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Ahmed Z, Xiang W, Wang F, Nawaz M, Kuthu ZH, Lei C, Xu D. Whole-genome resequencing deciphers patterns of genetic diversity, phylogeny, and evolutionary dynamics in Kashmir cattle. Anim Genet 2024; 55:511-526. [PMID: 38726735 DOI: 10.1111/age.13434] [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: 04/02/2024] [Revised: 04/02/2024] [Accepted: 04/11/2024] [Indexed: 07/04/2024]
Abstract
Kashmir cattle, which were kept by local pastoralists for centuries, are exceptionally resilient and adaptive to harsh environments. Despite its significance, the genomic characteristics of this cattle breed remain elusive. This study utilized whole genome sequences of Kashmir cattle (n = 20; newly sequenced) alongside published whole genomes of 32 distinct breeds and seven core cattle populations (n = 135). The analysis identified ~25.87 million biallelic single nucleotide polymorphisms in Kashmir cattle, predominantly in intergenic and intron regions. Population structure analyses revealed distinct clustering patterns of Kashmir cattle with proximity to the South Asian, African and Chinese indicine cattle populations. Genetic diversity analysis of Kashmir cattle demonstrated lower inbreeding and greater nucleotide diversity than analyzed global breeds. Homozygosity runs indicated less consanguineous mating in Kashmir cattle compared with European taurine breeds. Furthermore, six selection sweep detection methods were used within Kashmir cattle and other cattle populations to identify genes associated with vital traits, including immunity (BOLA-DQA5, BOLA-DQB, TNFAIP8L, FCRL4, AOAH, HIF1AN, FBXL3, MPEG1, CDC40, etc.), reproduction (GOLGA4, BRWD1, OSBP2, LEO1 ADCY5, etc.), growth (ADPRHL1, NRG2, TCF12, TMOD4, GBP4, IGF2, RSPO3, SCD, etc.), milk composition (MRPS30 and CSF1) and high-altitude adaptation (EDNRA, ITPR2, AGBL4 and SCG3). These findings provide essential genetic insights into the characteristics and establish the foundation for the scientific conservation and utilization of Kashmir cattle breed.
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Affiliation(s)
- Zulfiqar Ahmed
- College of Animal Science and Technology, Huazhong Agriculture University, Wuhan, China
- NCLBG&G, Department of Livestock and Poultry Production, Faculty of Veterinary and Animal Sciences, University of Poonch Rawalakot, Azad Jammu and Kashmir, Pakistan
| | - Weixuan Xiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Fuwen Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Mohsin Nawaz
- NCLBG&G, Department of Livestock and Poultry Production, Faculty of Veterinary and Animal Sciences, University of Poonch Rawalakot, Azad Jammu and Kashmir, Pakistan
| | - Zulfiqar Hussan Kuthu
- NCLBG&G, Department of Livestock and Poultry Production, Faculty of Veterinary and Animal Sciences, University of Poonch Rawalakot, Azad Jammu and Kashmir, Pakistan
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Dequan Xu
- College of Animal Science and Technology, Huazhong Agriculture University, Wuhan, China
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2
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Badia-Bringué G, Canive M, Vázquez P, Garrido JM, Fernández A, Juste RA, Jiménez JA, González-Recio O, Alonso-Hearn M. Genome-Wide Association Study Reveals Quantitative Trait Loci and Candidate Genes Associated with High Interferon-gamma Production in Holstein Cattle Naturally Infected with Mycobacterium Bovis. Int J Mol Sci 2024; 25:6165. [PMID: 38892353 PMCID: PMC11172856 DOI: 10.3390/ijms25116165] [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: 04/18/2024] [Revised: 05/27/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
Mycobacterium bovis (Mb) is the causative agent of bovine tuberculosis (bTb). Genetic selection aiming to identify less susceptible animals has been proposed as a complementary measure in ongoing programs toward controlling Mb infection. However, individual animal phenotypes for bTb based on interferon-gamma (IFNɣ) and its use in bovine selective breeding programs have not been explored. In the current study, IFNɣ production was measured using a specific IFNɣ ELISA kit in bovine purified protein derivative (bPPD)-stimulated blood samples collected from Holstein cattle. DNA isolated from the peripheral blood samples collected from the animals included in the study was genotyped with the EuroG Medium Density bead Chip, and the genotypes were imputed to whole-genome sequences. A genome-wide association analysis (GWAS) revealed that the IFNɣ in response to bPPD was associated with a specific genetic profile (heritability = 0.23) and allowed the identification of 163 SNPs, 72 quantitative trait loci (QTLs), 197 candidate genes, and 8 microRNAs (miRNAs) associated with this phenotype. No negative correlations between this phenotype and other phenotypes and traits included in the Spanish breeding program were observed. Taken together, our results define a heritable and distinct immunogenetic profile associated with strong production of IFNɣ in response to Mb.
