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Panigrahi M, Rajawat D, Nayak SS, Jain K, Nayak A, Rajput AS, Sharma A, Dutt T. A comprehensive review on genomic insights and advanced technologies for mastitis prevention in dairy animals. Microb Pathog 2025; 199:107233. [PMID: 39694196 DOI: 10.1016/j.micpath.2024.107233] [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: 10/29/2024] [Revised: 12/12/2024] [Accepted: 12/15/2024] [Indexed: 12/20/2024]
Abstract
Mastitis is a multi-etiological disease that significantly impacts milk production and reproductive efficiency. It is highly prevalent in dairy populations subjected to intensive selection for higher milk yield and where inbreeding is common. The issue is amplified by climate change and poor hygiene management, making disease control challenging. Key obstacles include antibiotic resistance, maximum residue levels, horizontal gene transfer, and limited success in breeding for resistance. Predictive genomics offers a promising solution for mastitis prevention by identifying genetic traits linked with susceptibility to mastitis. This review compiles the research and findings on genomics and its allied approaches, such as pan-genomics, epigenetics, proteomics, and transcriptomics, for diagnosing, understanding, and treating mastitis. In dairy production, artificial intelligence (AI), particularly deep learning (DL) techniques like convolutional neural networks (CNNs), has demonstrated significant potential to enhance milk production and improve farm profitability. It highlights the integration of advanced technologies like machine learning (ML), CRISPR, and pan-genomics to improve our knowledge of mastitis epidemiology, pathogen evolution, and the development of more effective diagnostic, preventive and therapeutic strategies for dairy herds. Genomic advancements provide critical insights into the complexities of mastitis, offering new avenues for understanding its dynamics. Integrating these findings with key predisposing factors can drive targeted prevention and more effective disease management.
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Affiliation(s)
- Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122, UP, India.
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122, UP, India
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122, UP, India
| | - Karan Jain
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122, UP, India
| | - Ambika Nayak
- Division of Microbiology, Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122, UP, India
| | - Atul Singh Rajput
- Livestock Production and Management Section, Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122, UP, India
| | - Anurodh Sharma
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122, UP, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122, UP, India
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Lohova E, Pilmane M, Šerstņova K, Melderis I, Gontar Ł, Kochański M, Drutowska A, Maróti G, Prieto-Simón B. Analysis of Inflammatory and Regulatory Cytokines in the Milk of Dairy Cows with Mastitis: A Comparative Study with Healthy Animals. Immunol Invest 2024; 53:1397-1421. [PMID: 39287131 DOI: 10.1080/08820139.2024.2404623] [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] [Indexed: 09/19/2024]
Abstract
Bovine mastitis remains a major problem in the global dairy cattle industry. The acute invasion of udder by pathogens induces innate immune response as the first defence mechanism in subclinical and clinical mastitis. The aim of the study was to determine inflammatory and regulatory cytokines IL-2, IL-4, TGF-β1, IL-17A, beta-defensin 3 and IL-10 and their potential changes in milk of dairy cows with subclinical and clinical mastitis, and to compare the findings with healthy animals. Milk samples from 15 holstein Friesian breed cows were used in the study. Cows were divided into three groups based on their health status (5 healthy, 5 subclinical and 5 clinical animals). All samples were tested using immunohistochemistry to evaluate IL-2, IL-4, IL-10, IL17A, TGF-β1 and β-Def 3 proteins. Expression of all proteins was detected in all milk samples. High expression of IL-2, IL-4, IL17A, TGF-β1 was detected in healthy cows' milk and in milk of cows with subclinical and clinical mastitis. However, expression of IL-10 and β-Def 3 in milk samples of healthy cows was significantly higher compared to the milk of cows with subclinical and clinical mastitis (p < .001). IL-10 and β-Def 3 can be considered as informative biomarkers in diagnosis of subclinical and clinical mastitis.
