Work Package Agricultural systems and land management
Improvement of livestock, in terms of health, welfare and productivity (both in terms of quantity and quality of farm products such as milk and meat) is key for the future sustainability of farming. While significant progress has been made in terms of selective breeding for production traits such as weight gain and milk production, less progress has been made on improving more complex or difficult to record traits such as feed conversion efficiency, disease resistance and animal behaviours. Furthermore, as traits are influenced by both genetic and environmental factors, optimising livestock environments through altered on-farm management practices may provide additional improvements in animal health, welfare and productivity.
Aim of Research
To improve livestock for traits and management practices important for sustainability of livestock farming at an animal and farm system level. The work will focus on improving animal health and welfare, improving the quality and health attributes of meat and milk products, and increasing animal/farm system resilience (i.e. the ability of animals or management systems to cope with stresses such as infectious diseases, behavioural stresses or changes in climate). An integral component of this RD is the development of novel biomarkers for difficult-to-record traits such as resilience to parasite infections and feed conversion efficiency, which may be used in livestock selective breeding programmes. Further work will explore management systems aimed at reducing the impact of infectious diseases and aggressive behaviours.
In this year, the work involved final refinement and validation of methodologies developed in the research programme, and collation and disseminating of these methods to promote their use in the field.
Work on the rumen microbiome refined the number of microbial genes to a core number of heritable genes which accurately estimate feed conversion efficiency and methane emissions in cattle throughout the growing to finishing period. This allows early selection of low methane emitting animals with high feed efficiency. The results were disseminated to the cattle industry and scientific community via publications, webinars and the media.
To consolidate current knowledge on nitrogen isotopic fractionation measurements, another proxy of feed conversion efficiency, two systematic reviews (meta-analyses) of the scientific literature were performed, one on lactating dairy cows and one on growing beef cattle. This ‘gold-standard’ approach to evaluating scientific evidence, highlighted the potential of this technique for feed efficiency breeding and/or identifying cows for targeted feeding.
Methods to measure heritable immune and nutritional traits in dairy cattle through routinely recorded milk infra-red (MIR) spectral data were validated on a commercial dairy farm, which demonstrated that MIR-based prediction of milk calcium, an important micronutrient, is feasible from existing MIR-data.
Final analysis of resilience of beef cattle to climate change (i.e. the ability to cope with extreme weather events) using over 1.5 million individual animals, confirmed that resilience varies between cattle breeds, with British breeds being more resilient that continental or dairy breeds to changes in climate. Such information will allow future selection of cattle breeds which are less affected by extreme weather events.
Finally management strategies for improved on farm parasite control and to reduce aggressing in pigs were promoted through revised industry guidelines (e.g. SCOPS (Sustainable Control Of Parasites in Sheep) guidance to sheep farmers), farmer and veterinary engagement (e.g. farmer websites, podcasts) and scientific publications.
- Identification of core rumen microbial information that can be used for early selection of low methane emitting animals with high feed conversion efficiency.
- Final systematic review of nitrogen fractionation measurements as a proxy for feed conversion efficiency in beef and dairy cattle.
- Validation of the use of milk mid-infrared spectral data to predict milk nutrient levels in dairy cattle.
- Identification of breed-specific differences in resilience to climate change.
- Improved guidance for parasite control in sheep.
- Improved guidance for reducing aggression in pigs.
In year 5, much of the work involved validating methodologies developed in the research programme for use in the field, and disseminating these results to end users.
Work on the rumen microbiome showed that selection for improved feed conversion efficiency and reduced methane emissions can be more effective if based on rumen microbial gene information rather than individually measured feed conversion efficiency or methane emissions recorded by respiration chambers. This concept of microbiome-driven breeding in cattle, which is less costly than recording feed conversion rates and methane production on individual animals, was presented at key stakeholder meetings and through the national press.
A large scale analysis of Irish, French, Swiss and UK cattle demonstrated that nitrogen isotopic fractionation measurements are consistently associated with feed conversion efficiency, confirming that previous results are widely applicable across different cattle populations. Furthermore, detailed methodologies for nitrogen isotopic fractionation measurements in cattle were disseminated through technical publication to allow wider uptake of these measurements by the cattle sector.