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Affiliation(s)
- Gerard Badia-Bringué
- Department of Animal Health, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - María Canive
- Department of Animal Health, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Patricia Vázquez
- Department of Animal Health, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Joseba M. Garrido
- Department of Animal Health, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Almudena Fernández
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28040 Madrid, Spain
| | - Ramón A. Juste
- Department of Animal Health, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | | | - Oscar González-Recio
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28040 Madrid, Spain
| | - Marta Alonso-Hearn
- Department of Animal Health, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
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3
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Duda HC, von Toerne C, Korbonits L, Didier A, Scholz AM, Märtlbauer E, Hauck SM, Deeg CA. Cathepsin S Is More Abundant in Serum of Mycobacterium avium subsp. paratuberculosis-Infected Dairy Cows. Metabolites 2024; 14:215. [PMID: 38668343 PMCID: PMC11051907 DOI: 10.3390/metabo14040215] [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: 03/09/2024] [Revised: 04/05/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
Mycobacterium avium subsp. paratuberculosis (MAP) is the causative agent of bovine paratuberculosis, a chronic granulomatous enteritis leading to economic losses and posing a risk to human health due to its zoonotic potential. The pathogen cannot reliably be detected by standard methods, and immunological procedures during the infection are not well understood. Therefore, the aim of our study was to explore host-pathogen interactions in MAP-infected dairy cows and to improve diagnostic tests. Serum proteomics analysis using quantitative label-free LC-MS/MS revealed 60 differentially abundant proteins in MAP-infected dairy cows compared to healthy controls from the same infected herd and 90 differentially abundant proteins in comparison to another control group from an uninfected herd. Pathway enrichment analysis provided new insights into the immune response to MAP and susceptibility to the infection. Furthermore, we found a higher abundance of Cathepsin S (CTSS) in the serum of MAP-infected dairy cows, which is involved in multiple enriched pathways associated with the immune system. Confirmed with Western blotting, we identified CTSS as a potential biomarker for bovine paratuberculosis. This study enabled a better understanding of procedures in the host-pathogen response to MAP and improved detection of paratuberculosis-diseased cattle.
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Affiliation(s)
- Heidi C. Duda
- Chair of Physiology, Department of Veterinary Sciences, Ludwig Maximilian University of Munich, D-82152 Martinsried, Germany
| | - Christine von Toerne
- Metabolomics and Proteomics Core, Helmholtz Center Munich, German Research Center for Environmental Health, D-85763 Neuherberg, Germany (S.M.H.)
| | - Lucia Korbonits
- Chair of Physiology, Department of Veterinary Sciences, Ludwig Maximilian University of Munich, D-82152 Martinsried, Germany
| | - Andrea Didier
- Chair of Hygiene and Technology of Milk, Department of Veterinary Sciences, Ludwig Maximilian University of Munich, D-85764 Oberschleißheim, Germany; (A.D.)
| | - Armin M. Scholz
- Livestock Center of the Faculty of Veterinary Medicine, Ludwig Maximilian University of Munich, D-85764 Oberschleißheim, Germany;
| | - Erwin Märtlbauer
- Chair of Hygiene and Technology of Milk, Department of Veterinary Sciences, Ludwig Maximilian University of Munich, D-85764 Oberschleißheim, Germany; (A.D.)
| | - Stefanie M. Hauck
- Metabolomics and Proteomics Core, Helmholtz Center Munich, German Research Center for Environmental Health, D-85763 Neuherberg, Germany (S.M.H.)
| | - Cornelia A. Deeg
- Chair of Physiology, Department of Veterinary Sciences, Ludwig Maximilian University of Munich, D-82152 Martinsried, Germany
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4
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Lee J, Mun H, Koo Y, Park S, Kim J, Yu S, Shin J, Lee J, Son J, Park C, Lee S, Song H, Kim S, Dang C, Park J. Enhancing Genomic Prediction Accuracy for Body Conformation Traits in Korean Holstein Cattle. Animals (Basel) 2024; 14:1052. [PMID: 38612291 PMCID: PMC11011013 DOI: 10.3390/ani14071052] [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: 12/31/2023] [Revised: 03/18/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
The Holstein breed is the mainstay of dairy production in Korea. In this study, we evaluated the genomic prediction accuracy for body conformation traits in Korean Holstein cattle, using a range of π levels (0.75, 0.90, 0.99, and 0.995) in Bayesian methods (BayesB and BayesC). Focusing on 24 traits, we analyzed the impact of different π levels on prediction accuracy. We observed a general increase in accuracy at higher levels for specific traits, with variations depending on the Bayesian method applied. Notably, the highest accuracy was achieved for rear teat angle when using deregressed estimated breeding values including parent average as a response variable. We further demonstrated that incorporating parent average into deregressed estimated breeding values enhances genomic prediction accuracy, showcasing the effectiveness of the model in integrating both offspring and parental genetic information. Additionally, we identified 18 significant window regions through genome-wide association studies, which are crucial for future fine mapping and discovery of causal mutations. These findings provide valuable insights into the efficiency of genomic selection for body conformation traits in Korean Holstein cattle and highlight the potential for advancements in the prediction accuracy using larger datasets and more sophisticated genomic models.
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Affiliation(s)
- Jungjae Lee
- Department of Animal Science and Technology, College of Biotechnology and Natural Resources, Chung-Ang University, Anseong 17546, Republic of Korea;
| | - Hyosik Mun
- Korea Animal Improvement Association, Seoul 06668, Republic of Korea; (H.M.); (Y.K.); (S.P.); (J.K.); (S.Y.); (J.S.); (C.P.); (S.K.)
| | - Yangmo Koo
- Korea Animal Improvement Association, Seoul 06668, Republic of Korea; (H.M.); (Y.K.); (S.P.); (J.K.); (S.Y.); (J.S.); (C.P.); (S.K.)
| | - Sangchul Park
- Korea Animal Improvement Association, Seoul 06668, Republic of Korea; (H.M.); (Y.K.); (S.P.); (J.K.); (S.Y.); (J.S.); (C.P.); (S.K.)
| | - Junsoo Kim
- Korea Animal Improvement Association, Seoul 06668, Republic of Korea; (H.M.); (Y.K.); (S.P.); (J.K.); (S.Y.); (J.S.); (C.P.); (S.K.)
