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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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Cao H, Fang C, Liu LL, Farnir F, Liu WJ. Identification of Susceptibility Genes Underlying Bovine Respiratory Disease in Xinjiang Brown Cattle Based on DNA Methylation. Int J Mol Sci 2024; 25:4928. [PMID: 38732144 PMCID: PMC11084705 DOI: 10.3390/ijms25094928] [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: 03/16/2024] [Revised: 04/25/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024] Open
Abstract
DNA methylation is a form of epigenetic regulation, having pivotal parts in controlling cellular expansion and expression levels within genes. Although blood DNA methylation has been studied in humans and other species, its prominence in cattle is largely unknown. This study aimed to methodically probe the genomic methylation map of Xinjiang brown (XJB) cattle suffering from bovine respiratory disease (BRD), consequently widening cattle blood methylome ranges. Genome-wide DNA methylation profiling of the XJB blood was investigated through whole-genome bisulfite sequencing (WGBS). Many differentially methylated regions (DMRs) obtained by comparing the cases and controls groups were found within the CG, CHG, and CHH (where H is A, T, or C) sequences (16,765, 7502, and 2656, respectively), encompassing 4334 differentially methylated genes (DMGs). Furthermore, GO/KEGG analyses showed that some DMGs were involved within immune response pathways. Combining WGBS-Seq data and existing RNA-Seq data, we identified 71 significantly differentially methylated (DMGs) and expressed (DEGs) genes (p < 0.05). Next, complementary analyses identified nine DMGs (LTA, STAT3, IKBKG, IRAK1, NOD2, TLR2, TNFRSF1A, and IKBKB) that might be involved in the immune response of XJB cattle infected with respiratory diseases. Although further investigations are needed to confirm their exact implication in the involved immune processes, these genes could potentially be used for a marker-assisted selection of animals resistant to BRD. This study also provides new knowledge regarding epigenetic control for the bovine respiratory immune process.
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Affiliation(s)
- Hang Cao
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; (H.C.); (L.-L.L.)
| | - Chao Fang
- Faculte de Medecine Veterinaire, Universite de Liege, Quartier Vallee 2, Avenue de Cureghem 6 (B43), 4000 Liege, Belgium;
| | - Ling-Ling Liu
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; (H.C.); (L.-L.L.)
| | - Frederic Farnir
- Faculte de Medecine Veterinaire, Universite de Liege, Quartier Vallee 2, Avenue de Cureghem 6 (B43), 4000 Liege, Belgium;
| | - Wu-Jun Liu
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; (H.C.); (L.-L.L.)
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Nakamura R, Sasaki M, Shoji N, Takahashi M, Watanabe A, Iijima K, Hasegawa K, Oyama K, Mannen H. Estimation of genetic parameters for visceral diseases of fattening Japanese Black cattle in Shimane Prefecture, Japan. Anim Sci J 2024; 95:e13930. [PMID: 38400812 DOI: 10.1111/asj.13930] [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: 10/10/2023] [Revised: 01/22/2024] [Accepted: 02/05/2024] [Indexed: 02/26/2024]
Abstract
In this study, the genetic parameters of major visceral diseases were estimated using the postmortem inspection records of 9057 fattening Japanese Black cattle in Shimane Prefecture, Japan, and the genetic correlation between visceral diseases and carcass traits was analyzed. There were six visceral diseases with a prevalence of 5% or higher, namely, pleurisy, pneumonia, bovine abdominal fat necrosis (BFN), rumenitis, hemorrhagic hepatitis, and perihepatitis. Variance components were estimated using the Gibbs sampling method, and the heritability of the visceral disease ranged from 0.07 to 0.49 for perihepatitis and BFN, respectively. Significant negative genetic correlations were identified between pleurisy and rib thickness (-0.32), BFN and carcass weight (-0.29), and BFN and rib eye area (-0.22). No significant genetic correlation was observed among the visceral diseases. The least squares analysis of variance suggested that some visceral diseases decrease the value of carcass traits. In particular, carcass weight and rib eye area in individuals with BFN were 11.7 kg and 1.87 cm2 lower than those of healthy cattle, respectively. Thus, it was inferred that genetic factors were involved in the visceral diseases of fattening Japanese Black cattle in Shimane Prefecture.
