Source: UNIVERSITY OF MISSOURI submitted to
TRI-PARTITE COLLABORATIVE: IDENTIFICATION OF REGULATORY ELEMENT VARIANTS IMPEDING IMMUNE RESPONSE TO PATHOGENS CAUSING BOVINE RESPIRATORY DISEASE
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
TERMINATED
Funding Source
AFRI COMPETITIVE GRANT
Reporting Frequency
Annual
Accession No.
1012457
Grant No.
2017-67015-26760
Project No.
MOC00055801
Proposal No.
2016-09375
Multistate No.
(N/A)
Program Code
A1221
Project Start Date
Jun 1, 2017
Project End Date
May 31, 2021
Grant Year
2017
Project Director
Taylor, J. F.
Recipient Organization
UNIVERSITY OF MISSOURI
(N/A)
COLUMBIA,MO 65211
Performing Department
Animal Sciences
Non Technical Summary
This project builds upon the work accomplished in the USDA NIFA AFRI project2011-68004-30367"Integrated program for reducing bovine respiratory disease complex in beef and dairy cattle." In that project, we conducted an optimized challenge experiment in which naive cattle were experimentally challenegd with one of three viruses or bacteria that are responsible for respiratory disease. Immune function tissues were harvested from these animals after they were euthenized at the peak of clinical signs and were analyzed to identify the cascades of genes that were involved in the normal immune response of these animals to infection by a disease causing pathogen. A significant number of these genes were found to be located in regions of the genome which we also established in the project to harbor DNA variants that affected the risk of animals contracting respiratory disease. However, we were able to establish that the majority of these risk variants did not appear to be within the product produced by the immune function genes. Therefore the genetic variants that influence an animal's risk of respiratory disease appear to not change the structure or function of proteins but actually influence the regulation of expression of these genes. In particular, we have consideable evidence that some of these variants may result in the certain immune function genes completely failing to appropriately respond to an infection by a pathogen.while we now have whole genome sequences on nearly 3,000 animals from which we have reliably cataloged the identity of nearly 40 million variants that are reasonably common among cattle, we have no idea which of these variants liein regulatory regions of genome, becausevery little is known about the regions of the genome which are regulatory in livestock. The tools to identify these regions have been developed in the human genome project and a project known as the Functional Annotation of Animal Genomes has been initiated to apply these tools to tissues harvested from animals to identify regulatory regions. Unfortunately, again, these tools were developed for use with fresh tissue samples and many important experiments in livestock have preserved frozen tissue samples. Consequently, we shall first optimize tools for the functional annotation of regulatory regions so that they can be applied to frozen tissue samples. We will then apply these tools to the six immune function related tissues that were collected and frozen on 27 animals that were either controls or challenged by a single virualor bacterial pathogen that is known to cause respiratory disease in cattle. From this approach, we shall identify the regions of the cattle genome that are responsible for regulating the expression of the genes that are involved in the normal immune response to disease causing pathogens. This work will also be conducted by our partners in Ireland who will also perform a challenge experiment in which animals will be challnged by two of the viruses that were used in our challenege experiment and that are responsible for most of the bovine respiratory disease in Ireland. In this study we will have the luxury of collecting fresh tissues from which to perform the functional analyses to identify regulatory regions.The next step in the research will be to utilize an extensive catalog of genetic variation obtained from the whole genome sequences of nearly 3,000 animals to identify those variants that are common (at a frequency of 1% or more in cattle) and that are also located in regions of the genome that regulate the genes that are involved in the normal immune response to infection by disease causing pathogens. These variants are now candidates for having direct effects of the genetic capability of animals to mount an effective immune response to pathogen infections. To test which of the candidates are directly causal, we shall place the variants of genotyping assays that are routinely used by the cattle industries in Ireland and the US and the resulting genotyping tool will provide us the opportunity to genotype unaffected and diseased cattle to assess which of the variants that lie in regulatory regions actually directly affect the immune response of the animal by being strongly different in frequency between diseased and unaffected animals. Once this step has been completed, we will have identified the variants that have the largest effect in the genome on disease suspectibility and we will be directly able to estimate the genetic merit of individual animals for resistance (or susceptibility) to respiratory disease. These can directly be used by cattle breeders to slect for cattle that are more resisatnt to disease and this will reduce the prevalence of respiratory disease in cattle populations world-wide.
Animal Health Component
100%
Research Effort Categories
Basic
50%
Applied
25%
Developmental
25%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
3033310110025%
3033310110125%
3033410110025%
3033410110125%
Knowledge Area
303 - Genetic Improvement of Animals;