| | - Seongpil Yu
- Korea Animal Improvement Association, Seoul 06668, Republic of Korea; (H.M.); (Y.K.); (S.P.); (J.K.); (S.Y.); (J.S.); (C.P.); (S.K.)
| | - Jiseob Shin
- Dairy Cattle Improvement Center of NH-Agree Business Group, National Agricultural Cooperative Federation, Goyang 10292, Republic of Korea; (J.S.); (S.L.); (H.S.)
| | - Jaegu Lee
- Animal Breeding and Genetics Division, National Institute of Animal Science, Rural Development Administration, Cheonan 31000, Republic of Korea;
| | - Jihyun Son
- Korea Animal Improvement Association, Seoul 06668, Republic of Korea; (H.M.); (Y.K.); (S.P.); (J.K.); (S.Y.); (J.S.); (C.P.); (S.K.)
| | - Chanhyuk Park
- Korea Animal Improvement Association, Seoul 06668, Republic of Korea; (H.M.); (Y.K.); (S.P.); (J.K.); (S.Y.); (J.S.); (C.P.); (S.K.)
| | - Seokhyun Lee
- Dairy Cattle Improvement Center of NH-Agree Business Group, National Agricultural Cooperative Federation, Goyang 10292, Republic of Korea; (J.S.); (S.L.); (H.S.)
| | - Hyungjun Song
- Dairy Cattle Improvement Center of NH-Agree Business Group, National Agricultural Cooperative Federation, Goyang 10292, Republic of Korea; (J.S.); (S.L.); (H.S.)
| | - Sungjin Kim
- Korea Animal Improvement Association, Seoul 06668, Republic of Korea; (H.M.); (Y.K.); (S.P.); (J.K.); (S.Y.); (J.S.); (C.P.); (S.K.)
| | - Changgwon Dang
- Animal Breeding and Genetics Division, National Institute of Animal Science, Rural Development Administration, Cheonan 31000, Republic of Korea;
| | - Jun Park
- Department of Animal Biotechnology, Jeonbuk National University, Jeonju 54896, Republic of Korea
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5
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Stephen MA, Burke CR, Steele N, Pryce JE, Meier S, Amer PR, Phyn CVC, Garrick DJ. Genome-wide association study of anogenital distance and its (co)variances with fertility in growing and lactating Holstein-Friesian dairy cattle. J Dairy Sci 2023; 106:7846-7860. [PMID: 37641287 DOI: 10.3168/jds.2023-23427] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 05/10/2023] [Indexed: 08/31/2023]
Abstract
Anogenital distance (AGD) is a moderately heritable trait that can be measured at a young age that may provide an opportunity to indirectly select for improved fertility in dairy cattle. In this study, we characterized AGD and its genetic and phenotypic relationships with a range of body stature and fertility traits. We measured AGD, shoulder height, body length, and body weight in a population of 5,010 Holstein-Friesian and Holstein-Friesian × Jersey crossbred heifers at approximately 11 mo of age (AGD1). These animals were born in 2018 across 54 seasonal calving, pasture-based dairy herds. A second measure of AGD was collected in a subset of herds (n = 17; 1,956 animals) when the animals averaged 29 mo of age (AGD2). Fertility measures included age at puberty (AGEP), then time of calving, breeding, and pregnancy during the first and second lactations. We constructed binary traits reflecting the animal's ability to calve during the first 42 d of their herd's seasonal calving period (CR42), be presented for breeding during the first 21 d of the seasonal breeding period (PB21) and become pregnant during the first 42 d of the seasonal breeding period (PR42). The posterior mean of sampled heritabilities for AGD1 was 0.23, with 90% of samples falling within a credibility interval (90% CRI) of 0.20 to 0.26, whereas the heritability of AGD2 was 0.29 (90% CRI 0.24 to 0.34). The relationship between AGD1 and AGD2 was highly positive, with a genetic correlation of 0.89 (90% CRI 0.82 to 0.94). Using a GWAS analysis of 2,460 genomic windows based on 50k genotype data, we detected a region on chromosome 20 that was highly associated with variation in AGD1, and a second region on chromosome 13 that was moderately associated with variation in AGD1. We did not detect any genomic regions associated with AGD2 which was measured in fewer animals. The genetic correlation between AGD1 and AGEP was 0.10 (90% CRI 0.00 to 0.19), whereas the genetic correlation between AGD2 and AGEP was 0.30 (90% CRI 0.15 to 0.44). The timing of calving, breeding, and pregnancy (CR42, PB21, and PR42) during first or second lactations exhibited moderate genetic relationships with AGD1 (0.19 to 0.52) and AGD2 (0.46 to 0.63). Genetic correlations between AGD and body stature traits were weak (≤0.16). We conclude that AGD is a moderately heritable trait, which may have value as an early-in-life genetic predictor for reproductive success during lactation.
