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Sarviaho K, Uimari P, Martikainen K. Signatures of positive selection after the introduction of genomic selection in the Finnish Ayrshire population. J Dairy Sci 2024:S0022-0302(24)00548-4. [PMID: 38490540 DOI: 10.3168/jds.2024-24105] [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: 08/21/2023] [Accepted: 02/15/2024] [Indexed: 03/17/2024]
Abstract
The Finnish Ayrshire (FAY) belongs to the Nordic Red breeds and is characterized by high milk yield, high milk components, good fertility, and functional conformation. The FAY breeding program is based on genomic selection. Despite the benefits of selection on breeding values, autozygosity in the genome may increase due to selection, and increased autozygosity may cause inbreeding depression in selected traits. However, there is lack of studies concerning selection signatures in the FAY after genomic selection introduction. The aim of this study was to identify signatures of selection in FAY after the introduction of genomic selection. Genomic data included 45,834 SNPs. The genotyped animals were divided into 2 groups: animals born before genomic selection introduction (6,108 cows) and animals born after genomic selection introduction (47,361 cows). We identified the selection signatures using 3 complementary methods: 2 based on identification of selection signatures from runs of homozygosity (ROH) islands and one based on the decay of site-specific extended haplotype between populations at SNP sites (Rsb). In total, we identified 34 ROH islands on chromosomes 1, 3, 6, 8, 12-15, 17, 19, 22, and 26 in FAY animals born before genomic selection (between 1980 and 2011) and 30 ROH islands on chromosomes 1-3, 13-17, 22, and 25-26 in FAY animals born after genomic selection introduction (between 2015 and 2020). We additionally detected 22 ΔROH islands on chromosomes 2-3, 11, 13, 14, 16, 18, 20, and 25-26. Finally, a total of 31 Rsb regions on chromosomes 2, 3, 14, 18, 20, and 25 were identified. Based on the results, genomic selection has favored certain alleles and haplotypes on genomic regions related to traits relevant in the FAY breeding program: milk production, fertility, growth, beef production traits, and feed efficiency. Several genes related to these traits, e.g., PLA2G4A, MECR, CHUK, COX15, RICTOR, SHISA9, and SEMA4G overlapped or partially overlapped the observed selection signature regions. The association of genotypes within these regions and their effects on traits relevant in the FAY breeding program should be studied and genetic regions undergoing selection monitored in the FAY population.
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Affiliation(s)
- Katri Sarviaho
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland.
| | - Pekka Uimari
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Katja Martikainen
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
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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.
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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
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Masembe C, Benda KK, Opoola O, Francis MJ, Ndinawe RP, Beine P, Mukiibi R. A case of forensic genomics in Uganda reveals animal ownership and low exotic genetic introgression in indigenous cattle. Vet Med Sci 2023; 9:2844-2851. [PMID: 37725326 PMCID: PMC10650367 DOI: 10.1002/vms3.1272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 08/30/2023] [Accepted: 09/05/2023] [Indexed: 09/21/2023] Open
Abstract
BACKGROUND The cattle industry contributes to Uganda's agricultural output. It faces challenges that include theft and parentage ascertainment. These challenges can benefit from recent molecular genomics and bioinformatics technologies. OBJECTIVES We employed genomic analyses to establish potential ownership of a group of nine cattle that were being claimed by two farmers in Uganda. We investigated the genetic relationship of Ugandan cattle with regional indigenous breeds as well as exotic breeds that are currently present in Uganda. In addition, we investigated regions that are likely to be under selection in the Ugandan cattle. METHODS Hair samples were collected from seven and two animals from farmers A and B, respectively. They were genotyped for 53,218 Single Nucleotide Polymorphism markers. To establish genetic relationships between the sampled animals, we performed genomic analyses including, principal component analysis (PCA), hierarchical clustering analysis and identity by state/descent. We also performed admixture and runs of homozygosity analyses to assess the ancestry composition and identify regions potentially under selection in Ugandan cattle, respectively. RESULTS The seven animals from Farmer A were genetically close to each other but showed minimal relationship with the disputed animals. The two animals from Farmer B were genetically distant from each other but showed greater similarity to four of the disputed animals. Four of the disputed animals showed great dissimilarity from the animals of both farmers. Comparison of these with the reference breeds revealed minimal European exotic genetic introgression into these animals, but rather high similarity to the Sheko. Results also revealed high homozygosity in the major histocompatibility complex regions. CONCLUSIONS Our results demonstrate the use of currently available genomic tools to empirically establish the ownership of cattle; these could be scaled up as a resourceful and viable tool that could be employed to support conflict resolution where reliable livestock identification is unavailable.