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Affiliation(s)
- Ryoichi Nakamura
- Livestock Technology Center, Shimane Prefectural Government, Izumo, Japan
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Makiko Sasaki
- Meat Sanitation and Inspection Station, Shimane Prefectural Government, Oda, Japan
| | - Nobutaka Shoji
- Meat Sanitation and Inspection Station, Shimane Prefectural Government, Oda, Japan
| | - Masaru Takahashi
- Livestock Technology Center, Shimane Prefectural Government, Izumo, Japan
| | - Akihiro Watanabe
- Livestock Technology Center, Shimane Prefectural Government, Izumo, Japan
| | - Kumi Iijima
- Livestock Technology Center, Shimane Prefectural Government, Izumo, Japan
| | - Kiyotoshi Hasegawa
- Livestock Technology Center, Shimane Prefectural Government, Izumo, Japan
| | - Kenji Oyama
- Food Resources Education and Research Center, Graduate School of Agricultural Science, Kobe University, Kasai, Japan
| | - Hideyuki Mannen
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
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Keele JW, McDaneld TG, Kuehn LA. Use of overlapping DNA pools to discern genetic differences despite pooling error. J Anim Sci 2023; 101:skad166. [PMID: 37227930 PMCID: PMC10263113 DOI: 10.1093/jas/skad166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 05/22/2023] [Indexed: 05/27/2023] Open
Abstract
Genotyping pools of commercial cattle and individual seedstock animals may reveal hidden relationships between sectors enabling use of commercial data for genetic evaluation. However, commercial data capture may be compromised by inexact pool formation. We aimed to estimate the concordance between distances or genomic covariance among pooling allele frequencies (PAFs) of DNA pools comprised of 100 animals with 0% or 50% overlap of animals in common between pools. Cattle lung samples were collected from a commercial beef processing plant on a single day. Six pools of 100 animals each were constructed so that overlap between pools was 0% or 50%. Two pools of all 200 animals were constructed to estimate PAFs for all 200 animals. Frozen lung tissue (0.01 g) from each animal was weighed into a tube containing a pool; there were two pools of 200 animals each and six pools of 100 animals each. Every contribution of an individual animal was an independent measurement to insure independence of pooling errors. Lung samples were kept on dried ice during the pooling process to keep them from thawing. The eight pools were then assayed for approximately 100,000 single nucleotide polymorphisms (SNP). PAF for each SNP and pool was based on the relative intensity of the two dyes used to detect the alleles rather than genotype calls which are not tractable from pooling data. Euclidean distances and genomic relationships among the PAFs for the eight pools were estimated and distances were tested for concordance with pool overlap using permutation-based analysis of distance. Distances among pools were concordant with the planned overlap of animals shared between pools (P = 0.0024); pool overlap accounted for 70% of the variation and pooling error accounted for 30%. Pools containing 100 animals with no overlap were the most distant from one another and pools with 50% overlap were the least distant. This work shows that we can discern differences in distance between pairs of overlapping DNA pools sharing 0% and 50% of the animals. Genomic correlations among nonoverlapping pools indicated that nonoverlapping pool pairs did not share many related animals because genomic correlations were near zero for these pairs. On the other hand, one pair of nonoverlapping pools likely contained related animals between pools because the correlation was 0.21. Pools sharing 50% overlap ranged in genomic relationship between 0.21 and 0.39 (N = 12).
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Affiliation(s)
- John W Keele
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, USA
| | - Tara G McDaneld
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, USA
| | - Larry A Kuehn
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, USA
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Cao H, Fang C, Wang Q, Liu LL, Liu WJ. Transcript Characteristics on the Susceptibility Difference of Bovine Respiratory Disease. Int J Genomics 2023; 2023:9934684. [PMID: 37180342 PMCID: PMC10175020 DOI: 10.1155/2023/9934684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 04/18/2023] [Accepted: 04/21/2023] [Indexed: 05/16/2023] Open
Abstract
Bovine respiratory disease (BRD) is one of the major health issues in the cattle industry, resulting in significant financial crises globally. There is currently no good treatment, and cattle are made resistant to pneumonia through disease-resistant breeding. The serial blood samples from six Xinjiang brown (XJB) calves were collected for the RNA sequencing (RNA-seq). The obtained six samples were grouped into two groups, in each group as infected with BRD and healthy calves, respectively. In our study, the differential expression mRNAs were detected by using RNA-seq and constructed a protein-protein interaction (PPI) network related to the immunity in cattle. The key genes were identified by protein interaction network analysis, and the results from RNA-seq were verified using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). A total of 488 differentially expressed (DE) mRNAs were identified. Importantly, the enrichment analysis of these identified DEGs classified them as mainly enriched in the regulation and immune response processes. The 16 hub genes were found to be related to immune pathways categorized by PPIs analysis. Results revealed that many hub genes were related to the immune response to respiratory disease. These results will provide the basis for a better understanding of the molecular mechanism of bovine resistance to BRD.
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Affiliation(s)
- Hang Cao
- College of Animal Science, Xinjiang Agricultural University, Urumqi, Xinjiang 830052, China
| | - Chao Fang
- College of Animal Science, Xinjiang Agricultural University, Urumqi, Xinjiang 830052, China
| | - Qiong Wang
- College of Animal Science, Xinjiang Agricultural University, Urumqi, Xinjiang 830052, China
| | - Ling-Ling Liu
- College of Animal Science, Xinjiang Agricultural University, Urumqi, Xinjiang 830052, China
| | - Wu-Jun Liu
- College of Animal Science, Xinjiang Agricultural University, Urumqi, Xinjiang 830052, China
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Vargas Jurado N, Kuehn LA, Keele JW, Lewis RM. Accuracy of GEBV of sires based on pooled allele frequency of their progeny. G3-GENES GENOMES GENETICS 2021; 11:6321233. [PMID: 34510188 DOI: 10.1093/g3journal/jkab231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/17/2021] [Indexed: 11/12/2022]
Abstract
Despite decreasing genotyping costs, in some cases individually genotyping animals is not economically feasible (e.g., in small ruminants). An alternative is to pool DNA, using the pooled allele frequency (PAF) to garner information on performance. Still, the use of PAF for prediction (estimation of genomic breeding values; GEBVs) has been limited. Two potential sources of error on accuracy of GEBV of sires, obtained from PAF of their progeny themselves lacking pedigree information, were tested: (i) pool construction error (unequal contribution of DNA from animals in pools), and (ii) technical error (variability when reading the array). Pooling design (random, extremes, K-means), pool size (5, 10, 25, 50, and 100 individuals), and selection scenario (random, phenotypic) also were considered. These factors were tested by simulating a sheep population. Accuracy of GEBV-the correlation between true and estimated values-was not substantially affected by pool construction or technical error, or selection scenario. A significant interaction, however, between pool size and design was found. Still, regardless of design, mean accuracy was higher for pools of 10 or less individuals. Mean accuracy of GEBV was 0.174 (SE 0.001) for random pooling, and 0.704 (SE 0.004) and 0.696 (SE 0.004) for extreme and K-means pooling, respectively. Non-random pooling resulted in moderate accuracy of GEBV. Overall, pooled genotypes can be used in conjunction with individual genotypes of sires for moderately accurate predictions of their genetic merit with little effect of pool construction or technical error.
