With more than 50 billion chickens reared every year for both eggs (layers) and meat (broilers), poultry is one of the largest and fastest growing food systems worldwide. Poultry already outcompetes other meat markets and by 2025 more than half of all the meat produced globally is forecasted to be chicken. In the UK, growth in the poultry sector has soared in recent years, with an estimated contribution of £3.3bn to UK GDP in 2014. According to Defra, the UK poultry meat production increased to 1.8 million tonnes in 2017, with broilers accounting for around 85%. Currently, the UK is about 75% self-sufficient in poultry meat, and poultry meat represents the only UK livestock sector capable of quickly scaling-up production to support increased self-sufficiency of the UK. Ensuring consistently high fertility rates is key for meeting the demands of this expanding market. Fertility in these flocks is notoriously variable and tends to decline as birds get older, through reproductive ageing. Poor male fertilising efficiency requires increased female exposure to males, which has additional repercussions because males are often aggressive to females, which reduces female condition, health and overall fecundity. Even small improvements in the fertility of breeding stocks have vast financial consequences; e.g. a 1% variation in fertility in broiler flocks was estimated to be worth hundreds of millions of US$ in the US market. It is becoming increasing clear that in several organisms, the proteins contained in the male seminal fluid can have a drastic influence on fertility by modulating sperm swimming velocity, sperm storage within the female reproductive tract, probability of fertilisation and female behaviour after mating including female receptivity to further matings. The advent of proteomics and the publication of a draft genome of the chicken present a unique opportunity to investigate the role of seminal fluid proteins in poultry fertility. Our recent work has characterised the seminal fluid proteome of natural ejaculates of a population of red junglefowl (the species that has given rise to the domestic chicken) and has shown that the seminal fluid proteome of these birds is complex with more than 1500 seminal fluid proteins (SFPs) identified so far, including proteins involved in various known biological functions e.g. immune responses and antibacterial defences, as well as sperm maturation and sperm motility. Our work has shown that some of these SFPs are associated with in vitro measures of sperm quality. Importantly, our work has further shown that the seminal fluid proteome undergoes rapid and marked compositional changes in response to socio-sexual factors such as the sexual familiarity of a female partner and the social dominance of a male, and longer term changes, as males age, with males that are able to retain high sperm quality in advanced age having a distinct seminal fluid proteome. In this project, we capitalise on this wealth of preliminary knowledge to develop a research programme, to identify seminal fluid proteins (SFPs) that are important in maintaining lifelong fertility in male poultry. We use the red junglefowl as benchmark experimental system that has not been influenced by domestication and artificial selection, to characterise proteomic repertoires associated with rapid responses to socio-sexual conditions (objective 1) and reproductive ageing (obj. 2), and identify SFP signatures causally linked to fertility. We then confirm the role of seminal fluid in driving variation in fertility (obj. 3), and validate the commercial relevance and applicability of these findings by investigating patterns of intra- and inter-male variation in fertility-linked SFPs in commercial meat-production domestic chicken lines (broiler breeders, obj. 4). Collectively, these results will help us identify proteins linked to poultry fertility, which will inform new strategies to improve fertility in commercial stocks.

Marek's disease (MD) causes paralysis and tumours in chickens. It is caused by serotype 1 strains of the Marek's disease virus (MDV-1) which is shed from skin of infected chickens and persists for many months in dust in contaminated poultry houses. It is highly contagious and spreads to other chickens by inhalation. MD is a major disease affecting poultry health, welfare, and productivity, with annual estimated loss to the global poultry industry of $2 billion. MD is endemic in UK poultry but is effectively controlled by live vaccine viruses, which are harmless relatives of MDV-1, and include CVI988, HVT, and MDV serotype 2 (MDV-2). MDV-2 vaccines are widely used in the Americas and Asia but not in the UK. However, by testing samples collected from poultry farms, we found MDV-2 is widespread in the UK. MDV-2 strains circulate freely and naturally at high levels and persist long-term in the flock, but little is known about them; are they derived from vaccine strains which 'escaped' from imported poultry, or are they naturally occurring strains? Chickens can be infected with