Aetiopathogenesis and genomic architecture of resistance to claw horn disruption lesions in dairy cattle
Lead Research Organisation:
Royal Veterinary College
Department Name: Clinical Sciences and Services
Abstract
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Technical Summary
The project will (i) determine and evaluate factors affecting the development of claw horn disruption lesions (CHDL) in dairy cattle; (ii) identify genomic markers (SNPs) and regions associated with animal resistance to CHDL development; (iii) identify and characterise causal genes and regulatory regions underlying pathways and networks associated with CHDL; (iv) develop and evaluate breeding tools and strategies for enhanced animal resistance to CHDL while at the same time improving other important dairy cattle traits. The study will involve 3,000 pedigree Holstein cows. Animals will be repeatedly examined by a qualified veterinarian for CHDL. In addition, mobility and foot conformation scores, digital cushion thickness, body condition score, claw temperature and backfat thickness will be recorded along with environmental temperature and animal activity and resting patterns. Blood levels of hormones, immuno-modulating cytokines, non-esterified fatty acids and beta-hydroxybutyric acid will also be measured. Statistical analysis of all these data, using mixed models, will reveal the impact of foot structure and anatomy, periparturient hormonal profile and inflammatory status, fat mobilisation and metabolic stress, and environmental and management conditions on CHDL. Interactions among factors will be also assessed. All animals will have genome-wide genotypes generated to identify SNPs and genomic regions associated with CHDL. Additive and dominance effects of significant SNPs and genomic heritabilities will be derived. Whole-genome sequencing and RNA-sequencing results on a subset of animals with extreme phenotypes and genotypes will be combined with pathways analyses and functional interpretation to reveal the underlying molecular mechanisms of CHDL development. All results will inform simulation studies to assess breeding strategies and tools (including a trait-specific SNP array) to enable breeding for resistance to CHDL development.
Planned Impact
Compromised foot health leads to pain, reduced cow mobility and lameness, and constitutes a major welfare issue in dairy cattle. Painful lesions such as those disrupting the claw horn of the foot account for 90% of cases, represent the primary reason for veterinary interventions and lead to involuntary culling of affected animals, thereby posing serious threats to the sustainability and profitability of dairy farms. Many consider that lameness is currently the most significant welfare issue affecting dairy cattle in the UK because of the level of discomfort caused, the number of animals affected and the average duration of clinical episodes. Furthermore, studies have shown a significant adverse effect of lameness on milk yield both before and after a cow is diagnosed as lame that can last up to nine months. The total current cost to the UK dairy sector is estimated at £250 million or higher annually.
This project proposes a holistic approach to identify the key factors leading to the development of claw horn disruption lesions (CHDL). The project will develop a unique veterinary database and will combine complementary scientific expertise in order to develop a thorough understanding of the aetiopathogenesis of CHDL, while also developing practical knowledge and tools that can be used in genetic improvement programmes. Envisaged benefits from the outcomes are expected to apply at multiple levels:
1. Early identification of animals prone to development of CHDL will assist selection and replacement strategies, and minimise animal suffering.
2. Dairy farmers will directly benefit from reduced incidence of CHDL leading to decreased cost of involuntary culling. More animals will then be available for selection to improve productivity and other important traits. Fewer foot health problems will also signify enhanced animal welfare.
3. The dairy industry will benefit from advances and optimisation of genetic improvement programmes brought about by outcomes of the project. Currently, the economic benefits of genetic improvement in the UK exceed £100 million/year; about half of this is being realised by improvements in cow health and longevity. Project results will enhance animal health and welfare, and underpin the sustainability of the sector.
4. Improved health and welfare of the milking cows will enhance the public profile of dairy products and, eventually, the image of the sector and acceptability by consumers.
5. Benefits in the dairy industry will permeate the entire food producing animal sector, where outcomes from this project could be used as models for other relevant activities.
6. Environmental benefits are expected to accrue because of the reduced number of on-farm replacements necessary to replace cows culled due to poor foot health. On-farm replacements currently account for nearly one third of the methane produced by dairy cattle.
7. Policy makers and government could use outcomes and evidence from this project in the formulation and regulation of actions aiming at enhancing animal welfare and the social acceptability and environmental image of the livestock sector.
8. Identification of key mechanisms involved in the pathogenesis of CHDL may lead to specific targeting of inflammatory mechanisms to improve foot health and be of interest to the pharmaceutical industry.
9. Scientific benefits in the form of publications, presentations and collaborations are anticipated. Staff involved in the project will receive training and develop scientific and professional skills in laboratory, computational and numerical analyses.
10. The UK economy as a whole will benefit through the links between the scientific partners in the project and industry, ensuring quick uptake and implementation of the research results, contributing to enhanced farm output, health and living standards.
This is a 3-year grant but benefits from the outcomes are expected to continue long after the completion of the project.
This project proposes a holistic approach to identify the key factors leading to the development of claw horn disruption lesions (CHDL). The project will develop a unique veterinary database and will combine complementary scientific expertise in order to develop a thorough understanding of the aetiopathogenesis of CHDL, while also developing practical knowledge and tools that can be used in genetic improvement programmes. Envisaged benefits from the outcomes are expected to apply at multiple levels:
1. Early identification of animals prone to development of CHDL will assist selection and replacement strategies, and minimise animal suffering.
2. Dairy farmers will directly benefit from reduced incidence of CHDL leading to decreased cost of involuntary culling. More animals will then be available for selection to improve productivity and other important traits. Fewer foot health problems will also signify enhanced animal welfare.
3. The dairy industry will benefit from advances and optimisation of genetic improvement programmes brought about by outcomes of the project. Currently, the economic benefits of genetic improvement in the UK exceed £100 million/year; about half of this is being realised by improvements in cow health and longevity. Project results will enhance animal health and welfare, and underpin the sustainability of the sector.
4. Improved health and welfare of the milking cows will enhance the public profile of dairy products and, eventually, the image of the sector and acceptability by consumers.
5. Benefits in the dairy industry will permeate the entire food producing animal sector, where outcomes from this project could be used as models for other relevant activities.
6. Environmental benefits are expected to accrue because of the reduced number of on-farm replacements necessary to replace cows culled due to poor foot health. On-farm replacements currently account for nearly one third of the methane produced by dairy cattle.
7. Policy makers and government could use outcomes and evidence from this project in the formulation and regulation of actions aiming at enhancing animal welfare and the social acceptability and environmental image of the livestock sector.
8. Identification of key mechanisms involved in the pathogenesis of CHDL may lead to specific targeting of inflammatory mechanisms to improve foot health and be of interest to the pharmaceutical industry.
9. Scientific benefits in the form of publications, presentations and collaborations are anticipated. Staff involved in the project will receive training and develop scientific and professional skills in laboratory, computational and numerical analyses.
10. The UK economy as a whole will benefit through the links between the scientific partners in the project and industry, ensuring quick uptake and implementation of the research results, contributing to enhanced farm output, health and living standards.
This is a 3-year grant but benefits from the outcomes are expected to continue long after the completion of the project.