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Affiliation(s)
| | - Larry A Kuehn
- Genetics, Breeding, and Animal Health Research Unit, U.S. Meat Animal Research Center, USDA-ARS, Clay Center, NE 68933, USA
| | - John W Keele
- Genetics, Breeding, and Animal Health Research Unit, U.S. Meat Animal Research Center, USDA-ARS, Clay Center, NE 68933, USA
| | - Ronald M Lewis
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
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Abrams AN, McDaneld TG, Keele JW, Chitko-McKown CG, Kuehn LA, Gonda MG. Evaluating Accuracy of DNA Pool Construction Based on White Blood Cell Counts. Front Genet 2021; 12:635846. [PMID: 33613648 PMCID: PMC7893106 DOI: 10.3389/fgene.2021.635846] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 01/14/2021] [Indexed: 11/13/2022] Open
Abstract
Pooling individual samples prior to DNA extraction can mitigate the cost of DNA extraction and genotyping; however, these methods need to accurately generate equal representation of individuals within pools. The objective of this study was to determine accuracy of pool construction of blood samples based on white blood cell counts compared to two common DNA quantification methods. Fifty individual bovine blood samples were collected, and then pooled with all individuals represented in each pool. Pools were constructed with the target of equal representation of each individual animal based on number of white blood cells, spectrophotometric readings, spectrofluorometric readings, and whole blood volume with 9 pools per method and a total of 36 pools. Pools and individual samples that comprised the pools were genotyped using a commercially available genotyping array. ASReml was used to estimate variance components for individual animal contribution to pools. The correlation between animal contributions between two pools was estimated using bivariate analysis with starting values set to the result of a univariate analysis. Adonis test on distance matrix from the animal correlation showed clustering with method, and higher correlations between methods than within (P < 1 × 10-6). White blood cell count was predictive of sample representation when compared to pooling based on DNA concentration. Therefore, constructing pools using white blood cell counts prior to DNA extraction may reduce cost associated with DNA extraction and genotyping and improve representation of individuals in a pool.
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Affiliation(s)
- Amy N Abrams
- Department of Animal Science, South Dakota State University, Brookings, SD, United States.,Department of Animal Science, Berry College, Mount Berry, GA, United States
| | - Tara G McDaneld
- Genetics, Breeding, and Animal Health Research Unit, U.S. Meat Animal Research Center, USDA-ARS, Clay Center, NE, United States
| | - John W Keele
- Genetics, Breeding, and Animal Health Research Unit, U.S. Meat Animal Research Center, USDA-ARS, Clay Center, NE, United States
| | - Carol G Chitko-McKown
- Animal Health Genomics Research Unit, U.S. Meat Animal Research Center, USDA-ARS, Clay Center, NE, United States
| | - Larry A Kuehn
- Genetics, Breeding, and Animal Health Research Unit, U.S. Meat Animal Research Center, USDA-ARS, Clay Center, NE, United States
| | - Michael G Gonda
- Department of Animal Science, South Dakota State University, Brookings, SD, United States
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Johnston D, Kim J, Taylor JF, Earley B, McCabe MS, Lemon K, Duffy C, McMenamy M, Cosby SL, Waters SM. ATAC-Seq identifies regions of open chromatin in the bronchial lymph nodes of dairy calves experimentally challenged with bovine respiratory syncytial virus. BMC Genomics 2021; 22:14. [PMID: 33407093 PMCID: PMC7789798 DOI: 10.1186/s12864-020-07268-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 11/23/2020] [Indexed: 12/13/2022] Open
Abstract
Background Bovine Respiratory Syncytial Virus (BRSV) is a cause of Bovine Respiratory Disease (BRD). DNA-based biomarkers contributing to BRD resistance are potentially present in non-protein-coding regulatory regions of the genome, which can be determined using ATAC-Seq. The objectives of this study were to: (i) identify regions of open chromatin in DNA extracted from bronchial lymph nodes (BLN) of healthy dairy calves experimentally challenged with BRSV and compare them with those from non-challenged healthy control calves, (ii) elucidate the chromatin regions that were differentially or uniquely open in the BRSV challenged relative to control calves, and (iii) compare the genes found in regions proximal to the differentially open regions to the genes previously found to be differentially expressed in the BLN in response to BRSV and to previously identified BRD susceptibility loci. This was achieved by challenging clinically healthy Holstein-Friesian calves (mean age 143 ± 14 days) with either BRSV inoculum (n = 12) or with sterile phosphate buffered saline (PBS) (n = 6) and preparing and sequencing ATAC-Seq libraries from fresh BLN tissues. Results Using Diffbind, 9,144 and 5,096 differentially accessible regions (P < 0.05, FDR < 0.05) were identified between BRSV challenged and control calves employing DeSeq2 and EdgeR, respectively. Additionally, 8,791 chromatin regions were found to be uniquely open in BRSV challenged calves. Seventy-six and 150 of the genes that were previously found to be differentially expressed using RNA-Seq, were located within 2 kb downstream of the differentially accessible regions, and of the regions uniquely open in BRSV challenged calves, respectively. Pathway analyses within ClusterProfiler indicated that these genes were involved in immune responses to infection and participated in the Th1 and Th2 pathways, pathogen recognition and the anti-viral response. There were 237 differentially accessible regions positioned within 40 previously identified BRD susceptibility loci. Conclusions The identified open chromatin regions are likely to be involved in the regulatory response of gene transcription induced by infection with BRSV. Consequently, they may contain variants which impact resistance to BRD that could be used in breeding programmes to select healthier, more robust cattle. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07268-5.
