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Wang N, Li Y, Li X, Li H, Bian C, Chen X, Jafari H, Chen N, Lei C. Genome-wide analysis of genetic diversity and selection signatures in Fuzhou cattle. Anim Genet 2025; 56:e70015. [PMID: 40324879 DOI: 10.1111/age.70015] [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: 01/13/2025] [Revised: 04/17/2025] [Accepted: 04/21/2025] [Indexed: 05/07/2025]
Abstract
The Fuzhou cattle breed, native to northeast China, is widely recognized for its adaptability, disease resistance, and docility. Despite being known for these qualities, its population has declined recently, and there is a significant lack of genomic studies on this species. We sequenced 21 samples from a primary breeding farm to determine the genetic structure, diversity, and selection signature to address this. Additionally, we combined 100 published genomic datasets from diverse geographical regions to characterize the genomic variation of Fuzhou cattle. There were 53 752 978 bi-allelic SNPs retained for downstream analysis. In population structure analysis, Fuzhou cattle show a predominantly East Asian taurine ancestry, with strong genetic affinities to Hanwoo and Yanbian cattle. Despite high nucleotide diversity within the Bos taurine lineage, genetic diversity analysis also revealed significant levels of inbreeding in Fuzhou cattle populations, indicating the need for conservation. Utilizing various methods such as θπ, iHS, FST, π-ratio, and XP-EHH, we identified genes associated with traits like growth, meat quality, energy metabolism, and immunity. Several genes related to cold adaptation were identified, including PLIN5, PLB1, and CPT2. These findings provide a basis for conservation strategies to safeguard the genetic resources of Fuzhou cattle.
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Affiliation(s)
- Nan Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yushan Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xinyi Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Hao Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Chenqi Bian
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xinyu Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Halima Jafari
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Ningbo Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
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2
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Cocco R, Sechi S, Marín-García PJ, Liotta L, Llobat L. Seroprevalence of zoonotic pathogens and related haematological and biochemical profiles in Fonni's dogs in rural conditions. Vet Microbiol 2025; 305:110540. [PMID: 40339256 DOI: 10.1016/j.vetmic.2025.110540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2025] [Revised: 04/21/2025] [Accepted: 04/26/2025] [Indexed: 05/10/2025]
Abstract
Fonni's dog is a canine breed autochthonous to the Mediterranean area, specifically from Sardinia (Italy). A total of 190 dogs were examined to determine the seroprevalence of different pathogens endemic in this region and related haematological profile. The seropositivity of pathogens was 65.0 %, 41.3 %, 28.7 %, and 18.9 % for Rickettsia spp., Ehrlichia canis, Anaplasma. phagocytophilum, and Bartonella spp., respectively. Leishmania infantum and Toxoplasma gondii presented the same seroprevalence (5.6 %) respectively. The number of pathogens in co-seropositivity did not change the haematological parameters evaluated, whereas the age had an effect on several of them, including albumin (ALB), alkaline phosphatase (ALP), calcium (CAL), total cholesterol (COL), creatine phosphokinase (CPK), creatinine (CRE), aspartate aminotransferase (GOT), lipase (LIP), phosphorus (P), total protein (PRO) and triglycerides (TRI). Pathogens evaluated influenced different parameters. Specifically, Rickettsia spp. decreased CPK activity, creatine and glucose levels and increased phosphorus. T. gondii increased CPK activity and decreased glucose levels, and E. canis decreased gamma glutamyl transferase (GGT) activity. Finally, L. infantum seropositivity decreased CPK and increased GOT activities. The results observed in Fonni's dogs related to seroprevalence of L. infantum and associated haematological parameters indicate that this canine breed could exhibit different behaviour from that of other canine breeds when faced with this pathogen. Further studies are necessary to elucidate the cause of these differences.