Publications
Anagnostopoulos A
(2021)
A study on the use of thermal imaging as a diagnostic tool for the detection of digital dermatitis in dairy cattle.
in Journal of dairy science
Anagnostopoulos A
(2024)
Association between a genetic index for digital dermatitis resistance and the presence of digital dermatitis, heel horn erosion, and interdigital hyperplasia in Holstein cows.
in Journal of dairy science
Anagnostopoulos A
(2024)
Association between a genetic index for digital dermatitis resistance and the presence of digital dermatitis, heel horn erosion, and interdigital hyperplasia in Holstein cows.
in Journal of dairy science
Anagnostopoulos A
(2021)
A study on the use of thermal imaging as a diagnostic tool for the detection of digital dermatitis in dairy cattle.
in Journal of dairy science
Attree E
(2024)
Identification of DNA methylation markers for age and Bovine Respiratory Disease in dairy cattle: A pilot study based on Reduced Representation Bisulfite Sequencing.
in Communications biology
B.E. Griffiths
A prospective cohort study examining factors associated with the digital cushion thickness in dairy cattle
in Journal of Dairy Science
| Description | Individual cow phenotypic, genotypic and pedigree data were collected on approximately. 2,500 cows in four herds. Multiple records were collected at different time-points in the cows' life and at the end the database included more than 10,000 phenotypic records. All animals were genotyped with a genome-wide DNA array. After imputation, 80,000 informative Single Nucleotide Polymorphism markers were retained in each genotype. Data were analysed to examine the genomic background of claw horn disruption lesions (CHDL) development and severity, as well as of digital cushion thickness, a foot structure trait. Analyses conducted have attested to the presence of considerable genetic variation in the studied CHDL traits. Depending on the lesion and time-point of measurement, trait heritability estimates ranged from 0.06 to 0.21 for susceptibility, 0.04-0.26 for severity, and around 0.24 for recovery. The range and magnitude of these estimates are as expected for health-related traits. The low to moderate heritability values reflect substantial environmental variance, which is expected in the commercial dairy cattle population. Nevertheless, genetic variance, reflecting inherent differences among individual animals, was present and significant suggesting that there is potential to identify and select breeding animals with an enhanced capacity to withstand and/or successfully cope with CHDL. This was corroborated by the examination of estimated Genomic Breeding Values of individual cows and their sires that illustrated the differences between desirable (resistant) and undesirable (susceptible) animal genotypes. All these results were published in the scientific literature. Heritability of digital cushion thickness was between 0.12 and 0.31, and its estimated genetic correlation with lesion severity was moderate and significant (between -0.21 and -0.25) suggesting that no or milder lesions may be expected for animal with genetically thick and robust digital cushion. This result has also been published. In addition, the current genetic evaluation for foot health, termed by the industry as the lameness advantage index, was analysed jointly with project data, and found to be associated with CHDL. Therefore, this index is recommended to be considered in herds aiming to reduce lameness. These results were published. Genomic association analyses also took place to examine the association of genomic markers and regions with CHDL phenotypes. In general, these analyses revealed a largely complex, polygenic architecture of the studied traits. Nevertheless, there were certain markers and genomic regions with potentially larger effects on CHDL than others. Mapping results on the most recent bovine reference genome suggested that some of these regions harbour annotated genes known to be associated with the cows' innate immune function, inflammation, energy metabolism, and nervous system. Relevant results have been published in the scientific literature. Furthermore, whole-genome sequencing, total RNA-seq and reduced representation bisulfite sequencing were performed on blood and foot biopsy samples on a subset of 24 animals with extreme phenotypes and genotypes, i.e., totally healthy vs. severely affected individuals. Twenty-five differentially expressed genes associated with CHDL were identified including genes involved in immune and keratin pathways. These results provide deep insights into the genetic architecture underlying CHDL and inform genetic improvement of CHDL resistance in dairy cattle. Results have been published. Moreover, 30 differentially expressed long-non coding RNAs and 9896 differentially methylated genes associated with CHDL were identified providing further insights. Interestingly, 5 of the differentially expressed genes were also differentially methylated in CHDL cases and controls. Specifically, functional analyses revealed that pathways implicated in CHDL resistance include those related with innate immune response, inflammation, keratinisation, ossification and neuronal development. Importantly immune genes involved in macrophage activation and the complement cascade have been identified as differentially expressed between cows with CHDL and healthy controls. A number of genes identified as differentially expressed were also identified as differentially methylated, including a gene of the complement cascade C1q A chain and involved in wound healing; coagulation factor XIII A chain. Correlation between differentially expressed genes and lncRNA differential expression was also identified (in particular correlation with expression of KIR3DL1). Genes involved in the structural formation and integrity of the hood have also been implicated in CHDL resistance. Keratinisation genes KRTAP27-1 and KRTAP3-3 were found to be differentially expressed (increased in cases). Further, calcium ion activities were found to be enriched functions with CHI3L2, SPP1 and AMTN differentially expressed. Neuronal development and remodelling and synapse organisation were also all identified as enriched pathways among the differentially expressed genes from PBL and foot tissue samples along with behavioural response to pain. A role of neuronal signalling has been previously implicated and in this five SNPs of interest were identified in exonic regions of the DAB1 gene. Cows with thinner digital cushions during the transition period were at greater risk of developing sole lesions (sole ulcers and sole haemorrhage) but not white line lesions. However, in older cows prior to calving a thicker digital cushion increased the risk of developing a sole lesion in early lactation, which could reflect older cows having experienced previous lameness events resulting in chronic changes within the hoof and reduced capacity of the digital cushion to function. Sole temperature, which could indicate the presence of damage and inflammation, was found to be increased prior to calving in cows which went on to develop sole lesions in early lactation. In preventative foot trimming, foot angle and heel depth are widely used to assess claw conformation and functionality, in broadly normal shaped claws, minor deviations away from target angles and depths were not found to be associated with the development of either sole or white line lesions. Thicker sole horn in the transition period was however found to be protective against the development of sole lesions. Whilst preventative foot trimming is essential to prevent imbalances within and between the claws which cause areas of increased pressure and pinching, care must be taken when trimming to maintain adequate sole horn to protect the sensitive tissues against external forces. The digital cushion plays an important role in the development of sole lesions, yet in heifers this cushion in not fully developed until late in lactation. Both the effect of calving (loosening of the connective tissue in the hoof associated with calving), and fat