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Affiliation(s)
- Dayle Johnston
- Animal and Bioscience Research Department, Animal & Grassland Research and Innovation Centre, Teagasc, Grange, Co. Meath, Ireland
| | - JaeWoo Kim
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - Jeremy F Taylor
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - Bernadette Earley
- Animal and Bioscience Research Department, Animal & Grassland Research and Innovation Centre, Teagasc, Grange, Co. Meath, Ireland
| | - Matthew S McCabe
- Animal and Bioscience Research Department, Animal & Grassland Research and Innovation Centre, Teagasc, Grange, Co. Meath, Ireland
| | - Ken Lemon
- Veterinary Sciences Division, Agri-Food and Biosciences Institute, Stormont, Belfast, Northern Ireland
| | - Catherine Duffy
- Veterinary Sciences Division, Agri-Food and Biosciences Institute, Stormont, Belfast, Northern Ireland
| | - Michael McMenamy
- Veterinary Sciences Division, Agri-Food and Biosciences Institute, Stormont, Belfast, Northern Ireland
| | - S Louise Cosby
- Veterinary Sciences Division, Agri-Food and Biosciences Institute, Stormont, Belfast, Northern Ireland
| | - Sinéad M Waters
- Animal and Bioscience Research Department, Animal & Grassland Research and Innovation Centre, Teagasc, Grange, Co. Meath, Ireland.
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Abstract
Genomic variation exists in cattle that affects their susceptibility to the complex of pathogens responsible for bovine respiratory disease (BRD). Heritability estimates and genome-wide association analyses (GWAA) support the role of host genomic variation in BRD susceptibility. Heritability estimates for BRD susceptibility range from 0.02 to 0.29 depending on the population, the definition of the disease, and the accuracy of diagnosis. GWAA have identified genomic regions (loci) associated with BRD in beef and dairy cattle based on a variety of BRD diagnostic criteria. National standards need to be developed for BRD diagnostics and reporting to facilitate selection. Commercial genotyping is available to predict BRD susceptibility in dairy cattle and for the selection of replacement animals. Disease pathogen profiles vary by region and can result in genetic heterogeneity where different loci are important for susceptibility to different BRD pathogens. Although the identification of the BRD pathogens may not be critical for treatment, it is of paramount importance in identifying loci that render cattle susceptible to the disease. Identification of loci associated with host susceptibility to BRD provides a foundation for genomic selection to reduce disease and opens the possibilities to a better understanding of how the host defends itself.
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10
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Alexandre PA, Porto-Neto LR, Karaman E, Lehnert SA, Reverter A. Pooled genotyping strategies for the rapid construction of genomic reference populations1. J Anim Sci 2019; 97:4761-4769. [PMID: 31710679 PMCID: PMC6915231 DOI: 10.1093/jas/skz344] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 11/06/2019] [Indexed: 01/24/2023] Open
Abstract
The growing concern with the environment is making important for livestock producers to focus on selection for efficiency-related traits, which is a challenge for commercial cattle herds due to the lack of pedigree information. To explore a cost-effective opportunity for genomic evaluations of commercial herds, this study compared the accuracy of bulls' genomic estimated breeding values (GEBV) using different pooled genotype strategies. We used ten replicates of previously simulated genomic and phenotypic data for one low (t1) and one moderate (t2) heritability trait of 200 sires and 2,200 progeny. Sire's GEBV were calculated using a univariate mixed model, with a hybrid genomic relationship matrix (h-GRM) relating sires to: 1) 1,100 pools of 2 animals; 2) 440 pools of 5 animals; 3) 220 pools of 10 animals; 4) 110 pools of 20 animals; 5) 88 pools of 25 animals; 6) 44 pools of 50 animals; and 7) 22 pools of 100 animals. Pooling criteria were: at random, grouped sorting by t1, grouped sorting by t2, and grouped sorting by a combination of t1 and t2. The same criteria were used to select 110, 220, 440, and 1,100 individual genotypes for GEBV calculation to compare GEBV accuracy using the same number of individual genotypes and pools. Although the best accuracy was achieved for a given trait when pools were grouped based on that same trait (t1: 0.50-0.56, t2: 0.66-0.77), pooling by one trait impacted negatively on the accuracy of GEBV for the other trait (t1: 0.25-0.46, t2: 0.29-0.71). Therefore, the combined measure may be a feasible alternative to use the same pools to calculate GEBVs for both traits (t1: 0.45-0.57, t2: 0.62-0.76). Pools of 10 individuals were identified as representing a good compromise between loss of accuracy (~10%-15%) and cost savings (~90%) from genotype assays. In addition, we demonstrated that in more than 90% of the simulations, pools present higher sires' GEBV accuracy than individual genotypes when the number of genotype assays is limited (i.e., 110 or 220) and animals are assigned to pools based on phenotype. Pools assigned at random presented the poorest results (t1: 0.07-0.45, t2: 0.14-0.70). In conclusion, pooling by phenotype is the best approach to implementing genomic evaluation using commercial herd data, particularly when pools of 10 individuals are evaluated. While combining phenotypes seems a promising strategy to allow more flexibility to the estimates made using pools, more studies are necessary in this regard.
