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Novo LC, Parker Gaddis KL, Wu XL, McWhorter TM, Burchard J, Norman HD, Dürr J, Fourdraine R, Peñagaricano F. Genetic Parameters and Genetic Trends for Johne's Disease in U.S. Holsteins: An Updated Study. J Dairy Sci 2024:S0022-0302(24)00515-0. [PMID: 38428495 DOI: 10.3168/jds.2023-23788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 02/01/2024] [Indexed: 03/03/2024]
Abstract
Johne's disease (JD) is an infectious enteric disease in ruminants, causing substantial economic loss annually worldwide. This work aimed to estimate JD's genetic parameters and the phenotypic and genetic trends by incorporating recent data. It also explores the feasibility of a national genetic evaluation for JD susceptibility in Holstein cattle in the United States (US). The data were extracted from a Johne's disease data repository, maintained at the Council on Dairy Cattle Breeding (CDCB), and initially supplied by 2 dairy records processing centers. The data comprised 365,980 Holstein cows from 1,048 herds participating in a voluntary control program for JD. Two protocol kits, Idexx Paratuberculosis Screening Ab Test (IDX) and Parachek® 2 (PCK), were used to analyze milk samples with the Enzyme-Linked Immunosorbent Assay (ELISA) technique. Test results from the first 5 parities were considered. An animal was considered infected if it had at least one positive outcome. The overall average of JD incidence was 4.72% in these US Holstein cattle. Genotypes of 78,964 SNP markers were used for 25,000 animals randomly selected from the phenotyped population. Variance components and genetic parameters were estimated based on 3 models, namely, a pedigree-only threshold model (THR), a single-step threshold model (ssTHR), and a single-step linear model (ssLR). The posterior heritability estimates of JD susceptibility were low to moderate: 0.11 to 0.16 based on the 2 threshold models and 0.05 to 0.09 based on the linear model. The average reliability of estimated breeding values of JD susceptibility using single-step analysis for animals with or without phenotypes varied from 0.18 (THR) to 0.22 (ssLR) for IDX and from 0.14 (THR) to 0.18 (ssTHR and ssLR) for PCK. Despite no prior direct genetic selection against JD, the estimated genetic trends of JD susceptibility were negative and highly significant (P-value <0.01). The correlations of bulls' predicted transmitting abilities with economically important traits such as milk yield, milk protein, milk fat, somatic cell score, and mastitis were low, indicating a non-overlapping genetic selection process with traits in current genetic evaluations. Our results suggest the feasibility of reducing the JD incidence rate by incorporating it into the national genetic evaluation programs.
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Affiliation(s)
- Larissa C Novo
- Department of Animal and Dairy Sciences, University of Wisconsin, Madison, WI 53706, USA; Council on Dairy Cattle Breeding, Bowie, MD 20716, USA.
| | | | - Xiao-Lin Wu
- Department of Animal and Dairy Sciences, University of Wisconsin, Madison, WI 53706, USA; Council on Dairy Cattle Breeding, Bowie, MD 20716, USA
| | - T M McWhorter
- Council on Dairy Cattle Breeding, Bowie, MD 20716, USA
| | | | | | - João Dürr
- Council on Dairy Cattle Breeding, Bowie, MD 20716, USA
| | | | - Francisco Peñagaricano
- Department of Animal and Dairy Sciences, University of Wisconsin, Madison, WI 53706, USA
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Sanchez MP, Tribout T, Fritz S, Guatteo R, Fourichon C, Schibler L, Delafosse A, Boichard D. New insights into the genetic resistance to paratuberculosis in Holstein cattle via single-step genomic evaluation. Genet Sel Evol 2022; 54:67. [PMID: 36243688 PMCID: PMC9569073 DOI: 10.1186/s12711-022-00757-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 09/24/2022] [Indexed: 11/10/2022] Open
Abstract
Background Bovine paratuberculosis, or Johne’s disease (JD), is a contagious and incurable disease caused by Mycobacterium avium subsp. paratuberculosis (MAP). It has adverse effects on animal welfare and is very difficult to control, leading to serious economic consequences. An important line of defense to this disease is host genetic resistance to MAP, which, when it will be more fully understood, could be improved through selective breeding. Using a large dataset of Holstein cows (161,253 animals including 56,766 cows with ELISA serological phenotypes and 12,431 animals with genotypes), we applied a single-step single nucleotide polymorphism (SNP) best linear unbiased prediction approach to investigate the genetic determinism underlying resistance to this disease (heritability estimate and identification of relevant genomic regions) and estimated genetic trends, reliability, and relative risk factors associated with genomic predictions. Results Resistance to JD was moderately