To validate methods to measure heritable immune and nutritional traits in dairy cattle through milk infra-red (MIR) spectral data, a range of immune and nutritional traits were quantified in milk samples from a commercial dairy farm to allow validation of the MIR methodology in a commercial setting.
Field studies in sheep tested combined use of vaccination and drug treatments to control parasitic worms, and identified best practice guidance for use of long-acting anthelmintic drugs to avoid development of anthelmintic resistance and reduced lamb performance. This information has been disseminated through the updated SCOPS (Sustainable Control Of Parasites in Sheep) guidance to sheep farmers, suitably qualified persons (SQPs) and vets.
Management strategies to reduce aggression and reduce the need for tail docking in pigs were developed, with results conveyed to stakeholders though scientific and industry publications, and industry talks.
Finally, work continued on better understanding climate resilience in dairy cows and how this can be improved though genetic selection.
- Demonstration that selective breeding based on rumen microbial information (microbiome-driven (indirect) genomic selection) is highly effective at improving feed efficiency and reducing methane emissions in beef cattle.
- Validation of nitrogen fractionation measurements as a proxy for feed conversion efficiency in a range of European cattle populations.
- Optimised methods developed for nitrogen isotopic fractionation measurements, which are associated with improved feed efficiency, in cattle.
- Improved guidance for use of long-acting anthelmintic drug treatments in sheep to maintain productivity in the face of parasite challenge.
- Early socialisation of pigs can be used to reduce pig aggression.
- Environmental enrichment of pigs around weaning was shown to reduce tail damage (thus reducing the requirement for tail docking) and increased pig growth.
In year 4, work focused on understanding how stable (repeatable) a number of the livestock traits under investigation are, and how the genetics of the animal influences the traits. This is important as it will determine whether breeding for the traits is possible, and whether one or more trait measurements is required. Further work was conducted on farm management systems developed within this RD, including cost-benefit analyses to explore the economic feasibility of implementing these management systems.
It was found that the relationship between the rumen microbes and feed conversion efficiency was stable throughout the growing period of beef cattle. It was also found that genes within rumen microbes associated with feed conversion efficiency are under significant genetic control. This means that breeding for improved feed conversion efficiency in beef cattle can be achieved by analysing rumen microbial genes at only one time time-point during the growing period, which is far more efficient than using costly measurements of feed intake and feed conversion efficiency. Further work was performed to understand the stability of milk micronutrient levels in cow’s milk, specifically the effects of season and diet, and to demonstrate that nitrogen isotopic fractionation measurements in dairy cow milk, which are associated with feed conversion efficiency, are stable over time. The influence of livestock genetics on vaccine responsiveness was also investigated, and while the study did not indicate a strong genetic effect on vaccine responses in sheep, a novel method of analysing livestock genetics using archived serum samples was developed.
Work continued on exploring the potential of routinely recorded milk mid-infrared (MIR) spectral data to estimate livestock traits, including nitrogen isotopic fractionation measurements and the ability of dairy cows to cope with extreme weather events.
Finally, work was performed to understand the implications of livestock management systems developed in this programme of work, including cost-benefit analysis of management systems aimed at reducing livestock aggression, and how different methods of parasite control influence the types of parasites present on farm.
- Rumen microbial genes predicting feed conversion efficacy are both heritable and stable during the growing period in beef cattle and can therefore be used to breed for improved feed conversion efficiency.
- Nitrogen isotopic fractionation measurements in dairy cow milk, which are associated with feed conversion efficiency, are stable over time.
- A new method of studying animal genetics using archived serum samples was developed.
- Routinely and cheaply recorded milk mid-infrared spectral data can be used to predict how dairy cows cope with extreme weather.
- Cost-benefit analysis demonstrated that early life interventions in pigs to reduce pig aggression delivers a net economic benefit to the farmer.