mobilisation have been linked to how the digital cushion thickness changes during the course of a lactation, with the digital cushion found to be thinnest at calving or during early lactation. We found that how the digital cushion thickness changes over the course of the lactation is dependent on which farm the cows came from, indicating that farm characteristics, management and perhaps genetics may play a role in how the digital cushion thickness changes over the course of a lactation. Moreover, a subset of cows have had serum biomarkers for fat mobilisation (bhb and NEFAs) and hormonal profiles (relaxin and insulin) measured from stored serum samples. The inflammatory status, using serum concentrations of Interleukin 1-alpha, Interlukin-6 and Interleukin-10, has also been assessed in these cows. Blood Lipopolysaccharide has also been assayed. Previous research has found that inflammation associated with lameness predisposes cows to future lameness events whilst at calving, cows which are given a non-steroidal anti-inflammatory drug (NSAID) were less likely to develop future lameness in the following lactation. Our results have highlighted cows with more inflammation shortly after calving were more likely to develop sole lesions in early lactation, with the inflammatory process still ongoing in early lactation. This inflammation may be the result of direct mechanical damage, such as with compression from the pedal bone "sinking" when the ligaments become lax at calving. Alternatively, fat mobilisation is an inflammatory process and therefore this inflammation, could indicate a possible role of negative energy balance and fat mobilisation from the digital cushion shortly after calving. Relaxin, which has been indicated as the hormone responsible for the calving effect was not associated with the development of sole lesions, and therefore a different hormone, such as oestrogen, may instead be responsible. Finally, simulation studies were conducted to assess breeding strategies to include results in genetic improvement programmes. Different scenarios were examined, with emphasis on CHDL in selective breeding ranging from 0 to 75% of the breeding goal. A useful balance of emphasis of 75% on cow productivity and 25% on CHDL resistance was revealed where the overall benefit is maximised. |
| Exploitation Route | The outcomes of this project could be used in breeding programmes aiming to improve cattle resistance to CHDL as well as in the identification of novel drug and vaccine targets discovery to control cattle lameness |
| Sectors | Agriculture Food and Drink Healthcare Pharmaceuticals and Medical Biotechnology |
| Description | Integrating clinical, data-driven and in-vitro approaches to the study of host-pathogen interactions in bovine digital dermatitis |
| Amount | £457,510 (GBP) |
| Funding ID | BB/X008878/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 06/2023 |
| End | 03/2026 |
| Title | ENA data availability PRJEB71365 - Reduced representation bisulfite sequencing (RRBS) of dairy cows and calves |
| Description | Raw methylation data for dairy cows and calves collected has been made publicly available in ENA under the project accession PRJEB71365. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2024 |
| Provided To Others? | Yes |
| Impact | Public availability of data facilitates it's use by other researchers in the field contributing to the collaborative research community efforts. |
| URL | https://www.ebi.ac.uk/ena/browser/view/PRJEB71365 |
| Title | Generation and analysis of Whole Genome Sequence data from animals with claw horn disruption lesions (CHDL) and healthy controls |
| Description | Total DNA was extracted from PBL cells using the DNeasy Blood & Tissue kit (Qiagen, Hilden, Germany) with a few modifications. Library preparation was performed using Novogene's NGS DNA Library Prep Set. Whole Genome Sequencing (150bp paired-end reads and average coverage of 30X reads) using Illumina Technology was performed on the Novaseq6000 instrument and S4 (NovaSeq PE150) flow cell. The sequencing reads were mapped to the ARS-UCD1.2 using BWA-MEM and variant calling was performed using GATK4 tools according to Best Practices. The WGS analysis is on going. |
| Type Of Material | Data analysis technique |
| Year Produced | 2022 |
| Provided To Others? | No |
| Impact | The WGS analysis is on going. The aim of this analysis is to identify putative candidate genes and mutations located within the candidate regions for CHDL susceptibility identified by a GWAS study performed in 3,000 cows. Hopefully, this analysis will shed more light in the genetic background of CHDL susceptibility in dairy cattle. |
| Title | Generation and analysis of mRNA Sequence data from Peripheral Blood Leucocytes (PBL) collected from animals with claw horn disruption lesions (CHDL) and healthy controls |
| Description | Total RNA from PBL was extracted using the RNeasy Mini kit (Qiagen, Hilden, Germany). Total RNA-Sequencing library preparation was performed using Illumina TruSeq ribo-zero gold kit (Illumina, San Diego, USA). Paired-end, 2 x150bp, reads were obtained using the NovaSeq 6000 instrument with NovaSeq 6000 S4 reagent kit v1.5. Total coverage was 50M reads per sample. The generated sequence reads were QC using FastQC and further trimmed using Trimmomatic v0.39. Then sequence reads that passed QC were mapped to the ARS-UCD1.2 bovine genome assembly using STAR v2.7.0 with default parameters. Read counts per gene were obtained using the gene annotation file corresponding to the ARS-UCD1.2 bovine genome assembly (Ensemble release 104) and the featureCounts v2.0.2. Differentially expressed genes between cases and controls were identified using DESeq2 v1.35.0. Results of mRNA seq analysis: Ten DEG genes were found between CHDL cases and controls. We found enrichment for molecular function regulation, calcium ion binding, hormone activity, endopeptase activvity and regulation and signaling receptor activity and regulation. In addition, the mineralisation associated genes SPARC and CLEC3B were downregulated and upregulated in CHDL cases, respectively. Moreover, three genes (YAP1, DSP and PALLD) associated with keratinocyte development were upregulated in the CHDL cases, which may suggest the presence of a reparative mechanism in the CHDL cases. |
| Type Of Material | Data analysis technique |
| Year Produced | 2022 |
| Provided To Others? | No |
| Impact | The results of this study have been included in a conference paper which has been submitted in the World Congress of Applied Livestock Genomics which will take place this June 2022. These results give new insights in the underlying pathways related to CHDL susceptibility in dairy cattle. The conference paper will be published when accepted. |
| Title | Generation and analysis of Long non-coding (lnc) RNA Sequencing data from Peripheral Blood Leucocytes (PBL) and foot biopsy tissue samples from cows with claw horn disruption lesions (CHDL) and healthy controls |