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Affiliation(s)
- Raffaela Cocco
- Department of Veterinary Sciences, Teaching Veterinary Hospital, Sassari 07100, Italy
| | - Sara Sechi
- Department of Veterinary Sciences, Teaching Veterinary Hospital, Sassari 07100, Italy
| | - Pablo Jesús Marín-García
- Department of Animal Production and Health, Public Veterinary Health and Food Science and Technology, School of Veterinary Medicine, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia 46113, Spain
| | - Luigi Liotta
- Department of Veterinary Sciences, University of Messina, Messina 98168, Italy.
| | - Lola Llobat
- Molecular Mechanisms of Zoonotic Diseases (MMOPS) Research group, Department of Animal Production and Health, Public Veterinary Health and Food Science and Technology, School of Veterinary Medicine, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia 46113, Spain.
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3
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Poutougnigni Matenchi Y, Hegarty M. Genomic diversity of Cameroonian Gudali and Gudali-cross cattle. Sci Rep 2025; 15:15066. [PMID: 40301666 PMCID: PMC12041558 DOI: 10.1038/s41598-025-99799-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2024] [Accepted: 04/23/2025] [Indexed: 05/01/2025] Open
Abstract
Information on population structure and diversity in cattle breeds is critical for understanding environmental adaptation, as well as optimal utilisation of genetic resources and breed improvement. In this study, we investigated at the genomic level the population structure, genetic diversity and admixture of the local Gudali breed and its crossbred with the Italian Simmental (Simgud) in three agroecological zones of Cameroon. A total of 717 Gudali and 139 Simgud were genotyped using the GeneSeek® Genomic ProfilerTM (GGP) Bovine 100K array and analyzed together with reference breed data from public databases. Principal component (PCA) and admixture analysis separated European Bos taurus from Asian Bos indicus, African Bos taurus and African Bos indicus breeds. These analyses showed that, except for recently admixed cattle, all African indigenous breeds are either pure African Bos taurus (N'dama) or admixtures of African Bos taurus and Bos indicus. Analysis revealed an ancient admixture from Asian origin in Gudali and a more recent and ongoing European introgression. Simgud is an unmanaged crossbreed expected to be primarily a 50% admixture of Gudali and Simmental. We show here that Simgud is, in actuality, composed of two genetic groups representing admixture of between ∼25% to ∼50% Simmental proportion. Diversity analysis revealed high average heterozygosity ([Formula: see text], [Formula: see text]) for the Gudali and ([Formula: see text] , [Formula: see text]) for Simgud respectively. Inbreeding measures based on the mean FIS coefficient were 0.03 for Gudali and 0.07 for Simgud. A general decline in effective population size was observed in Gudali from a large population (Ne=2475), 959 generations (4797 years ago), back to 13 generations (65 years) (Ne=1404) ago. These results were expected, given the breeding efforts that began in 1952 with the introduction of various exotic (imported taurine) breeds and the Gudali selection initiative. This has affected the effective population size of Gudali, despite the general increase in cattle population in the ranches over that period. These results highlight the need for a structured breeding program in Cameroon for improving productivity, while maintaining a large genetic base of the pure Gudali population.
