M.P. Coffey
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Multi-omics data integration towards sustainable bovine production, health and welfare: the case of painful foot lesions Open
Claw horn disruption lesions (CHDL) are painful non-infectious foot lesions with significant animal welfare and socioeconomic impacts on the dairy industry. Lameness caused by CHDL is the main cause of involuntary culling, considerably red…
Genome-wide association studies of dairy cattle resistance to digital dermatitis recorded at four distinct lactation stages Open
Digital dermatitis (DD) is an endemic infectious hoof disease causing lameness in dairy cattle. The aim of the present study was to investigate the genetic profile of DD development using phenotypic and genotypic data on 2192 Holstein cows…
Detection of genetic variability in dairy cattle infectivity for bovine tuberculosis Open
This study investigated the genetics of bovine tuberculosis (bTB) infectivity in Holstein-Friesian dairy cows using British national data. The analyses included cows with recorded sires from herds affected by bTB outbreaks between 2000 and…
UKCropDiversity‐HPC: A collaborative high‐performance computing resource approach for sustainable agriculture and biodiversity conservation Open
Societal Impact Statement Diverse gene pools are fundamental to crop improvement, biodiversity maintenance and environmental management. The UKCropDiversity‐HPC high‐performance computing resource enables seven UK institutes to perform pla…
Mapping the locus for ocular melanosis in Cairn Terriers Open
Objective To map the disease locus for familial ocular melanosis (OM) in the Cairn Terrier. Animals Studied Cairn Terriers with OM and normal control dogs. Procedure A genome‐wide association study (GWAS) was performed using 63 OM‐affected…
Association between a genetic index for digital dermatitis resistance and the presence of digital dermatitis, heel horn erosion, and interdigital hyperplasia in Holstein cows Open
Digital dermatitis (DD) is a polybacterial disease endemic to most UK dairy farms. It poses a major financial and welfare threat and is characterized by high incidence and recurrence rates. We aimed to investigate the association between t…
Field method for preservation of total mercury in waters, including those associated with artisanal scale gold mining Open
A method was developed for sampling and preserving total Hg from water samples, recovering >75% Hg over 4 weeks of storage. The method was assessed using water samples at artisanal gold mining sites in Kenya.
The Role of Technology in Undergraduate Bioscience Laboratory Learning: Bridging the Gap between Theory and Practice Open
Integration of technology is widespread in laboratory teaching, whose purpose includes building theoretical understanding and practical skills. How second-year bioscience undergraduate students at a UK university use technology to construc…
Use of dry-matter intake recorded at multiple time periods during lactation increases the accuracy of genomic prediction for dry-matter intake and residual feed intake in dairy cattle Open
Context Feed is the largest expense on a dairy farm, therefore improving feed efficiency is important. Recording dry-matter intake (DMI) is a prerequisite for calculating feed efficiency. Genetic variation of feed intake and feed efficienc…
Modelling growth in Suffolk and Charollais sheep populations using random regression models and validation of constrained polynomial correlation values Open
Random regression modelling has been used across multiple animal species to model longitudinal data. The random regression model for growth accounts for the genetic correlation between measures of the same trait over time and the wide envi…
Single-step genome-wide association analyses of claw horn lesions in Holstein cattle using linear and threshold models Open
Background Lameness in dairy cattle is primarily caused by foot lesions including the claw horn lesions (CHL) of sole haemorrhage (SH), sole ulcers (SU), and white line disease (WL). This study investigated the genetic architecture of the …
Challenges and Opportunities in Applying Genomic Selection to Ruminants Owned by Smallholder Farmers Open
Genomic selection has transformed animal and plant breeding in advanced economies globally, resulting in economic, social and environmental benefits worth billions of dollars annually. Although genomic selection offers great potential in l…
Automated Processing and Phenotype Extraction of Ovine Medical Images Using a Combined Generative Adversarial Network and Computer Vision Pipeline Open
The speed and accuracy of phenotype detection from medical images are some of the most important qualities needed for any informed and timely response such as early detection of cancer or detection of desirable phenotypes for animal breedi…
Predicting pregnancy status from mid-infrared spectroscopy in dairy cow milk using deep learning Open