| Description | The quality of sequence reads was assessed using FastQC before and after quality control, which included quality-based read trimming and adapter removal using Trimmomatic v0.39. Reads longer than 32 bp and with a Phred score =33 were retained. Quality-controlled reads were mapped to the ARS-UCD1.2 bovine genome assembly using STAR v2.7.0, and transcripts were assembled using StringTie v2.1.0. Assembled transcripts were merged using the merge option of StringTie, resulting in non-redundant assembled transcripts. Transcripts were then compared with Ensembl bovine gene annotation (release 104) using Cuffcompare from Cufflink v2.2.0 to identify transcripts overlapping with known protein-coding and non-coding regions (lncRNA) and transcripts non-overlapping with any known protein-coding and non-coding regions (lincRNA). We used the transcript classification codes of Cuffcompare to select transcripts categorized as "u", "x", "i", "u", "j", "s" and "e" with a length of =200 nt to identify lncRNA. Transcripts categorized as "u" with a length of =200 nt were considered lincRNA. The coding probability of these transcripts was estimated using three tools, CPC2, CPAT v2.0.0, and CNCI v2.0.0. Only transcripts passing all three tools were considered non-coding potential and used for downstream analysis. Transcripts with high protein-coding potential were removed using two metrics: open reading frames (ORF) encoding a protein >100 amino acids and similarity to the UniProt protein database based on a 1E-5 threshold. This filtering was carried out using Transdecoder, including the BLASTp step. The coding probability cutoff was determined to be 0.38 using 20-fold cross-validation of the outputs of the CPAT models (Figure 1). To quantify expression levels of the identified lncRNA and lincRNA transcripts, we used Kallisto v0.46.2 to generate transcript-level abundance estimates. We indexed the lncRNA and lincRNA transcripts using the default parameters of Kallisto. The trimmed and filtered reads were then aligned to this index using Kallisto with 100 bootstraps. The resulting transcript-level abundance estimates were then imported into R using the tximport package. Then the quantification data were subsequently imported into DESeq2 v1.34.1 for normalization and differential expression analysis. Differentially expressed lncRNAs and lincRNAs were defined as those with an adjusted P-value < 0.05 and an absolute log2 fold change > 1. To explore the functions of significant DE lncRNA, we used bedtools to obtain the genes 100kb of each lncRNA. From analysis of the foot tissue samples, 35 genes were found within 100kb of significantly DE lncRNA and 24 genes from analysis of DE lnc in PBL samples. Specifically, for PBLs 29 lnc correspondito 24 protein coding genes and 16 linc to 15 protein coding genes. For foot tissue 35 lnc correspond to 35 protein coding genes and 35 linc to 35 protein coding genes. |
| Type Of Material | Data analysis technique |
| Year Produced | 2023 |
| Provided To Others? | No |
| Impact | Better understanding of the role of lnc in CHDL susceptibility |
| Title | Generation and analysis of RRBS data from blood samples from cows with claw horn disruption lesions (CHDL) and healthy controls |
| Description | Blood samples from cows with CHDL and healthy controls collected by collaborating veterinarians. Reduced representation bisulfite sequencing was performed on extracted DNA and using Diogene. Methylation was identified usign Bismark and methylation call files were analysed using methylkit. Differentially methylated bases between cases and controls were identified and nearest gene transcription start sites annotated to combine and compare results to identified differentially expressed genes by RNA-seq. |
| Type Of Material | Data analysis technique |
| Year Produced | 2022 |
| Provided To Others? | No |
| Impact | DNA methylation data collected and differences between control and CHDL animals identified. 9896 genes were found to be differentially methylated with five overlapping with the RNA-seq dataset, having also been identified to be significantly differentially expressed. Thee genes were found to enrich pathways involved in immune system regulation, the innate immune system and in signalling pathways |
| Title | Generation and analysis of data collected from PBL samples from cows with CHDL and healthy controls for eQTL analysis |
| Description | Data from the GWAS analysis was used to identify SNPs within GWAS windows and determine animal genotypes. The gene expression from the RNA-seq analysis of PBL samples was combined with the SNP and genotype data for an eQTL analysis. eQTL analysis was performed in R using MatrixEQTL. |
| Type Of Material | Data analysis technique |
| Year Produced | 2023 |
| Provided To Others? | No |
| Impact | Identification of eQTL's with potential importance in the susceptibility/resistance to CHDL |
| Title | Generation and analysis of data collected from foot tissue biopsy samples from cows with CHDL and healthy controls for eQTL analysis |
| Description | Data from the GWAS analysis was used to identify SNPs within GWAS windows and determine animal genotypes. The gene expression from the RNA-seq analysis of foot tissue samples was combined with the SNP and genotype data for an eQTL analysis. eQTL analysis was performed in R using MatrixEQTL. |
| Type Of Material | Data analysis technique |
| Year Produced | 2023 |
| Provided To Others? | No |
| Impact | Identification of eQTL's with potential importance in the susceptibility/resistance to CHDL |
| Title | Generation and analysis of mRNA Sequence data from foot tissue biopsies collected from animals with claw horn disruption lesions (CHDL) and healthy controls |
| Description | Total RNA from foot tissue was extracted using the RNeasy Mini kit (Qiagen, Hilden, Germany). Total RNA-Sequencing library preparation was performed using Illumina TruSeq ribo-zero gold kit (Illumina, San Diego, USA). Paired-end, 2 x150bp, reads were obtained using the NovaSeq 6000 instrument with NovaSeq 6000 S4 reagent kit v1.5. Total coverage was 50M reads per sample. The generated sequence reads were QC using FastQC and further trimmed using Trimmomatic v0.39. Then sequence reads that passed QC were mapped to the ARS-UCD1.2 bovine genome assembly using STAR v2.7.0 with default parameters. Read counts per gene were obtained using the gene annotation file corresponding to the ARS-UCD1.2 bovine genome assembly (Ensemble release 104) and the featureCounts v2.0.2. Differentially expressed genes between cases and controls were identified using DESeq2 v1.35.0. Results of mRNA seq analysis: Fifteen DEG genes were found between CHDL cases and controls. Gene set enrichment showed enrichment of pathways including: defense response, positive regulation of response to stimulus, innate and inflammatory immune response and organic acid metabolic process. |
| Type Of Material | Data analysis technique |
| Year Produced | 2022 |
| Provided To Others? | No |
| Impact | The results of this study were included in a conference paper submitted in the World Congress of Applied Livestock Genomics in June 2022. These results give new insights in the underlying pathways related to CHDL susceptibility in dairy cattle. |
| Title | Generation and analysis of the effect of variants identified by WGS associated with CHDL |
| Description | Genomic variants in 24 dairy cattle (12 CHDL cases and 12 controls) were analysed by whole genome sequencing (WGS) following the GATK4 pipeline. Variants identified by WGS in the top 10 genomic windows associated with CHDL as identified by genome wide association study (GWAS) were analysed by ensembl varient effect predictior (VEP) program including the algorithm for sorting intolerant from tolerant (SIFT) mutations. A total of 7898 variants were analysed by VEP with 7007 (88.7%) identified as existing variants and 891 (11.3%) novel variants overlapping 29 genes and 68 transcripts. Of the identified variants, 5 were identified of high impact, 45 of moderate and 77 of low. eleterious mutations were identified as 7 missense variants with modifier impact in: GALNT16, ERH, ENSBTAG00000050645, C8B and ENSBTAG00000059494. Identified variants were statistically analysed by chi-squared test to identify the distribution in case and control animals. Statistically significant chi-squared distributions were identified for ENSBTAG00000059494 and FYB2 between case and control animals. |
| Type Of Material | Data analysis technique |
| Year Produced | 2024 |
| Provided To Others? | No |
| Impact | Two statistically significant high impact SNPs have been identified to differentiate between case and control animals for CHDL. These results combined with the other data generated in this project have provided novel insights in CHDL susceptibility and has helped to prioritise genetic variants of interest which could be used to advance future breeding programmes aiming to increase resistance to CHDL. |
| Title | Generation of a dataset of samples from extreme Holstein cows to characterise CHDL susceptibility |