heritable (0.14) and 16 genomic regions were detected that accounted for at least 0.05% of the breeding values variance (GV) in resistance to JD, and were located on chromosomes 1, 3, 5, 6, 7, 19, 20, 21, 23, 25, and 27, with the highest percentage of variance explained by regions on chromosomes 23 (0.36% GV), 5 (0.22% GV), 1 (0.14% GV), and 3 (0.13% GV). When estimated for the whole chromosomes, the autosomes with the largest overall contributions were chromosomes 3 (5.3% GV), 10 (4.8%), 23 (4.7%), 1 (3.6%), 7 (3.4%), 5 (2.9%), 12 (2.5%), 11 (2.2%), and 13 (2%). We estimated a slightly favorable genetic trend in resistance to JD over the last two decades, which can be explained by a low positive genetic correlation between resistance to JD and total merit index (+ 0.06). Finally, in a validation population of 907 cows, relatively reliable genomic predictions (reliability = 0.55) were obtained, which allowed the identification of cows at high risk of infection. Conclusions This study provides new insights into the genetic determinism of resistance to JD and shows that this trait can be predicted from SNP genotypes. It has led to the implementation of a single-step genomic evaluation that should rapidly become an effective tool for controlling paratuberculosis on French Holstein farms.
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Affiliation(s)
- Marie-Pierre Sanchez
- Université Paris Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France.
| | - Thierry Tribout
- Université Paris Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Sébastien Fritz
- Université Paris Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France.,Eliance, 149 Rue de Bercy, 75012, Paris, France
| | | | | | | | | | - Didier Boichard
- Université Paris Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
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McGovern SP, Purfield DC, Ring SC, Carthy TR, Graham DA, Berry DP. Candidate genes associated with the heritable humoral response to Mycobacterium avium ssp. paratuberculosis in dairy cows have factors in common with gastrointestinal diseases in humans. J Dairy Sci 2019; 102:4249-4263. [PMID: 30852025 DOI: 10.3168/jds.2018-15906] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 01/20/2019] [Indexed: 01/09/2023]
Abstract
Infection of cattle with bovine paratuberculosis (i.e., Johne's disease) is caused by Mycobacterium avium ssp. paratuberculosis (MAP) and results in a chronic incurable gastroenteritis. This disease, which has economic ramifications for the cattle industry, is increasing in detected prevalence globally; subclinically infected animals can silently shed the bacterium into the environment for years, exposing contemporaries and hampering disease-control programs. The objective of the present study was to first quantify the genetic parameters for humoral response to MAP in dairy cattle. This was followed by a genome-based association analysis and subsequent downstream bioinformatic analyses from imputed whole genome sequence SNP data. After edits, ELISA test records were available on 136,767 cows; analyses were also undertaken on a subset of 33,818 of these animals from herds with at least 5 MAP ELISA-positive cows, with at least 1 of those positive cows being homebred. Variance components were estimated using univariate animal and sire linear mixed models. The heritability calculated from the animal model for humoral response to MAP using alternative phenotype definitions varied from 0.02 (standard error = 0.003) to 0.05 (standard error = 0.008). The genome-based associations were undertaken within a mixed model framework using weighted deregressed estimated breeding values as a dependent variable on 1,883 phenotyped animals that were ≥87.5% Holstein-Friesian. Putative susceptibility quantitative trait loci (QTL) were identified on Bos taurus autosome 1, 3, 5, 6, 8, 9, 10, 11, 13, 14, 18, 21, 23, 25, 26, 27, and 29; mapping the most significant SNP to genes within and overlapping these QTL revealed that the most significant associations were with the 10 functional candidate genes KALRN, ZBTB20, LPP, SLA2, FI3A1, LRCH3, DNAJC6, ZDHHC14, SNX1, and HAS2. Pathway analysis failed to reveal significantly enriched biological pathways, when both bovine-specific pathway data and human ortholog data were taken into account. The existence of genetic variation for MAP susceptibility in a large data set of dairy cows signifies the potential of breeding programs for reducing MAP susceptibility. Furthermore, the identification of susceptible QTL facilitates greater biological understanding of bovine paratuberculosis and potential therapeutic targets for future investigation. The novel molecular similarities identified between bovine paratuberculosis and human inflammatory bowel disease suggest potential for human therapeutic interventions to be translated to veterinary medicine and vice versa.