Subject Of Investigation
3310 - Beef cattle, live animal; 3410 - Dairy cattle, live animal;

Field Of Science
1101 - Virology; 1100 - Bacteriology;
Goals / Objectives
This is a tripartite collaborative research project with partners from Teagasc in the Republic of Ireland and the Agri-Food and Biosciences Institute in Northern Ireland. The long-term goal of this team is to sustainably reduce the prevalence of Bovine Respiratory Disease (BRD) world-wide via the identification of large-effect causal variants underlying risk of BRD and the rapid deployment of assays containing these variants enabling genomic selection in the US and Irish cattle populations. The team will strengthen the international competitiveness of US and Irish agriculture and will enable increased food production via the reduction of animal losses and costs associated with treating sick animals. The work will also result in the reduction of the need for antibiotic use in animal agriculture thus reducing the rate of evolution of antibiotic resistance in the bacterial pathogens and symbionts that are present within treated cattle.We have previously conducted genome-wide association analyses in cattle that are controls or BRD cases and have found that at least 20% of the variation in the risk of disease is genetically determined and that there appear to be a large number of large effect variants that underlie risk of disease. This should probably not be surprising considering that there is a large suite of pathogens that are capable of causing respiratory disease in cattle. We have also performed a global gene expression profiling study of lung and lymphoid tissues harvested from cattle that were experimentally challenged with single pathogens responsible for BRD and have found that many of the genes that are normally involved in the immune response to challenge by these pathogens are located in regions of the genomes that have large effects on risk of disease. That is, the joint conclusions of the genome-wide association study and genome-wide gene expression study of immune function tissues is that mutations in regions of the genome that regulate the expression of genes involved in the immune response to pathogens can reduce the adequacy of the immune response and increase the risk of disease. Thus, we hypothesize that by identifying the mutations in regions of the genome that regulate the genes that are involved with the immune response to BRD pathogens, we shall identify the large-effect variants responsible for increasing the risk of disease. By incorporating these variants of the genotyping assays that are used by the cattle industry to deploy genomic selection for production traits, we shall also be able to select animals with better functioning immune systems that are more capable of resisting the pathogens that cause BRD and as a result the prevalence of BRD will decrease.We have already performed the genome-wide association studies for risk of BRD and likewise, we have already performed the challenge experiments and global transcript analysis of lymphoid tissues from the experimentally challenged animals. Together, these analyses indicate the locations in the genome of the genes responsible for the normal immune response to infection and whether there appear to mutations in these genes or the elements that regulate these genes that impact the risk of disease. By performing association analyses using variants imputed to the level of whole genome sequence (over 12 million variants in the genome-wide association analysis) we conclude that the majority of the large-effect risk variants do not lie in genes themselves but are in the upstream regions that regulate the expression of these genes. Because nearly 3,000 animals have already had their genomes sequenced to date, we have an excellent catalog of the locations and nature of variation within the bovine genome. What we currently lack, is the annotation of regions of the genome that are involved in the functional regulation of genes.We shall tackle this by employing two techniques known as FAIRE-seq and ATAC-seq that identify regions of open chromatin within the lymphoid tissues of the animals that were experimentally challenged with pathogens responsible for BRD. Regions of open chromatin are stretches of DNA that have been released from compact wrapping around histones to allow the binding of transcription factors or enhancers to act on the transcription of nearby genes. Thus regions of open chromatin represent regulatory regions of the genome. By performing capture experiments that sequence the DNA in these regions from the lymphoid tissues (e.g., bronchial lymph nodes, nasopharyngeal lymph nodes and lung tissues) we shall be able to identify the regions of the genome that are responsible for regulating the normal immune response to infection by pathogens that cause BRD. At this point we can intersect these regions with the catalog of genomic variation identified by sequencing more than 3,000 animals to identify candidate variants for the BRD risk loci of large effect discovered in genome-wide association studies. Finally, these variants can be incorporated into the next generations of industry SNP chips to gather the data that will allow the validation of which variants directly influence risk of BRD and also to deliver genomic estimates of breeding value for risk of BRD to the industry to allow selection to improve the resistance of animals to the pathogens responsible for BRD.
Project Methods
In the USDA NIFA supported Bovine Respiratory Disease CAP project, we conducted two experimental challenge experiments with pathogenic agents. In the first experiment, Angus x Hereford steers were challenged with bovine respiratory syncytial virus, infectious bovine rhinotracheitis virus, bovine viral diarrhea virus, Mannheimia haemolytica, Pasteurella multocida or Mycoplasma bovis to determine the appropriate pathogen dosage and the time course for each experimental infection so that tissue samples could be harvested at the time of maximal clinical signs. A second optimized experiment was then conducted in which groups of four animals were challenged with one of the viruses or and 4 animals were mock challenged as controls. One animal challenged with M. bovis was euthanized early due to extreme disease and tissues were not collected, leaving 27 animals from which healthy lung and lung lesions and the lymphoid tissues retropharyngeal lymph node, nasopharyngeal lymph node, bronchial lymph node and pharyngeal tonsil were collected. Tissue samples were frozen on dry ice before being transferred to the laboratory where they were