| Description | Foot biopsy and blood samples were collected from 24 (12 extreme CHDL cases (days in milk (DIM:198 ? 102) and 12 healthy control (DIM: 195 ? 100)) Holstein dairy cows in order to be used in genomic, transcriptomic and functional analysis to characterise CHDL susceptibility in dairy cattle. The animals were selected based on the CHDL score and genomic estimated breeding values (GEBV) of CHDL. The CHDL was a combined SH, SU and WLD score. Controls and cases were sampled in pairs within the same herd, ensuring they were of similar age, parity, and lactation stage to minimise any systematic noise. From the blood samples peripheral blood leukocytes (PBL) were isolated by lysis of erythrocytes. PBL were counted and stored in liquid nitrogen and -80C until further processing. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | No |
| Impact | This dataset will be used for post-GWAS analyses to identify candidate pathways and gene networks for CHDL susceptibility. When analyses will be completed the relevant data will become publicly available and the results will be presented in international conferences and published. |
| Title | Identification of differentially expressed genes in foot tissue and PBLs in cows with sole haemorrhages |
| Description | We identified 9 significantly differentially expressed genes in the foot tissue of cows with SH and 111 in PBLs using RNA-seq data analysed in Kallisto and DESeq2. These were statistically significant based on an FDR adjusted P value of <= 0.10, inclusion of a lfc filter of >=1 or <=-1. |
| Type Of Material | Data analysis technique |
| Year Produced | 2025 |
| Provided To Others? | No |
| Impact | This data provides a greater insight into the underlying molecular mechanisms of behind susceptibility to sole hemorrhages in dairy cattle populations. |
| Title | Identification of differentially expressed genes in foot tissue and PBLs in cows with sole ulcer |
| Description | We identified 5 significantly differentially expressed genes in the foot tissue of cows with SU and 1 in PBLs using RNA-seq data analysed in Kallisto and DESeq2. These were statistically significant based on an FDR adjusted P value of <= 0.10, inclusion of a lfc filter of >=1 or <=-1. |
| Type Of Material | Data analysis technique |
| Year Produced | 2025 |
| Provided To Others? | No |
| Impact | This data provides a greater insight into the underlying molecular mechanisms of behind susceptibility to sole ulcers in dairy cattle populations. |
| Title | Identification of differentially expressed genes in foot tissue and PBLs in cows with white line disease |
| Description | We identified 9 significantly differentially expressed genes in the foot tissue of cows with WL and 111 in PBLs using RNA-seq data analysed in Kallisto and DESeq2. These were statistically significant based on an FDR adjusted P value of <= 0.10 and inclusion of a lfc filter of >=1 or <=-1. |
| Type Of Material | Data analysis technique |
| Year Produced | 2025 |
| Provided To Others? | No |
| Impact | This data provides a greater insight into the underlying molecular mechanisms of behind susceptibility to white line disease in dairy cattle populations. |
| Title | Phenotypic database of closely monitored cows for claw horn disruption lesion |
| Description | A detailed database of 271 closely monitored cows for claw horn disruption lesions (CHDL) has been developed. This database contains all the CHDL records of these cows. Based on these phenotypes we have ranked cows according to their susceptibility in developing CHDL. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | No |
| Impact | This database was developed from our consortium for internal use in order to facilitate the selection of the most appropriate animals-in the extreme of phenotypes- to collect samples for downstream functional analysis including WGS, RNA-Seq and protein work. |
| Title | WGS analysis of dairy cattle with sole haemorrhages |
| Description | Genomic variants in 24 dairy cattle (12 sole haemorrhage cases and 12 controls) were analysed by whole genome sequencing (WGS) following the GATK4 pipeline. Genetic variants were identified by WGS to be analysed by variant effect prediction. Quality control of sequence data was performed using FastQC v0.11.9 (Andrews, 2010) and adapter and quality trimming performed using Trimmomatic v0.39 (Bolger and Usadel, 2014), included quality based read trimming and adapter removal, with -phred33 and minimum length of 32. Reads that passed quality control from each cow were aligned to the Bos taurus genome (ARSUCD 1.2) using Burrows-Wheeler Alignment tool (BWA v0.7.10; Li and Durbin, 2009), with the default parameters. We subsequently used SAMtools v1.9 (Li et al., 2009) to sort and index the alignment results and then used Picard toolkit v2.22 (https://broadinstitute.github.io/picard/) to identify and remove potential PCR duplicate reads. The quality scores of the aligned reads were processed according to the best practice for the Genome Analysis Toolkit (GATK v4.1.6; McKenna et al., 2010) following the best practice. Briefly, the quality scores of the aligned reads were recalibrate using GATK4's BaseRecalibrator and ApplyBQSR tool. Variants were called from the recalibrated BAM file using GATK4's HaplotypeCaller tool. Then the single-sample GVCFs were imported into GenomicsDB by using GenomicsDBImport before joint genotyping. After that, the indexed and selected SNPs were subjected to filtering based on the following criteria using the GATK VariantFiltration module as follow: (a) quality by depth (QD) >2.0; (b) quality score (QUAL) > 30; (c) strand odds ratio (SOR) < 3.0; (d) Fisher strand bias (FS) < 60.0; (e) mapping quality (MQ) > 40.0; (f) MQRanksum > -12.5; and (g) ReadPosRankSum > -8.0. The indexed and selected indels were subjected to filtering based on the following criteria as follow: (a) quality by depth (QD) >2.0; (b) quality score (QUAL) > 30; (c) Fisher strand bias (FS) < 200.0; and (d) ReadPosRankSum > -20.0. Finally, the SNPs and indels were merged by MergeVcfs tool from Picard. Filtered variants were then intersected with known genes using Bedtools (Quinlan and Hall, 2010). |
| Type Of Material | Data analysis technique |
| Year Produced | 2023 |
| Provided To Others? | No |
| Impact | Statistically significantly SNPs have been identified, between case and control animals for sole haemorrhage. These combined with other data generated in this project lead investigators to prioritising genetic mutations that could be candidates for selection in breeding strategies for genetic improvement to increase resistance to sole haemorrhage. The identified SNPs were filtered to within GWAS windows as previously identified for variant effect prediction and eQTL analysis. |
| Title | WGS analysis of dairy cattle with sole ulcer |
| Description | Genomic variants in 24 dairy cattle (12 sole ulcer cases and 12 controls) were analysed by whole genome sequencing (WGS) following the GATK4 pipeline. Genetic variants were identified by WGS to be analysed by variant effect prediction.Quality control of sequence data was performed using FastQC v0.11.9 (Andrews, 2010) and adapter and quality trimming performed using Trimmomatic v0.39 (Bolger and Usadel, 2014), included quality based read trimming and adapter removal, with -phred33 and minimum length of 32. Reads that passed quality control from each cow were aligned to the Bos taurus genome (ARSUCD 1.2) using Burrows-Wheeler Alignment tool (BWA v0.7.10; Li and Durbin, 2009), with the default parameters. We subsequently used SAMtools v1.9 (Li et al., 2009) to sort and index the alignment results and then used Picard toolkit v2.22 (https://broadinstitute.github.io/picard/) to identify and remove potential PCR duplicate reads. The quality scores of the aligned reads were processed according to the best practice for the Genome Analysis Toolkit (GATK v4.1.6; McKenna et al., 2010) following the best practice. Briefly, the quality scores of the aligned reads were recalibrate using GATK4's BaseRecalibrator and ApplyBQSR tool. Variants were called from the recalibrated BAM file using GATK4's HaplotypeCaller tool. Then the single-sample GVCFs were imported into GenomicsDB by using GenomicsDBImport before joint genotyping. After that, the indexed and selected SNPs were subjected to filtering based on the following criteria using the GATK VariantFiltration module as follow: (a) quality by depth (QD) >2.0; (b) quality score (QUAL) > 30; (c) strand odds ratio (SOR) < 3.0; (d) Fisher strand bias (FS) < 60.0; (e) mapping quality (MQ) > 40.0; (f) MQRanksum > -12.5; and (g) ReadPosRankSum > -8.0. The indexed and selected indels were subjected to filtering based on the following criteria as follow: (a) quality by depth (QD) >2.0; (b) quality score (QUAL) > 30; (c) Fisher strand bias (FS) < 200.0; and (d) ReadPosRankSum > -20.0. Finally, the SNPs and indels were merged by MergeVcfs tool from Picard. Filtered variants were then intersected with known genes using Bedtools (Quinlan and Hall, 2010). |