Accurately identifying pregnancy status is imperative for a profitable dairy enterprise. Mid-infrared (MIR) spectroscopy is routinely used to determine fat and protein concentrations in milk samples. Mid-infrared spectra have successfully …
Genetic parameters for carcase measurements and age at slaughter in commercial cattle Open
Genetic parameters were estimated for cold carcase weight (CCW), carcase conformation (CON), carcase fat class (FAT), age at slaughter (AGE) and average daily carcase gain (ADCG) in 14 common UK breeds of cattle. These included crossbred a…
293 ASAS-EAAP Talk: #Phenotypeisking Open
The objective of this text is to describe the changing face of phenotypes collection for use in national genetic and genomic evaluations of dairy cattle and to offer possible new scenarios that may exist. Dairy cattle have been chosen as a…
A comparison of 4 different machine learning algorithms to predict lactoferrin content in bovine milk from mid-infrared spectra Open
Lactoferrin (LF) is a glycoprotein naturally present in milk. Its content varies throughout lactation, but also with mastitis; therefore it is a potential additional indicator of udder health beyond somatic cell count. Condequently, there …
Predicting bovine tuberculosis status of dairy cows from mid-infrared spectral data of milk using deep learning Open
Bovine tuberculosis (bTB) is a zoonotic disease in cattle that is transmissible to humans, distributed worldwide, and considered endemic throughout much of England and Wales. Mid-infrared (MIR) analysis of milk is used routinely to predict…
Life-long telomere attrition predicts health and lifespan in a large mammal Open
Telomere length measured in blood cells is predictive of subsequent adult health and survival across a range of vertebrate species. However, we currently do not know whether such associations result from among-individual differences in tel…
The Genetic Architecture of Bovine Telomere Length in Early Life and Association With Animal Fitness Open
Health and survival are key goals for selective breeding in farm animals. Progress, however, is often limited by the low heritability of these animal fitness traits in addition to measurement difficulties. In this respect, relevant early-l…
Energy profiling of dairy cows from routine milk mid-infrared analysis Open
The balance of body energy within and across lactations can have health and fertility consequences for the dairy cow. This study aimed to create a large calibration data set of dairy cow body energy traits across the cow's productive life,…
View article: Can We Breed Cattle for Lower Bovine TB Infectivity?
Can We Breed Cattle for Lower Bovine TB Infectivity? Open
Host resistance and infectivity are genetic traits affecting infectious disease transmission. This Perspective discusses the potential exploitation of genetic variation in cattle infectivity, in addition to resistance, to reduce the risk, …
Forensic use of the genomic relationship matrix to validate and discover livestock pedigrees Open
Correct pedigree is essential to produce accurate genetic evaluations of livestock populations. Pedigree validation has traditionally been undertaken using microsatellites and more recently, based on checks on opposing homozygotes using si…
View article: The impact of modelling and pooled data on the accuracy of genomic prediction in small holder dairy data
The impact of modelling and pooled data on the accuracy of genomic prediction in small holder dairy data Open
The lack of data recording in smallholder dairy cattle system implies that the availability of molecular data could offer some quick wins in terms of using the genomic information in genomic evaluation and therefore genomic selection (GS).…
Characterization of copy number variants in a large multibreed population of beef and dairy cattle using high-density single nucleotide polymorphism genotype data1 Open
Copy number variants (CNVs) are a form of genomic variation that changes the structure of the genome through deletion or duplication of stretches of DNA. The objective of the present study was to characterize CNVs in a large multibreed pop…
Immune-associated traits measured in milk of Holstein-Friesian cows as proxies for blood serum measurements Open
Previous work has highlighted that immune-associated (IA) traits measurable in blood are associated with health, productivity, and reproduction in dairy cows. The aim of the present study was to determine relationships between IA traits me…
Longitudinal changes in telomere length and associated genetic parameters in dairy cattle analysed using random regression models Open
Telomeres cap the ends of linear chromosomes and shorten with age in many organisms. In humans short telomeres have been linked to morbidity and mortality. With the accumulation of longitudinal datasets the focus shifts from investigating …