ultimately stored in a -80OC freezer. The sampled animals had not been vaccinated against pathogens and steers seronegative, or with the lowest titers against each bacterial and viral pathogen, were selected to establish the normal immune response of cattle to infection by these pathogens.Results for the bronchial lymph node RNA-seq analyses are published and results for the analyses of the remaining tissues have been completed. In the association analysis conducted in Holstein calves we found 116 genomic regions harboring variants associated with respiratory disease susceptibility. These 116 regions harbor 649 genes (UMD3.1 reference assembly), of which, 142 were differentially expressed between the experimentally challenged and control animals in the bronchial lymph nodes and 247 in the remaining tissues. Of particular interest, no expression was detected for 156 genes in the tissues of the experimentally challenged animals while expression was detected in the controls and no expression was detected for 55 genes in the tissues of the controls while expression was detected in the experimentally challenged animals. Among these genes are 54 potential upstream regulators located in the quantitative trait locus regions that encode transcription factors, cytokines, transporters, phosphatases and protein kinases such as IL15, TGM2, FADD, SRC and IL6ST and these molecules activate a cascade of post-infection events.Variants within regulatory regions that affect the expression of these genes will be identified in a two step process. First we shall use FAIRE-seq and ATAC-seq to identify the regulatory regions and then we shall use whole genome sequence data available in our laboratory (~600 animals) and via the 1000 Bull Genomes project (~2,000 animals) to identify the common variants that are located within these regulatory regions and that are candidates for affecting the normal expression of immune function genes by disrupting transcription factor or other regulatory protein binding sites.FAIRE-seq (Formaldehyde-Assisted Isolation of Regulatory Elements) and ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) are approaches for the identification of genomic regions in which nucleosomes have been evicted from the chromatin to allow transcription factors or other regulatory proteins to bind to regulatory elements within the regions of open chromatin. In FAIRE-seq, cells or dissociated tissues are cross-linked with formaldehyde, lysed and the DNA is sheared by sonication. The sheared DNA is phenol/chloroform extracted and purified to produce a reduced representation comprising typically from 1-3% of the genome that represents the open chromatin. FAIRE is based on differences in formaldehyde cross-linking efficiencies between DNA and nucleosomes or sequence-specific DNA-binding proteins. DNA in nucleosome-depleted regions of chromatin is much less efficiently cross-linked to protein and the DNA that is not cross-linked to protein will segregate to the aqueous phase during phenol/chloroform extraction. Conversely, DNA that is covalently linked to proteins demonstrates hydrophilic properties and becomes trapped between the organic and aqueous phases. FAIRE has been shown to identify additional distal regulatory elements not recovered by DNase-seq, although it remains unclear what these sites represent. FAIRE overcomes the sequence-specific cleavage bias observed with MNase and DNase I and thus represents an ancillary or perhaps even alternative approach to these assays. In ATAC-seq, hyperactive Tn5 transposase is loaded in vitro with high-throughput DNA sequencing adaptors to simultaneously fragment and tag the genome with sequencing adaptors in a process called "Tagmentation." The Tn5 transposase preferentially integrates the adaptors into regions of accessible chromatin, whereas steric hindrance in less accessible chromatin makes such transposition less probable. The resulting PCR amplifiable DNA fragments are suitable for high-throughput sequencing and are highly enriched for regions of open chromatin.FAIRE-seq has now largely been surpassed by ATAC-seq because the FAIRE-seq protocol requires a great deal of optimization and a 3 day process to generate a sequencing library, whereas the much simpler two-step ATAC-seq protocol arrives at this point after about only 3 hours of lab work. In FAIRE, the adequacy of fixation depends heavily on the tissue size and composition, and must be optimized. Additionally, sonication parameters must be optimized for each experiment because of variation in cell number, composition, sonicator and probe type, and adequacy of fixation. The most common reason for a failed FAIRE experiment is underfixation of the cells. Further, relative to ChIP-seq or DNase-seq experiments, FAIRE has a lower signal-to-noise ratio and the sites detected by FAIRE can, at times, be only marginally enriched above the background signal. Conversely, ATAC-seq has a signal-to-noise ratio that is similar to DNase-seq. On the other hand, FAIRE can be used with frozen tissue as the starting material, requiring only the additional step of pulverization of the frozen tissue into a coarse powder before fixation. While the published ATAC-seq protocol has been optimized for 50,000 cells of starting material, when tissue samples are analyzed, the amount of starting material must be optimized to a DNA yield that is equivalent to that from 50,000 cells to ensure that the correct volume of Tn5 transposase is utilized in the Tagmentation reaction. Further, it is not clear that the protocol will be effective when used with frozen tissues which may have suffered DNA damage and the established protocol recommends starting with fresh, unfixed cells in a homogeneous, single-cell suspension to maximize methodological sensitivity. Preservation of the native chromatin architecture and the original nucleosome distribution patterns is essential for ATAC-seq. Freezing samples prior to the purification of nuclei can be detrimental to nuclear integrity and chromatin structure, possibly restricting the application of ATAC-seq to freshly-isolated nuclei.Because the tissues available to us from the challenge experiment were frozen on dry ice prior to their being frozen at -80OC we shall optimize both protocols using fresh and frozen tissue samples harvested from animals slaughtered at the University of Missouri College of Veterinary Medicine. Once the protocols have been optimized, we shall analyze all of the frozen samples (5 tissues from each of 27 animals) to identify regulatory regions in the tissues of control animals and those challenged with disease causing pathogens.