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Affiliation(s)
- M A Stephen
- DairyNZ Ltd., Hamilton 3240, New Zealand; AL Rae Centre for Genetics and Breeding-Massey University, Ruakura, Hamilton 3214, New Zealand.
| | - C R Burke
- DairyNZ Ltd., Hamilton 3240, New Zealand
| | - N Steele
- DairyNZ Ltd., Hamilton 3240, New Zealand
| | - J E Pryce
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, Victoria 3083, Australia; School of Applied Systems Biology, La Trobe University, Bundoora, Victoria 3083, Australia
| | - S Meier
- DairyNZ Ltd., Hamilton 3240, New Zealand
| | | | - C V C Phyn
- DairyNZ Ltd., Hamilton 3240, New Zealand
| | - D J Garrick
- DairyNZ Ltd., Hamilton 3240, New Zealand; AL Rae Centre for Genetics and Breeding-Massey University, Ruakura, Hamilton 3214, New Zealand
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Banos G. Selective breeding can contribute to bovine tuberculosis control and eradication. Ir Vet J 2023; 76:19. [PMID: 37620894 PMCID: PMC10464393 DOI: 10.1186/s13620-023-00250-z] [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: 10/26/2022] [Accepted: 07/25/2023] [Indexed: 08/26/2023] Open
Abstract
Bovine tuberculosis (bTB) persists in many countries having a significant impact on public health and livestock industry finances. The incidence and prevalence of new cases in parts of the UK and elsewhere over the past decades warrant intensified efforts towards achieving Officially Tuberculosis Free (OTF) status in the respective regions. Genetic selection aiming to identify and remove inherently susceptible animals from breeding has been proposed as an additional measure in ongoing programmes towards controlling the disease. The presence of genetic variation among individual animals in their capacity to respond to Mycobacterium bovis exposure has been documented and heritability estimates of 0.06-0.18 have been reported. Despite their moderate magnitude, these estimates suggest that host resistance to bTB is amenable to improvement with selective breeding. Although relatively slow, genetic progress can be constant, cumulative and permanent, thereby complementing ongoing disease control measures. Importantly, mostly no antagonistic genetic correlations have been found between bTB resistance and other animal traits suggesting that carefully incorporating the former in breeding decisions should not adversely affect bovine productivity. Simulation studies have demonstrated the potential impact of genetic selection on reducing the probability of a breakdown to occur or the duration and severity of a breakdown that has already been declared. Furthermore, research on the bovine genome has identified multiple genomic markers and genes associated with bTB resistance. Nevertheless, the combined outcomes of these studies suggest that host resistance to bTB is a complex, polygenic trait, with no single gene alone explaining the inherent differences between resistant and susceptible animals. Such results support the development of accurate genomic breeding values that duly capture the collective effect of multiple genes to underpin selective breeding programmes. In addition to improving host resistance to bTB, scientists and practitioners have considered the possibility of reducing host infectivity. Ongoing studies have suggested the presence of genetic variation for infectivity and confirmed that bTB eradication would be accelerated if selective breeding considered both host resistance and infectivity traits. In conclusion, research activity on bTB genetics has generated knowledge and insights to support selective breeding as an additional measure towards controlling and eradicating the disease.
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Affiliation(s)
- Georgios Banos
- Scotland's Rural College (SRUC), Department of Animal and Veterinary Sciences, Easter Bush, Midlothian, EH25 9RG, UK.
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Mariotti FR, Supino D, Landolina N, Garlanda C, Mantovani A, Moretta L, Maggi E. IL-1R8: A molecular brake of anti-tumor and anti-viral activity of NK cells and ILC. Semin Immunol 2023; 66:101712. [PMID: 36753974 DOI: 10.1016/j.smim.2023.101712] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 12/30/2022] [Accepted: 01/09/2023] [Indexed: 02/07/2023]
Abstract
Interleukin-1 receptor family members (ILRs) and Toll-Like Receptors (TLRs) play pivotal role in immunity and inflammation and are expressed by most cell types including cells of both the innate and adaptive immune system. In this context, IL-1 superfamily members are also important players in regulating function and differentiation of adaptive and innate lymphoid cells. This system is tightly regulated in order to avoid uncontrolled activation, which may lead to detrimental inflammation contributing to autoimmune or allergic responses. IL-1R8 (also known as TIR8 or SIGIRR) is a member of the IL-1R family that acts as a negative regulator dampening ILR and TLR signaling and as a co-receptor for human IL-37. Human and mouse NK cells, that are key players in immune surveillance of tumors and infections, express high level of IL-1R8. In this review, we will summarize our current understanding on the structure, expression and function of IL-1R8 and we will also discuss the emerging role of IL-1R8 as an important checkpoint regulating NK cells function in pathological conditions including cancer and viral infections.
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Affiliation(s)
- Francesca R Mariotti
- Tumor Immunology Unit, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
| | | | - Nadine Landolina
- Tumor Immunology Unit, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
| | - Cecilia Garlanda
- IRCCS, Humanitas Research Hospital, 20089 Rozzano, Italy; Department of Biomedical Science, Humanitas University, 20072 Pieve Emanuele, Italy
| | - Alberto Mantovani
- IRCCS, Humanitas Research Hospital, 20089 Rozzano, Italy; Department of Biomedical Science, Humanitas University, 20072 Pieve Emanuele, Italy; The William Harvey Research Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, United Kingdom
| | - Lorenzo Moretta
- Tumor Immunology Unit, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
| | - Enrico Maggi
- Translational Immunology Unit, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy.