| Type Of Material | Data analysis technique |
| Year Produced | 2023 |
| Provided To Others? | No |
| Impact | Statistically significantly SNPs have been identified, between case and control animals for sole ulcer. These combined with other data generated in this project lead investigators to prioritising genetic mutations that could be candidates for selection in breeding strategies for genetic improvement to increase resistance to sole ulcer. The identified SNPs were filtered to within GWAS windows as previously identified for variant effect prediction and eQTL analysis. |
| Title | WGS analysis of dairy cattle with white line disease |
| Description | Whole genome sequencing (WGS) was performed for 24 of the cows involved in the GWAS study, selected as phenotypic extremes (12 white line disease cases and 12 controls) were analysed by whole genome sequencing (WGS) following the GATK4 pipeline. Genetic variants were identified by WGS to be analysed by variant effect prediction. Quality control of sequence data was performed using FastQC v0.11.9 (Andrews, 2010) and adapter and quality trimming performed using Trimmomatic v0.39 (Bolger and Usadel, 2014), included quality based read trimming and adapter removal, with -phred33 and minimum length of 32. Reads that passed quality control from each cow were aligned to the Bos taurus genome (ARSUCD 1.2) using Burrows-Wheeler Alignment tool (BWA v0.7.10; Li and Durbin, 2009), with the default parameters. We subsequently used SAMtools v1.9 (Li et al., 2009) to sort and index the alignment results and then used Picard toolkit v2.22 (https://broadinstitute.github.io/picard/) to identify and remove potential PCR duplicate reads. The quality scores of the aligned reads were processed according to the best practice for the Genome Analysis Toolkit (GATK v4.1.6; McKenna et al., 2010) following the best practice. Briefly, the quality scores of the aligned reads were recalibrate using GATK4's BaseRecalibrator and ApplyBQSR tool. Variants were called from the recalibrated BAM file using GATK4's HaplotypeCaller tool. Then the single-sample GVCFs were imported into GenomicsDB by using GenomicsDBImport before joint genotyping. After that, the indexed and selected SNPs were subjected to filtering based on the following criteria using the GATK VariantFiltration module as follow: (a) quality by depth (QD) >2.0; (b) quality score (QUAL) > 30; (c) strand odds ratio (SOR) < 3.0; (d) Fisher strand bias (FS) < 60.0; (e) mapping quality (MQ) > 40.0; (f) MQRanksum > -12.5; and (g) ReadPosRankSum > -8.0. The indexed and selected indels were subjected to filtering based on the following criteria as follow: (a) quality by depth (QD) >2.0; (b) quality score (QUAL) > 30; (c) Fisher strand bias (FS) < 200.0; and (d) ReadPosRankSum > -20.0. Finally, the SNPs and indels were merged by MergeVcfs tool from Picard. Filtered variants were then intersected with known genes using Bedtools (Quinlan and Hall, 2010). |
| Type Of Material | Data analysis technique |
| Year Produced | 2023 |
| Provided To Others? | No |
| Impact | Statistically significantly SNPs have been identified, between case and control animals for white line disease. These combined with other data generated in this project lead investigators to prioritising genetic mutations that could be candidates for selection in breeding strategies for genetic improvement to increase resistance to white line disease. The identified SNPs were filtered to within GWAS windows as previously identified for variant effect prediction and eQTL analysis. |
| Title | eQTL analysis of dairy cows with sole haemorrhages compared to healthy controls in PBL and foot tissue samples |
| Description | Using cows identified with sole haemorrhages compared to healthy controls; data from the GWAS analysis was used to identify SNPs within GWAS windows and determine animal genotypes. The gene expression from the RNA-seq analysis of foot tissue samples was combined with the SNP and genotype data for an eQTL analysis. Separately gene expression from the RNA-seq analysis of PBL samples was combined with the SNP and genotype data for another eQTL analysis. eQTL analyses were performed in R using MatrixEQTL. We identified 16982 cis eQTLs in foot tissue and 12480 PBLs corresponding to 189 and 200 genes respectively. Functional enrichment analyses by PANTHER of these found enrichment of biological process' including immunoglobulin mediated immune response (GO:0016064, 16.76 fold change), B cell mediated immunity (GO:0019724, 16.55 fold change), lymphocyte mediated immunity (GO:0002449, 13.54 fold change), adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains (GO:0002460, 11.55 fold change), leukocyte mediated immunity (GO:0002443, 10.64 fold change), adaptive immune response (GO:0002250, 6.72 fold change) and immune effector process (GO:0002252, 5.46 fold change). Functional enrichment analysis by DAVID resulted in one significantly enriched GO biological process (p=0.05, padj=0.05): complement activation, classical pathway. |
| Type Of Material | Data analysis technique |
| Year Produced | 2024 |
| Provided To Others? | No |
| Impact | Identification of eQTL's with potential importance in the susceptibility/resistance to sole haemorrhages |
| Title | eQTL analysis of dairy cows with sole ulcers compared to healthy controls in PBL and foot tissue samples |
| Description | Using cows identified with sole ulcers compared to healthy controls; data from the GWAS analysis was used to identify SNPs within GWAS windows and determine animal genotypes. The gene expression from the RNA-seq analysis of foot tissue samples was combined with the SNP and genotype data for an eQTL analysis. Separately gene expression from the RNA-seq analysis of PBL samples was combined with the SNP and genotype data for another eQTL analysis. eQTL analyses were performed in R using MatrixEQTL. We identified 34513 cis eQTLs in foot tissue and 47157 PBLs corresponding to 275 and 333 genes respectively. Functional enrichment analyses of these found enrichment of biological process' including iTransmembrane protein family 132 middle, regulation of transcription by RNA polymerase II, RNA-binding, DNA repair and protein transport. |
| Type Of Material | Data analysis technique |
| Year Produced | 2024 |
| Provided To Others? | No |
| Impact | Identification of eQTL's with potential importance in the susceptibility/resistance to sole ulcers |
| Title | eQTL analysis of dairy cows with white line disease compared to healthy controls in PBL and foot tissue samples |
| Description | Using cows identified with white line disease compared to healthy controls; data from the GWAS analysis was used to identify SNPs within GWAS windows and determine animal genotypes. The gene expression from the RNA-seq analysis of foot tissue samples was combined with the SNP and genotype data for an eQTL analysis. Separately gene expression from the RNA-seq analysis of PBL samples was combined with the SNP and genotype data for another eQTL analysis. eQTL analyses were performed in R using MatrixEQTL. We identified 45225 cis eQTLs in foot tissue and 38175 PBLs corresponding to 318 and 333 genes respectively. Functional enrichment analyses of these found enrichment of biological process' including interleukin-27-mediated signaling pathway and regulation of ribonuclease activity. |
