BACKGROUND This study aimed to determine the association between the lameness advantage genetic index and four outcomes: sole haemorrhage (SH), sole ulcers (SU), white line lesions (WL), and lameness during mobility scoring. METHODS We... more
BACKGROUND This study aimed to determine the association between the lameness advantage genetic index and four outcomes: sole haemorrhage (SH), sole ulcers (SU), white line lesions (WL), and lameness during mobility scoring. METHODS We enrolled 2352 Holstein cows from four predominantly housed dairy herds in the UK. Cows were mobility scored and foot lesions recorded at four time points from before calving to late lactation. Cows were genotyped and genetic indexes were assigned to each cow following national genetic evaluations. Lameness records and genetic indexes were matched for 2107 cows. Four separate multivariable logistic regression models, which included farm and parity as covariables, were used to quantify the association between the lameness advantage index and whether animals were affected by SH, SU, WL, or lameness. RESULTS The odds ratios (95% confidence intervals) for one-point increases in the lameness advantage index were 0.79 (0.72-0.86), 0.68 (0.59-0.78), 0.94 (0.84-1.04), and 0.82 (0.74-0.91) for SH, SU, WL, and lameness, respectively. The same trends were present when the sire's lameness advantage index was evaluated in place of the animal's own, although the strength of this association was generally weaker. CONCLUSION The lameness advantage index is associated with SH, SU, and lameness, therefore selection on the lameness advantage index could be considered in herds aiming to reduce lameness. Where genomic testing of heifers is not conducted, sire lameness advantage index may still be effective to reduce SH and SU incidence.
Research Interests:
Additive and dominance effects for significant SNPs identified by genome-wide association analysis. (DOCX 13 kb)
Research Interests:
Genetic parameters of three bovine tuberculosis traits. (DOCX 14 kb)
Research Interests:
Manhattan plots displaying results of chromosomal association analyses of three bovine tuberculosis susceptibility traits: (a) phenotype 1, positive reactors to the skin test with positive post-mortem results; (b) phenotype 2, positive... more
Manhattan plots displaying results of chromosomal association analyses of three bovine tuberculosis susceptibility traits: (a) phenotype 1, positive reactors to the skin test with positive post-mortem results; (b) phenotype 2, positive reactors to the skin test regardless of post-mortem results; (c) phenotype 3, as phenotype 2 plus non-reactors and inconclusive reactors with positive post-mortem examination results. Dashed and solid lines represent suggestive and genome-wide thresholds, respectively. (DOCX 2254 kb)
Research Interests:
Research Interests:
Research Interests: Biology, Medicine, Analytics, Sensors, Big Data, and 4 morePhenomics, Genotype, Dairy Cattle, and Animal Frontiers
Genetic evaluations for resistance to bovine tuberculosis (bTB) were calculated based on British national data including individual animal tuberculin skin test results, postmortem examination (presence of bTB lesions and bacteriological... more
Genetic evaluations for resistance to bovine tuberculosis (bTB) were calculated based on British national data including individual animal tuberculin skin test results, postmortem examination (presence of bTB lesions and bacteriological culture for Mycobacterium bovis), animal movement and location information, production history, and pedigree records. Holstein cows with identified sires in herds with bTB breakdowns (new herd incidents) occurring between the years 2000 and 2014 were considered. In the first instance, cows with a positive reaction to the skin test and a positive postmortem examination were defined as infected. Values of 0 and 1 were assigned to healthy and infected animal records, respectively. Data were analyzed with mixed models. Linear and logit function heritability estimates were 0.092 and 0.172, respectively. In subsequent analyses, breakdowns were split into 2-mo intervals to better model time of exposure and infection in the contemporary group. Intervals with...