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Affiliation(s)
- S P McGovern
- Department of Microbiology, University College Cork, Coláiste na hOllscoile Corcaigh, College Road, Cork City, Co. Cork, Ireland T12 CY82
| | - D C Purfield
- Teagasc, Animal & Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland P61 C996
| | - S C Ring
- Irish Cattle Breeding Federation, Highfield House, Shinagh, Bandon, Co. Cork, Ireland P72 X050
| | - T R Carthy
- Teagasc, Animal & Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland P61 C996
| | - D A Graham
- Animal Health Ireland, 4-5 The Archways, Carrick-on-Shannon, Co. Leitrim, Ireland N41 WN27
| | - D P Berry
- Teagasc, Animal & Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland P61 C996.
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McAloon CG, Roche S, Ritter C, Barkema HW, Whyte P, More SJ, O'Grady L, Green MJ, Doherty ML. A review of paratuberculosis in dairy herds - Part 1: Epidemiology. Vet J 2019; 246:59-65. [PMID: 30902190 DOI: 10.1016/j.tvjl.2019.01.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 01/24/2019] [Accepted: 01/25/2019] [Indexed: 11/24/2022]
Abstract
Bovine paratuberculosis is a chronic infectious disease of cattle caused by Mycobacterium avium subspecies paratuberculosis (MAP). This is the first in a two-part review of the epidemiology and control of paratuberculosis in dairy herds. Paratuberculosis was originally described in 1895 and is now considered endemic among farmed cattle worldwide. MAP has been isolated from a wide range of non-ruminant wildlife as well as humans and non-human primates. In dairy herds, MAP is assumed to be introduced predominantly through the purchase of infected stock with additional factors modulating the risk of persistence or fade-out once an infected animal is introduced. Faecal shedding may vary widely between individuals and recent modelling work has shed some light on the role of super-shedding animals in the transmission of MAP within herds. Recent experimental work has revisited many of the assumptions around age susceptibility, faecal shedding in calves and calf-to-calf transmission. Further efforts to elucidate the relative contributions of different transmission routes to the dissemination of infection in endemic herds will aid in the prioritisation of efforts for control on farm.
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Affiliation(s)
- Conor G McAloon
- Section of Herd Health and Animal Husbandry, School of Veterinary Medicine, University College Dublin, Ireland.
| | - Steven Roche
- Department of Population Medicine, University of Guelph, 50 Stone Rd., Guelph, ON, N1G 2W1, Canada
| | - Caroline Ritter
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, 2500 University Drive, Calgary, AB, T2N 1N4, Canada
| | - Herman W Barkema
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, 2500 University Drive, Calgary, AB, T2N 1N4, Canada
| | - Paul Whyte
- Section of Herd Health and Animal Husbandry, School of Veterinary Medicine, University College Dublin, Ireland
| | - Simon J More
- Section of Herd Health and Animal Husbandry, School of Veterinary Medicine, University College Dublin, Ireland
| | - Luke O'Grady
- Section of Herd Health and Animal Husbandry, School of Veterinary Medicine, University College Dublin, Ireland
| | - Martin J Green
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Leicestershire, LE12 5RD, United Kingdom
| | - Michael L Doherty
- Section of Herd Health and Animal Husbandry, School of Veterinary Medicine, University College Dublin, Ireland
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Gao Y, Jiang J, Yang S, Cao J, Han B, Wang Y, Zhang Y, Yu Y, Zhang S, Zhang Q, Fang L, Cantrell B, Sun D. Genome-wide association study of Mycobacterium avium subspecies Paratuberculosis infection in Chinese Holstein. BMC Genomics 2018; 19:972. [PMID: 30591025 PMCID: PMC6307165 DOI: 10.1186/s12864-018-5385-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 12/18/2018] [Indexed: 02/06/2023] Open
Abstract
Background Paratuberculosis is a contagious, chronic and enteric disease in ruminants, which is caused by Mycobacterium avium subspecies paratuberculosis (MAP) infection, resulting in enormous economic losses worldwide. There is currently no effective cure for MAP infection or a vaccine, it is thus important to explore the genetic variants that contribute to host susceptibility to infection by MAP, which may provide a better understanding of the mechanisms of paratuberculosis and benefit animal genetic improvement. Herein we performed a genome-wide association study (GWAS) to identify genomic regions and candidate genes associated with susceptibility to MAP infection in dairy cattle. Results Using Illumina Bovine 50 K (54,609 SNPs) and GeneSeek HD (138,893 SNPs) chips, two analytical approaches were performed, GRAMMAR-GC and ROADTRIPS in 937 Chinese Holstein cows, among which