| Type Of Material | Data analysis technique |
| Year Produced | 2024 |
| Provided To Others? | No |
| Impact | Identification of eQTL's with potential importance in the susceptibility/resistance to white line disease |
| Title | lncRNA analysis of dairy cattle with CHDL |
| Description | The quality of sequence reads was assessed using FastQC before and after quality control, which included quality-based read trimming and adapter removal using Trimmomatic v0.39. Reads longer than 32 bp and with a Phred score =33 were retained. Quality-controlled reads were mapped to the ARS-UCD1.2 bovine genome assembly using STAR v2.7.0, and transcripts were assembled using StringTie v2.1.0. Assembled transcripts were merged using the merge option of StringTie, resulting in non-redundant assembled transcripts. Transcripts were then compared with Ensembl bovine gene annotation (release 104) using Cuffcompare from Cufflink v2.2.0 to identify transcripts overlapping with known protein-coding and non-coding regions (lncRNA) and transcripts non-overlapping with any known protein-coding and non-coding regions (lincRNA). We used the transcript classification codes of Cuffcompare to select transcripts categorized as "u", "x", "i", "u", "j", "s" and "e" with a length of =200 nt to identify lncRNA. Transcripts categorized as "u" with a length of =200 nt were considered lincRNA. The coding probability of these transcripts was estimated using three tools, CPC2, CPAT v2.0.0, and CNCI v2.0.0. The coding probability cutoff was determined to be 0.38 using 20-fold cross-validation of the outputs of the CPAT models (Figure 1). Only transcripts passing all three tools were considered non-coding potential and used for downstream analysis. Transcripts with high protein-coding potential were removed using two metrics: open reading frames (ORF) encoding a protein >100 amino acids and similarity to the UniProt protein database based on a 1E-5 threshold. This filtering was carried out using Transdecoder, including the BLASTp step. In addition, the filtered lncRNA/lincRNA were compared against Rfam, to identify and exclude known small ncRNAs or structured RNAs that may have been inadvertently included in the lncRNA dataset. To quantify expression levels of the identified lncRNA transcripts, we used Kallisto v0.46.2 to generate transcript-level abundance estimates. We indexed the lncRNA transcripts using the default parameters of Kallisto. The trimmed and filtered reads were then aligned to this index using Kallisto quant with 100 bootstraps. The resulting transcript-level abundance estimates were then imported into R using the tximport package. Then the quantification data were subsequently imported into DESeq2 v1.34.1 for normalization and differential expression analysis. Differentially expressed lncRNAs were defined as those with an adjusted P-value < 0.05 and an absolute log2 fold change > 1. Subsequently, coexpression analysis was conducted between the differentially expressed lncRNA transcripts and differentially expressed genes identified between the CHDL and Control groups in both foot tissue and PBL. Significant coexpression was determined based on an adjusted P-value threshold of < 0.05, signifying statistical significance in the associations between the expression profiles of lncRNAs and genes across the two experimental conditions. |
| Type Of Material | Data analysis technique |
| Year Produced | 2023 |
| Provided To Others? | No |
| Impact | Principal Component Analysis (PCA) was performed to investigate the overall patterns of variation in the expression profiles of lncRNAs between CHDL case and control groups. The analysis successfully elucidated a cumulative variance of 69% in foot tissue and 79% in PBL, encapsulating the major sources of variability present in both datasets. The dataset of foot tissue encompassed 14 samples, comprising 7 CHDL cases and 7 controls. It included expression data for a total of 13,352 identified lncRNAs with 11,706 identified lincRNAs. The peripheral blood leukocytes (PBL) dataset comprised 24 samples, consisting of 12 cases and 12 controls. It encompassed expression data for a total of 63,266 identified lncRNAs with 37,541 lincRNAs. The PCA plot revealed a scattered distribution of samples across the principal component space, with no discernible clustering or separation between the CHDL case and control groups in both foot tissue and PBL. In the comparative analysis between CHDL and Control groups in foot tissue, a total of 34 differentially expressed lncRNA transcripts were discerned. Notably, among these, a single lncRNA transcript exhibited downregulation in the CHDL case group relative to the Control group. The differentially expressed lncRNA transcripts primarily fell into the categories of intergenic ("u") and intronic ("i"). Specifically, the majority of these transcripts were associated with a single exon (exon number 1). A total of 30 differentially expressed lncRNA transcripts were identified between CHDL and Control groups in PBL. Among these transcripts, 10 lncRNA transcripts exhibited upregulation in the CHDL group compared to the Control group. Specifically, the majority of the differentially expressed lncRNA transcripts belonged to the intergenic category ("u"), while others were classified as intronic ("i"). Two transcripts were assigned a class code of "s," indicating their localization within introns matched on the opposite strand. All these identified transcripts were located within exon numbers 1 and 2. Based on the co-expression analysis results between the differentially expressed lncRNAs and differentially expressed genes in foot tissue, it is evident that except for lncRNAs XLOC_038968 and XLOC_044640, the remaining differentially expressed lncRNAs exhibited a propensity to enhance the expression levels of the following differentially expressed genes: ENSBTAG00000053420, bta-mir-2285cu, 7SK, ENSBTAG00000042498, KIR3DL1, U6, ENSBTAG00000042477, FUT9, ENSBTAG00000048831, ENSBTAG00000048419, BPIFB1, and KNCN. However, these two lncRNAs (XLOC_038968 and XLOC_044640) enhance the expression of genes ENSBTAG00000022373 and ENSBTAG00000049986. Based on the co-expression analysis results between the differentially expressed long non-coding RNAs (lncRNAs) and differentially expressed genes in peripheral blood leukocytes (PBL), distinct regulatory patterns were observed. Specifically, lncRNAs XLOC_000733, XLOC_041028, XLOC_011112, XLOC_060330, and XLOC_020621 were found to enhance the expression of genes ENSBTAG00000048406 and ENSBTAG00000038893, while concurrently downregulating the expression of gene ENSBTAG00000053198. Conversely, lncRNA XLOC_050961 exhibited an enhancing effect on the expression of genes ENSBTAG00000025260, AMTN, KRTAP27-1, ENSBTAG00000054136, ENSBTAG00000052798, KRTAP3-3, and ENSBTAG00000051867. |
| Description | Collaboration with SRUC and University of Liverpool |
| Organisation | Scotland's Rural College |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | This project is a Joint application between SRUC, University of Liverpool and RVC. RVC is responsible for the post-genomic functional work of this project. |
| Collaborator Contribution | This project is a Joint application between SRUC, University of Liverpool and RVC. University of Liverpool and SRUC are responsible for the collection of data, immunological profile of animals and genetic analysis. |
| Impact | Multi-disciplinary collaboration among vet, animal scientists, geneticists, immunologists, computational biologists, molecular biologists. |
| Start Year | 2018 |
| Description | Collaboration with SRUC and University of Liverpool |
| Organisation | University of Liverpool |
| Department | School of Veterinary Science Liverpool |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | This project is a Joint application between SRUC, University of Liverpool and RVC. RVC is responsible for the post-genomic functional work of this project. |
| Collaborator Contribution | This project is a Joint application between SRUC, University of Liverpool and RVC. University of Liverpool and SRUC are responsible for the collection of data, immunological profile of animals and genetic analysis. |