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Affiliation(s)
| | - Matthew Hegarty
- Department of Life Sciences, Aberystwyth University, Penglais Campus, Aberystwyth, Ceredigion, SY23 3FL, UK
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Martínez-Sáez L, Lopreiato V, Liotta L, Cavallo C, Amato A, Marín-García PJ, Llobat L. Seroprevalence of Leishmania spp. in Cattle Breeds of the Mediterranean Region: Effect of the Breed in the Immune Response. Transbound Emerg Dis 2025; 2025:3277232. [PMID: 40302747 PMCID: PMC12017099 DOI: 10.1155/tbed/3277232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2024] [Accepted: 02/21/2025] [Indexed: 05/02/2025]
Abstract
Leishmania spp. is an intracellular obligate protozoan that causes the zoonotic disease leishmaniosis. Although the dog has always been considered the main reservoir, the number of species involved in transmission of the parasite is increasingly numerous and includes both domestic species, such as cats or horses, wildlife species, and livestock such as pigs, sheep, or cows. In the latter, the presence of Leishmania spp. has been detected in some countries of South America, Asia, and Africa. In Europe, and specifically in the Mediterranean region where leishmaniasis is endemic, there are no data in this regard, although cow blood has been detected in sandflies, which act as the vector for this parasite. This study analyzed the seroprevalence of Leishmania spp. in 75 lactating cows of three different cattle breeds (Modicana, Simmental, and Holstein) from Southern Italy, finding an overall seroprevalence of 17.33%. Cytokine serum levels related to immune response were analyzed and the presence of Leishmania spp. infection did not change the levels of cytokines interleukin 1β (IL-1β), IL-6, IL-10, interferon gamma (IFN-γ), and tumor necrosis factor alpha (TNF-α). Interaction between breed and infection was observed, the IL-1β being higher in Modicana breed than in Simmental and Holstein when infection was present. This breed had medium levels of IL-6 without infection, with high levels being observed in Simmental and low levels in Holstein. Furthermore, Simmental cows showed higher levels of IL-6 with infection than without infection. These results suggest that the livestock species could play a relevant role in Leishmania spp. transmission in endemic regions, and with different immune responses depending on the breed. Additional research is required to ascertain the role of livestock species in parasite transmission and evaluate the immune response of autochthonous breeds.
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Affiliation(s)
- Lola Martínez-Sáez
- Molecular Mechanisms of Zoonotic Diseases (MMOPS) Research Group, Department of Animal Production and Health, Public Health and Food Science and Technology (PASAPTA), Medicine Veterinary Faculty, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain
| | - Vicenzo Lopreiato
- Department of Veterinary Sciences, University of Messina, Messina, Italy
| | - Luigi Liotta
- Department of Veterinary Sciences, University of Messina, Messina, Italy
| | - Carmelo Cavallo
- Department of Veterinary Sciences, University of Messina, Messina, Italy
| | - Annalisa Amato
- Department of Veterinary Sciences, University of Messina, Messina, Italy
| | - Pablo Jesús Marín-García
- Department of Animal Production and Health, Public Health and Food Science and Technology (PASAPTA), Medicine Veterinary Faculty, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain
| | - Lola Llobat
- Molecular Mechanisms of Zoonotic Diseases (MMOPS) Research Group, Department of Animal Production and Health, Public Health and Food Science and Technology (PASAPTA), Medicine Veterinary Faculty, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain
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5
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Tijjani A, Kambal S, Terefe E, Njeru R, Ogugo M, Ndambuki G, Missohou A, Traore A, Salim B, Ezeasor C, D'andre H C, Obishakin ET, Diallo B, Talaki E, Abdoukarim IY, Nash O, Osei-Amponsah R, Ravaorimanana S, Issa Y, Zegeye T, Mukasa C, Tiambo C, Prendergast JGD, Kemp SJ, Han J, Marshall K, Hanotte O. Genomic Reference Resource for African Cattle: Genome Sequences and High-Density Array Variants. Sci Data 2024; 11:801. [PMID: 39030190 PMCID: PMC11271538 DOI: 10.1038/s41597-024-03589-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 07/01/2024] [Indexed: 07/21/2024] Open
Abstract
The diversity in genome resources is fundamental to designing genomic strategies for local breed improvement and utilisation. These resources also support gene discovery and enhance our understanding of the mechanisms of resilience with applications beyond local breeds. Here, we report the genome sequences of 555 cattle (208 of which comprise new data) and high-density (HD) array genotyping of 1,082 samples (537 new samples) from indigenous African cattle populations. The new sequences have an average genome coverage of ~30X, three times higher than the average (~10X) of the over 300 sequences already in the public domain. Following variant quality checks, we identified approximately 32.3 million sequence variants and 661,943 HD autosomal variants mapped to the Bos taurus reference genome (ARS-UCD1.2). The new datasets were generated as part of the Centre for Tropical Livestock Genetics and Health (CTLGH) Genomic Reference Resource for African Cattle (GRRFAC) initiative, which aspires to facilitate the generation of this livestock resource and hopes for its utilisation for complete indigenous breed characterisation and sustainable global livestock improvement.