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Affiliation(s)
- Elizabeta Lohova
- The Institute of Anatomy and Anthropology, Rīga Stradiņš University, Rīga, Latvia
| | - Mara Pilmane
- The Institute of Anatomy and Anthropology, Rīga Stradiņš University, Rīga, Latvia
| | - Ksenija Šerstņova
- The Institute of Anatomy and Anthropology, Rīga Stradiņš University, Rīga, Latvia
| | - Ivars Melderis
- The Institute of Anatomy and Anthropology, Rīga Stradiņš University, Rīga, Latvia
| | - Łukasz Gontar
- Research and Innovation Centre Pro-Akademia, Centrum Badan i Innowacji Pro-Akademia, Konstantynów Łódzki, Poland
| | - Maksymilian Kochański
- Research and Innovation Centre Pro-Akademia, Centrum Badan i Innowacji Pro-Akademia, Konstantynów Łódzki, Poland
| | - Andzelika Drutowska
- Research and Innovation Centre Pro-Akademia, Centrum Badan i Innowacji Pro-Akademia, Konstantynów Łódzki, Poland
| | - Gergely Maróti
- Seqomics Biotechnology Ltd., Morahalom, Hungary
- Biological Research Center, Plant Biology Institute, Szeged, Hungary
| | - Beatriz Prieto-Simón
- Department of Electronic Engineering, Universitat Rovira i Virgili, Tarragona, Spain
- ICREA, Barcelona, Spain
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Ghiasi H, Khaldari M, Taherkhani R. Identification of hub genes associated with somatic cell score in dairy cow. Trop Anim Health Prod 2023; 55:349. [PMID: 37796357 DOI: 10.1007/s11250-023-03766-2] [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: 10/26/2022] [Accepted: 09/19/2023] [Indexed: 10/06/2023]
Abstract
CONTEXT Somatic cell count (SCC) is used as an indicator of udder health. The log transformation of SCC is called somatic cell score (SCS). AIM Several QTL and genes have been identified that are associated with SCS. This study aimed to identify the most important genes associated with SCS. METHODS This study compiled 168 genes that were reported to be significantly linked to SCS. Pathway analysis and network analysis were used to identify hub genes. KEY RESULTS Pathway analysis of these genes identified 73 gene ontology (GO) terms associated with SCS. These GO terms are associated with molecular function, biological processes, and cellular components, and the identified pathways are directly or indirectly linked with the immune system. In this study, a gene network was constructed, and from this network, the 17 hub genes (CD4, CXCL8, TLR4, STAT1, TLR2, CXCL9, CCR2, IGF1, LEP, SPP1, GH1, GHR, VWF, TNFSF11, IL10RA, NOD2, and PDGFRB) associated to SCS were identified. The subnetwork analysis yielded 10 clusters, with cluster 1 containing all identified hub genes (except for the VWF gene). CONCLUSION Most hub genes and pathways identified in our study were mainly involved in inflammatory and cytokine responses. IMPLICATIONS Result obtained in current study provides knowledge of the genetic basis and biological mechanisms controlling SCS. Therefore, the identified hub genes may be regarded as the main gene for the genomic selection of mastitis resistance.
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Affiliation(s)
- Heydar Ghiasi
- Department of Animal Science, Faculty of Agricultural Science, Payame Noor University, Tehran, 19395-4697, Iran.
| | - Majid Khaldari
- Department of Animal Science, Faculty of Agriculture, Lorestan University, Khorram-Abad, Iran
| | - Reza Taherkhani
- Department of Animal Science, Faculty of Agricultural Science, Payame Noor University, Tehran, 19395-4697, Iran
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Al-Sharif M, Abdo M, Shabrawy OE, El-Naga EMA, Fericean L, Banatean-Dunea I, Ateya A. Investigating Polymorphisms and Expression Profile of Immune, Antioxidant, and Erythritol-Related Genes for Limiting Postparturient Endometritis in Holstein Cattle. Vet Sci 2023; 10:370. [PMID: 37368756 DOI: 10.3390/vetsci10060370] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 05/18/2023] [Accepted: 05/22/2023] [Indexed: 06/29/2023] Open
Abstract
This study looked at genetic polymorphisms and transcript levels of immune, antioxidant, and erythritol-related markers for postparturient endometritis prediction and tracking in Holstein dairy cows. One hundred and thirty female dairy cows (65 endometritis affected and 65 apparently healthy) were used. Nucleotide sequence variations between healthy and endometritis-affected cows were revealed using PCR-DNA sequencing for immune (TLR4, TLR7, TNF-α, IL10, NCF4, and LITAF), antioxidant (ATOX1, GST, and OXSR1), and erythritol-related (TKT, RPIA, and AMPD1) genes. Chi-square investigation exposed a noteworthy variance amongst cow groups with and without endometritis in likelihood of dispersal of all distinguished nucleotide variants (p < 0.05). The IL10, ATOX1, and GST genes were expressed at substantially lower levels in endometritis-affected cows. Gene expression levels were considerably higher in endometritis-affected cows than in resistant ones for the genes TLR4, TLR7, TNF-α, NCF4, LITAF, OXSR1, TKT, RPIA, and AMPD1. The sort of marker and vulnerability or resistance to endometritis had a significant impact on the transcript levels of the studied indicators. The outcomes might confirm the importance of nucleotide variants along with gene expression patterns as markers of postparturient endometritis susceptibility/resistance and provide a workable control plan for Holstein dairy cows.