| Impact | Multi-disciplinary collaboration among vet, animal scientists, geneticists, immunologists, computational biologists, molecular biologists. |
| Start Year | 2018 |
| Description | BCVA "Foot anatomy and structure and its association with the development of claw horn disruption lesions in dairy cattle" |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Conference presentation B.E. Griffiths, M. Barden, A. Anagnostopoulos, C. Bedford, H. Higgins, A. Psifidi, G. Banos and G. Oikonomou. BCVA Congress 2022, 19-21 October, 2022, Telford International Centre |
| Year(s) Of Engagement Activity | 2022 |
| Description | BSAS "Association between a genetic index for digital dermatitis resistance and the incidence of foot lesions in Holstein cows" |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Conference presentation A. Anagnostopoulos, M. Barden, B.E. Griffiths, C. Bedford, M. Winters, B. Li, M. Coffey, A. Psifidi, G. Banos, G. Oikonomou. BSAS 2023, 28-30 March, Birmingham, UK |
| Year(s) Of Engagement Activity | 2023 |
| Description | BSAS "Association between a genetic index for digital dermatitis resistance and the incidence of foot lesions in Holstein cows" |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Presentation at British Society of Animal Science (BSAS) in 2022 Authors: Alkiviadis Anagnostopoulos1, Matthew Barden1, Bethany E. Griffiths1, Cherril Bedford1, Marco Winters2, Bingjie Li3, Mike Coffey3, Androniki Psifidi4, Georgios Banos3, Georgios Oikonomou1 |
| Year(s) Of Engagement Activity | 2022 |
| Description | BSAS "Serum biomarkers for fat mobilisation and hormonal profiles and their association with sole ulcers in dairy cows" |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | B. Griffiths, A. Anagnostopoulos, M. Barden, C. Bedford, M. Rudd, J. Graham-Brown, S. Carter, A. Psifidi, G. Banos, G. Oikonomou. BSAS 2023, 28-30 March, Birmingham, UK |
| Year(s) Of Engagement Activity | 2023 |
| Description | BSAS "The association of serum biomarkers for fat mobilisation and hormonal profiles with sole ulcers in dairy cows." |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Presentation and British Society of Animal Science (BSAS) Authors: Bethany Griffiths1, Alkiviadis Anagnostopoulos1, Matthew Barden1, Cherrill Bedford1, Mollie Rudd1, John Graham- Brown1, Stuart Carter1, Androniki Psifidi2, Georgios Banos3, Georgios Oikonomou1 |
| Year(s) Of Engagement Activity | 2022 |
| Description | Conference presentation - International Conference on Lameness in Ruminants - Investigating the role of long noncoding RNAs on claw horn disruption lesions susceptibility in dairy cattle |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Conference presentation at the International Conference on Lameness in Ruminants 16-20th September 2024 presenting lncRNA work conducted in this project. Presentation title: Investigating the role of long noncoding RNAs on claw horn disruption lesions susceptibility in dairy cattle. Authors: X. Dai, D. Xia, C. Xu, D. Werling, G. Banos, G. Oikonomou, and A. Psifidi |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.lamenessinruminants2024.com/ |
| Description | Conference presentation in the Animal Genetics and Diseases, Wellcome Genome Campus Conference Centre, Hinxton, Cambridge, UK |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | In this conference I presented a lightening talk and a poster entitled: "Aetiopathogenesis and genomic architecture of resistance to lameness in dairy cattle". This presentation sparked questions and discussions afterwards and attracted a lot of interest. |
| Year(s) Of Engagement Activity | 2019 |
| Description | ISAG "Integration of Reduced Representation Bisulphite Sequencing with RNA Sequencing data provides further insights in Claw Horn Disruption Lesions susceptibility in dairy cattle" |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Poster presentation at ISAG 2023: Elizabeth Attree, Xiaoxia Dai, Dong Xia, Matthew Barden, Bethany Eloise Griffiths, Alkiviadis Anagnostopoulos, Dirk Werling, George Oikonomou, Georgios Banos and Androniki Psifidi. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.isag.us/2023/ |
| Description | Invited seminar at The Roslin Institute, University of Edinburgh entitled: : "Integrating genetics and omics data to dissect host resistance to disease". |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | I presented in this scientific seminar the different research projects I am currently involved in with an emphasis on the work we are doing in the "One Health Poultry Hub" and the "Aetiopathogenesis and genomic architecture of resistance to claw horn disruption lesions in dairy cattle" project. This was a well attended seminar, with lots of questions and discussion afterwards. Interest expressed for future collaborative work. |
| Year(s) Of Engagement Activity | 2020 |
| Description | Night at the Vet College public engagement |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Schools |
| Results and Impact | Participation in public engagement at the Night at the Vet college event by research stand advertising past, current and future research, key research outcomes and educating visitors on research group overall aims. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.rvc.ac.uk/study/rvc-is-open-for-all/visit-us/night-at-the-vet-college |
| Description | PAG "Understanding the Genomic Architecture of Claw Horn Disruption Lesions in Dairy Cattle" |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Poster presentation at PAG 2023 Authors: Elizabeth Attree1, Xiaoxia Dai1, Bingjie Li2, Dong Xia1, Matthew Barden3, Bethany Eloise Griffiths3, Dirk Werling4, George Oikonomou3, Georgios Banos2 and Androniki Psifidi1 |
| Year(s) Of Engagement Activity | 2023 |
| Description | Participation in an open day event - Night at the Vet college |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Schools |
| Results and Impact | Participation in an open day event at the RVC presenting past and ongoing research projects from the group explaining how genetics research can improve animal health and welfare. The event was designed to engage future students and their families as well as young children to RVC research activities and inspire future scientists. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.rvc.ac.uk/study/rvc-is-open-for-all/visit-us/night-at-the-vet-college |
| Description | Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP) " Understanding the genetic architecture of claw horn lesions in different lactation stages in Holstein cattle" |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Presentation: " Understanding the genetic architecture of claw horn lesions in different lactation stages in Holstein cattle" scientific debate of results with researchers from around the world |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.wageningenacademic.com/doi/abs/10.3920/978-90-8686-940-4_674 |
| Description | Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP) "Transcriptomic characterisation of claw horn disruption lesions in the peripheral blood leucocytes of dairy cattle" |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presentation : Transcriptomic characterisation of claw horn disruption lesions in the peripheral blood leucocytes of dairy cattle" Scientific debate of results and impact with researchers from around the world |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.wageningenacademic.com/doi/abs/10.3920/978-90-8686-940-4_555 |
| Description | press release |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Press release from the RVC, the University of Liverpool and the SRUC on the new award related to cattle lameness (https://www.vettimes.co.uk/news/cash-boost-for-cattle-lameness/https://www.feedstuffs.com/nutrition-health/uk-study-seeks-root-cause-dairy-cow-lameness ) |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.rvc.ac.uk/news-and-events/rvc-news/new-research-into-250-million-problem-of-lameness-in-... |