individuals genotyped by the 50 K chip were imputed to HD SNPs with Beagle software. Consequently, 15 and 11 significant SNPs (P < 5 × 10− 5) were identified with GRAMMAR-GC and ROADTDRIPS, respectively. A total of 10 functional genes were in proximity to (i.e., within 1 Mb) these SNPs, including IL4, IL5, IL13, IRF1, MyD88, PACSIN1, DEF6, TDP2, ZAP70 and CSF2. Functional enrichment analysis showed that these genes were involved in immune related pathways, such as interleukin, T cell receptor signaling pathways and inflammatory bowel disease (IBD), implying their potential associations with susceptibility to MAP infection. In addition, by examining the publicly available cattle QTLdb, a previous QTL for MAP was found to be overlapped with one of regions detected currently at 32.5 Mb on BTA23, where the TDP2 gene was anchored. Conclusions In conclusion, we identified 26 SNPs located on 15 chromosomes in the Chinese Holstein population using two GWAS strategies with high density SNPs. Integrated analysis of GWAS, biological functions and the reported QTL information helps to detect positional candidate genes and the identification of regions associated with susceptibility to MAP traits in dairy cattle. Electronic supplementary material The online version of this article (10.1186/s12864-018-5385-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yahui Gao
- Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jianping Jiang
- Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Shaohua Yang
- Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jie Cao
- College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Bo Han
- Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yachun Wang
- Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yi Zhang
- Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Ying Yu
- Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Shengli Zhang
- Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Qin Zhang
- Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Lingzhao Fang
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA
| | - Bonnie Cantrell
- Department of Animal and Veterinary Sciences, University of Vermont, Burlington, VT, 05405, USA
| | - Dongxiao Sun
- Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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Kirkpatrick BW, Lett BM. Short communication: Heritability of susceptibility to infection by Mycobacterium avium ssp. paratuberculosis in Holstein cattle. J Dairy Sci 2018; 101:11165-11169. [DOI: 10.3168/jds.2018-15021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 08/03/2018] [Indexed: 01/09/2023]
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Brito LF, Mallikarjunappa S, Sargolzaei M, Koeck A, Chesnais J, Schenkel F, Meade K, Miglior F, Karrow N. The genetic architecture of milk ELISA scores as an indicator of Johne's disease (paratuberculosis) in dairy cattle. J Dairy Sci 2018; 101:10062-10075. [DOI: 10.3168/jds.2017-14250] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 07/12/2018] [Indexed: 01/28/2023]
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Gao Y, Cao J, Zhang S, Zhang Q, Sun D. Short communication: Heritability estimates for susceptibility to Mycobacterium avium ssp. paratuberculosis infection in Chinese Holstein cattle. J Dairy Sci 2018; 101:7274-7279. [DOI: 10.3168/jds.2017-13264] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 02/07/2018] [Indexed: 11/19/2022]
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Pritchard T, Mrode R, Coffey M, Bond K, Wall E. The genetics of antibody response to paratuberculosis in dairy cattle. J Dairy Sci 2017; 100:5541-5549. [DOI: 10.3168/jds.2016-12300] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2016] [Accepted: 03/18/2017] [Indexed: 11/19/2022]
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Richardson IW, Berry DP, Wiencko HL, Higgins IM, More SJ, McClure J, Lynn DJ, Bradley DG. A genome-wide association study for genetic susceptibility to Mycobacterium bovis infection in dairy cattle identifies a susceptibility QTL on chromosome 23. Genet Sel Evol 2016; 48:19. [PMID: 26960806 PMCID: PMC4784436 DOI: 10.1186/s12711-016-0197-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 02/29/2016] [Indexed: 01/08/2023] Open
Abstract