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8
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Hasankhani A, Bahrami A, Mackie S, Maghsoodi S, Alawamleh HSK, Sheybani N, Safarpoor Dehkordi F, Rajabi F, Javanmard G, Khadem H, Barkema HW, De Donato M. In-depth systems biological evaluation of bovine alveolar macrophages suggests novel insights into molecular mechanisms underlying Mycobacterium bovis infection. Front Microbiol 2022; 13:1041314. [PMID: 36532492 PMCID: PMC9748370 DOI: 10.3389/fmicb.2022.1041314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 11/04/2022] [Indexed: 08/26/2023] Open
Abstract
OBJECTIVE Bovine tuberculosis (bTB) is a chronic respiratory infectious disease of domestic livestock caused by intracellular Mycobacterium bovis infection, which causes ~$3 billion in annual losses to global agriculture. Providing novel tools for bTB managements requires a comprehensive understanding of the molecular regulatory mechanisms underlying the M. bovis infection. Nevertheless, a combination of different bioinformatics and systems biology methods was used in this study in order to clearly understand the molecular regulatory mechanisms of bTB, especially the immunomodulatory mechanisms of M. bovis infection. METHODS RNA-seq data were retrieved and processed from 78 (39 non-infected control vs. 39 M. bovis-infected samples) bovine alveolar macrophages (bAMs). Next, weighted gene co-expression network analysis (WGCNA) was performed to identify the co-expression modules in non-infected control bAMs as reference set. The WGCNA module preservation approach was then used to identify non-preserved modules between non-infected controls and M. bovis-infected samples (test set). Additionally, functional enrichment analysis was used to investigate the biological behavior of the non-preserved modules and to identify bTB-specific non-preserved modules. Co-expressed hub genes were identified based on module membership (MM) criteria of WGCNA in the non-preserved modules and then integrated with protein-protein interaction (PPI) networks to identify co-expressed hub genes/transcription factors (TFs) with the highest maximal clique centrality (MCC) score (hub-central genes). RESULTS As result, WGCNA analysis led to the identification of 21 modules in the non-infected control bAMs (reference set), among which the topological properties of 14 modules were altered in the M. bovis-infected bAMs (test set). Interestingly, 7 of the 14 non-preserved modules were directly related to the molecular mechanisms underlying the host immune response, immunosuppressive mechanisms of M. bovis, and bTB development. Moreover, among the co-expressed hub genes and TFs of the bTB-specific non-preserved modules, 260 genes/TFs had double centrality in both co-expression and PPI networks and played a crucial role in bAMs-M. bovis interactions. Some of these hub-central genes/TFs, including PSMC4, SRC, BCL2L1, VPS11, MDM2, IRF1, CDKN1A, NLRP3, TLR2, MMP9, ZAP70, LCK, TNF, CCL4, MMP1, CTLA4, ITK, IL6, IL1A, IL1B, CCL20, CD3E, NFKB1, EDN1, STAT1, TIMP1, PTGS2, TNFAIP3, BIRC3, MAPK8, VEGFA, VPS18, ICAM1, TBK1, CTSS, IL10, ACAA1, VPS33B, and HIF1A, had potential targets for inducing immunomodulatory mechanisms by M. bovis to evade the host defense response. CONCLUSION The present study provides an in-depth insight into the molecular regulatory mechanisms behind M. bovis infection through biological investigation of the candidate non-preserved modules directly related to bTB development. Furthermore, several hub-central genes/TFs were identified that were significant in determining the fate of M. bovis infection and could be promising targets for developing novel anti-bTB therapies and diagnosis strategies.
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Affiliation(s)
- Aliakbar Hasankhani
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Abolfazl Bahrami
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
- Biomedical Center for Systems Biology Science Munich, Ludwig-Maximilians-University, Munich, Germany
| | - Shayan Mackie
- Faculty of Science, Earth Sciences Building, University of British Columbia, Vancouver, BC, Canada
| | - Sairan Maghsoodi
- Faculty of Paramedical Sciences, Kurdistan University of Medical Sciences, Kurdistan, Iran
| | - Heba Saed Kariem Alawamleh
- Department of Basic Scientific Sciences, AL-Balqa Applied University, AL-Huson University College, AL-Huson, Jordan
| | - Negin Sheybani
- Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Tehran, Iran
| | - Farhad Safarpoor Dehkordi
- Halal Research Center of IRI, FDA, Tehran, Iran
- Department of Food Hygiene and Quality Control, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Fatemeh Rajabi
- Department of Agronomy and Plant Breeding, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Ghazaleh Javanmard
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Hosein Khadem
- Department of Agronomy and Plant Breeding, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Herman W. Barkema
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Marcos De Donato
- Regional Department of Bioengineering, Tecnológico de Monterrey, Monterrey, Mexico
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Addo S, Jung L. An insight into the runs of homozygosity distribution and breed differentiation in Mangalitsa pigs. Front Genet 2022; 13:909986. [DOI: 10.3389/fgene.2022.909986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 09/30/2022] [Indexed: 11/13/2022] Open
Abstract
Mangalitsa pigs exhibit three distinct coat color patterns based on which they are described as Red, Blond, and Swallow-bellied. The current study investigated genome-wide diversity and selection signatures in the three breeds using fixation index, runs of homozygosity and population structure analyses. The analyses were originally based on quality-controlled data on 77 Mangalitsa animals from Germany, including 23 Blond, 30 Swallow-bellied and 24 Red Mangalitsa genotyped with a customized version of the ProcineSNP60 v2 Genotyping Bead Chip. Also, 20 Hungarian Mangalitsa genotypes were included as outgroup data for comparison. Estimates of observed heterozygosity were 0.27, 0.28, and 0.29, and inbreeding coefficients estimated based on runs of homozygosity were 24.11%, 20.82%, and 16.34% for Blond, Swallow-bellied and Red Mangalitsa, respectively. ROH islands were detected in all breeds, however, none of these were shared amongst them. The KIF16B gene previously reported to play a role in synaptic signaling was found in a ROH island (SSC17: 16–26) in Swallow-bellied Mangalitsa. The same gene was found to harbor a significantly differentiated SNP (MARC0032380) while contrasting either Blond or Red to Swallow-belied Mangalitsa. In the Red Mangalitsa, some ROH islands were associated with genes that play a role in meat quality traits, i.e., ABCA12, VIL1, PLSCR5, and USP37. Our population structure analysis highlighted a separation of the three breeds, but also showed the closest relatedness between Red and Blond Mangalitsa pigs. Findings of this study improve our understanding of the diversity in the three breeds of Mangalitsa pigs.