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Affiliation(s)
- Abdulfatai Tijjani
- Centre for Tropical Livestock Genetics and Health (CTLGH), ILRI Ethiopia, P.O. Box 5689, Addis Ababa, Ethiopia.
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, 04609, USA.
| | - Sumaya Kambal
- Centre for Tropical Livestock Genetics and Health (CTLGH), ILRI Ethiopia, P.O. Box 5689, Addis Ababa, Ethiopia
- Department of Genetics and Animal Breeding, Faculty of Animal Production, University of Khartoum, Khartoum, Sudan
| | - Endashaw Terefe
- Department of Animal Science, College of Agriculture and Environmental Sciences, Arsi University, Asella, Ethiopia
| | - Regina Njeru
- International Livestock Research Institute, P.O. Box 30709, Nairobi, 00100, Kenya
| | - Moses Ogugo
- International Livestock Research Institute, P.O. Box 30709, Nairobi, 00100, Kenya
| | - Gideon Ndambuki
- International Livestock Research Institute, P.O. Box 30709, Nairobi, 00100, Kenya
| | - Ayao Missohou
- Ecole Inter-Etats des Sciences et Médecine Vétérinaires (EISMV), Dakar, Sénégal
| | - Amadou Traore
- Institut de l'Environnement et de Recherches Agricoles (INERA), Ouagadougou, Burkina Faso
| | - Bashir Salim
- Faculty of Veterinary Medicine, University of Khartoum, Khartoum, Sudan
- Camel Research Center, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Chukwunonso Ezeasor
- Department of Veterinary Pathology and Microbiology, University of Nigeria, Nsukka, Enugu State, Nigeria
| | - Claire D'andre H
- Rwanda Agricultural and Animal Resources Development Board, Kigali, Rwanda
| | - Emmanuel T Obishakin
- Biotechnology Division, National Veterinary Research Institute, Vom, Plateau State, Nigeria
| | | | - Essodina Talaki
- École Supérieure d'Agronomie de l'Université de Lomé, Lomé, Togo
| | - Issaka Y Abdoukarim
- Laboratoire de Biotechnologie Animale et de Technologie des Viandes, Abomey-Calavi, Benin
| | - Oyekanmi Nash
- Centre for Genomics Research and Innovation, NABDA, Abuja, Nigeria
| | - Richard Osei-Amponsah
- Department of Animal Science, College of Basic and Applied Sciences, University of Ghana, Legon, Ghana
| | | | - Youssouf Issa
- Institut National supérieur des Sciences et Techniques d'Abéché-INSTA/Tchad, Abéché, Chad
| | - Tsadkan Zegeye
- Mekelle Agricultural Research Center, Tigray Agricultural Research Institute, Mekelle, Ethiopia
| | - Christopher Mukasa
- National Animal Genetic Resources Centre and Data Bank (NAGRC&DB), Entebbe, Uganda
| | - Christian Tiambo
- International Livestock Research Institute, P.O. Box 30709, Nairobi, 00100, Kenya
| | - James G D Prendergast
- Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Stephen J Kemp
- International Livestock Research Institute, P.O. Box 30709, Nairobi, 00100, Kenya
| | - Jianlin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Yazhouwan National Laboratory, No. 8 Huanjin Road, Yazhou, Sanya, 572024, Hainan, P. R. China
| | - Karen Marshall
- International Livestock Research Institute, P.O. Box 30709, Nairobi, 00100, Kenya.
| | - Olivier Hanotte
- Centre for Tropical Livestock Genetics and Health (CTLGH), ILRI Ethiopia, P.O. Box 5689, Addis Ababa, Ethiopia.