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Affiliation(s)
- Pâmela A Alexandre
- Agriculture & Food, Commonwealth Scientific and Industrial Research Organization, Brisbane, QLD, Australia
| | - Laercio R Porto-Neto
- Agriculture & Food, Commonwealth Scientific and Industrial Research Organization, Brisbane, QLD, Australia
| | - Emre Karaman
- Center for Quantitative Genetics and Genomics, Aarhus University, Tjele, Denmark
| | - Sigrid A Lehnert
- Agriculture & Food, Commonwealth Scientific and Industrial Research Organization, Brisbane, QLD, Australia
| | - Antonio Reverter
- Agriculture & Food, Commonwealth Scientific and Industrial Research Organization, Brisbane, QLD, Australia
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11
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Quick AE, Ollivett TL, Kirkpatrick BW, Weigel KA. Genomic analysis of bovine respiratory disease and lung consolidation in preweaned Holstein calves using clinical scoring and lung ultrasound. J Dairy Sci 2019; 103:1632-1641. [PMID: 31759603 DOI: 10.3168/jds.2019-16531] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 10/04/2019] [Indexed: 11/19/2022]
Abstract
Bovine respiratory disease (BRD) is a leading cause of morbidity and mortality in dairy calves, with detrimental long-term effects that include stunted growth, increased age at first calving, and decreased milk production in first lactation. The objectives of this study were to establish a protocol for objective and efficient assessment of BRD phenotypes in preweaned dairy calves, develop a genomic reference population with well-defined clinical and subclinical phenotypes, identify chromosomal regions associated with BRD in a genome-wide association study, estimate genetic parameters of BRD, and predict genomic breeding values of dairy calves. A total of 1,107 Holstein calves from 6 dairy farms in southern Wisconsin were examined using clinical respiratory scoring and lung ultrasound at 3 and 6 wk of age. The clinical respiratory score was based on visual appraisal of eyes, nose, ears, cough, and temperature. Lung ultrasound scores were assigned based on the amount of consolidation present. Calves were genotyped with a commercially available SNP array and after quality control and imputation to higher density, 690,291 SNP markers and 1,014 individuals remained. Single-step genome-wide association study and single-step genomic best linear unbiased prediction were applied to binary 3- and 6-wk phenotypes considered as overall respiratory healthy versus affected (RESP3, RESP6) or as presence or absence of lung consolidation (CON3, CON6). Lung ultrasound combined with a clinical scoring system allowed for efficient and objective assessment for the prevalence of BRD. Proportions of variance attributed to 1-Mb non-overlapping windows suggested genomic regions that may contain putative candidate genes, most notably regions on Bos taurus autosomes 1, 6, 7, 10, 11, 12, 15, 17, 18, 27, and 28 that explained 0.70 to 1.45% of the genetic variance. Heritability estimates were higher at 3 wk (0.214 and 0.241 for CON3 and RESP3, respectively) than 6 wk (0.084 and 0.111 for CON6 and RESP6, respectively), and mean reliabilities of genomic estimated breeding vales for calves with genotypes and phenotypes ranged from 0.12 for CON6 to 0.30 for RESP3.
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Affiliation(s)
- Allison E Quick
- Department of Dairy Science, College of Agricultural and Life Sciences, University of Wisconsin, Madison 53706.
| | - Theresa L Ollivett
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin, Madison 53706
| | - Brian W Kirkpatrick
- Department of Animal Sciences, College of Agricultural and Life Sciences, University of Wisconsin, Madison 53706
| | - Kent A Weigel
- Department of Dairy Science, College of Agricultural and Life Sciences, University of Wisconsin, Madison 53706
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12
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McRae KM, Rowe SJ, Baird HJ, Bixley MJ, Clarke SM. Genome-wide association study of lung lesions and pleurisy in New Zealand lambs. J Anim Sci 2019; 96:4512-4520. [PMID: 30099550 PMCID: PMC6247835 DOI: 10.1093/jas/sky323] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 08/06/2018] [Indexed: 12/13/2022] Open
Abstract
Pneumonia is an important issue for sheep production, leading to reduced growth rate and a predisposition to pleurisy. The objective of this study was to identify loci associated with pneumonic lesions and pleurisy in New Zealand progeny test lambs. The lungs from 3,572 progeny-test lambs were scored for presence and severity of pneumonic lesions and pleurisy at slaughter. Animals were genotyped using the Illumina Ovine Infinium HD SNP BeadChip (606,006 markers). The heritability of lung lesion score and pleurisy were calculated using the genomic relationship matrix, and genome-wide association analyses were conducted using EMMAX and haplotype trend regression. At slaughter, 35% of lambs had pneumonic lesions, with 9% showing lesions on more than half of any individual lobe. The number of lambs recorded as having pleurisy by the processing plants was 9%. Heritability estimates for pneumonic lesions and pleurisy scores adjusted for heteroscedasticity (CPSa and PLEURa) were 0.16 (± 0.03) and 0.05 (± 0.02), respectively. Five single-nucleotide polymorphisms (SNPs) were significantly associated with pneumonic lesions at the genome-wide level, and additional 37 SNPs were suggestively significant. Four SNPs were significantly associated with pleurisy, with an additional 11 SNPs reaching the suggestive level of significance. There were no regions that overlapped between the 2 traits. Multiple SNPs were in regions that contained genes involved in either the DNA damage response or the innate immune response, including several that had previously been reported to have associations with respiratory disease. Both EMMAX and HTR analyses of pleurisy data showed a significant peak on chromosome 2, located downstream from the transcription factor SP3. SP3 activates or suppresses the expression of numerous genes, including several genes with known functions in the immune system. This study identified several SNPs associated with genes involved in both the innate immune response and the response to DNA damage that are associated with pneumonic lesions and pleurisy in lambs at slaughter. Additionally, the identification in sheep of several SNPs within genes that have previously been associated with the respiratory system in cattle, pigs, rats, and mice indicates that there may be common pathways that underlie the response to invasion by respiratory pathogens in multiple species.