any combination of MDV-1, MDV-2, and vaccine viruses at the same time (co-infection). We have found MDV-2 in healthy chicken flocks, as well as flocks that have MD. We would like to know whether co-infection with MDV-2 affects flock health and disease, and production parameters such as egg production and mortality, and whether certain MDV-2 strains could be used as effective recombinant vaccines against MD and other poultry diseases. Our objectives are to: (1) Investigate prevalence of naturally occurring MDV-2 infection in the field, and it's influence on flock productivity, immune responses and disease, (2) Characterise MDV-2 field isolates and (3) Exploit novel MDV-2 as potential viral vectors for novel recombinant vaccines. The project is a partnership with poultry industry vets. We will select two MDV-2-positive and two MDV-2-negative flocks for two bird types (broiler-breeder, layer) for regular sampling to collect blood samples from chickens and dust from the housing sheds. We will also collect data on flock health and productivity. At Pirbright, we will test the samples by 'polymerase chain reaction' to detect the genetic material of MDV-1, MDV-2 and vaccine viruses to show the kinetics of MDV-2 infection and shedding, and the frequency of co-infection with MDV-1 field strains and vaccine viruses. Using mathematical modelling, we will also investigate dynamics of transmission of MDV-2 within flocks. We will determine variability of MDV-2 strains by sequencing the virus genetic material and comparing with known MDV-2 strains. We will study the characteristics of selected MDV-2 strains by growing these viruses in cell culture then using them to infect chickens under controlled laboratory conditions to examine replication, persistence, clinical signs and transmission of MDV-2. Most MDV-2 strains have characteristics which make them suitable as vaccines against MD: they do not cause disease, they grow well in the chicken and persist for many months, and they are easily transmitted between chickens to maintain a high level of exposure of the flock to vaccine virus. Furthermore, MDV-2 can be genetically engineered to carry genes from other important poultry viral pathogens, e.g., infectious bursal disease virus (IBDV) and Newcastle disease virus (NDV); a recombinant 'vectored vaccine' like this could potentially protect chickens against IBD and ND as well as MD in a single vaccination. We will engineer an appropriate MDV-2 strain to create a 'rMDV2-IBD-ND' virus, then test its ability to protect chickens against these three diseases under controlled laboratory conditions. This study is important to understand the effect of widespread MDV-2 infection on health and productivity of commercial poultry flocks. A new recombinant MDV-2 vaccine would be a useful addition to the set of live virus vaccines used to control MD and other poultry diseases.

Higher agricultural productivity and sustainability is critical to meeting the global challenges of food security in the presence of climate change. Legume crops are a critical source of plant-based proteins for people and animals. As the world demand for animal products increases, the demand for vegetable proteins as animal feedstocks also rises and the UK in common with other countries faces a shortfall in domestic vegetable protein production capability. In the EU 70% of the protein fed to animals is imported, mostly soyabean or soya meal with soya meal accounting for 33% of the protein in UK livestock feeds. In 2011-12 UK imports of soya products reached 1.83 million tonnes, the majority of this being transgenic soya imported from South America. Increasing the amount of UK grown protein to replace imported soya products is recognised as a major challenge for the UK animal feed sector. In this LINK proposal we will develop and apply new genetic approaches to enhance the nutritional value (protein and water soluble carbohydrate) of the pea (Pisum sativum L.) seed, to increase the use of pea as a high quality feed in animal diets, reducing the UK protein deficit from the import of soya products and also delivering environmental benefits to livestock production systems. The proposal builds on knowledge gained in BBSRC, EU, Defra, Innovate UK and levy board-funded research on the genetics and agronomy of pulses that have led to the development of novel lines of pea with higher protein content. We will use our expertise in plant genomics, pea genetics and breeding, agronomy, plant chemistry and animal nutrition to integrate the germplasm with improved grain composition into improved pea varieties. With industry partners from the poultry and pig sector as well as crop developers, we will analyse the impact of replacing soya with these new pea varieties in feed rations on the growth of monogastrics and poultry and the economic and environmental impact of their inclusion. Although the focus is on poultry and monogastrics, the project will provide information on the value of including these new pea lines for other sectors (ruminants and aquaculture).