Research Interests:
Research Interests:
Research Interests:
Quantile-quantile plots of observed against expected P-values from genome-wide association analyses: (a) phenotype 1, positive reactors to the skin test with positive post-mortem results; (b) phenotype 2, positive reactors to the skin... more
Quantile-quantile plots of observed against expected P-values from genome-wide association analyses: (a) phenotype 1, positive reactors to the skin test with positive post-mortem results; (b) phenotype 2, positive reactors to the skin test regardless of post-mortem results; (c) phenotype 3, as phenotype 2 plus non-reactors and inconclusive reactors with positive post-mortem examination results. (DOCX 1200 kb)
Background: Here, we jointly summarise scientific evidence for genetic variation in resistance to infection with Mycobacterium bovis, the primary agent of bovine tuberculosis (TB), provided by two recent and separate studies of... more
Background: Here, we jointly summarise scientific evidence for genetic variation in resistance to infection with Mycobacterium bovis, the primary agent of bovine tuberculosis (TB), provided by two recent and separate studies of Holstein-Friesian dairy cow populations in Great Britain (GB) and Ireland. Methods: The studies quantified genetic variation within archived data from field and abattoir surveillance control programmes within each country. These data included results from the single intradermal comparative tuberculin test (SICTT), abattoir inspection for TB lesions and laboratory confirmation of disease status. Threshold animal models were used to estimate variance components for responsiveness to the SICTT and abattoir confirmed M. bovis infection. The link functions between the observed 0/1 scale and the liability scale were the complementary log-log in the GB, and logit link function in the Irish population. Results and discussion: The estimated heritability of susceptibil...
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... more
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 breeding. To improve both these qualities, the world is leveraging artificial intelligence and machine learning against this challenge. Most recently, deep learning has successfully been applied to the medical field to improve detection accuracies and speed for conditions including cancer and COVID-19. In this study, we applied deep neural networks, in the form of a generative adversarial network (GAN), to perform image-to-image processing steps needed for ovine phenotype analysis from CT scans of sheep. Key phenotypes such as gigot geometry and tissue distribution were determined using a computer vision (CV) pipeline. The results of the image processing using a trained GAN are strikingly similar (a similarity index of 98%) when used on unseen test image...
Research Interests:
Telomere length is predictive of adult health and survival across vertebrate species. However, we currently do not know whether such associations result from among-individual differences in telomere length determined genetically or by... more
Telomere length is predictive of adult health and survival across vertebrate species. However, we currently do not know whether such associations result from among-individual differences in telomere length determined genetically or by early-life environmental conditions, or from differences in the rate of telomere attrition over the course of life that might be affected by environmental conditions. Here, we measured relative leukocyte telomere length (RLTL) multiple times across the entire lifespan of dairy cattle in a research population that is closely monitored for health and milk production and where individuals are predominantly culled in response to health issues. Animals varied in their change in RLTL between subsequent measurements and RLTL shortened more during early life and following hotter summers which are known to cause heat stress in dairy cows. The average amount of telomere attrition calculated over multiple repeat samples of individuals predicted a shorter producti...
Research Interests: Medicine()
()
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... more
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 an exemplar, but some of the principles could be applied to other livestock species. National evaluations in many established countries have evolved over many decades into sophisticated layers of management, ownership and funding streams, but all have created large gains for farmers, dairy cows and consumers. Usually, milk recording data has been gathered for management purposes and passed the national evaluation centers freely in return for genetic evaluations that added value to the recording service. Conformation and functional phenotypes were often recorded by breed societies and sometimes evaluated by them. These long standing and established processes are becoming disrupted by the advent of genomic evaluation whereby limited and high-quality p...
Research Interests:
Research Interests:
This work was part of the EU RobustMilk project. In this work package, we have focused on two aspects of robustness, micro- and macro-environmental sensitivity and applied these to somatic cell count (SCC), one aspect of milk quality. We... more
This work was part of the EU RobustMilk project. In this work package, we have focused on two aspects of robustness, micro- and macro-environmental sensitivity and applied these to somatic cell count (SCC), one aspect of milk quality. We showed that it is possible to combine both categorical and continuous descriptions of the environment in one analysis of genotype by environment interaction. We also developed a method to estimate genetic variation in residual variance and applied it to both simulated and a large field data set of dairy cattle. We showed that it is possible to estimate genetic variation in both micro- and macro-environmental sensitivity in the same data, but that there is a need for good data structure. In a dairy cattle example, this would mean at least 100 bulls with at least 100 daughters each. We also developed methods for improved genetic evaluation of SCC. We estimated genetic variance for some alternative SCC traits, both in an experimental herd data and in f...