Background Bovine tuberculosis (bTB) infection in cattle is a significant economic concern in many countries, with annual costs to the UK and Irish governments of approximately €190 million and €63 million, respectively, for bTB control. The existence of host additive and non-additive genetic components to bTB susceptibility has been established. Methods Two approaches i.e. single-SNP (single nucleotide polymorphism) regression and a Bayesian method were applied to genome-wide association studies (GWAS) using high-density SNP genotypes (n = 597,144 SNPs) from 841 dairy artificial insemination (AI) sires. Deregressed estimated breeding values for bTB susceptibility were used as the quantitative dependent variable. Network analysis was performed using the quantitative trait loci (QTL) that were identified as significant in the single-SNP regression and Bayesian analyses separately. In addition, an identity-by-descent analysis was performed on a subset of the most prolific sires in the dataset that showed contrasting prevalences of bTB infection in daughters. Results A significant QTL region was identified on BTA23 (P value >1 × 10−5, Bayes factor >10) across all analyses. Sires with the minor allele (minor allele frequency = 0.136) for this QTL on BTA23 had estimated breeding values that conferred a greater susceptibility to bTB infection than those that were homozygous for the major allele. Imputation of the regions that flank this QTL on BTA23 to full sequence indicated that the most significant associations were located within introns of the FKBP5 gene. Conclusions A genomic region on BTA23 that is strongly associated with host susceptibility to bTB infection was identified. This region contained FKBP5, a gene involved in the TNFα/NFκ-B signalling pathway, which is a major biological pathway associated with immune response. Although there is no study that validates this region in the literature, our approach represents one of the most powerful studies for the analysis of bTB susceptibility to
date. Electronic supplementary material The online version of this article (doi:10.1186/s12711-016-0197-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ian W Richardson
- Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland. .,Animal and Grassland Research and Innovation Centre, Teagasc, Moorepark, Fermoy, Co. Cork, Ireland.
| | - Donagh P Berry
- Animal and Grassland Research and Innovation Centre, Teagasc, Moorepark, Fermoy, Co. Cork, Ireland.
| | - Heather L Wiencko
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Co. Meath, Ireland.
| | - Isabella M Higgins
- UCD Centre for Veterinary Epidemiology and Risk Analysis, UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Simon J More
- UCD Centre for Veterinary Epidemiology and Risk Analysis, UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland.
| | | | - David J Lynn
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Co. Meath, Ireland. .,South Australian Health and Medical Research Institute, North Terrace, Adelaide, SA, 5000, Australia. .,School of Medicine, Flinders University, Bedford Park, SA, 5042, Australia.
| | - Daniel G Bradley
- Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland.
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Richardson IW, Bradley DG, Higgins IM, More SJ, McClure J, Berry DP. Variance components for susceptibility to Mycobacterium bovis infection in dairy and beef cattle. Genet Sel Evol 2014; 46:77. [PMID: 25407624 PMCID: PMC4234858 DOI: 10.1186/s12711-014-0077-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 10/29/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Infection of livestock with bovine tuberculosis (bTB; Mycobacterium bovis) is of major economical concern in many countries; approximately 15 000 to 20 000 cattle are infected per year in Ireland. The objective of this study was to quantify the genetic variation for bTB susceptibility in Irish dairy and beef cattle. METHODS A total of 105 914 cow, 56 904 heifer and 21 872 steer single intra-dermal comparative tuberculin test records (i.e., binary trait) collected from the years 2001 to 2010 from dairy and beef herds were included in the analysis. Only animal level data pertaining to periods of herd bTB infection were retained. Variance components for bTB were estimated using animal linear and threshold mixed models and co-variances were estimated using sire linear mixed models. RESULTS Using a linear model, the heritability for susceptibility to bTB in the entire dataset was 0.11 and ranged from 0.08 (heifers in dairy herds) to 0.19 (heifers in beef herds) among the sub-populations investigated. Differences in susceptibility to bTB between breeds were clearly evident. Estimates of genetic correlations for bTB susceptibility between animal types (i.e., cows, heifers, steers) were all positive (0.10 to 0.64), yet different from one. Furthermore, genetic correlations for bTB susceptibility between environments that differed in herd prevalence of bTB ranged from 0.06 to 0.86 and were all different from one. CONCLUSIONS Genetic trends for bTB susceptibility observed in this study suggest a slight increase in genetic susceptibility to bTB in recent years. Since bTB is of economic importance and because all animals are routinely tested at least once annually in Ireland and some other countries, the presence of genetic variation for bTB susceptibility suggests that bTB susceptibility should be included in a national breeding program to halt possible deterioration in genetic susceptibility to bTB infection.