Progress 06/01/17 to 05/31/21

Outputs
Target Audience:The target audience for this project includes research scientists working to understand the regulation of the immune response to infections by the pathogens that cause Bovine Respiratory Disease. This includes scientists focused on understanding the basis for human respiratory diseases and developing therapies for these diseases and those working in the livestock sector where these diseases cause loss of production and production efficiency. These scientists include geneticists and immunologists interested in the transcriptional regulation of immune function genes and also in the development of therapies against disease and predictions of genetic merit for disease resistance based upon variants that lie within regulatory regions of the genome (risk of disease based upon genotype). Also included in the target audience are graduate and undergraduate students in the Life Sciences with interests in genetics and immunology. Finally, the work is ultimately targeted at members of the beef cattle production sector including Beef Breed Associations, producers, feedlot managers and owners with an interest in generating and producing beef from animals with an enhanced resistance to the pathogens responsible for resiratory disease. Changes/Problems:We were never satisfied with any of the results produced by using the published protocols for ATAC-seq from frozen tissues and were never able to modify these protocols to produce satisfactory results. In all cases we used biological and technical replicates to quantify the repeatability of the protocols under the hypothesis that the number of regulatory regions within the genome should be a tissue-specific event and that robust protocols should recapitulate this both in terms of the number of regions identified and the concordance between the detected regions in technical and biological replicates. We found that by far the best results were obtained using single nucleotide ATAC-seq approaches but were unable to complete the sequencing of the frozen brocnhical lymph node samples from the BRD challenge experiment within the time-frame and available budget of the project. What opportunities for training and professional development has the project provided?This project supported aspects of the training of Tamar Crum and Jesse Hoff who were PhD students at the University of Missouri under the primary supervision of Dr. Taylor. Dr. Crum developed an analytical pipeline called CRUMBLER which utilizes high-density SNP genotypes scored in cattle to estimate their breed composition. While this is not important in the US dairy industry where the majority of animals are purebred, it is very importnat in the US beef industry where the majority of production animals are crossbred. The CRUMBLER pipeline was used to estimate the brred compsotion of beef animals generated in the Bovine Respiratory Disease project which was incorporated into analyses of SNP association with disease phenotype to assist reduce analytical issues which inflate test statistics due to undetected confounding effects. Dr. Hoff performed an analysis in which we wished to determine if restricting the number of SNPs used in an analysis to those within QTL regions (which include regulatory variants) would result in an increase the realized heritability of resistance to Bovine Respiratory Disease due to an increased precision of estimation of SNP effects. Dr. JaeWoo Kim also traveled to Ireland in 2018 for two weeks to assisat our Irish collaborators with the sampling of tissues from experimentally challenged animals and the preparation of ATC-seq libraries from these tissues which were sequenced at the University of Missouri. Finally, Dr. Taylor served on the dissertation defense committee for Dayle Johnston, the Irish PhD student who led the research for our Irish collaborators as a postdoctoral fellow. He attended her PhD defense in Ireland in 2017. How have the results been disseminated to communities of interest?Results from this work have been conveyed to the scientific community through a series of peer reviewed journal articles which have been published in high-quality journals. On-going aspects of the research have been conveyed to members of the US Beef Cattle Industry through presentations at coferences such as the Beef Improvement Federation. Results have not yet advanced to the point that predictions of genetic merit of animals for disease resistance/susceptiblity can be transferred to the beef industry. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? From the outset of this project, we decided to focus on ATAC-seq as the most desirable approach for identifying regulatory regions of DNA using next-generation sequencing. To test the effectiveness of the various techniques for sequencing library preparations from frozen tissue, we designed a large number of experiments in which we applied the protocols to fresh bronchial lymph node samples and flash frozen bronchial lymph node samples harvested from the same animal with the inclusion of technical replicates. In the process, we modified a number of steps in the frozen tissue protocol to examine the effects of different numbers of tissue processing approaches, numbers of starting cells, total amount of transposase added and transposase incubation times, etc. To evaluate the effects of these experimental changes in each protocol, we evaluated the fragment size distributions for each produced library to detect the periodicity expected from histone spooling and also to examine the effects of background DNA contamination from random incorporation of transposase into DNA that was no longer histone bound due to cell damage and DNA release from freezing. Invariably, the produced libraries would reveal the characteristic expected size distribution but with a considerable amount of background DNA across the fragment size distribution from non-histone bound DNA. When these libraries were sequenced, the sequences were adapter trimmed, PCR duplicates were removed and fragments aligned to the ARS-UCD1.2 bovine reference assembly and "peaks" were called. In general, the presence of the background DNA reduced the number of peaks that were called to ~25K per sample when we expected to see 50-60K peaks based upon human data and the concordance between peaks called in technical replicates was only in the range 0.5-0.6, much lower than we expected for a high-quality data set. After 4 years of work, we were never able to produce ATAC-seq libraries from frozen tissue samples that generated sequence data that were of higher quality than this and so in the final months of the project, we conducted an experiment using a new approach - single nucleotide ATAC-seq sequencing. The advantage of this this approach is that one begins with a single intact nucleus and so there is no free non-histone bound DNA in solution to contaminate the library construction. In this final experiment we took two technical replicates from two animals (biological replicates) and generated snATC-seq libraries which were sequenced and analyzed as before. In this experiment, we obtained 54,799, 55,225, 55,386 and 56,471 peaks from the four libraries. Highly consistent results between both technical and biological replicates. The Jaccard similarity scores between technical replicates average 0.87 and between biological replicates averaged 0.76. These results are characteristic of well-behaved data. Moreover, the data reinforce the notion that ATAC peaks should be characteristic of a tissue and there should not be much biological variability in a well optimized assay. At this point, the project funds were spent and the one-year no-cost extension had expired. In our collaborations with our Irish counterparts, Dr. Kim spent two weeks in Ireland assisting with tissue harvest and processing into ATAC-seq libraries from experimentally challenged animals. The libraries were sequenced at the eUniversity of Missouri and the produced sequences were analyzed by Dayle Johnston, the Irish postdoc leading this aspect of the work for the Irish groups. This collaboration led to an extensive characterization of fresh bronchial lymph nodes from Irish dairy cattle experimentally challenged with Bovine Respiratory Syncytial virus. This collaboration led to 9 presentations at International Scientific meetings and 4 coauthored peer reviewed journal articles describing the performed experimental challenge and ATAC-seq profile of challenged versus control animals along with the bronchial lymph node mRNA and miRNA profiles of these animals. Finally, we performed an analysis to predict the genetic merit of US Holstein animals for susceptibility to Bovine Respiratory Disease using a genome-wide SNP set and a SNP set that had been reduced in the number of fit SNPs to those that were located within susceptibility QTL regions within the genome. Our conjecture was that by reducing the number of randomly selected SNPs to a subset that tagged regions harboring regulatory and protein amino acid variants that we could potentially increase the realized heritability of the trait. We also postulated that the accuracy of prediction of genetic merit for disease susceptibility would be increased in advanced generations of animals by limiting our focus to a SNP set that was more likely to contain causal variants. We discovered that the realized heritability (SNP-set heritability) did not differ between a genome-wide sampled SNP-set and the set selected based upon likelihood of causality. Despite fitting many fewer SNPs in the model, this likely reflects the fact that the large numbers of SNPs fit in each case were more than sufficient to tag the causal SNPs in the genome due to linkage disequilibrium. The more interesting question of whether the accuracy of prediction of merit in future generations of animals would be improved with the feature selected SNP-set could not be addressed because the animals utilized were from only single generation.