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Neupane M, Kiser JN, Neibergs HL. Gene set enrichment analysis of SNP data in dairy and beef cattle with bovine respiratory disease. Anim Genet 2018; 49:527-538. [PMID: 30229962 DOI: 10.1111/age.12718] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/21/2018] [Indexed: 02/01/2023]
Abstract
Bovine respiratory disease (BRD) is a complex disease that is associated with infection by bacterial and viral pathogens when cattle fail to adequately respond to stress. The objective of this study was to use gene set enrichment analysis of SNP data (GSEA-SNP) and a network analysis (ingenuity pathway analysis) to identify gene sets, genes within gene sets (leading-edge genes) and upstream regulators associated with BRD in pre-weaned dairy calves and beef feedlot cattle. BRD cases and controls were diagnosed using the McGuirk health scoring system. Holstein calves were sampled from commercial calf-raising facilities in California (1003 cases and 1011 controls) and New Mexico (376 cases and 372 controls). Commercial feedlot cattle were sampled from Colorado (500 cases and 499 controls) and Washington (504 cases and 497 controls). There were 102 and 237 unique leading-edge genes identified in the dairy calf and beef cattle populations respectively. Six leading-edge genes (ADIPOQ, HTR2A, MIF, PDE6G, PRDX3 and SNCA) were associated with BRD in both dairy and beef cattle. Network analysis identified glucose as the most influential upstream regulator in dairy cattle, whereas in beef cattle, TNF was the most influential upstream regulator. The genes, gene sets and upstream regulators associated with BRD have common functions associated with immunity, inflammation and pulmonary disease and provide insights into the mechanisms that are critical to BRD susceptibility in cattle.
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Affiliation(s)
- M Neupane
- Department Animal Sciences, Washington State University, P.O. Box 646310, Pullman, WA, 99164-6310, USA
| | - J N Kiser
- Department Animal Sciences, Washington State University, P.O. Box 646310, Pullman, WA, 99164-6310, USA
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- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA
| | - H L Neibergs
- Department Animal Sciences, Washington State University, P.O. Box 646310, Pullman, WA, 99164-6310, USA
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Human-Mediated Introgression of Haplotypes in a Modern Dairy Cattle Breed. Genetics 2018; 209:1305-1317. [PMID: 29848486 PMCID: PMC6063242 DOI: 10.1534/genetics.118.301143] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 05/24/2018] [Indexed: 12/20/2022] Open
Abstract
Domestic animals can serve as model systems of adaptive introgression and their genomic signatures. In part, their usefulness as model systems is due to their well-known histories. Different breeding strategies such as introgression and artificial selection have generated numerous desirable phenotypes and superior performance in domestic animals. The modern Danish Red Dairy Cattle is studied as an example of an introgressed population. It originates from crossing the traditional Danish Red Dairy Cattle with the Holstein and Brown Swiss breeds, both known for high milk production. This crossing happened, among other things due to changes in the production system, to raise milk production and overall performance. The genomes of modern Danish Red Dairy Cattle are heavily influenced by regions introgressed from the Holstein and Brown Swiss breeds and under subsequent selection in the admixed population. The introgressed proportion of the genome was found to be highly variable across the genome. Haplotypes introgressed from Holstein and Brown Swiss contained or overlapped known genes affecting milk production, as well as protein and fat content (CD14, ZNF215, BCL2L12, and THRSP for Holstein origin and ITPR2, BCAT1, LAP3, and MED28 for Brown Swiss origin). Genomic regions with high introgression signals also contained genes and enriched QTL associated with calving traits, body confirmation, feed efficiency, carcass, and fertility traits. These introgressed signals with relative identity-by-descent scores larger than the median showing Holstein or Brown Swiss introgression are mostly significantly correlated with the corresponding test statistics from signatures of selection analyses in modern Danish Red Dairy Cattle. Meanwhile, the putative significant introgressed signals have a significant dependency with the putative significant signals from signatures of selection analyses. Artificial selection has played an important role in the genomic footprints of introgression in the genome of modern Danish Red Dairy Cattle. Our study on a modern cattle breed contributes to an understanding of genomic consequences of selective introgression by demonstrating the extent to which adaptive effects contribute to shape the specific genomic consequences of introgression.