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Affiliation(s)
| | | | | | | | | | - Donagh P Berry
- Animal and Grassland Research and Innovation Center, Teagasc, Moorepark, Fermoy, Co, Cork, Ireland.
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Genome-wide association analysis and genomic prediction of Mycobacterium avium subspecies paratuberculosis infection in US Jersey cattle. PLoS One 2014; 9:e88380. [PMID: 24523889 PMCID: PMC3921184 DOI: 10.1371/journal.pone.0088380] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 01/06/2014] [Indexed: 01/22/2023] Open
Abstract
Paratuberculosis (Johne’s disease), an enteric disorder in ruminants caused by Mycobacterium avium subspecies paratuberculosis (MAP), causes economic losses in excess of $200 million annually to the US dairy industry. To identify genomic regions underlying susceptibility to MAP infection in Jersey cattle, a case-control genome-wide association study (GWAS) was performed. Blood and fecal samples were collected from ∼5,000 mature cows in 30 commercial Jersey herds from across the US. Discovery data consisted of 450 cases and 439 controls genotyped with the Illumina BovineSNP50 BeadChip. Cases were animals with positive ELISA and fecal culture (FC) results. Controls were animals negative to both ELISA and FC tests that matched cases on birth date and herd. Validation data consisted of 180 animals including 90 cases (positive to FC) and 90 controls (negative to ELISA and FC), selected from discovery herds and genotyped by Illumina BovineLD BeadChip (∼7K SNPs). Two analytical approaches were used: single-marker GWAS using the GRAMMAR-GC method and Bayesian variable selection (Bayes C) using GenSel software. GRAMMAR-GC identified one SNP on BTA7 at 68 megabases (Mb) surpassing a significance threshold of 5×10−5. ARS-BFGL-NGS-11887 on BTA23 (27.7 Mb) accounted for the highest percentage of genetic variance (3.3%) in the Bayes C analysis. SNPs identified in common by GRAMMAR-GC and Bayes C in both discovery and combined data were mapped to BTA23 (27, 29 and 44 Mb), 3 (100, 101, 106 and 107 Mb) and 17 (57 Mb). Correspondence between results of GRAMMAR-GC and Bayes C was high (70–80% of most significant SNPs in common). These SNPs could potentially be associated with causal variants underlying susceptibility to MAP infection in Jersey cattle. Predictive performance of the model developed by Bayes C for prediction of infection status of animals in validation set was low (55% probability of correct ranking of paired case and control samples).
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Evidence of birth seasonality and clustering of Mycobacterium avium subspecies paratuberculosis infection in US dairy herds. Prev Vet Med 2013; 112:276-84. [DOI: 10.1016/j.prevetmed.2013.07.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Revised: 07/25/2013] [Accepted: 07/26/2013] [Indexed: 11/21/2022]
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Bennett R, McClement I, McFarlane I. Modelling of Johne's disease control options in beef cattle: A decision support approach. Livest Sci 2012. [DOI: 10.1016/j.livsci.2012.03.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Shook GE, Chaffer M, Wu XL, Ezra E. Genetic parameters for paratuberculosis infection and effect of infection on production traits in Israeli Holsteins. Anim Genet 2012; 43 Suppl 1:56-64. [DOI: 10.1111/j.1365-2052.2012.02349.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- G. E. Shook
- Dairy Science Department; University of Wisconsin-Madison; Madison; WI; 53706; USA
| | - M. Chaffer
- Department of Bacteriology; Kimron Veterinary Institute; Bet Dagan; 50250; Israel
| | - X.-L. Wu
- Dairy Science Department; University of Wisconsin-Madison; Madison; WI; 53706; USA
| | - E. Ezra
- Israel Cattle Breeders Association; Caesarea; 38900; Israel
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Abstract
Multiple studies indicate that host animal genetics play a role in susceptibility to Mycobacterium avium subsp. paratuberculosis (MAP) infection. However, due to differences in methods used to define MAP-infected animals and controls and differences in methods of genetic analysis, there is as yet no clear consensus on the genes or markers to reliably define the MAP infection susceptibility of any animal species. Meta-analysis of combined studies and larger studies will help resolve the situation in the coming years.