It is estimated that environmental mitigation costs are in the region of $1 trillion per year of which ~$120 billion is provided largely by government and charitable foundations. Private investment is relatively small, providing a large untapped funding source that needs to be mobilised to help cover the massive shortfall. There are many impediments to private sector investment, including lack of appropriate and marketable financial instruments that can provide a satisfactory level of assurance regarding the outcome of environmental projects. The problem is exacerbated, in terms of biodiversity, due to the lack of financial value attributed to biodiversity and biodiversity assets. Current financial instruments that support the environment comprise mainly of green bonds. While the green bond market is expanding, these assets are not environmental performance related instead representing a commitment to simply fund more "straight forward" sustainable projects such as tree planting and renewable energy. As a result they have been linked to "green washing". FRIBO will identify with stakeholder partners (from the finance, land-use, wildlife, ecosystem service civil society and policy sectors) the opportunities and impediments to developing more fit-for-purpose performance related financial instruments that would be attractive to private investors while incentivising the delivery of real nature-based solutions (NBSs), with a focus on improved and measurable biodiversity outcomes. Examples of candidate instruments are Environmental Impact Bonds (EIBs); they link financial return to the success of the intervention by repaying the initial loan and interest using the financially valuable and marketable benefits of the project, such as carbon offsets, or cost reducing outcomes such as reduced flood damage, to pay off the full project costs. They are termed as "pay for performance" instruments. Sustainability Linked Bonds (SLBs) work in a similar way, but depend on meeting broader pre-defined sustainability goals such as reduction in GHG emissions to avoid penalty payments. FRIBO will analyse the linkages and drivers within the Finance-Biodiversity Nexus to assess opportunities and impediments to progress. Extensive stakeholder interaction, face to face, virtual and via surveys and questionnaires, will be conducted to identify key areas of research needed and critique optimum strategies for developing and incentivising the instruments. Challenges that will need to be taken into account are: how to measure and financially value biodiversity and biodiversity outcomes and NBSs in a market context (FRIBO will exploit links with existing NERC projects in this area), defining an improved biodiversity outcome; developing suitable biodiversity metrics; the role and function of Environmental Impact Assessments, the role and function of biodiversity in NBSs; the evaluation and quantification of wider societal benefits; identifying how to obtain additional payments for the wider biodiversity benefits that are realised in NBSs; the immaturity of EIBs and NBSs requires that their marketability within the financial sector requires study. Finally, there may be unintended consequences such as divesting/offshoring of environmental damage, non-equivalence of some "offsets" such as the carbon and biodiversity value of new tree plantations to offset deforestation of old growth forests;. Comprising a core group of researchers from Queen's University Belfast and Newcastle University, with a range of national and international partners, FRIBO will produce a Strategic Research Agenda that will identify the research required to address these challenges and accelerate investment in biodiversity related NBSs. In addition, FRIBO will produce an Implementation Roadmap that will outline key activities and timelines that need to be undertaken in order for stakeholders to implement Biodiversity focused "Rewards for performance" investment schemes.

Campylobacter spp. are extremely important food borne enteropathogenic bacteria, estimated to cause over 600,000 cases of infection in the UK each year with around 100 deaths. It is estimated that Campylobacter infections cost the UK economy around £1 billion per year. Infection is characterised by acute and sometimes bloody diarrhoea, particularly in children. The last few years have seen a marked rise in cases in compromised elderly populations and in such people, particularly those with bowel cancer, infection can be fatal. Chicken meat is the most important source and vehicle for human Campylobacter infections and around 80% of chickens on sale in the UK are Campylobacter-positive. Campylobacter are natural inhabitants of the intestinal tract of chickens and other food animals. Contamination of chicken meat takes two forms. Carcass surfaces can carry high levels of Campylobacter and this can lead to cross-contamination in both domestic and commercial catering. This is an important risk factor for infection. However, and perhaps more importantly, Campylobacter have been recovered from deep muscle tissues of up to 27% of chickens tested. Furthermore, liver tissues are also commonly contaminated. In these tissues the bacteria will be better protected from the effects of cooking. Undercooked chicken meat and chicken liver pate are internationally important vehicles of Campylobacter infection. To improve public health in the UK it is essential that the number of contaminated chickens on sale is reduced. The proposed research will examine the different systems in which UK chickens are grown to identify cost-effective farm-based control options. Our work will focus on chickens reared intensively in housed systems as these comprise ~90% of the UK market. The work will be in collaboration with the three biggest poultry producers in the UK and all the major UK food retailers are giving financial support. The proposed research builds on past studies which showed that chickens (broilers) reared under higher welfare systems are less likely to have Campylobacter than birds reared more intensively. The higher welfare systems generally use slower-growing birds and stock houses with fewer birds than the more intensive systems. Our work showed that birds reared in the more intensive system had poorer welfare, as shown by high rates of endemic disease and general health and leg problems. This might explain why these birds were more likely to be Campylobacter-positive, as birds compromised by poor health and/or welfare are more susceptible to these bacteria. These differences might be due to the birds used and/or the in-house environment and we will determine this. Our field work might also indicate that the slower-growing bird types may be inherently more Campylobacter-resistant. We will conduct longitudinal studies on flocks reared under different systems and determine when birds first become Campylobacter-positive and relate this to changes in bird health and welfare. We will also determine whether the spread of Campylobacter from the intestine of the birds to edible tissues like liver occurs on farm and if it is linked to poor welfare for endemic disease. Our aim is to provide the UK poultry industry with science-based and cost-effective control options, which will help it meet customer demands and comply with forth-coming EU legislation aimed at reducing the number of chickens that are Campylobacter-positive.