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Fraser RS, Lumsden JS, Lillie BN. Identification of polymorphisms in the bovine collagenous lectins and their association with infectious diseases in cattle. Immunogenetics 2018; 70:533-546. [PMID: 29744529 PMCID: PMC6061482 DOI: 10.1007/s00251-018-1061-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 05/01/2018] [Indexed: 12/30/2022]
Abstract
Infectious diseases are a significant issue in animal production systems, including both the dairy and beef cattle industries. Understanding and defining the genetics of infectious disease susceptibility in cattle is an important step in the mitigation of their impact. Collagenous lectins are soluble pattern recognition receptors that form an important part of the innate immune system, which serves as the first line of host defense against pathogens. Polymorphisms in the collagenous lectin genes have been shown in previous studies to contribute to infectious disease susceptibility, and in cattle, mutations in two collagenous lectin genes (MBL1 and MBL2) are associated with mastitis. To further characterize the contribution of variation in the bovine collagenous lectins to infectious disease susceptibility, we used a pooled NGS approach to identify short nucleotide variants (SNVs) in the collagenous lectins (and regulatory DNA) of cattle with (n = 80) and without (n = 40) infectious disease. Allele frequency analysis identified 74 variants that were significantly (p < 5 × 10−6) associated with infectious disease, the majority of which were clustered in a 29-kb segment upstream of the collectin locus on chromosome 28. In silico analysis of the functional effects of all the variants predicted 11 SNVs with a deleterious effect on protein structure and/or function, 148 SNVs that occurred within potential transcription factor binding sites, and 31 SNVs occurring within potential miRNA binding elements. This study provides a detailed look at the genetic variation of the bovine collagenous lectins and identifies potential genetic markers for infectious disease susceptibility.
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Affiliation(s)
- R S Fraser
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - J S Lumsden
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada.,St. George's University, True Blue, Grenada
| | - B N Lillie
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada.
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Kiser JN, Lawrence TE, Neupane M, Seabury CM, Taylor JF, Womack JE, Neibergs HL. Rapid Communication: Subclinical bovine respiratory disease - loci and pathogens associated with lung lesions in feedlot cattle. J Anim Sci 2018; 95:2726-2731. [PMID: 28727052 PMCID: PMC7110184 DOI: 10.2527/jas.2017.1548] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Bovine respiratory disease (BRD) is an economically important disease of feedlot cattle that is caused by viral and bacterial pathogen members of the BRD complex. Many cases of subclinical BRD go untreated and are not detected until slaughter, when lung lesions are identified. The objectives of this study were to identify which BRD pathogens were associated with the presence of lung lesions at harvest and to identify genomic loci that were associated with susceptibility to lung lesions as defined by consolidation of the lung and/or the presence of fibrin tissue. Steers from a Colorado feedlot (n = 920) were tested for the presence of viral and bacterial pathogens using deep pharyngeal and mid-nasal swabs collected on entry into the study. Pathogen profiles were compared between cattle with or without lung consolidation (LC), fibrin tissue in the lung (FT), a combination of LC and FT in the same lung (lung lesions [LL]), and hyperinflated lungs (HIF) at harvest. Genotyping was conducted using the Illumina BovineHD BeadChip. Genomewide association analyses (GWAA) were conducted using EMMAX (efficient mixed-model association eXpedited), and pseudoheritabilities were estimated. The pathogen profile comparisons revealed that LC (P = 0.01, odds ratio [OR] = 3.37) and LL cattle (P = 0.04, OR = 4.58) were more likely to be infected with bovine herpes virus-1 and that HIF cattle were more likely to be infected with Mycoplasma spp. (P = 0.04, OR = 4.33). Pseudoheritability estimates were 0.25 for LC, 0.00 for FT, 0.28 for LL, and 0.13 for HIF. Because pseudoheritability for FT was estimated to be 0, GWAA results for FT were not reported. There were 4 QTL that were moderately associated (P < 1 × 10−5) with only LC, 2 that were associated with only LL, and 1 that was associated with LC and LL. Loci associated with HIF included 12 that were moderately associated and 3 that were strongly associated (uncorrected P < 5 × 10−7). A 24-kb region surrounding significant lead SNP was investigated to identify positional candidate genes. Many positional candidate genes underlying or flanking the detected QTL have been associated with signal transduction, cell adhesion, or gap junctions, which have functional relevance to the maintenance of lung health. The identification of pathogens and QTL associated with the presence of lung abnormalities in cattle exhibiting subclinical BRD allows the identification of loci that may not be detected through manifestation of clinical disease alone.
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Runyan CA, Downey-Slinker ED, Ridpath JF, Hairgrove TB, Sawyer JE, Herring AD. Feed Intake and Weight Changes in Bos indicus-Bos taurus Crossbred Steers Following Bovine Viral Diarrhea Virus Type 1b Challenge Under Production Conditions. Pathogens 2017; 6:pathogens6040066. [PMID: 29231886 PMCID: PMC5750590 DOI: 10.3390/pathogens6040066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Revised: 12/07/2017] [Accepted: 12/08/2017] [Indexed: 11/24/2022] Open
Abstract
Bovine viral diarrhea virus (BVDV) has major impacts on beef cattle production worldwide, but the understanding of host animal genetic influence on illness is limited. This study evaluated rectal temperature, weight change and feed intake in Bos indicus crossbred steers (n = 366) that were challenged with BVDV Type 1b, and where family lines were stratified across three vaccine treatments of modified live (MLV), killed, (KV) or no vaccine (NON). Pyrexia classification based on 40.0 °C threshold following challenge and vaccine treatment were investigated for potential interactions with sire for weight change and feed intake following challenge. Pyrexia classification affected daily feed intake (ADFI, p = 0.05), and interacted with day (p < 0.001) for ADFI. Although low incidence of clinical signs was observed, there were marked reductions in average daily gain (ADG) and cumulative feed intake during the first 14 day post-challenge; ADG (CV of 104%) and feed efficiency were highly variable in the 14-day period immediately post-challenge as compared to the subsequent 14-day periods. A sire × vaccine strategy interaction affected ADFI (p < 0.001), and a sire by time period interaction affected ADG (p = 0.03) and total feed intake (p = 0.03). This study demonstrates that different coping responses may exist across genetic lines to the same pathogen, and that subclinical BVDV infection has a measurable impact on cattle production measures.