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Affiliation(s)
- Charles Masembe
- Department of Zoology, Entomology and Fisheries Sciences, College of Natural SciencesMakerere UniversityKampalaUganda
| | - Kirungi Katali Benda
- Department of Zoology, Entomology and Fisheries Sciences, College of Natural SciencesMakerere UniversityKampalaUganda
- National Animal Genetics Resources Centre and Data Bank (NAGRC&DB)EntebbeUganda
| | - Oluyinka Opoola
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of EdinburghEdinburghUK
- Centre for Tropical Livestock Genetics and Health (CTLGH)University of EdinburghEdinburghUK
| | - Mayega Johnson Francis
- Department of Zoology, Entomology and Fisheries Sciences, College of Natural SciencesMakerere UniversityKampalaUganda
| | - Ruth Pamela Ndinawe
- National Animal Genetics Resources Centre and Data Bank (NAGRC&DB)EntebbeUganda
| | - Peter Beine
- National Animal Genetics Resources Centre and Data Bank (NAGRC&DB)EntebbeUganda
| | - Robert Mukiibi
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of EdinburghEdinburghUK
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Ahlawat S, Choudhary V, Arora R, Kumar A, Kaur M, Chhabra P. Exploring the Transcriptome Dynamics of In Vivo Theileria annulata Infection in Crossbred Cattle. Genes (Basel) 2023; 14:1663. [PMID: 37761803 PMCID: PMC10530335 DOI: 10.3390/genes14091663] [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: 12/08/2022] [Revised: 12/20/2022] [Accepted: 12/27/2022] [Indexed: 09/29/2023] Open
Abstract
The molecular changes occurring in the host in response to in vivo Theileria annulata parasitic infection are not well understood. Therefore, the present study investigated the differential expression profiles of peripheral blood mononuclear cells (PBMCs) across Theileria annulata-infected and non-infected crossbred cows. The differential expression profiles from PBMCs of infected and non-infected crossbred cows were generated by RNA sequencing. A marked difference in the expression of genes associated with innate immunity (FTH1, ACTB, ISG15) was observed between the two groups. The over-represented pathways in Theileria annulata-infected cows were associated with the immune system and regulation of the mitotic cycle. Enriched genes and pathways in non-infected animals were associated with the maintenance of chromatin integrity and cell structure. The highly connected genes identified in this study form potential candidates for further investigation into host-parasite interactions in cattle. An improved understanding of the transcriptomic dynamics during theileriosis would lead to underpinning molecular level differences related to the health status of cattle.
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Affiliation(s)
- Sonika Ahlawat
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - Vikas Choudhary
- Department of Animal Husbandry and Dairying, Karnal 132001, Haryana, India
| | - Reena Arora
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - Ashish Kumar
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - Mandeep Kaur
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - Pooja Chhabra
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
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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.
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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
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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.
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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
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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.
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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.)