- Cells, Organism and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, UK.
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Boschiero C, Neupane M, Yang L, Schroeder SG, Tuo W, Ma L, Baldwin RL, Van Tassell CP, Liu GE. A Pilot Detection and Associate Study of Gene Presence-Absence Variation in Holstein Cattle. Animals (Basel) 2024; 14:1921. [PMID: 38998033 PMCID: PMC11240624 DOI: 10.3390/ani14131921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 06/18/2024] [Accepted: 06/26/2024] [Indexed: 07/14/2024] Open
Abstract
Presence-absence variations (PAVs) are important structural variations, wherein a genomic segment containing one or more genes is present in some individuals but absent in others. While PAVs have been extensively studied in plants, research in cattle remains limited. This study identified PAVs in 173 Holstein bulls using whole-genome sequencing data and assessed their associations with 46 economically important traits. Out of 28,772 cattle genes (from the longest transcripts), a total of 26,979 (93.77%) core genes were identified (present in all individuals), while variable genes included 928 softcore (present in 95-99% of individuals), 494 shell (present in 5-94%), and 371 cloud genes (present in <5%). Cloud genes were enriched in functions associated with hormonal and antimicrobial activities, while shell genes were enriched in immune functions. PAV-based genome-wide association studies identified associations between gene PAVs and 16 traits including milk, fat, and protein yields, as well as traits related to health and reproduction. Associations were found on multiple chromosomes, illustrating important associations on cattle chromosomes 7 and 15, involving olfactory receptor and immune-related genes, respectively. By examining the PAVs at the population level, the results of this research provided crucial insights into the genetic structures underlying the complex traits of Holstein cattle.
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Affiliation(s)
- Clarissa Boschiero
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
- Department of Veterinary Medicine, University of Maryland, College Park, MD 20742, USA
| | - Mahesh Neupane
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Liu Yang
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA
| | - Steven G Schroeder
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Wenbin Tuo
- Animal Parasitic Diseases Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Li Ma
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA
| | - Ransom L Baldwin
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Curtis P Van Tassell
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - George E Liu
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
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Jaimes-Dueñez J, Tique-Oviedo M, Arias-Vega L, Castiblanco-Diaz E, Rivero-Rodriguez L, Marin-Cossio L, Gongora-Orjuela A, Jimenez-Leaño A. Epidemiological assessment of Anaplasma marginale, Babesia bigemina, and Babesia bovis infections in Colombian creole cattle breeds: A molecular survey in northeastern Colombia. Vet Parasitol Reg Stud Reports 2024; 50:101011. [PMID: 38644043 DOI: 10.1016/j.vprsr.2024.101011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 02/28/2024] [Accepted: 03/05/2024] [Indexed: 04/23/2024]
Abstract
Anaplasmosis and babesiosis are globally distributed arthropod-borne diseases known for causing substantial economic losses due to their high morbidity and mortality rates. This study aims to assess the frequency and epidemiological features associated with the infection of Anaplasma marginale, Babesia bigemina, and Babesia bovis in three Creole cattle breeds (Chino Santandereano (Chino), Casanareño (CAS), and Sanmartinero (SM)) in northeastern Colombia. Between June 2019 and March 2020, a total of 252 Creole cattle were sampled, with Chino, CAS, and SM accounting for 42.8%, 29.5%, and 29.5% of the samples, respectively. Blood samples were subjected to molecular analysis to detect the DNA of A. marginale, B. bigemina, and B. bovis, using species-specific primers. Additionally, Packed Cell Volume (PCV), total serum proteins, and body condition were evaluated. Molecular analyses revealed the presence of B. bigemina, A. marginale, and B. bovis in 83.7% (211/252; 95% CI = 79.1%-88.3%), 59.9% (151/252; 95% CI = 53.8%-66.1%), and 40.9% (103/252; 95% CI = 34.7%-46.9%) of the samples, respectively, with 69% (174/252; 95% CI = 57.8%-80.3%) exhibiting coinfections. Notably, in infected animals, no significant alterations in PCV, total serum proteins, or body condition were observed. Multivariate analyses indicated a statistically significant association between the frequency of A. marginale infection and the breed and season, with a higher frequency in SM during the rainy season (P < 0.05). To our knowledge, this is the first molecular survey that evaluates multiple arthropod-borne pathogens in Colombian Creole breeds. The results revel a high frequency of B. bigemina and A. marginale infections, coupled with a notable frequency of coinfections, all without significant alteration in the PCV, total serum proteins and body conditions. Our findings enhance the understanding of the epidemiological aspects of arthropod-borne pathogens in Colombian Creole breed and contribute to the improvement of sanitary programs for these animals.