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Immunological and pathological responses of red deer resistant or susceptible genotypes, to experimental challenge with Mycobacterium avium subsp. paratuberculosis. Vet Immunol Immunopathol 2011; 143:131-42. [PMID: 21782254 DOI: 10.1016/j.vetimm.2011.06.035] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2011] [Revised: 06/20/2011] [Accepted: 06/27/2011] [Indexed: 11/21/2022]
Abstract
This study aimed to monitor the clinical, immunological and pathological changes in red deer for 49 weeks after experimental oral challenge with Mycobacterium avium subsp. paratuberculosis (MAP) and to assess the heritability of resistance in the offspring of two red stags. Eighteen young deer, which were bred from unselected hinds and sired by two stags resistant (R) or susceptible (S) to paratuberculosis, were challenged with MAP and monitored for 49 weeks. Biopsy samples of the jejunal lymph node were collected at Weeks 4 and 13 and at necropsy after euthanasia of clinically affected animals or when electively killed at Week 49. Three animals (two S and one R) developed clinical disease and were euthanised. The nine S offspring had significantly more severe lesions than the nine R offspring (Mantel-Haenszel Chi-square P=0.017). The average Lesion Severity Score (LSS) of R offspring was 5.9 (mild), and 7/9 had no or very mild lesions. In contrast, the LSS of S offspring averaged 11.7 (severe), and 7/9 had severe lesions. Most of the resistant, but not the susceptible, animals showed evidence of resolving lesions and a reduction in the number of MAP between 13 and 49 weeks after challenge. One R offspring appeared to completely cure itself, and progressed from mild culture-positive paratuberculosis lesions at Week 13 to having no signs of disease or infection 36 weeks later. This study showed significant heritable resistance/susceptibility to paratuberculosis and key differences in immunological responses in the first 3 months after challenge, indicating different paths to relative success or failure to control MAP. In general, R deer had higher IFN-γ levels, low antibody titres and fewer MAP, while S deer had lower IFN-γ levels, higher antibody and more MAP.
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Bermingham ML, Brotherstone S, Berry DP, More SJ, Good M, Cromie AR, White IM, Higgins IM, Coffey M, Downs SH, Glass EJ, Bishop SC, Mitchell AP, Clifton-Hadley RS, Woolliams JA. Evidence for genetic variance in resistance to tuberculosis in Great Britain and Irish Holstein-Friesian populations. BMC Proc 2011; 5 Suppl 4:S15. [PMID: 21645294 PMCID: PMC3108209 DOI: 10.1186/1753-6561-5-s4-s15] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Background Here, we jointly summarise scientific evidence for genetic variation in resistance to infection with Mycobacterium bovis, the primary agent of bovine tuberculosis (TB), provided by two recent and separate studies of Holstein-Friesian dairy cow populations in Great Britain (GB) and Ireland. Methods The studies quantified genetic variation within archived data from field and abattoir surveillance control programmes within each country. These data included results from the single intradermal comparative tuberculin test (SICTT), abattoir inspection for TB lesions and laboratory confirmation of disease status. Threshold animal models were used to estimate variance components for responsiveness to the SICTT and abattoir confirmed M. bovis infection. The link functions between the observed 0/1 scale and the liability scale were the complementary log-log in the GB, and logit link function in the Irish population. Results and discussion The estimated heritability of susceptibility to TB, as judged by responsiveness to the SICTT, was 0.16 (0.012) and 0.14 (0.025) in the GB and Irish populations, respectively. For abattoir or laboratory confirmation of infection, estimates were 0.18 (0.044) and 0.18 (0.041) from the GB and the Irish populations, respectively. Conclusions Estimates were all significantly different from zero and indicate that exploitable variation exists among GB and Irish Holstein Friesian dairy cows for resistance to TB. Epidemiological analysis suggests that factors such as variation in exposure or imperfect sensitivity and specificity would have resulted in underestimation of the true values.