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Comparative Investigation of Gene Regulatory Processes Underlying Avian Influenza Viruses in Chicken and Duck. BIOLOGY 2022; 11:biology11020219. [PMID: 35205087 PMCID: PMC8868632 DOI: 10.3390/biology11020219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 01/07/2022] [Accepted: 01/25/2022] [Indexed: 11/30/2022]
Abstract
Simple Summary Avian influenza poses a great risk to gallinaceous poultry, while mallard ducks can withstand most virus strains. To date, the mechanisms underlying the susceptibility of chicken and the effective immune response of duck have not been completely understood. In this study, our aim is to investigate the transcriptional gene regulation governing the expression of important avian-influenza-induced genes and to reveal the master regulators stimulating an effective immune response after virus infection in ducks while dysfunctioning in chicken. Abstract The avian influenza virus (AIV) mainly affects birds and not only causes animals’ deaths, but also poses a great risk of zoonotically infecting humans. While ducks and wild waterfowl are seen as a natural reservoir for AIVs and can withstand most virus strains, chicken mostly succumb to infection with high pathogenic avian influenza (HPAI). To date, the mechanisms underlying the susceptibility of chicken and the effective immune response of duck have not been completely unraveled. In this study, we investigate the transcriptional gene regulation underlying disease progression in chicken and duck after AIV infection. For this purpose, we use a publicly available RNA-sequencing dataset from chicken and ducks infected with low-pathogenic avian influenza (LPAI) H5N2 and HPAI H5N1 (lung and ileum tissues, 1 and 3 days post-infection). Unlike previous studies, we performed a promoter analysis based on orthologous genes to detect important transcription factors (TFs) and their cooperation, based on which we apply a systems biology approach to identify common and species-specific master regulators. We found master regulators such as EGR1, FOS, and SP1, specifically for chicken and ETS1 and SMAD3/4, specifically for duck, which could be responsible for the duck’s effective and the chicken’s ineffective immune response.
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MIDESP: Mutual Information-Based Detection of Epistatic SNP Pairs for Qualitative and Quantitative Phenotypes. BIOLOGY 2021; 10:biology10090921. [PMID: 34571798 PMCID: PMC8469369 DOI: 10.3390/biology10090921] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/09/2021] [Accepted: 09/13/2021] [Indexed: 11/17/2022]
Abstract
Simple Summary The interactions between SNPs, which are known as epistasis, can strongly influence the phenotype. Their detection is still a challenge, which is made even more difficult through the existence of background associations that can hide correct epistatic interactions. To address the limitations of existing methods, we present in this study our novel method MIDESP for the detection of epistatic SNP pairs. It is the first mutual information-based method that can be applied to both qualitative and quantitative phenotypes and which explicitly accounts for background associations in the dataset. Abstract The interactions between SNPs result in a complex interplay with the phenotype, known as epistasis. The knowledge of epistasis is a crucial part of understanding genetic causes of complex traits. However, due to the enormous number of SNP pairs and their complex relationship to the phenotype, identification still remains a challenging problem. Many approaches for the detection of epistasis have been developed using mutual information (MI) as an association measure. However, these methods have mainly been restricted to case–control phenotypes and are therefore of limited applicability for quantitative traits. To overcome this limitation of MI-based methods, here, we present an MI-based novel algorithm, MIDESP, to detect epistasis between SNPs for qualitative as well as quantitative phenotypes. Moreover, by incorporating a dataset-dependent correction technique, we deal with the effect of background associations in a genotypic dataset to separate correct epistatic interaction signals from those of false positive interactions resulting from the effect of single SNP×phenotype associations. To demonstrate the effectiveness of MIDESP, we apply it on two real datasets with qualitative and quantitative phenotypes, respectively. Our results suggest that by eliminating the background associations, MIDESP can identify important genes, which play essential roles for bovine tuberculosis or the egg weight of chickens.