Publications

  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Taylor JF. 2017. Identification of Variants within Regulatory Regions: Immune Response to Pathogens Responsible for Respiratory Disease. Omics Workshop, Piracicaba, Brazil. April 26.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Taylor JF, RD Schnabel, B Simpson, JE Decker, MM Rolf, B Kinghorn, AL Van Eenennaam, M MacNeil, S Brown, MF Smith and D Patterson. 2017. GGP-F250 and Loss of Function Variants. Beef Improvement Federation. Athens, GA. June 2.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Rowan TN, JE Decker, JF Taylor and RD Schnabel. 2018. Impact of the new reference genome on genotype imputation accuracy. Presentation W151. Plant and Animal Genome Conference XXVI. San Diego. Jan 13.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: Taylor JF, JL Hoff, TN Rowan, JD Neal, JE Decker, RD Schnabel & BRD CAP Project. 2019. Identification of disease-causing pathogens and breeding for disease resistance in cattle. Biotechnology Applied to the Fight Against Hunger, University of Sao Paulo, Pirassununga, SP, Brazil, April 12.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: Taylor JF. 2019. Adventures in next-generation sequencing. University of Sao Paulo, Piracicaba, Brazil, April 16.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Decker JE, ML Wilson, RD Schnabel, R Weaber and JF Taylor. 2017. Using haplotype-based models and feature selection for genomic predictions in crossbred animals and multiple breeds. Gordon Research Conference in Quantitative Genetics and Genomics. Galvaston TX. Feb 27  Mar 3.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Neibergs HL, JN Kiser, M Neupane, CM Seabury, JF Taylor, MA Cornmesser, BRD Consortium and JE Womack. 2017. Genome wide association analysis identifies QTL associated with clinical and sub-clinical bovine respiratory disease. Midwest ASAS March 12-14, Omaha, NE.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Crum TE, RD Schnabel, JE Decker and JF Taylor. 2018. Inference of Admixture for Cattle with Complex Ancestry. Population, Evolutionary and Quantitative Genetics Conference. May 13-16, 2018. Madison, WI.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Johnston D, B Earley, MS Mccabe, G Blackshields, K Lemon, C Duffy, M Mcmenamy, SL Cosby, JW Kim, JF Taylor and SM Waters. 2018. Elucidation of genes/pathways involved in the host response to bovine respiratory syncytial virus. 7th International Symposium on Animal Functional Genomics. Nov 12-15. Adelaide, Australia.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: Johnston D, B Earley, MS McCabe, G Blackshields, K Lemon, C Duffy, M McMenamy, SL Cosby, J Kim, JF Taylor and SM Waters. 2019. Application of next generation sequencing for the elucidation of genes and pathways involved in the host response to bovine respiratory syncytial virus. The Microbiology Society annual meeting. April 8-11. Belfast.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: Johnston D, B Earley, M McCabe, G Blackshields, K Lemon, C Duffy, M McMenamy, J Kim, J Taylor, S Waters, SL Cosby, 2019. Experimental virus challenge in calves to model bovine and human respiratory disease. British Society of Immunology. Ulster Immunology Group 'Immunology without borders' 13 - 14 June 2019. Belfast, Northern Ireland.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: Johnston D, B Earley, MS McCabe, K Lemon, C Duffy, M McMenamy, SL Cosby, J Kim, JF Taylor & SM Waters. 2019. Characterisation of miRNAs and target genes involved in the dairy calf bronchial lymph node transcriptomic response to bovine respiratory syncytial virus. Association for Veterinary Teaching and Research Work. Teagasc Grange, Ireland. October 4.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: Johnston D, B Earley, MS McCabe, K Lemon, C Duffy, M McMenamy, SL Cosby, J Kim, JF Taylor & SM Waters. 2020. Elucidation of miRNAs and target genes involved in the dairy calf bronchial lymph node transcriptomic response to bovine respiratory syncytial virus. Society for Veterinary Epidemiology and Preventative Medicine. Westport Ireland. Mar 25-27.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: Johnston D, B Earley, M McCabe, G Blackshields, K Lemon, C Duffy, M McMenamy, SL Cosby, J Kim, J Taylor and Sinead Waters. 2020. Experimental virus challenge in calves to model bovine and human respiratory disease. Microbiology Society Annual Conference, Mar 30  Apr 3. Edinburgh, United Kingdom
  • Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: Johnston D, JW Kim, JF Taylor, B Earley, MS McCabe, K Lemon, C Duffy, M McMenamy, SL Cosby and SM Waters. 2020. Elucidation of regions of open chromatin in the bronchial lymph nodes of dairy calves experimentally challenged with Bovine Respiratory Syncytial Virus using ATAC-Seq. 2nd FAANG-Europe Workshop on Functional Annotation of Animal Genomes. Prague, Czech Republic. Feb 11 - 13.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: Johnston D, JW Kim, JF Taylor, B Earley, MS McCabe, K Lemon, C Duffy, M McMenamy, SL Cosby and SM Waters. 2020. Bovine Respiratory Syncytial Virus induces alterations in transcription of miRNAs and their target genes in the bronchial lymph node. 2nd FAANG-Europe Workshop on Functional Annotation of Animal Genomes. Prague, Czech Republic. Feb 11 - 13.
  • Type: Conference Papers and Presentations Status: Submitted Year Published: 2021 Citation: Johnston D, B Earley, M McCabe, G Blackshields, K Lemon, C Duffy, M McMenamy, R Bell, H Turkington, J Kim, J Taylor, S Cosby and S Waters. 2021. Experimental virus challenge in calves to identify host markers for Bovine Respiratory Syncytial Virus infection. British Society of Immunology Congress. Edinburgh UK. Nov 28  Dec 1.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Taylor JF, RD Schnabel and P Sutovsky. 2018. Review: Genomics of bull fertility. Animal. 12 (S1): s172183.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Hoff JL JE Decker, RD Schnabel, CM Seabury, HL Neibergs and JF Taylor. 2019. QTL-mapping and genomic prediction for bovine respiratory disease in U.S. Holsteins using sequence imputation and feature selection. BMC Genomics 20:555.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Crum T, RD Schnabel, JE Decker, LCA Regitano and JF Taylor. 2019. CRUMBLER: A tool for the prediction of ancestry in cattle. PLoS One 14:e0221471.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: Maldonado MBC, NB de Rezende Neto, ST Nagamatsu, MF Carazzolle, JL Hoff, LK Whitacre, RD Schnabel, SK Behura, SD McKay, JF Taylor, FL Lopes. 2019. Identification of bovine CpG SNPs as potential targets for epigenetic regulation via DNA methylation. PLoS One 14:e0222329.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Johnston D, B Earley, MS McCabe, K Lemon, C Duffy, M McMenamy, SL Cosby, JW Kim, G Blackshields, JF Taylor and SM Waters. 2019. Experimental challenge with bovine respiratory syncytial virus in dairy calves: bronchial lymph node transcriptome response. Sci Rep. 9:14736.
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Johnston D, JW Kim, JF Taylor, B Earley, MS McCabe, K Lemon, C Duffy, M McMenamy, SL Cosby and SM Waters. 2021. ATAC-Seq identifies regions of open chromatin in the bronchial lymph nodes of dairy calves experimentally challenged with Bovine Respiratory Syncytial Virus. BMC Genomics 22:14.
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Johnston D, B Earley, MS McCabe, JW Kim, JF Taylor, K Lemon, M McMenamy, C Duffy, SL Cosby and SM Waters. 2021. Elucidation of the host bronchial lymph node miRNA transcriptome response to bovine respiratory syncytial virus. Front Genet. 12:633125.
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Wang X, Z Ju, Q Jiang, J Zhong, C Liu, J Wang, JL Hoff, RD Schnabel, H Zhao, Y Gao, W Liu, L Wang, Y Gao, C Yang, M Hou, N Huang, LCA Regitano, LR Porto-Neto, JE Decker, JF Taylor and J Huang. 2021. Introgression, admixture, and selection facilitate genetic adaptation to high-altitude environments in cattle. Genomics. 113:1491-1503.
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Johnston D, B Earley, MS McCabe, JW Kim, JF Taylor, K Lemon, C Duffy, M McMenamy, SL Cosby and SM Waters. 2021. Messenger RNA biomarkers of Bovine Respiratory Syncytial Virus infection in the whole blood of dairy calves. Sci Rep. 11:9392.
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2021 Citation: Crum TE, RD Schnabel, JE Decker and JF Taylor. 2021 Taurine and indicine haplotype representation in advanced generation individuals from three American breeds. Front Genet 12:758394.