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Affiliation(s)
- Chase A Runyan
- Department of Animal Science, Texas A&M University, College Station, TX 77843, USA.
- Department of Agriculture, Angelo State University, San Angelo, TX 76909-0888, USA.
| | - Erika D Downey-Slinker
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA.
- Elanco Animal Health, Larchwood, IA 51241, USA.
| | - Julia F Ridpath
- USDA-ARS National Animal Disease Center, Ames, IA 50010, USA.
- Ridpath Consulting, LLC, Gilbert, IA 50105, USA.
| | - Thomas B Hairgrove
- Department of Animal Science, Texas A&M University, College Station, TX 77843, USA.
- Texas A&M AgriLife Extension, College Station, TX 77843, USA.
| | - Jason E Sawyer
- Department of Animal Science, Texas A&M University, College Station, TX 77843, USA.
- Texas A&M AgriLife Research, College Station, TX 77843, USA.
| | - Andy D Herring
- Department of Animal Science, Texas A&M University, College Station, TX 77843, USA.
- Texas A&M AgriLife Research, College Station, TX 77843, USA.
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Mahmoud M, Yin T, Brügemann K, König S. Phenotypic, genetic, and single nucleotide polymorphism marker associations between calf diseases and subsequent performance and disease occurrences of first-lactation German Holstein cows. J Dairy Sci 2017; 100:2017-2031. [DOI: 10.3168/jds.2016-11767] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 11/13/2016] [Indexed: 12/28/2022]
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Keele JW, Kuehn LA, McDaneld TG, Tait RG, Jones SA, Keel BN, Snelling WM. Genomewide association study of liver abscess in beef cattle. J Anim Sci 2016; 94:490-9. [PMID: 27065119 DOI: 10.2527/jas.2015-9887] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Fourteen percent of U.S. cattle slaughtered in 2011 had liver abscesses, resulting in reduced carcass weight, quality, and value. Liver abscesses can result from a common bacterial cause, , which inhabits rumen lesions caused by acidosis and subsequently escapes into the blood stream, is filtered by the liver, and causes abscesses in the liver. Our aim was to identify SNP associated with liver abscesses in beef cattle. We used lung samples as a DNA source because they have low economic value, they have abundant DNA, and we had unrestricted access to sample them. We collected 2,304 lung samples from a beef processing plant: 1,152 from animals with liver abscess and 1,152 from animals without liver abscess. Lung tissue from pairs of animals, 1 with abscesses and another without, were collected from near one another on the viscera table to ensure that pairs of phenotypically extreme animals came from the same lot. Within each phenotype (abscess or no abscess), cattle were pooled by slaughter sequence into 12 pools of 96 cattle for each phenotype for a total of 24 pools. The pools were constructed by equal volume of frozen lung tissue from each animal. The DNA needed to allelotype each pool was then extracted from pooled lung tissue and the BovineHD Bead Array (777,962 SNP) was run on all 24 pools. Total intensity (TI), an indicator of copy number variants, was the sum of intensities from red and green dyes. Pooling allele frequency (PAF) was red dye intensity divided TI. Total intensity and PAF were weighted by the inverse of their respective genomic covariance matrices computed over all SNP across the genome. A false discovery rate ≤ 5% was achieved for 15 SNP for PAF and 20 SNP for TI. Genes within 50 kbp from significant SNP were in diverse pathways including maintenance of pH homeostasis in the gastrointestinal tract, maintain immune defenses in the liver, migration of leukocytes from the blood into infected tissues, transport of glutamine into the kidney in response to acidosis to facilitate production of bicarbonate to increase pH, aggregate platelets to liver injury to facilitate liver repair, and facilitate axon guidance. Evidence from the 35 detected SNP associations combined with evidence of polygenic variation indicate that there is adequate genetic variation in incidence rate of liver abscesses, which could be exploited to select sires for reduced susceptibility to subacute acidosis and associated liver abscess.
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Raszek MM, Guan LL, Plastow GS. Use of Genomic Tools to Improve Cattle Health in the Context of Infectious Diseases. Front Genet 2016; 7:30. [PMID: 27014337 PMCID: PMC4780072 DOI: 10.3389/fgene.2016.00030] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 02/18/2016] [Indexed: 12/15/2022] Open
Abstract
Although infectious diseases impose a heavy economic burden on the cattle industry, the etiology of many disorders that affect livestock is not fully elucidated, and effective countermeasures are often lacking. The main tools available until now have been vaccines, antibiotics and antiparasitic drugs. Although these have been very successful in some cases, the appearance of parasite and microbial resistance to these treatments is a cause of concern. Next-generation sequencing provides important opportunities to tackle problems associated with pathogenic illnesses. This review describes the rapid gains achieved to track disease progression, identify the pathogens involved, and map pathogen interactions with the host. Use of novel genomic tools subsequently aids in treatment development, as well as successful creation of breeding programs aimed toward less susceptible livestock. These may be important tools for mitigating the long term effects of combating infection and helping reduce the reliance on antibiotic treatment.
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Affiliation(s)
- Mikolaj M Raszek
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta Edmonton, AB, Canada
| | - Le L Guan
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta Edmonton, AB, Canada
| | - Graham S Plastow
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta Edmonton, AB, Canada
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