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Cortes-Hernández JG, Ruiz-López FJ, Vásquez-Peláez CG, García-Ruiz A. Runs of homocigosity and its association with productive traits in Mexican Holstein cattle. PLoS One 2022; 17:e0274743. [PMID: 36121861 PMCID: PMC9484644 DOI: 10.1371/journal.pone.0274743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 09/03/2022] [Indexed: 11/21/2022] Open
Abstract
The objective of this study was to describe the runs of homozygosity (ROH) detected in the Mexican Holstein population and to associate them with milk, fat and protein yields, and conformation final score. After imputation and genomic quality control, 4,227 genotyped animals with 100,806 SNPs markers each were used. ROH with a minimum length of 1 Mb and a minimum of 10 SNPs were included in the analysis. One heterozygous SNP marker and five missing genotypes per ROH were allowed. A total of 425,098 ROH were found in the studied population (71.83 ± 10.73 ROH per animal), with an average length and coverage of 4.80 ± 0.77 Mb, and 276.89 Mb, respectively. The average chromosome length covered by ROH was 10.40 ± 3.70 Mb. ROH between 1 and 2 Mb were the most frequent in the population (51.33%) while those between 14 and 16 Mb were the least frequent (1.20%). Long chromosomes showed a larger number of ROH. Chromosomes 10 and 20, had a greater percentage of their length covered by ROH because they presented a largest number of long ROH (>8 Mb). From the total ROH, 17 were detected in 1,847 animals and distributed among different chromosomes, and were associated with milk, fat and protein yield and percentage, and conformation final score. Of the ROH with effects on production traits, the majority were found with a length between 1 and 4 Mb. These results show evidence of genomic regions preserved by genetic selection and associated with the improvement of the productivity and functionality of dairy cattle.
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Affiliation(s)
- José G. Cortes-Hernández
- Programa de Maestría y Doctorado en Ciencias de la Producción y de la Salud Animal, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Felipe J. Ruiz-López
- Centro Nacional de Investigación Disciplinaria en Fisiología y Mejoramiento Animal, Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias, Ajuchitlán Colón Querétaro, México
| | - Carlos G. Vásquez-Peláez
- Departamento de Genética y Bioestadística de la Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Adriana García-Ruiz
- Centro Nacional de Investigación Disciplinaria en Fisiología y Mejoramiento Animal, Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias, Ajuchitlán Colón Querétaro, México
- * E-mail:
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11
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Supino D, Minute L, Mariancini A, Riva F, Magrini E, Garlanda C. Negative Regulation of the IL-1 System by IL-1R2 and IL-1R8: Relevance in Pathophysiology and Disease. Front Immunol 2022; 13:804641. [PMID: 35211118 PMCID: PMC8861086 DOI: 10.3389/fimmu.2022.804641] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 01/03/2022] [Indexed: 12/11/2022] Open
Abstract
Interleukin-1 (IL-1) is a primary cytokine of innate immunity and inflammation. IL-1 belongs to a complex family including ligands with agonist activity, receptor antagonists, and an anti-inflammatory cytokine. The receptors for these ligands, the IL-1 Receptor (IL-1R) family, include signaling receptor complexes, decoy receptors, and negative regulators. Agonists and regulatory molecules co-evolved, suggesting the evolutionary relevance of a tight control of inflammatory responses, which ensures a balance between amplification of innate immunity and uncontrolled inflammation. IL-1 family members interact with innate immunity cells promoting innate immunity, as well as with innate and adaptive lymphoid cells, contributing to their differentiation and functional polarization and plasticity. Here we will review the properties of two key regulatory receptors of the IL-1 system, IL-1R2, the first decoy receptor identified, and IL-1R8, a pleiotropic regulator of different IL-1 family members and co-receptor for IL-37, the anti-inflammatory member of the IL-1 family. Their complex impact in pathology, ranging from infections and inflammatory responses, to cancer and neurologic disorders, as well as clinical implications and potential therapeutic exploitation will be presented.