Research Interests:
Research Interests:
Feed costs are a significant proportion of total costs in most dairy production systems and there is strong evidence for substantial genetic variation in total feed intake. However, a large component of this variation is unfavorably... more
Feed costs are a significant proportion of total costs in most dairy production systems and there is strong evidence for substantial genetic variation in total feed intake. However, a large component of this variation is unfavorably correlated with important maintenance and production functions of the animal. Ideally, selection indexes for improved feed efficiency would consider total feed intake that explicitly accounts for the feed required for valuable energy sinks such as milk production, high fertility and adequate body reserves. Residual feed intake (RFI), which is defined at the phenotypic level as the difference between actual feed intake and predicted feed intake, is a potential selection criterion to improve efficiency of feed utilization. However, there are other potential approaches that might have desirable attributes when considered in the context of well-established genetic evaluation systems with breeding objective definitions that are accepted by industry. In this s...
Research Interests: Dairy Science, Animal Production, Longevity, Pregnancy, Female, and 5 moreAnimals, Cattle, Age Factors, Food Sciences, and Seasons
Bull insemination records and Interbull genetic evaluation results for a very large number of elite dairy sires used globally since 1980 were used to quantify the benefits of genetic improvement in the UK dairy industry. The aggregate... more
Bull insemination records and Interbull genetic evaluation results for a very large number of elite dairy sires used globally since 1980 were used to quantify the benefits of genetic improvement in the UK dairy industry. The aggregate benefits of genetic improvement in the UK dairy industry are estimated to have been between £2.2 billion and £2.4 billion since 1980. Importation of superior gene stocks has played a substantial role in delivering these benefits, both directly from imported semen, and from use of this semen to breed UK born bulls of high merit. While the USA has contributed a large proportion of this imported genetic gain, Interbull results suggest that bulls from many other countries were of comparable or superior genetic merit for use in the UK, and that bulls first proven in the UK have been on a par with imported bulls for a number of years. There is also an indication that foreign proven bulls used in the UK in 2008 and 2009, were superior (for use in the UK) to t...
Research Interests: Business()
()
Pedigree collected by the Interbeef service permitted to assess genetic diversity of 5 European Limousin cattle populations respectively from Denmark, France, Ireland, Sweden and UnitedKingdom using pedigree analyses. Analyzed populations... more
Pedigree collected by the Interbeef service permitted to assess genetic diversity of 5 European Limousin cattle populations respectively from Denmark, France, Ireland, Sweden and UnitedKingdom using pedigree analyses. Analyzed populations included 1 652 734 calves with age-adjusted weaning weights whose 91.9% were recorded in France, 4.9% in United-Kingdom, 1.8% in Denmark, 0.9% in Sweden and 0.5% in Ireland. Pedigree file included 2 409 659 animals whose 82.5% originated from FRA, 11.1% from DNK, 4.9% from UK, 0.8% from IRL, and 0.7% from SWE. Gene flows were rather limited between populations, except from France towards other countries. Pedigree knowledge was good in all 5 subpopulations and allowed tracing pedigree back to the French population. Therefore, between 71% and 96% founders of calves born between 1989 and 2008 were of French origin. In each population, it was shown that founders but also ancestors had unbalanced genetic contributions: the main 10 ancestors explained 20...
Research Interests:
Research Interests: Biology()
()
Research Interests: Biology()
()
Research Interests: Biology()
()
Research Interests: Biology()
()
Gembloux Agro-Bio Tech, University of Liege, Animal Science Unit Passage des Deportes, 2 – 5030 GEMBLOUX Tel :++ 32 (0) 81 62 25 82 Fax : ++ 32 (0) 81 62 21 15 hsoyeurt@ulg.ac.be Mid-Infrared Predictions of Fatty Acids in Bovine Milk:... more
Gembloux Agro-Bio Tech, University of Liege, Animal Science Unit Passage des Deportes, 2 – 5030 GEMBLOUX Tel :++ 32 (0) 81 62 25 82 Fax : ++ 32 (0) 81 62 21 15 hsoyeurt@ulg.ac.be Mid-Infrared Predictions of Fatty Acids in Bovine Milk: Final Results of the RobustMilk Project H. Soyeurt1,2, S. McParland3, D. Berry3 , E. Wall4, M. Coffey4, N. Gengler1, F. Dehareng5 & P. Dardenne5 1 University of Liege, Gembloux Agro-Bio Tech, Animal Science Unit, B-5030 Gembloux, Belgium, 2 National Fund for Scientific Research, B-1000 Brussels, Belgium, 3 Animal and Grassland Research & Innovation Centre, Teagasc Moorepark, Fermoy, Cork, Ireland, 4 Sustainable Livestock Systems Group, Scottish Agricultural College, Bush Estate, Penicuik, Midlothian, United Kingdom, 5 Agricultural Walloon Research Centre, Valorisation of Agricultural Products Department, B-5030 Gembloux, Belgium.
