokines levels were measured in healthy endemic controls (n = 40), stage 1 (n = 10), early stage 2 (n = 19), and late stage 2 patients (n = 23) and in a cohort of SERO TL+ individuals (n = 60) who were followed up for two years to assess the evolution of their parasitological and serological status. In contrast to HAT patients which T-cell responses appeared to be activated with increased levels of IL2, IL4, and IL10, SERO TL+ exhibited high levels of proinflammatory cytokines (IL6, IL8 and TNFα) and an almost absence of IL12p70. In SERO TL+, high levels of IL10 and low levels of TNFα were associated with an increased risk of developing HAT whereas high levels of IL8 predicted that serology would become negative. Further studies using high throughput technologies, hopefully will provide a more detailed view of the critical molecules or pathways underlying the trypanotolerant phenotype. Whereas immunological mechanisms involved in the control of trypanosome infections have been extensively studied in animal models, knowledge of how Trypanosoma brucei gambiense interacts with its human hosts lags far behind. In this study we measured cytokine levels in sleeping sickness patients and individuals who were apparently able to control infection to subdetection levels over long periods of time or who were engaged in a process of self-cure as demonstrated by the disappearance of specific antibodies. In contrast to patients, trypanotolerant subjects were characterized by a strong inflammatory response with elevated levels of IL8, IL6, and TNFα. This study indicates that both protective immune responses and markers of disease development exist in human T. brucei. gambiense infection and constitute an important step forward to identify new diagnostic or therapeutic targets in the fight against sleeping sickness.
Collapse
Affiliation(s)
- Hamidou Ilboudo
- Centre International de Recherche-Développement sur l'Elevage en zones Subhumides (CIRDES), Unité de Recherches sur les Bases Biologiques de la Lutte Intégrée, Bobo-Dioulasso, Burkina Faso
| | - Rachel Bras-Gonçalves
- Institut de Recherche pour le Développement (IRD), UMR IRD-CIRAD 177 INTERTRYP, Campus International de Baillarguet, Montpellier, France
| | - Mamadou Camara
- Ministère de la Santé et de l'Hygiène Publique, Programme National de Lutte contre la Trypanosomose Humaine Africaine, Conakry, Guinée
| | - Laurence Flori
- Centre de coopération Internationale en Recherche Agronomique pour le développement (CIRAD), UMR IRD-CIRAD 177 INTERTRYP, Campus International de Baillarguet, Montpellier, France
- Institut National de la Recherche Agronomique (INRA), UMR 1313 GABI, F78350 Jouy-en-Josas, France
| | - Oumou Camara
- Ministère de la Santé et de l'Hygiène Publique, Programme National de Lutte contre la Trypanosomose Humaine Africaine, Conakry, Guinée
| | - Hassane Sakande
- Centre International de Recherche-Développement sur l'Elevage en zones Subhumides (CIRDES), Unité de Recherches sur les Bases Biologiques de la Lutte Intégrée, Bobo-Dioulasso, Burkina Faso
| | - Mamadou Leno
- Ministère de la Santé et de l'Hygiène Publique, Programme National de Lutte contre la Trypanosomose Humaine Africaine, Conakry, Guinée
| | - Elodie Petitdidier
- Institut de Recherche pour le Développement (IRD), UMR IRD-CIRAD 177 INTERTRYP, Campus International de Baillarguet, Montpellier, France
| | - Vincent Jamonneau
- Centre International de Recherche-Développement sur l'Elevage en zones Subhumides (CIRDES), Unité de Recherches sur les Bases Biologiques de la Lutte Intégrée, Bobo-Dioulasso, Burkina Faso
- Institut de Recherche pour le Développement (IRD), UMR IRD-CIRAD 177 INTERTRYP, Campus International de Baillarguet, Montpellier, France
| | - Bruno Bucheton
- Institut de Recherche pour le Développement (IRD), UMR IRD-CIRAD 177 INTERTRYP, Campus International de Baillarguet, Montpellier, France
- Ministère de la Santé et de l'Hygiène Publique, Programme National de Lutte contre la Trypanosomose Humaine Africaine, Conakry, Guinée
- * E-mail:
| |
Collapse
|
49
|