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Tarekegn GM, Khayatzadeh N, Liu B, Osama S, Haile A, Rischkowsky B, Zhang W, Tesfaye K, Dessie T, Mwai OA, Djikeng A, Mwacharo JM. Ethiopian indigenous goats offer insights into past and recent demographic dynamics and local adaptation in sub-Saharan African goats. Evol Appl 2021; 14:1716-1731. [PMID: 34295359 PMCID: PMC8287980 DOI: 10.1111/eva.13118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 07/15/2020] [Accepted: 08/13/2020] [Indexed: 12/13/2022] Open
Abstract
Knowledge on how adaptive evolution and human socio-cultural and economic interests shaped livestock genomes particularly in sub-Saharan Africa remains limited. Ethiopia is in a geographic region that has been critical in the history of African agriculture with ancient and diverse human ethnicity and bio-climatic conditions. Using 52K genome-wide data analysed in 646 individuals from 13 Ethiopian indigenous goat populations, we observed high levels of genetic variation. Although runs of homozygosity (ROH) were ubiquitous genome-wide, there were clear differences in patterns of ROH length and abundance and in effective population sizes illustrating differences in genome homozygosity, evolutionary history, and management. Phylogenetic analysis incorporating patterns of genetic differentiation and gene flow with ancestry modelling highlighted past and recent intermixing and possible two deep ancient genetic ancestries that could have been brought by humans with the first introduction of goats in Africa. We observed four strong selection signatures that were specific to Arsi-Bale and Nubian goats. These signatures overlapped genomic regions with genes associated with morphological, adaptation, reproduction and production traits due possibly to selection under environmental constraints and/or human preferences. The regions also overlapped uncharacterized genes, calling for a comprehensive annotation of the goat genome. Our results provide insights into mechanisms leading to genome variation and differentiation in sub-Saharan Africa indigenous goats.
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Affiliation(s)
- Getinet M. Tarekegn
- Department of Animal Production and TechnologySchool of Animal Sciences and Veterinary MedicineBahir Dar UniversityBahir DarEthiopia
- Department of Animal Breeding and GeneticsSwedish University of Agricultural Sciences (SLU)UppsalaSweden
| | - Negar Khayatzadeh
- Department of Sustainable Agricultural SystemsDivision of Livestock SciencesUniversity of Natural Resources and Life SciencesViennaAustria
| | - Bin Liu
- Inner Mongolia Agricultural UniversityHohhotChina
| | - Sarah Osama
- The University of QueenslandSaint LuciaQLDAustralia
| | - Aynalem Haile
- Small Ruminant GenomicsInternational Centre for Agricultural Research in the Dry Areas (ICARDA)Addis AbabaEthiopia
| | - Barbara Rischkowsky
- Small Ruminant GenomicsInternational Centre for Agricultural Research in the Dry Areas (ICARDA)Addis AbabaEthiopia
| | | | - Kassahun Tesfaye
- Department of Microbial, Cellular and Molecular BiologyAddis Ababa UniversityAddis AbabaEthiopia
| | - Tadelle Dessie
- International Livestock Research Institute (ILRI)Addis AbabaEthiopia
| | - Okeyo A. Mwai
- International Livestock Research Institute (ILRI)NairobiKenya
| | - Appolinaire Djikeng
- Animal and Veterinary Sciences Group, SRUC and Centre for Tropical Livestock Genetics and Health (CTLGH)The Roslin InstituteEaster BushMidlothianUK
| | - Joram M. Mwacharo
- Small Ruminant GenomicsInternational Centre for Agricultural Research in the Dry Areas (ICARDA)Addis AbabaEthiopia
- Animal and Veterinary Sciences Group, SRUC and Centre for Tropical Livestock Genetics and Health (CTLGH)The Roslin InstituteEaster BushMidlothianUK
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11
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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.