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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.
| | - Marisol Tique-Oviedo
- Grupo de Investigación en Ciencias Animales - GRICA, Facultad de Medicina Veterinaria y Zootecnia, Universidad Cooperativa de Colombia UCC, Bucaramanga, Colombia
| | - Laura Arias-Vega
- Grupo de Investigación en Ciencias Animales - GRICA, Facultad de Medicina Veterinaria y Zootecnia, Universidad Cooperativa de Colombia UCC, Bucaramanga, Colombia
| | - Edinson Castiblanco-Diaz
- Grupo de Investigación en Ciencias Animales - GRICA, Facultad de Medicina Veterinaria y Zootecnia, Universidad Cooperativa de Colombia UCC, Bucaramanga, Colombia
| | - Leslie Rivero-Rodriguez
- Grupo de Investigación en Ciencias Animales - GRICA, Facultad de Medicina Veterinaria y Zootecnia, Universidad Cooperativa de Colombia UCC, Bucaramanga, Colombia
| | - Laura Marin-Cossio
- Grupo de Investigación en Reproducción y Genética Animal - GIRGA, Facultad de Medicina Veterinaria y Zootecnia, Universidad de los Llanos, Villavicencio, Colombia
| | - Agustín Gongora-Orjuela
- Grupo de Investigación en Reproducción y Genética Animal - GIRGA, Facultad de Medicina Veterinaria y Zootecnia, Universidad de los Llanos, Villavicencio, Colombia
| | - Angela Jimenez-Leaño
- Grupo de Investigación en Ciencias Animales - GRICA, Facultad de Medicina Veterinaria y Zootecnia, Universidad Cooperativa de Colombia UCC, Bucaramanga, Colombia
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8
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Ayalew W, Wu X, Tarekegn GM, Sisay Tessema T, Naboulsi R, Van Damme R, Bongcam-Rudloff E, Edea Z, Enquahone S, Yan P. Whole-Genome Resequencing Reveals Selection Signatures of Abigar Cattle for Local Adaptation. Animals (Basel) 2023; 13:3269. [PMID: 37893993 PMCID: PMC10603685 DOI: 10.3390/ani13203269] [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: 09/01/2023] [Revised: 10/02/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
Over time, indigenous cattle breeds have developed disease resistance, heat tolerance, and adaptability to harsh environments. Deciphering the genetic mechanisms underlying adaptive traits is crucial for their improvement and sustainable utilization. For the first time, we performed whole-genome sequencing to unveil the genomic diversity, population structure, and selection signatures of Abigar cattle living in a tropical environment. The population structure analysis revealed that Abigar cattle exhibit high nucleotide diversity and heterozygosity, with low runs of homozygosity and linkage disequilibrium, suggesting a genetic landscape less constrained by inbreeding and enriched by diversity. Using nucleotide diversity (Pi) and population differentiation (FST) selection scan methods, we identified 83 shared genes that are likely associated with tropical adaption. The functional annotation analysis revealed that some of these genes are potentially linked to heat tolerance (HOXC13, DNAJC18, and RXFP2), immune response (IRAK3, MZB1, and STING1), and oxidative stress response (SLC23A1). Given the wider spreading impacts of climate change on cattle production, understanding the genetic mechanisms of adaptation of local breeds becomes crucial to better respond to climate and environmental changes. In this context, our finding establishes a foundation for further research into the mechanisms underpinning cattle adaptation to tropical environments.