Wu Y, Fan H, Wang Y, Zhang L, Gao X, Chen Y, Li J, Ren H, Gao H. Genome-wide association studies using haplotypes and individual SNPs in Simmental cattle. PLoS One 2014; 9:e109330. [PMID: 25330174 PMCID: PMC4203724 DOI: 10.1371/journal.pone.0109330] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 09/10/2014] [Indexed: 01/05/2023] Open
Abstract
Recent advances in high-throughput genotyping technologies have provided the opportunity to map genes using associations between complex traits and markers. Genome-wide association studies (GWAS) based on either a single marker or haplotype have identified genetic variants and underlying genetic mechanisms of quantitative traits. Prompted by the achievements of studies examining economic traits in cattle and to verify the consistency of these two methods using real data, the current study was conducted to construct the haplotype structure in the bovine genome and to detect relevant genes genuinely affecting a carcass trait and a meat quality trait. Using the Illumina BovineHD BeadChip, 942 young bulls with genotyping data were introduced as a reference population to identify the genes in the beef cattle genome significantly associated with foreshank weight and triglyceride levels. In total, 92,553 haplotype blocks were detected in the genome. The regions of high linkage disequilibrium extended up to approximately 200 kb, and the size of haplotype blocks ranged from 22 bp to 199,266 bp. Additionally, the individual SNP analysis and the haplotype-based analysis detected similar regions and common SNPs for these two representative traits. A total of 12 and 7 SNPs in the bovine genome were significantly associated with foreshank weight and triglyceride levels, respectively. By comparison, 4 and 5 haplotype blocks containing the majority of significant SNPs were strongly associated with foreshank weight and triglyceride levels, respectively. In addition, 36 SNPs with high linkage disequilibrium were detected in the GNAQ gene, a potential hotspot that may play a crucial role for regulating carcass trait components.
Collapse
Affiliation(s)
- Yang Wu
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China
| | - Huizhong Fan
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China
| | - Yanhui Wang
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China
| | - Lupei Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China
| | - Xue Gao
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China
| | - Yan Chen
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China
| | - Junya Li
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China
| | - HongYan Ren
- Department of life sciences, National Natural Science Foundation of China, Beijing, China
- * E-mail: (HG); (HR)
| | - Huijiang Gao
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China
- * E-mail: (HG); (HR)
| |
Collapse
|
50
|
La Greca F, Haynes C, Stijlemans B, De Trez C, Magez S. Antibody-mediated control of Trypanosoma vivax infection fails in the absence of tumour necrosis factor. Parasite Immunol 2014; 36:271-6. [PMID: 24697754 DOI: 10.1111/pim.12106] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 02/17/2014] [Indexed: 11/28/2022]
Abstract
Trypanosoma vivax causes a wasting disease affecting livestock breeding and agriculture in developing countries of sub-Sahara Africa and South America. Being an extracellular parasite, control of T. vivax has been proposed to be mediated by host antibodies. However, the use of a comparative infection model of wild-type (WT) and tumour necrosis factor (TNF) knockout (TNF(-/-) ) mice shows that the latter is unable to control first-peak parasitaemia, despite the presence of specific antitrypanosome antibodies. In contrast, WT mice parasitaemia peak control coincides with a combined early onset of TNF production and induction of specific antibodies. TNF is mainly produced by liver-associated monocytes and neutrophils. In this study, no other correlation between cellular immunomodulations and peak parasitaemia control was observed, underscoring the importance of the role of TNF in the control of T. vivax infections.
Collapse
Affiliation(s)
- F La Greca
- Research Unit of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium; Department of Structural Biology Brussels, VIB, Brussels, Belgium
| | | | | | | | | |
Collapse
|