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Affiliation(s)
- Mona Al-Sharif
- Department of Biology, College of Science, University of Jeddah, Jeddah 21589, Saudi Arabia
| | - Mohamed Abdo
- Department of Animal Histology and Anatomy, School of Veterinary Medicine, Badr University in Cairo (BUC), Cairo 11829, Egypt
- Department of Anatomy and Embryology, Faculty of Veterinary Medicine, University of Sadat City, Sadat City 32897, Egypt
| | - Omnia El Shabrawy
- Department of Biochemistry and Chemistry of Nutrition, Faculty of Veterinary Medicine, Menofia University, Menofia 32951, Egypt
| | - Eman M Abu El-Naga
- Department of Theriogenology, Faculty of Veterinary Medicine, Aswan University, Aswan 81528, Egypt
| | - Liana Fericean
- Department of Biology and Plant Protection, Faculty of Agricultural Sciences, University of Life Sciences King Michael I, 300645 Timisoara, Romania
| | - Ioan Banatean-Dunea
- Department of Biology and Plant Protection, Faculty of Agricultural Sciences, University of Life Sciences King Michael I, 300645 Timisoara, Romania
| | - Ahmed Ateya
- Department of Development of Animal Wealth, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt
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Mallikarjunappa S, Shandilya UK, Sharma A, Lamers K, Bissonnette N, Karrow NA, Meade KG. Functional analysis of bovine interleukin-10 receptor alpha in response to Mycobacterium avium subsp. paratuberculosis lysate using CRISPR/Cas9. BMC Genet 2020; 21:121. [PMID: 33138773 PMCID: PMC7607837 DOI: 10.1186/s12863-020-00925-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 10/20/2020] [Indexed: 12/21/2022] Open
Abstract
Background The interleukin-10 receptor alpha (IL10RA) gene codes for the alpha chain of the IL-10 receptor which binds the cytokine IL-10. IL-10 is an anti-inflammatory cytokine with immunoregulatory function during the pathogenesis of many inflammatory disorders in livestock, including Johne’s disease (JD). JD is a chronic enteritis in cattle caused by Mycobacterium avium subsp. paratuberculosis (MAP) and is responsible for significant economic losses to the dairy industry. Several candidate genes including IL10RA have been found to be associated with JD. The aim of this study was to better understand the functional significance of IL10RA in the context of immune stimulation with MAP cell wall lysate. Results An IL10RA knock out (KO) bovine mammary epithelial cell (MAC-T) line was generated using the CRISPR/cas9 (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 9) gene editing system. These IL10RA KO cells were stimulated with the immune stimulant MAP lysate +/− IL-10, or with LPS as a positive control. In comparison to unedited cells, relative quantification of immune-related genes after stimulation revealed that knocking out IL10RA resulted in upregulation of pro-inflammatory cytokine gene expression (TNFA, IL1A, IL1B and IL6) and downregulation of suppressor of cytokine signaling 3 (SOCS3), a negative regulator of pro-inflammatory cytokine signaling. At the protein level knocking out IL10RA also resulted in upregulation of inflammatory cytokines - TNF-α and IL-6 and chemokines - IL-8, CCL2 and CCL4, relative to unedited cells. Conclusions The findings of this study illustrate the broad and significant effects of knocking out the IL10RA gene in enhancing pro-inflammatory cytokine expression and further support the immunoregulatory role of IL10RA in eliciting an anti-inflammatory response as well as its potential functional involvement during the immune response associated with JD.