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Affiliation(s)
- Wondossen Ayalew
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China;
- Institute of Biotechnology, Addis Ababa University, Addis Ababa P.O. Box 1176, Ethiopia; (G.M.T.); (T.S.T.)
| | - Xiaoyun Wu
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China;
| | - Getinet Mekuriaw Tarekegn
- Institute of Biotechnology, Addis Ababa University, Addis Ababa P.O. Box 1176, Ethiopia; (G.M.T.); (T.S.T.)
- Scotland’s Rural College (SRUC), Roslin Institute Building, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Tesfaye Sisay Tessema
- Institute of Biotechnology, Addis Ababa University, Addis Ababa P.O. Box 1176, Ethiopia; (G.M.T.); (T.S.T.)
| | - Rakan Naboulsi
- Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institute, Tomtebodavägen 18A, 17177 Stockholm, Sweden
| | - Renaud Van Damme
- Department of Animal Breeding and Genetics, Bioinformatics Section, Swedish University of Agricultural Sciences, P.O. Box 7023, S-750 07 Uppsala, Sweden; (R.V.D.); (E.B.-R.)
| | - Erik Bongcam-Rudloff
- Department of Animal Breeding and Genetics, Bioinformatics Section, Swedish University of Agricultural Sciences, P.O. Box 7023, S-750 07 Uppsala, Sweden; (R.V.D.); (E.B.-R.)
| | - Zewdu Edea
- Ethiopian Bio and Emerging Technology Institute, Addis Ababa P.O. Box 5954, Ethiopia;
| | - Solomon Enquahone
- Institute of Biotechnology, Addis Ababa University, Addis Ababa P.O. Box 1176, Ethiopia; (G.M.T.); (T.S.T.)
| | - Ping Yan
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China;
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Oke O, Oso O, Logunleko M, Uyanga V, Akinyemi F, Okeniyi F, Akosile O, Baloyi J, Onagbesan O. Adaptation of the White Fulani cattle to the tropical environment. J Therm Biol 2022; 110:103372. [DOI: 10.1016/j.jtherbio.2022.103372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/11/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022]
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10
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Genetic diversity and population structure of four Nigerian indigenous cattle breeds. Trop Anim Health Prod 2022; 54:132. [PMID: 35260931 DOI: 10.1007/s11250-022-03132-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 02/24/2022] [Indexed: 10/18/2022]
Abstract
A total of thirty-eight (38) Nigerian indigenous cattle were used to evaluate the genetic relatedness, diversity, and population structure of four indigenous cattle breeds. Blood samples were collected from the experimental animals into vacutainer tubes containing EDTA, and genomic DNA extracted, quantified, and evaluated for integrity. Fourteen (14) microsatellite primers were used for polymerase chain reaction (PCR) and PCR amplification performed under standard conditions followed by electrophoresis in 2.5% Metaphor Agarose gel. Genomic parameter estimates included allele number (Na), observed (Ho) and expected (He) heterozygosity, polymorphism information content (PIC), test of Hardy-Weinberg equilibrium, and genetic diversity; pairwise Nei's genetic distance, Wright's F-statistics (FIT, FST, and FIS), and gene flow (Nm); and breed relationship, population structure, and degree of admixture. A total of 112 alleles were detected and mean number of alleles was 4.02 ± 0.190, while mean fixation index was 0.461 ± 0.068. Mean Ho and He were 0.352 ± 0.05 and 0.605 ± 0.018, respectively. Pairwise estimates of genetic differentiation, FST, were significantly different (p < 0.001) implying distinct breeds. Estimates of Nm were less than 4 but greater than 1, indicating that the cattle breeds do not belong to one panmictic population. Estimates of pairwise genetic distance revealed that White Fulani and Sokoto Gudali were more closely related than Muturu and N'Dama. The results of STRUCTURE, principal coordinate, and phylogenetic analyses revealed four clusters which implies that the breeds were genetically distinct. It is recommended that the four cattle breeds can be used to develop composites with higher genetic potentials for beef production and resistance to endemic diseases and pests. Further efforts should be made to conserve and genetically improve these breeds to meet present and future production and breeding imperatives.