In year 3, studies of the rumen microbiome in cattle were performed to better understand the relationship between the rumen microbes, meat quality, and stress. This work demonstrated that certain microbial genes in cattle can predict levels of linoleic acids within meat, which are beneficial to human health, having anti-cancer properties. The work also demonstrated that animal stress has a big impact on the rumen microbiome. Further studies in cattle showed that nutrient levels of serum and milk of dairy cattle are under genetic control, indicating that selective breeding for nutrients associated with healthier cows and healthier milk is possible.
Work also demonstrated that milk mid-infrared (MIR) spectral data, which is routinely recorded on milk at a national level, could be used to estimate milk production efficiency and milk nutrient levels in dairy cattle. These MIR-based predictions could then be used for selective breeding programmes aimed at improving milk production efficiency and nutritional quality. We also demonstrated that levels of specific serum antibodies (natural antibodies) associated with production efficiency in dairy cows are highly correlated in milk and serum, indicating that these measurements can be performed on milk samples which are less invasive to collect compared to serum. In a further genetic study, it was shown that selection of grazing lambs which require less anti-parasitic drugs to maintain growth rates was not possible, as genetics played little role in determining whether a lamb required treatment.
Finally, work was undertaken to improve livestock management systems, including the best use of anti-parasitic drugs in sheep flocks to control parasites while minimising drug resistance, and the development of new systems to monitor aggression in pigs.
- Rumen microbial genes can predict meat quality and healthiness
- Routinely and cheaply recorded milk mid-infrared spectral data can be used to predict milk nutrient levels and production efficiency in dairy cows.
- Nutrient levels in milk and serum of dairy cows is under genetic control, meaning they could be improved by selective breeding.
In year 2, improvements were made in the ability to predict feed conversion efficiency in cattle using rumen microbial genes or nitrogen isotopic fractionation: these measures could be used to select animals with higher feed conversion efficiencies without the need to monitor feed intake and milk and meat production, which is both time-consuming and costly.
Analyses of immune response traits in cattle and sheep have identified associations between specific immune traits (either cellular immune traits or antibody levels) and nutrient levels in blood and milk, anti-parasitic drug requirement, and the ability of animals to respond to vaccination. Furthermore, cellular immune-associated traits are genetically correlated with key functional traits in dairy cows such as calving difficulty, still birth and lameness and could provide a useful tool in improving animal health, fitness, and fertility through selective breeding programmes.
Climate resilience studies in cattle demonstrated that animal production is compromised at both higher and lower temperatures and humidity. Importantly, daughters of bulls differed in their response to temperature and humidity, highlighting the potential to identify animals that are better able to cope with extremes of weather.
Finally further work was performed on management strategies to optimise lamb growth using novel anthelmintic treatment regimes, and on ways to reduce aggression in pigs. In pig studies it was shown that pig avoidance of aggression at regrouping results in less fight lesions in the short term but more lesions in the longer term. This information could be used to develop new approaches to reduce pig aggression. By studying tail lesions in the abattoir it was shown that the prevalence of tail biting on farm is severely underestimated. Tail docking was found to be highly effective at reducing tail biting - In a study of 2000 pigs no tail damage was observed in tail docked pigs, whereas 23.0% of the undocked pigs were tail bitten; however, the pros and cons of tail docking need to be considered as docking is a painful procedure.
- Cross SEFARI working shows that cellular immune-associated traits are genetically correlated with key functional traits in dairy cows such as calving difficulty, still birth and lameness and could provide a useful tool in improving animal health, fitness and fertility.
- Pig avoidance of aggressive behaviour at regrouping leads to fewer lesions in the short term but more lesions in the longer term. This offer novel strategies to reduce pig aggression.
- Tail docking in pigs was effective in reducing tail biting damage on a commercial farm, but is itself a controversial practice.
- Royal award for SEFARI research: The Langhill Dairy Experiment, supported by the SRP and a source of data and samples for this RD, has been recognised with the award of the Queen’s Anniversary Prize in recognition of the excellence, innovation and impact of the research conducted using this dairy herd.