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Affiliation(s)
- Sanjay Mallikarjunappa
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Co. Meath, Ireland.,Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Umesh K Shandilya
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Ankita Sharma
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Kristen Lamers
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Nathalie Bissonnette
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, J1M 0C8, Canada
| | - Niel A Karrow
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Kieran G Meade
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Co. Meath, Ireland.
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Hasenauer FC, Rossi UA, Caffaro ME, Raschia MA, Maurizio E, Poli MA, Rossetti CA. Association of TNF rs668920841 and INRA111 polymorphisms with caprine brucellosis: A case-control study of candidate genes involved in innate immunity. Genomics 2020; 112:3925-3932. [PMID: 32629097 DOI: 10.1016/j.ygeno.2020.06.050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 05/25/2020] [Accepted: 06/28/2020] [Indexed: 01/24/2023]
Abstract
Caprine brucellosis is an infectious, contagious zoonotic disease caused by Brucella melitensis. Multiple factors, including host genetics, can influence the outcome of the exposure to Brucella; and it is expected that genetic variants that affect the host innate immune response could have a key role in Brucella infection and pathogenesis. In this study, we evaluated if polymorphisms in innate immunity-related genes are associated with results of Brucella infection in goats. Nine polymorphisms within interferon gamma (IFNG), tumor necrosis factor (TNF), MyD88 innate immune signal transduction adaptor (MYD88), interleukin 10 (IL10) and IL-10 receptor subunit alpha (IL10RA) genes and two molecular markers (BMS2753 and INRA111) were resolved by PCR-capillary electrophoresis in samples from 81 seronegative and 61 seropositive goats for brucellosis. A heterozygous genotype at INRA111, a microsatellite near the VRK serine/threonine kinase 2 (VRK2) gene, was associated with absence of Brucella-specific antibodies in goats naturally exposed to the pathogen (P = .004). Conversely, variants in the TNF gene (rs668920841) and near the IFN gamma receptor 1 (IFNGR1) gene (microsatellite BMS2753) were significantly associated with presence of Brucella-specific antibodies at allelic (P = .042 and P = .046) and genotypic level (P = .012 and P = .041, respectively). Moreover, an in silico analysis predicted a functional role of the insertion-deletion polymorphism rs668920841 on the transcriptional regulation of the caprine TNF gene. Altogether, these results contribute to the identification of genetic factors that have a putative effect on the resistance / susceptibility phenotype of goats to Brucella infection.
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Affiliation(s)
- F C Hasenauer
- Instituto de Patobiología, CICVyA, INTA, Nicolás Repetto y de Los Reseros s/n, Hurlingham, B1686, Buenos Aires, Argentina; CONICET, Godoy Cruz 2290, C1425 CABA, Argentina
| | - U A Rossi
- Instituto de Patobiología, CICVyA, INTA, Nicolás Repetto y de Los Reseros s/n, Hurlingham, B1686, Buenos Aires, Argentina; CONICET, Godoy Cruz 2290, C1425 CABA, Argentina
| | - M E Caffaro
- Instituto de Genética "Ewald A. Favret", CICVyA, INTA, Nicolás Repetto y de Los Reseros s/n, Hurlingham, B1686, Buenos Aires, Argentina
| | - M A Raschia
- Instituto de Genética "Ewald A. Favret", CICVyA, INTA, Nicolás Repetto y de Los Reseros s/n, Hurlingham, B1686, Buenos Aires, Argentina
| | - E Maurizio
- Instituto de Patobiología, CICVyA, INTA, Nicolás Repetto y de Los Reseros s/n, Hurlingham, B1686, Buenos Aires, Argentina; CONICET, Godoy Cruz 2290, C1425 CABA, Argentina
| | - M A Poli
- Instituto de Genética "Ewald A. Favret", CICVyA, INTA, Nicolás Repetto y de Los Reseros s/n, Hurlingham, B1686, Buenos Aires, Argentina
| | - C A Rossetti
- Instituto de Patobiología, CICVyA, INTA, Nicolás Repetto y de Los Reseros s/n, Hurlingham, B1686, Buenos Aires, Argentina.