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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:
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Biscarini F, Mastrangelo S, Catillo G, Senczuk G, Ciampolini R. Insights into Genetic Diversity, Runs of Homozygosity and Heterozygosity-Rich Regions in Maremmana Semi-Feral Cattle Using Pedigree and Genomic Data. Animals (Basel) 2020; 10:E2285. [PMID: 33287320 PMCID: PMC7761732 DOI: 10.3390/ani10122285] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 11/27/2020] [Accepted: 11/30/2020] [Indexed: 12/24/2022] Open
Abstract
Semi-feral local livestock populations, like Maremmana cattle, are the object of renewed interest for the conservation of biological diversity and the preservation and exploitation of unique and potentially relevant genetic material. The aim of this study was to estimate genetic diversity parameters in semi-feral Maremmana cattle using both pedigree- and genomic-based approaches (FIS and FROH), and to detect regions of homozygosity (ROH) and heterozygosity (ROHet) in the genome. The average heterozygosity estimates were in the range reported for other cattle breeds (HE=0.261, HO=0.274). Pedigree-based average inbreeding (F) was estimated at 4.9%. The correlation was low between F and genomic-based approaches (r=0.03 with FIS, r=0.21 with FROH), while it was higher between FIS and FROH (r=0.78). The low correlation between F and FROH coefficients may be the result of the limited pedigree depth available for the animals involved in this study. The ROH islands identified in Maremmana cattle included candidate genes associated with climate adaptation, carcass traits or the regulation of body weight, fat and energy metabolism. The ROHet islands contained candidate genes associated with nematode resistance and reproduction traits in livestock. The results of this study confirm that genome-based measures like FROH may be useful estimators of individual autozygosity, and may provide insights on pedigree-based inbreeding estimates in cases when animals' pedigree data are unavailable, thus providing a more detailed picture of the genetic diversity.
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Affiliation(s)
- Filippo Biscarini
- CNR-IBBA (National Research Council, Institute of Agricultural Biology and Biotechnology), 20133 Milan, Italy
| | - Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128 Palermo, Italy;
| | - Gennaro Catillo
- CREA Research Centre for Animal Production and Acquaculture, CREA, 00015 Monterotondo, Italy;
| | - Gabriele Senczuk
- Dipartimento di Agricoltura, Ambiente e Alimenti, University of Molise, 86100 Campobasso, Italy;
| | - Roberta Ciampolini
- Dipartimento di Scienze Veterinarie—Università di Pisa, 56124 Pisa, Italy;
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Ramzan F, Klees S, Schmitt AO, Cavero D, Gültas M. Identification of Age-Specific and Common Key Regulatory Mechanisms Governing Eggshell Strength in Chicken Using Random Forests. Genes (Basel) 2020; 11:genes11040464. [PMID: 32344666 PMCID: PMC7230204 DOI: 10.3390/genes11040464] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 04/08/2020] [Accepted: 04/21/2020] [Indexed: 12/21/2022] Open
Abstract
In today's chicken egg industry, maintaining the strength of eggshells in longer laying cycles is pivotal for improving the persistency of egg laying. Eggshell development and mineralization underlie a complex regulatory interplay of various proteins and signaling cascades involving multiple organ systems. Understanding the regulatory mechanisms influencing this dynamic trait over time is imperative, yet scarce. To investigate the temporal changes in the signaling cascades, we considered eggshell strength at two different time points during the egg production cycle and studied the genotype-phenotype associations by employing the Random Forests algorithm on chicken genotypic data. For the analysis of corresponding genes, we adopted a well established systems biology approach to delineate gene regulatory pathways and master regulators underlying this important trait. Our results indicate that, while some of the master regulators (Slc22a1 and Sox11) and pathways are common at different laying stages of chicken, others (e.g., Scn11a, St8sia2, or the TGF- β pathway) represent age-specific functions. Overall, our results provide: (i) significant insights into age-specific and common molecular mechanisms underlying the regulation of eggshell strength; and (ii) new breeding targets to improve the eggshell quality during the later stages of the chicken production cycle.
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Affiliation(s)
- Faisal Ramzan
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany; (F.R.); (S.K.); (A.O.S.)
- Department of Animal Breeding and Genetics, University of Agriculture Faisalabad, 38000 Faisalabad, Pakistan
| | - Selina Klees
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany; (F.R.); (S.K.); (A.O.S.)
| | - Armin Otto Schmitt
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany; (F.R.); (S.K.); (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; (F.R.); (S.K.); (A.O.S.)
- Center for Integrated Breeding Research (CiBreed), Albrecht-Thaer-Weg 3, Georg-August University, 37075 Göttingen, Germany
- Correspondence:
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14
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Genetic diversity and population structure of six ethiopian cattle breeds from different geographical regions using high density single nucleotide polymorphisms. Livest Sci 2020. [DOI: 10.1016/j.livsci.2020.103979] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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