Research Interests:
Research Interests:
Research Interests:
The declining energy balance characteristics of modern dairy cows have been implicated in a reduction of fertility throughout a number of countries. The link between various aspects of energy balance in early lactation and fertility has... more
The declining energy balance characteristics of modern dairy cows have been implicated in a reduction of fertility throughout a number of countries. The link between various aspects of energy balance in early lactation and fertility has been difficult to define using traditional statistical methods. One reason for this may be that both traits are continuously varying over time in different patterns and it could be the sequence of events that is more important than the quantitative link between them. Cows from a research herd were progesterone profiled for the first 140 days of lactation to identify luteal cycling activity. Behavioural oestrus was also recorded. Cows were weighed daily and condition scored weekly and these data used to monitor energy balance. Characteristics of both energy balance and luteal cycles were used to identify a key sequence of events which may precipitate the day of first observed heat. In 58% of lactations first heat was observed once cows had gone into p...
Research Interests: Biology()
()
In dairy production, feed efficiency relates to amount of energy corrected milk that can be produced per unit of energy consumed. As feeding costs account for the bulk of overheads in dairy production, incorporating feed efficiency into... more
In dairy production, feed efficiency relates to amount of energy corrected milk that can be produced per unit of energy consumed. As feeding costs account for the bulk of overheads in dairy production, incorporating feed efficiency into genetic and genomic breeding programmes has enormous potential for reducing costs to producers as well as having positive implications from an environmental sustainability standpoint. Feed efficiency has long been incorporated into breeding programmes in the pig and poultry industry, and much progress has been made in the last decade in the dairy cattle sector using proxy traits. Dairy goat breeding programmes are relatively new, and to date, much of the breeding focus has been on increasing milk yield and quality. Feed efficiency and body weight in the present population have been shown to have a heritable component (average h2 0.25; Desire et al., 2017), with sufficient genetic variation to respond to traditional selective breeding. The accuracy of...
A 50K bovine DNA array allows large scale genotyping of dairy cattle for around 50 thousand markers (Single Nucleotide Polymorphisms -SNP). This development opens the door to genomic prediction and selection, and also facilitates gene... more
A 50K bovine DNA array allows large scale genotyping of dairy cattle for around 50 thousand markers (Single Nucleotide Polymorphisms -SNP). This development opens the door to genomic prediction and selection, and also facilitates gene detection, mapping and association studies. Any such application requires knowledge of the Linkage Disequilibrium (LD) state of the markers. The objective of this work was to examine the LD in two divergent genetic lines of dairy cows genotyped with the 50K bovine DNA array.
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... more
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 population of beef and dairy bulls. The CNVs were called on the autosomes of 5,551 cattle from 22 different beef and dairy breeds, using 2 freely available software suites, QuantiSNP and PennCNV. All CNVs were classified into either deletions or duplications. The median concordance between PennCNV and QuantiSNP, per animal, was 18.5% for deletions and 0% for duplications. The low concordance rate between PennCNV and QuantiSNP indicated that neither algorithm, by itself, could identify all CNVs in the population. In total, PennCNV and QuantiSNP collectively identified 747,129 deletions and 432,523 duplications; 80.2% of all duplications and 69.1% of all deletions were present only once in the population. Only 0.154% of all CNVs identified were present ...
Research Interests:
Research Interests:
Abattoir data are an important source of information for the genetic evaluation of carcass traits, but also for on-farm management purposes. The present study aimed to quantify the contribution of herd environment to beef carcass... more
Abattoir data are an important source of information for the genetic evaluation of carcass traits, but also for on-farm management purposes. The present study aimed to quantify the contribution of herd environment to beef carcass characteristics (weight, conformation score and fat score) with particular emphasis on generating finishing herd-specific profiles for these traits across different ages at slaughter. Abattoir records from 46,115 heifers and 78,790 steers aged between 360 and 900days, and from 22,971 young bulls aged between 360 and 720days, were analysed. Finishing herd-year and animal genetic (co)variance components for each trait were estimated using random regression models. Across slaughter age and gender, the ratio of finishing herd-year to total phenotypic variance ranged from 0.31 to 0.72 for carcass weight, 0.21 to 0.57 for carcass conformation and 0.11 to 0.44 for carcass fat score. These parameters indicate that the finishing herd environment is an important cont...