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Haubert L, Kroning IS, Iglesias MA, da Silva WP. First report of the Staphylococcus aureus isolate from subclinical bovine mastitis in the South of Brazil harboring resistance gene dfrG and transposon family Tn 916-1545. Microb Pathog 2017; 113:242-247. [DOI: 10.1016/j.micpath.2017.10.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 10/10/2017] [Accepted: 10/13/2017] [Indexed: 01/03/2023]
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Kopper JJ, Patterson JS, Mansfield LS. Metronidazole—but not IL-10 or prednisolone—rescues Trichuris muris infected C57BL/6 IL-10 deficient mice from severe disease. Vet Parasitol 2015; 212:239-52. [DOI: 10.1016/j.vetpar.2015.07.038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 07/24/2015] [Accepted: 07/31/2015] [Indexed: 10/23/2022]
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Thompson-Crispi K, Atalla H, Miglior F, Mallard BA. Bovine mastitis: frontiers in immunogenetics. Front Immunol 2014; 5:493. [PMID: 25339959 PMCID: PMC4188034 DOI: 10.3389/fimmu.2014.00493] [Citation(s) in RCA: 122] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 09/23/2014] [Indexed: 12/24/2022] Open
Abstract
Mastitis is one of the most prevalent and costly diseases in the dairy industry with losses attributable to reduced milk production, discarded milk, early culling, veterinary services, and labor costs. Typically, mastitis is an inflammation of the mammary gland most often, but not limited to, bacterial infection, and is characterized by the movement of leukocytes and serum proteins from the blood to the site of infection. It contributes to compromised milk quality and the potential spread of antimicrobial resistance if antibiotic treatment is not astutely applied. Despite the implementation of management practises and genetic selection approaches, bovine mastitis control continues to be inadequate. However, some novel genetic strategies have recently been demonstrated to reduce mastitis incidence by taking advantage of a cow's natural ability to make appropriate immune responses against invading pathogens. Specifically, dairy cattle with enhanced and balanced immune responses have a lower occurrence of disease, including mastitis, and they can be identified and selected for using the high immune response (HIR) technology. Enhanced immune responsiveness is also associated with improved response to vaccination, increased milk, and colostrum quality. Since immunity is an important fitness trait, beneficial associations with longevity and reproduction are also often noted. This review highlights the genetic regulation of the bovine immune system and its vital contributions to disease resistance. Genetic selection approaches currently used in the dairy industry to reduce the incidence of disease are reviewed, including the HIR technology, genomics to improve disease resistance or immune response, as well as the Immunity(+)™ sire line. Improving the overall immune responsiveness of cattle is expected to provide superior disease resistance, increasing animal welfare and food quality while maintaining favorable production levels to feed a growing population.