Progress 06/01/20 to 05/31/21

Outputs
Target Audience:See Final Report Changes/Problems:See Final Report What opportunities for training and professional development has the project provided?See Final Report How have the results been disseminated to communities of interest?See Final Report What do you plan to do during the next reporting period to accomplish the goals?See Final Report

Impacts
What was accomplished under these goals? See Final Report

Publications


    Progress 06/01/19 to 05/31/20

    Outputs
    Target Audience:See Final Report Changes/Problems:See Final Report What opportunities for training and professional development has the project provided?See Final Report How have the results been disseminated to communities of interest?See Final Report What do you plan to do during the next reporting period to accomplish the goals?See Final Report

    Impacts
    What was accomplished under these goals? See Final Report

    Publications


      Progress 06/01/18 to 05/31/19

      Outputs
      Target Audience:See Final Report Changes/Problems:See Final Report What opportunities for training and professional development has the project provided?See Final Report How have the results been disseminated to communities of interest?See Final Report What do you plan to do during the next reporting period to accomplish the goals?See Final Report

      Impacts
      What was accomplished under these goals? See Final Report

      Publications


        Progress 06/01/17 to 05/31/18

        Outputs
        Target Audience:See final Report Changes/Problems:See Final Report What opportunities for training and professional development has the project provided?See Final Report How have the results been disseminated to communities of interest?See Final Report What do you plan to do during the next reporting period to accomplish the goals?See Final Report

        Impacts
        What was accomplished under these goals? See Final Report

        Publications