Research Interests:
The significant social and economic loss as a result of bovine tuberculosis (bTB) presents a continuous challenge to cattle industries in the UK and worldwide. However, host genetic variation in cattle susceptibility to bTB provides an... more
The significant social and economic loss as a result of bovine tuberculosis (bTB) presents a continuous challenge to cattle industries in the UK and worldwide. However, host genetic variation in cattle susceptibility to bTB provides an opportunity to select for resistant animals and further understand the genetic mechanisms underlying disease dynamics. The present study identified genomic regions associated with susceptibility to bTB using genome-wide association (GWA), regional heritability mapping (RHM) and chromosome association approaches. Phenotypes comprised de-regressed estimated breeding values of 804 Holstein-Friesian sires and pertained to three bTB indicator traits: i) positive reactors to the skin test with positive post-mortem examination results (phenotype 1); ii) positive reactors to the skin test regardless of post-mortem examination results (phenotype 2) and iii) as in (ii) plus non-reactors and inconclusive reactors to the skin tests with positive post-mortem exami...
Research Interests: Genetics()
()
Data collected from an experimental Holstein-Friesian research herd were used to determine genetic and phenotypic parameters of innate and adaptive cellular immune-associated traits. Relationships between immune-associated traits and... more
Data collected from an experimental Holstein-Friesian research herd were used to determine genetic and phenotypic parameters of innate and adaptive cellular immune-associated traits. Relationships between immune-associated traits and production, health, and fertility traits were also investigated. Repeated blood leukocyte records were analyzed in 546 cows for 9 cellular immune-associated traits, including percent T cell subsets, B cells, NK cells, and granulocytes. Variance components were estimated by univariate analysis. Heritability estimates were obtained for all 9 traits, the highest of which were observed in the T cell subsets percent CD4(+), percent CD8(+), CD4(+):CD8(+) ratio, and percent NKp46(+) cells (0.46, 0.41, 0.43 and 0.42, respectively), with between-individual variation accounting for 59 to 81% of total phenotypic variance. Associations between immune-associated traits and production, health, and fertility traits were investigated with bivariate analyses. Strong gen...
Research Interests: Dairy Science, Fertility, Lactation, Animal Production, Female, and 5 moreAnimals, Phenotype, Milk, Cattle, and Food Sciences
The effect of subclinical paratuberculosis (or Johne's disease) risk status on performance, health, and fertility was studied in 58,096 UK Holstein-Friesian cows with 156,837 lactations across lactations 1 to 3. Low-, medium-, and... more
The effect of subclinical paratuberculosis (or Johne's disease) risk status on performance, health, and fertility was studied in 58,096 UK Holstein-Friesian cows with 156,837 lactations across lactations 1 to 3. Low-, medium-, and high-risk group categories were allocated to cows determined by a minimum of 4 ELISA milk tests taken at any time during their lactating life. Lactation curves of daily milk, protein, and fat yields and protein and fat percentage, together with loge-transformed somatic cell count, were estimated using a random regression model to quantify differences between risk groups. The effect of subclinical paratuberculosis risk groups on fertility, lactation-average somatic cell count, and mastitis were analyzed using linear regression fitting risk group as a fixed effect. Milk yield losses associated with high-risk cows compared with low-risk cows in lactations 1, 2, and 3 for mean daily yield were 0.34, 1.05, and 1.61kg; likewise, accumulated 305-d yields were...
Research Interests:
Bovine tuberculosis (bTB) is a disease of significant economic importance and is a persistent animal health problem with implications for public health worldwide. Control of bTB in the UK has relied on diagnosis through the single... more
Bovine tuberculosis (bTB) is a disease of significant economic importance and is a persistent animal health problem with implications for public health worldwide. Control of bTB in the UK has relied on diagnosis through the single intradermal comparative cervical test (SICCT). However, limitations in the sensitivity of this test hinder successful eradication and the control of bTB remains a major challenge. Genetic selection for cattle that are more resistant to bTB infection can assist in bTB control. The aim of this study was to conduct a quantitative genetic analysis of SICCT measurements collected during bTB herd testing. Genetic selection for bTB resistance will be partially informed by SICCT-based diagnosis; therefore it is important to know whether, in addition to increasing bTB resistance, this might also alter genetically the epidemiological characteristics of SICCT. Our main findings are that: (1) the SICCT test is robust at the genetic level, since its hierarchy and compa...