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Affiliation(s)
- Kathleen Thompson-Crispi
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada
- Center for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, Canada
| | - Heba Atalla
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada
- Center for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, Canada
- Department of Biomedical Science, University of Guelph, Guelph, ON, Canada
- Department of Animal and Poultry Science, University of Guelph, Guelph, ON, Canada
| | - Filippo Miglior
- Center for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, Canada
- Canadian Dairy Network, Guelph, ON, Canada
| | - Bonnie A. Mallard
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada
- Center for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, Canada
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Cochran SD, Cole JB, Null DJ, Hansen PJ. Discovery of single nucleotide polymorphisms in candidate genes associated with fertility and production traits in Holstein cattle. BMC Genet 2013; 14:49. [PMID: 23759029 PMCID: PMC3686577 DOI: 10.1186/1471-2156-14-49] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 05/23/2013] [Indexed: 11/22/2022] Open
Abstract
Background Identification of single nucleotide polymorphisms (SNPs) for specific genes involved in reproduction might improve reliability of genomic estimates for these low-heritability traits. Semen from 550 Holstein bulls of high (≥ 1.7; n = 288) or low (≤ −2; n = 262) daughter pregnancy rate (DPR) was genotyped for 434 candidate SNPs using the Sequenom MassARRAY® system. Three types of SNPs were evaluated: SNPs previously reported to be associated with reproductive traits or physically close to genetic markers for reproduction, SNPs in genes that are well known to be involved in reproductive processes, and SNPs in genes that are differentially expressed between physiological conditions in a variety of tissues associated in reproductive function. Eleven reproduction and production traits were analyzed. Results A total of 40 SNPs were associated (P < 0.05) with DPR. Among these were genes involved in the endocrine system, cell signaling, immune function and inhibition of apoptosis. A total of 10 genes were regulated by estradiol. In addition, 22 SNPs were associated with heifer conception rate, 33 with cow conception rate, 36 with productive life, 34 with net merit, 23 with milk yield, 19 with fat yield, 13 with fat percent, 19 with protein yield, 22 with protein percent, and 13 with somatic cell score. The allele substitution effect for SNPs associated with heifer conception rate, cow conception rate, productive life and net merit were in the same direction as for DPR. Allele substitution effects for several SNPs associated with production traits were in the opposite direction as DPR. Nonetheless, there were 29 SNPs associated with DPR that were not negatively associated with production traits. Conclusion SNPs in a total of 40 genes associated with DPR were identified as well as SNPs for other traits. It might be feasible to include these SNPs into genomic tests of reproduction and other traits. The genes associated with DPR are likely to be important for understanding the physiology of reproduction. Given the large number of SNPs associated with DPR that were not negatively associated with production traits, it should be possible to select for DPR without compromising production.
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Affiliation(s)
- Sarah D Cochran
- Department of Animal Sciences, D.H. Barron Reproductive and Perinatal Biology Research Program, and Genetics Institute, University of Florida, Gainesville, FL 32611-0910, USA
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Olbromski R, Siadkowska E, Zelazowska B, Zwierzchowski L. Allelic gene expression imbalance of bovine IGF2, LEP and CCL2 genes in liver, kidney and pituitary. Mol Biol Rep 2012. [PMID: 23184004 PMCID: PMC3538019 DOI: 10.1007/s11033-012-2161-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Allelic expression imbalance (AEI) is an important genetic factor being the cause of differences in phenotypic traits that can be heritable. Studying AEI can be useful in searching for factors that modulate gene expression and help to understand molecular mechanisms underlying phenotypic changes. Although it was commonly recognized in many species and we know many genes show allelic expression imbalance, this phenomena was not studied on a larger scale in cattle. Using the pyrosequencing method we analyzed a set of 29 bovine genes in order to find those that have preferential allelic expression. The study was conducted in three tissues: liver, pituitary and kindey. Out of the studied group of genes 3 of them—LEP (leptin), IGF2 (insulin-like growth factor 2), CCL2 (chemokine C–C motif ligand 2) showed allelic expression imbalance.
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Affiliation(s)
- R Olbromski
- Department of Molecular Biology, Institute of Genetics and Animal Breeding, Polish Academy of Sciences (IGAB PAS), Jastrzębiec, 05-552, Magdalenka, Poland.