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Genetic Analyses and Genome-Wide Association Studies on Pathogen Resistance of Bos taurus and Bos indicus Cattle Breeds in Cameroon. Genes (Basel) 2021; 12:genes12070976. [PMID: 34206759 PMCID: PMC8307268 DOI: 10.3390/genes12070976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/23/2021] [Accepted: 06/24/2021] [Indexed: 11/16/2022] Open
Abstract
Autochthonous taurine and later introduced zebu cattle from Cameroon differ considerably in their resistance to endemic pathogens with little to no reports of the underlying genetic make-up. Breed history and habitat variations are reported to contribute significantly to this diversity worldwide, presumably in Cameroon as well, where locations diverge in climate, pasture, and prevalence of infectious agents. In order to investigate the genetic background, the genotypes of 685 individuals of different Cameroonian breeds were analysed by using the BovineSNP50v3 BeadChip. The variance components including heritability were estimated and genome-wide association studies (GWAS) were performed. Phenotypes were obtained by parasitological screening and categorised in Tick-borne pathogens (TBP), gastrointestinal nematodes (GIN), and onchocercosis (ONC). Estimated heritabilities were low for GIN and TBP (0.079 (se = 0.084) and 0.109 (se = 0.103) respectively) and moderate for ONC (0.216 (se = 0.094)). Further than revealing the quantitative nature of the traits, GWAS identified putative trait-associated genomic regions on five chromosomes, including the chromosomes 11 and 18 for GIN, 20 and 24 for TBP, and 12 for ONC. The results imply that breeding for resistant animals in the cattle population from Northern Cameroon might be possible for the studied pathogens; however, further research in this field using larger datasets will be required to improve the resistance towards pathogen infections, propose candidate genes or to infer biological pathways, as well as the genetic structures of African multi-breed populations.
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Using Bioelements Isotope Ratios and Fatty Acid Composition to Deduce Beef Origin and Zebu Feeding Regime in Cameroon. Molecules 2021; 26:molecules26082155. [PMID: 33918075 PMCID: PMC8069081 DOI: 10.3390/molecules26082155] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/02/2021] [Accepted: 04/04/2021] [Indexed: 11/16/2022] Open
Abstract
The purpose of this study was to address the lack of knowledge regarding the stable isotopic composition of beef from zebu cattle reared in tropical Africa. Sixty beef carcasses belonging to the most common zebu breeds (Goudali, white Fulani, and red Mbororo) were selected and classified according to their subcutaneous fat color (white, cream or yellow). The stable isotope ratios of five bioelements—H, O, C, N, and S—in muscle fractions and the fatty acids composition were analyzed. Zebu meat from Cameroon shows peculiar δ13C values, related to the almost exclusive intake of grazed tropical grasses with photosynthetic cycle C4. It also shows δ2H and δ18O values higher than those reported in other areas of the world and correlated with the isotopic composition of animal drinking water. The white subcutaneous fat (“white type”) zebu showed higher δ2H and lower δ13C than the “yellow type”, that is correlated with a higher content of polyunsaturated fatty acid (PUFA) and a lower amount of saturated fatty acid (SFA) and monounsaturated fatty acid (MUFA). Multielement analysis seems to provide promising results for tracing the regional origin of Cameroon beef and some aspects of the livestock system, such as the nutritional status of the animals.
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