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Affiliation(s)
- Domenico Supino
- Department of Immunology and Inflammation, IRCCS Humanitas Research Hospital, Rozzano, Italy
| | - Luna Minute
- Department of Immunology and Inflammation, IRCCS Humanitas Research Hospital, Rozzano, Italy.,Department of Biomedical Science, Humanitas University, Pieve Emanuele, Italy
| | - Andrea Mariancini
- Department of Immunology and Inflammation, IRCCS Humanitas Research Hospital, Rozzano, Italy.,Department of Biomedical Science, Humanitas University, Pieve Emanuele, Italy
| | - Federica Riva
- Department of Veterinary Medicine, University of Milan, Milan, Italy
| | - Elena Magrini
- Department of Immunology and Inflammation, IRCCS Humanitas Research Hospital, Rozzano, Italy
| | - Cecilia Garlanda
- Department of Immunology and Inflammation, IRCCS Humanitas Research Hospital, Rozzano, Italy.,Department of Biomedical Science, Humanitas University, Pieve Emanuele, Italy
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12
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Identification of Copy Number Variations and Genetic Diversity in Italian Insular Sheep Breeds. Animals (Basel) 2022; 12:ani12020217. [PMID: 35049839 PMCID: PMC8773107 DOI: 10.3390/ani12020217] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/14/2022] [Accepted: 01/16/2022] [Indexed: 02/05/2023] Open
Abstract
Copy number variants (CNVs) are one of the major contributors to genetic diversity and phenotypic variation in livestock. The aim of this work is to identify CNVs and perform, for the first time, a CNV-based population genetics analysis with five Italian sheep breeds (Barbaresca, Comisana, Pinzirita, Sarda, and Valle del Belìce). We identified 10,207 CNVs with an average length of 1.81 Mb. The breeds showed similar mean numbers of CNVs, ranging from 20 (Sarda) to 27 (Comisana). A total of 365 CNV regions (CNVRs) were determined. The length of the CNVRs varied among breeds from 2.4 Mb to 124.1 Mb. The highest number of shared CNVRs was between Comisana and Pinzirita, and only one CNVR was shared among all breeds. Our results indicated that segregating CNVs expresses a certain degree of diversity across all breeds. Despite the low/moderate genetic differentiation among breeds, the different approaches used to disclose the genetic relationship showed that the five breeds tend to cluster in distinct groups, similar to the previous studies based on single-nucleotide polymorphism markers. Gene enrichment was described for the 37 CNVRs selected, considering the top 10%. Out of 181 total genes, 67 were uncharacterized loci. Gene Ontology analysis showed that several of these genes are involved in lipid metabolism, immune response, and the olfactory pathway. Our results corroborated previous studies and showed that CNVs represent valuable molecular resources for providing useful information for separating the population and could be further used to explore the function and evolutionary aspect of sheep genome.
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13
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Mazorra-Carrillo JL, Alcaraz-López OA, López-Rincón G, Villarreal-Ramos B, Gutiérrez-Pabello JA, Esquivel-Solís H. Host Serum Proteins as Potential Biomarkers of Bovine Tuberculosis Resistance Phenotype. Front Vet Sci 2021; 8:734087. [PMID: 34869715 PMCID: PMC8637331 DOI: 10.3389/fvets.2021.734087] [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: 06/30/2021] [Accepted: 10/25/2021] [Indexed: 12/19/2022] Open
Abstract
Eradication of bovine tuberculosis (bTB) continues to be a worldwide challenge. The lack of reliable vaccines dampens the control and eradication programs of Mycobacterium bovis infection and spread. Selection and breeding of cattle resistant to M. bovis infection would greatly enhance the effectiveness of bTB eradication programs. Here, we have evaluated the potential of serum proteins as biomarkers of cattle resistance to bTB in Holstein-Friesian cows, 6-8-year-old, born and raised in similar conditions in herds with bTB prevalence >30%. Serum proteins obtained from uninfected cows (bTB-resistant; R) were compared to those from infected cows (bTB-susceptible; S), defined by a negative or positive bTB diagnosis, respectively. bTB diagnosis included: (i) single intradermal (caudal fold) tuberculin test, (ii) whole blood IFN-gamma test, (iii) gross visible lesions in lymph nodes and lungs by inspection at the abattoir, and (iv) a bacteriological culture for M. bovis. Using 2D-GE and LC-ESI-MS/MS, we found higher expression levels of primary amine oxidase (AO), complement component 5 (C5), and serotransferrin (TF) in R cattle than S cattle. In-house developed and standardized ELISAs for these novel biomarkers showed the best sensitivities of 72, 77, 77%, and specificities of 94, 94, 83%, for AO, C5, and TF, respectively. AUC-ROC (95% CI) values of 0.8935 (0.7906-0.9964), 0.9290 (0.8484-1.010), and 0.8580 (0.7291-0.9869) were obtained at cut-off points of 192.0, 176.5 ng/ml, and 2.1 mg/ml for AO, C5, and TF, respectively. These proteins are involved in inflammatory/immunomodulatory responses to infections and may provide a novel avenue of research to determine the mechanisms of protection against bTB. Overall, our results indicate that these proteins could be novel biomarkers to help identify cattle resistant to bTB, which in turn could be used to strengthen the effectiveness of existing eradication programs against bTB.
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Affiliation(s)
- Jorge Luis Mazorra-Carrillo
- Biotecnología Médica y Farmacéutica, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, Guadalajara, Mexico
| | - Omar Antonio Alcaraz-López
- Biotecnología Médica y Farmacéutica, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, Guadalajara, Mexico.,Laboratorio de Investigación en Tuberculosis Bovina, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Gonzalo López-Rincón
- Biotecnología Médica y Farmacéutica, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, Guadalajara, Mexico
| | - Bernardo Villarreal-Ramos
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, United Kingdom.,Centre of Excellence for Bovine Tuberculosis, Institute for Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - José A Gutiérrez-Pabello
- Laboratorio de Investigación en Tuberculosis Bovina, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Hugo Esquivel-Solís
- Biotecnología Médica y Farmacéutica, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, Guadalajara, Mexico
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14
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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.