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Yuan Z, Li J, Li J, Gao X, Xu S. SNPs identification and its correlation analysis with milk somatic cell score in bovine MBL1 gene. Mol Biol Rep 2012; 40:7-12. [PMID: 23114911 DOI: 10.1007/s11033-012-1934-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 10/01/2012] [Indexed: 10/27/2022]
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Leach RJ, O'Neill RG, Fitzpatrick JL, Williams JL, Glass EJ. Quantitative trait loci associated with the immune response to a bovine respiratory syncytial virus vaccine. PLoS One 2012; 7:e33526. [PMID: 22438944 PMCID: PMC3305305 DOI: 10.1371/journal.pone.0033526] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Accepted: 02/15/2012] [Indexed: 12/05/2022] Open
Abstract
Infectious disease is an important problem for animal breeders, farmers and governments worldwide. One approach to reducing disease is to breed for resistance. This linkage study used a Charolais-Holstein F2 cattle cross population (n = 501) which was genotyped for 165 microsatellite markers (covering all autosomes) to search for associations with phenotypes for Bovine Respiratory Syncytial Virus (BRSV) specific total-IgG, IgG1 and IgG2 concentrations at several time-points pre- and post-BRSV vaccination. Regions of the bovine genome which influenced the immune response induced by BRSV vaccination were identified, as well as regions associated with the clearance of maternally derived BRSV specific antibodies. Significant positive correlations were detected within traits across time, with negative correlations between the pre- and post-vaccination time points. The whole genome scan identified 27 Quantitative Trait Loci (QTL) on 13 autosomes. Many QTL were associated with the Thymus Helper 1 linked IgG2 response, especially at week 2 following vaccination. However the most significant QTL, which reached 5% genome-wide significance, was on BTA 17 for IgG1, also 2 weeks following vaccination. All animals had declining maternally derived BRSV specific antibodies prior to vaccination and the levels of BRSV specific antibody prior to vaccination were found to be under polygenic control with several QTL detected. Heifers from the same population (n = 195) were subsequently immunised with a 40-mer Foot-and-Mouth Disease Virus peptide (FMDV) in a previous publication. Several of these QTL associated with the FMDV traits had overlapping peak positions with QTL in the current study, including the QTL on BTA23 which included the bovine Major Histocompatibility Complex (BoLA), and QTL on BTA9 and BTA24, suggesting that the genes underlying these QTL may control responses to multiple antigens. These results lay the groundwork for future investigations to identify the genes underlying the variation in clearance of maternal antibody and response to vaccination.
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Affiliation(s)
- Richard J Leach
- Department of Genetics and Genomics, The Roslin Institute and Royal, Dick, School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, United Kingdom.
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Pighetti GM, Elliott AA. Gene polymorphisms: the keys for marker assisted selection and unraveling core regulatory pathways for mastitis resistance. J Mammary Gland Biol Neoplasia 2011; 16:421-32. [PMID: 21997401 DOI: 10.1007/s10911-011-9238-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Accepted: 09/23/2011] [Indexed: 12/11/2022] Open
Abstract
One of the most frequent mammary diseases impacting lactating animals is mastitis, an inflammation of the mammary gland most commonly caused by bacterial infection. The severity of mastitis is greatly influenced by the invading organism and the subsequent immune response which must recognize the foreign organism, recruit immune cells, eliminate the invading pathogen, and resolve the inflammatory response. The speed, strength, and duration of this response and subsequent disease susceptibility are critically tied to the genetic background of an animal. However, the genetic contribution has been difficult to identify due to the complex interactions that must occur for effective disease resistance. Recent studies have utilized polymorphisms to better define the genes and chromosomal regions that contribute to mastitis resistance. This review will examine these studies with primary emphasis in bovine systems, as the most work regarding mastitis has been conducted in this species.
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Affiliation(s)
- Gina M Pighetti
- Department of Animal Science, The University of Tennessee, Knoxville, TN 37996, USA.
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Verschoor CP, Pant SD, You Q, Schenkel FS, Kelton DF, Karrow NA. Single nucleotide polymorphisms alter the promoter activity of bovine MIF. Anim Biotechnol 2011; 22:143-50. [PMID: 21774622 DOI: 10.1080/10495398.2011.580219] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Macrophage migration inhibitory factor (MIF) is a unique pro-inflammatory cytokine whose chief functions include modulating TLR4 expression, and suppressing the anti-inflammatory effects of glucocorticoids. Not surprisingly, MIF is involved in a number of inflammatory diseases and single nucleotide polymorphisms (SNPs) have been implicated in modulating disease severity. The objective of the present study was to determine if SNPs in 5' region of bovine MIF affects its promoter activity. Three SNPs were identified, -1078A>G, -395A>G, and -400G>C, all of which fall within predicted transcription factor binding regions. Reporter gene assays indicate that the identified SNPs have a significant effect of modulating MIF promoter activity. Finally, gene association analysis suggests a significant relationship of -395A>G with the susceptibility to Mycobacterium avium ssp. paratuberculosis infection, the causative agent of Johne's disease. Given the relationships revealed in the current study, it is clear that the role of MIF in bovine diseases such as Johne's disease merits further investigation.