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Affiliation(s)
| | - Susan Brotherstone
- Institute of Evolutionary Biology, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, UK
| | - Donagh P Berry
- Moorepark Production Research Centre, Fermoy, Co. Cork, Ireland
| | - Simon J More
- Centre for Veterinary Epidemiology and Risk Analysis, UCD School of Agriculture, Food Science and Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Margaret Good
- Department of Agriculture, Fisheries and Food, Kildare St., Dublin 2, Ireland
| | - Andrew R Cromie
- The Irish Cattle Breeding Federation, Bandon, Co. Cork, Ireland
| | - Ian Ms White
- Institute of Evolutionary Biology, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, UK
| | - Isabella M Higgins
- Centre for Veterinary Epidemiology and Risk Analysis, UCD School of Agriculture, Food Science and Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Mike Coffey
- Scottish Agricultural College, Bush Estate, Penicuik, Midlothian EH26 0PH, UK
| | - Sara H Downs
- Veterinary Laboratories Agency-Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Elizabeth J Glass
- The Roslin Institute, Roslin Biocentre, Roslin, Midlothian EH25 9RG, UK
| | - Stephen C Bishop
- The Roslin Institute, Roslin Biocentre, Roslin, Midlothian EH25 9RG, UK
| | - Andy P Mitchell
- Veterinary Laboratories Agency-Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | | | - John A Woolliams
- The Roslin Institute, Roslin Biocentre, Roslin, Midlothian EH25 9RG, UK
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Berry DP, Bermingham ML, Good M, More SJ. Genetics of animal health and disease in cattle. Ir Vet J 2011; 64:5. [PMID: 21777492 PMCID: PMC3102331 DOI: 10.1186/2046-0481-64-5] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Accepted: 03/31/2011] [Indexed: 11/16/2022] Open
Abstract
There have been considerable recent advancements in animal breeding and genetics relevant to disease control in cattle, which can now be utilised as part of an overall programme for improved cattle health. This review summarises the contribution of genetic makeup to differences in resistance to many diseases affecting cattle. Significant genetic variation in susceptibility to disease does exist among cattle suggesting that genetic selection for improved resistance to disease will be fruitful. Deficiencies in accurately recorded data on individual animal susceptibility to disease are, however, currently hindering the inclusion of health and disease resistance traits in national breeding goals. Developments in 'omics' technologies, such as genomic selection, may help overcome some of the limitations of traditional breeding programmes and will be especially beneficial in breeding for lowly heritable disease traits that only manifest themselves following exposure to pathogens or environmental stressors in adulthood. However, access to large databases of phenotypes on health and disease will still be necessary. This review clearly shows that genetics make a significant contribution to the overall health and resistance to disease in cattle. Therefore, breeding programmes for improved animal health and disease resistance should be seen as an integral part of any overall national disease control strategy.
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Affiliation(s)
- Donagh P Berry
- Animal and Grassland Research and Innovation Centre, Teagasc, Moorepark, Co, Cork, Ireland.
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Bermingham ML, More SJ, Good M, Cromie AR, Higgins IM, Berry DP. Genetic correlations between measures of Mycobacterium bovis infection and economically important traits in Irish Holstein-Friesian dairy cows. J Dairy Sci 2011; 93:5413-22. [PMID: 20965357 DOI: 10.3168/jds.2009-2925] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2009] [Accepted: 08/01/2010] [Indexed: 11/19/2022]
Abstract
Mycobacterium bovis is the primary agent of tuberculosis (TB) in cattle. The failure of Ireland and some other countries to reach TB-free status indicates a need to investigate complementary control strategies. One such approach would be genetic selection for increased resistance to TB. Previous research has shown that considerable genetic variation exists for susceptibility to the measures of M. bovis infection, confirmed M. bovis infection, and M. bovis-purified protein derivative (PPD) responsiveness. The objective of this study was to estimate the genetic and phenotypic correlations between economically important traits and these measures of M. bovis infection. A total of 20,148 and 17,178 cows with confirmed M. bovis infection and M. bovis-PPD responsiveness records, respectively, were available for inclusion in the analysis. First- to third-parity milk, fat, and protein yields, somatic cell count, calving interval, and survival, as well as first-parity body condition score records, were available on cows that calved between 1985 and 2007. Bivariate linear-linear and threshold-linear sire mixed models were used to estimate (co)variance components. The genetic correlations between economically important traits and the measures of M. bovis infection estimated from the linear-linear and threshold-linear sire models were similar. The genetic correlations between susceptibility to confirmed M. bovis infection and economically important traits investigated in this study were all close to zero. Mycobacterium bovis-PPD responsiveness was positively genetically correlated with fat production (0.39) and body condition score (0.36), and negatively correlated with somatic cell score (-0.34) and survival (-0.62). Hence, selection for increased survival may indirectly reduce susceptibility to M. bovis infection, whereas selection for reduced somatic cell count and increased fat production and body condition score may increase susceptibility to M. bovis infection.
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Affiliation(s)
- M L Bermingham
- Moorepark Production Research Centre, Fermoy, Co. Cork, Ireland.
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