- Prize winning science: Based on scientific excellence and community impact SEFARI researchers won the prestigious PLOS Genetics Research Prize 2017 for their work showing the potential use of rumen microbial information to reduce methane emissions in beef cattle
The research in year 1 explored a number of phenotypic and genetic traits, and their association with important livestock measures of productivity. Rumen microbiome information at various levels (bacterial phyla, bacterial genera and metabolic genes) and nitrogen isotopic fractionation measurements were shown to be associated with feed conversion efficiency in ruminant livestock. In the case of rumen microbiome information, it was concluded that the microbial community should be determined at the genus level for accurate feed conversion efficiency measurements.
Individual cow production data from the Langhill Dairy Experiment was linked to Meteorological Office weather data and showed that production efficiency is compromised at high temperatures and humidity, with feed intakes reduced by over 10% in animal selected for high milk production traits.
Pig behavioural studies demonstrated that particular social networks, rather than individual behaviours, were associated with lower levels of aggression. This new understanding of pig behaviour could be used to develop better management systems aimed at reducing aggression in pigs and thus improving animal health and welfare.
Finally, work was undertaken to generate data and experimental systems for subsequent studies in Year 2 and 3: immune, genetic, nutritional, behavioural and environmental resilience traits were recorded in a number of livestock species (sheep, cattle and pigs) for future genetic or phenotypic association studies. Paddocks were seeded with defined parasitic worms for future studies to determine how best to use anti-parasitic drugs in terms of improved parasite control and reduced selection of drug-resistant parasites.
- Ruminal bacterial phyla can predict feed conversion efficiency in cattle.
- The Langhill Dairy Experiment was used to quantify the effects of weather on feed intake and efficiency in dairy cattle and showed that production efficiency is reduced at high temperatures and humidity.
- Social networks are important for predicting aggression in pigs.
Building on the work from this programme, microbiome research will focus on how best to reduce greenhouse gas emissions from cattle and to understand whether particular microbiomes are better at controlling bacterial and parasitic diseases in sheep and cattle. Milk mid-infrared spectral data will be evaluated for the ability to predict cattle feed intake and fitness, including freedom from viral and bacterial diseases such as Bovine viral diarrhoea (BVD) and Johne’s disease. Research on gastro-intestinal parasite control in sheep and cattle will be expanded to include assessment of the environmental impact of anthelmintic drugs on the environment, and explore alternatives to anthelmintics such as grazing systems, phoretic mites and vaccines. Further work will be performed to optimise farming systems including feeding and genetics, to promote climate resilience in cattle.
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- Troy, S.M., Duthie, C.-A., Ross, D.W., Hyslop, J.J., Roehe, R., Waterhouse, A., Rooke, J.A. (2016). A comparison of methane emissions from beef cattle measured using methane hoods with those measured using respiration chambers. Animal Feed Science and Technology 211, 227–240. https://www.sciencedirect.com/science/article/pii/S0377840115300791#!
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- Duthie, C.-A., Haskell, M., Hyslop, J.J., Waterhouse, A., Wallace, R.J., Roehe, R., Rooke, J.A. (2017). The impact of divergent breed types and diets on methane emissions, rumen characteristics and performance of finishing beef cattle. Animal 10, 786–795. https://www.cambridge.org/core/journals/animal/article/impact-of-divergent-breed-types-and-diets-on-methane-emissions-rumen-characteristics-and-performance-of-finishing-beef-cattle/AE4AB4EC03AA0BE46FA910EB5CDF8ADF
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- Stewart, R., Auffret, M.D., Warr, A., Snelling, T., Dewhurst, R.J., Walker, A.W., Roehe, R. and Watson, M. (2018). Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen. Nature Communications 9: 870. https://www.nature.com/articles/s41467-018-03317-6/
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- Duthie, C.-A., Troy, S.M., Hyslop, J.J., Ross, D.W., Roehe, R., Rooke, J.A. (2018). The effect of dietary addition of nitrate or increase in lipid concentrations, alone or in combination, on performance and methane emissions of beef cattle. Animal 12, 280–287. https://www.cambridge.org/core/journals/animal/article/effect-of-dietary-addition-of-nitrate-or-increase-in-lipid-concentrations-alone-or-in-combination-on-performance-and-methane-emissions-of-beef-cattle/042AD9AB21B81F20CB3AD11450179DB5
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