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Affiliation(s)
- C P Verschoor
- Centre for Genetic Improvement of Livestock, Department of Animal and Poultry Science, University of Guelph, Guelph, Ontario, Canada
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Verschoor CP, Pant SD, Biggar GA, Schenkel FS, Sharma BS, Karrow NA. Identification of SNPs in interferon gamma, interleukin-22, and their receptors and associations with health and production-related traits in Canadian Holstein bulls. Anim Biotechnol 2011; 22:7-15. [PMID: 21328101 DOI: 10.1080/10495398.2011.536078] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Genetic variants in a number of immunoregulatory genes have been previously associated with health and production traits in dairy cattle. Therefore, in the following study, the genes coding interferon gamma (IFNG), IFNG receptor 1 and 2 domains, interleukin-22 (IL22), and IL22 receptor alpha 1, were investigated for single nucleotide polymorphisms (SNPs) in Holstein bulls. These SNPs, along with SNPs previously identified in IL10, IL10 receptor, and transforming growth factor beta 1 (TGFB1) genes, were evaluated for statistical associations to estimated breeding values for milk somatic cell score (SCS), a trait highly correlated to mastitis incidence, and various production-related traits, including milk yield, protein yield, fat yield, and lactation persistency. While no significant associations were found between these SNPs and SCS, SNPs in IL10 receptor beta subunit showed a significant effect on protein yield and lactation persistency. While there is evidence that IL10 plays an important role during lactation, it is also likely that the effects of SNPs in IL10 receptor beta subunit on protein yield and lactation persistency are due to linkage disequilibrium with a neighboring QTL.
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Affiliation(s)
- Chris P Verschoor
- Centre for Genetic Improvement of Livestock, Department of Animal and Poultry Science, University of Guelph, Guelph, Ontario, Canada
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Verschoor CP, Pant SD, You Q, Schenkel FS, Kelton DF, Karrow NA. Polymorphisms in the gene encoding bovine interleukin-10 receptor alpha are associated with Mycobacterium avium ssp. paratuberculosis infection status. BMC Genet 2010; 11:23. [PMID: 20398313 PMCID: PMC2873551 DOI: 10.1186/1471-2156-11-23] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2009] [Accepted: 04/15/2010] [Indexed: 02/08/2023] Open
Abstract
Background Johne's disease is a chronic inflammatory bowel disease (IBD) of ruminants caused by Mycobacterium avium ssp. paratuberculosis (MAP). Since this pathogen has been implicated in the pathogenesis of human IBDs, the goal of this study was to assess whether single nucleotide polymorphism (SNPs) in several well-known candidate genes for human IBD are associated with susceptibility to MAP infection in dairy cattle. Methods The bovine candidate genes, interleukin-10 (IL10), IL10 receptor alpha/beta (IL10RA/B), transforming growth factor beta 1 (TGFB1), TGFB receptor class I/II (TGFBR1/2), and natural resistance-associated macrophage protein 1 (SLC11A1) were sequenced for SNP discovery using pooled DNA samples, and the identified SNPs were genotyped in a case-control association study comprised of 242 MAP negative and 204 MAP positive Holstein dairy cattle. Logistic regression was used to determine the association of SNPs and reconstructed haplotypes with MAP infection status. Results A total of 13 SNPs were identified. Four SNPs in IL10RA (984G > A, 1098C > T, 1269T > C, and 1302A > G) were tightly linked, and showed a strong additive and dominance relationship with MAP infection status. Haplotypes AGC and AAT, containing the SNPs IL10RA 633C > A, 984G > A and 1185C > T, were associated with an elevated and reduced likelihood of positive diagnosis by serum ELISA, respectively. Conclusions SNPs in IL10RA are associated with MAP infection status in dairy cattle. The functional significance of these SNPs warrants further investigation.
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Affiliation(s)
- Chris P Verschoor
- Centre for Genetic Improvement of Livestock, Department of Animal and Poultry Science, University of Guelph, 50 Stone Rd East, Guelph, Ontario, N1G2W1, Canada
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