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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
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15
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Çınar MU, Akyüz B, Arslan K, White SN, Neibergs HL, Gümüşsoy KS. The EDN2 rs110287192 gene polymorphism is associated with paratuberculosis susceptibility in multibreed cattle population. PLoS One 2020; 15:e0238631. [PMID: 32881967 PMCID: PMC7470282 DOI: 10.1371/journal.pone.0238631] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 08/20/2020] [Indexed: 12/12/2022] Open
Abstract
Paratuberculosis (pTB), also known as Johne's disease (JD), is a contagious, chronic, and granulomatous inflammatory disease of the intestines of ruminants which is caused by Mycobacterium avium subsp. paratuberculosis (MAP) infection, resulting in billions of dollars in economic losses worldwide. Since, currently, no effective cure is available for MAP infection, it is important to explore the genetic variants that affect the host MAP susceptibility. The aim of this study was to analyze a potential association between EDN2 synonymous gene mutations (rs110287192, rs109651404 and rs136707411), that modifies susceptibility to pTB. EDN2 rs110287192, rs109651404 and rs136707411 mutations were genotyped in 68 infected and 753 healthy animals from East Anatolian Red crossbred, Anatolian Black crossbred and Holstein breed cattle by using Custom TaqMan SNP Genotyping Assays. For pTB status, serum antibody levels S/P ≥ 1.0 were assessed in carriers of the different EDN2 genotypes. EDN2 rs110287192 mutation showed a significant association with bovine pTB (adj. p < 0.05). For rs110287192 locus, the odd ratios for GG and TG genotypes versus TT genotypes were 1.73; (95% CI = 0.34–8.59) and 0.53 (95% CI = 0.12–2.37) respectively, which indicated that proportion of TG heterozygotes were significantly higher in control animals as compared to pTB animals. On the other hand, while rs136707411 mutation showed a suggestive association with pTB status in the examined cattle population (nominal p < 0.05); no association was detected between rs109651404 genotypes and pTB status. Selecting animals against rs110287192-GG genotype may decrease the risk of pTB in cattle of the Bos taurus taurus subspecies.
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Affiliation(s)
- Mehmet Ulaş Çınar
- Department of Animal Science, Faculty of Agriculture, Erciyes University, Kayseri, Turkey
- Department of Veterinary Microbiology & Pathology, Washington State University, Pullman, WA, United States of America
- * E-mail:
| | - Bilal Akyüz
- Department of Genetics, Faculty of Veterinary Medicine, Erciyes University, Kayseri, Turkey
| | - Korhan Arslan
- Department of Genetics, Faculty of Veterinary Medicine, Erciyes University, Kayseri, Turkey
| | - Stephen N. White
- Department of Veterinary Microbiology & Pathology, Washington State University, Pullman, WA, United States of America
- Animal Disease Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Pullman, WA, United States of America
- Center for Reproductive Biology, Washington State University, Pullman, WA, United States of America
| | - Holly L. Neibergs
- Center for Reproductive Biology, Washington State University, Pullman, WA, United States of America
- Department of Animal Science, Washington State University, Pullman, WA, United States of America
| | - Kadir Semih Gümüşsoy
- Department of Microbiology, Erciyes University, Faculty of Veterinary Medicine, Kayseri, Turkey
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16
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Shabalina T, Yin T, König S. Survival analyses in Holstein cows considering direct disease diagnoses and specific SNP marker effects. J Dairy Sci 2020; 103:8257-8273. [DOI: 10.3168/jds.2020-18174] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 05/07/2020] [Indexed: 12/11/2022]
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Gonzalez M, Villa R, Villa C, Gonzalez V, Montano M, Medina G, Mahadevan P. Inspection of real and imputed genotypes reveled 76 SNPs associated to rear udder height in Holstein cattle. J Adv Vet Anim Res 2020; 7:234-241. [PMID: 32607355 PMCID: PMC7320818 DOI: 10.5455/javar.2020.g415] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 03/24/2020] [Accepted: 03/30/2020] [Indexed: 12/14/2022] Open
Abstract
Objective This paper presents the obtained result of a study that realizes to associate a set of real and imputed single nucleotide polymorphisms (SNP) genotypes to the rear udder height in Holstein cows. Materials and methods Forty-six Holstein cows from an arid zone of Mexico were phenotyped and genotyped for this study. Blood samples were used for DNA extraction, genotyping was performed with the Illumina BovineLD Bead chip which interrogates 6,912 SNPs genome-wide, and imputation was performed using the Findhap software. After QC filters, a total of 22,251 high quality and informative SNPs were inspected. Results The results showed the detection of 76 significant SNPs throughout the complete genome. Significant SNPs fall inside 111 Quantitative Loci Traits related to protein percentage, milk yield, and fat, among others, in chromosomes 1, 2, 3, 5, 6, 9, 10, 11, 12, 13, 19, 20, 21, 23, 26, 27, and 29. Similarly, results confirm that a genotype imputation is a convenient option for genome-wide covering when selecting economic traits with low-density real SNP panels. Conclusion This study contributes to establishing a low-cost and profitable strategy for applying genomic selection in developing countries.
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Affiliation(s)
- Mirvana Gonzalez
- Laboratory of Bioinformatics and Biofotonics, Engineering Institute, Autonomous University of Baja California, Mexicali, B.C, Mexico
| | - Rafael Villa
- Laboratory of Bioinformatics and Biofotonics, Engineering Institute, Autonomous University of Baja California, Mexicali, B.C, Mexico
| | - Carlos Villa
- Laboratory of Bioinformatics and Biofotonics, Engineering Institute, Autonomous University of Baja California, Mexicali, B.C, Mexico
| | - Victor Gonzalez
- Institute for Research in Veterinary Science, Autonomous University of Baja California, Mexicali, B.C, Mexico
| | - Martin Montano
- Institute for Research in Veterinary Science, Autonomous University of Baja California, Mexicali, B.C, Mexico
| | - Gerardo Medina
- Institute for Research in Veterinary Science, Autonomous University of Baja California, Mexicali, B.C, Mexico
| | - Pad Mahadevan
- Department of Biology, University of Tampa, Tampa, FL, USA
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