The small ruminant lentiviruses (SRLVs) cause the disease known as Maedi Visna (MV) in sheep. This is an insidious respiratory disease of sheep with severe economic impacts. It is difficult to detect and control due to a very long latent period between infection and testing positive. Farms often do not realise their animals are affected until over 50% of the flock is infected with a large number of animals thin and dying. There are no treatment or vaccination options and control is dependent on testing and culling affected animals over repeated rounds. The cost of control is prohibitive, and this disease makes heavily infected operations economically unviable. The disease has been highlighted by the Agriculture and Horticulture Development board (AHDB) as an "iceberg" disease where awareness of disease is low in farmers, hiding the scale and impact on production losses. To make matters worse the incidence of MV is increasing rapidly in the UK flock with prevalence rising from 1.4 % in 1995 to 9.4% in 2019. Northern Ireland has also experienced a breakdown in its previously MV-free status in 2022 and may not be able to regain it due to the number of flocks and length of time it has gone undetected. There is a critical need for viable options for protecting commercial flocks from this devastating disease. Breed differences in susceptibility to MV have long been recognised. Recent advances in small ruminant genetics and genomics have enabled the genetic loci responsible for these differences to be described. There is very strong genetic and epidemiological evidence for the glutamic acid to lysine mutation at amino acid 35 of the TMEM154 (transmembrane protein 154) providing resistance to both infection with and progression of MV. However, there are a number of fundamental things we need to know about the gene and the mutation before we could recommend a genetic selection programme using this marker. We do not know what this gene actually does in sheep (or any animal), how widespread in UK sheep breeds the resistant allele is, whether there are deleterious effects to the resistance mutation and whether the effectiveness of the MV resistance is dependent on the infecting strain of the virus. This research programme seeks to answer those questions to enable us to be sure we are recommending a safe and effective control option for reducing the impact of MV on UK sheep farms. The option of genetic selection for disease resistance is a popular one with sheep breeders, particularly as the scrapie elimination programme was very successful giving them a positive experience of genetic selection for disease resistance. The marker concerned is on the current SNP chip array used widely for sheep genetic selection and this programme will help drive uptake of the use of genetic markers in commercial sheep breeding.

Wheat rusts are a major threat to cereal production worldwide. As is common among rust pathogens, the wheat rusts require two hosts to complete their life cycles; stem and yellow rust undertake asexual reproduction on wheat and complete sexual reproduction on barberry (Berberis), where recombination can lead to emergence of novel genotypes. The eradication of barberry in the UK drove stem rust to almost complete extinction. However, over the past decade, barberry planting has been reinitiated and is advancing at speed in many major wheat growing regions. In the UK, this is largely driven by the habitat conservation programme for the endangered barberry carpet moth, Pareulype berberata. This is worrying because in the same time period we have seen an increasing number of sporadic stem rust epidemics in Europe, including severe outbreaks as far apart as Sweden and Sicily. Here in the UK in our preliminary study, we identified one wheat plant infected by stem rust in 2013 which illustrates the potential for stem rust to infect wheat crops in the UK. Furthermore, in 2017 we recorded for the first time in decades stem rust aecia on barberry in the UK. In parallel our collaborators in Sweden in the same year identified the first sexual population of wheat stem rust derived from barberry. The overall aim of this project is to characterize the composition of rust on Berberis to determine if this mass re-planting could be facilitating the future re-emergence of stem rust in the UK, whilst also enhancing wheat yellow rust diversity. This will provide vital information for the future design and deployment of surveillance and management strategies that fully consider the threat of Berberis. However, it must also carefully balance the desire to minimise the risk of intensifying wheat rust diversity with (where possible) protecting habitat for the barberry carpet moth. The proposed research aims to: (1) define the composition of rust on Berberis in the UK, (2), determine the risk of barberry-derived sexual rust populations to UK wheat and barley production, and (3) develop a UK risk model for wheat rust dispersal from Berberis and associated management actions. This research project will provide a wealth of information regarding the role of the sexual cycle in exacerbating the diversity of cereal rusts. Furthermore, it will provide vital information that will directly inform policy regarding the re-planting programme for Berberis across the UK and identify areas of high risk that should be avoided or (if plants are already present) regularly monitored. Herein, we aim to achieve a careful balance that manages the immediate needs of the farming community, ensures future resilience in UK wheat by accessing the susceptibility of breeding material to wheat stem rust, whilst conserving the biodiversity of UK fauna.

Doctoral Training Partnerships: a range of postgraduate training is funded by the Research Councils. For information on current funding routes, see the common terminology at https://www.ukri.org/apply-for-funding/how-we-fund-studentships/. Training grants may be to one organisation or to a consortia of research organisations. This portal will show the lead organisation only.

Doctoral Training Partnerships: a range of postgraduate training is funded by the Research Councils. For information on current funding routes, see the common terminology at https://www.ukri.org/apply-for-funding/how-we-fund-studentships/. Training grants may be to one organisation or to a consortia of research organisations. This portal will show the lead organisation only.

In the advanced agricultural production systems of Northern Europe, weed control in cereal crops has become one of the greatest challenges to sustainable intensification, accounting for higher yield losses and greater input costs than all other biological constraints (pests and diseases). The most problematic weeds in cereals in Northern Europe are the wild grasses, notably black-grass (Alopecurus myosuroides), which has become steadily more difficult to control over the last 30 years due to the evolution of herbicide resistance. This resistance assumes two forms: 1) Target site resistance (TSR), whereby the weeds become highly tolerant of herbicides due to mutations in the proteins targeted by these chemicals rendering them less sensitive to inhibition by that herbicide mode of action. 2) Metabolic or multiple herbicide resistance (MHR) where weeds become more tolerant of a broad range of herbicides, irrespective of their chemistry or mode of action, due to a general enhancement in the ability to detoxify crop protection agents. While TSR is now quite well understood and can be countered by the rotational use of herbicides with differing modes of action, the molecular basis and evolutionary drivers which promote MHR are poorly understood and the associated grass weeds very difficult to control using conventional methods. In this 4 year project, we propose to use a combination of molecular biology and biochemistry, ecology and evolution, modeling and integrated pest management to develop better tools to monitor and manage both TSR and MHR in black-grass under field conditions. The project represents a novel agri-systems approach, linking our latest understanding in the molecular biology of herbicide resistance to on farm monitoring and modeling based on a quantitative genetics approach to define the effectiveness of different intervention measures. Through a multidisciplinary consortium, we will integrate knowledge about MHR and TSR at the molecular and biochemical levels and relate this fundamental understanding to resistance phenotypes observed in the field. Selection and breeding experiments will examine the dynamics of selection for resistance, with the intention of determining the genetic architecture of MHR for the first time and its relation to other stresses and life history traits. Data from field monitoring and glasshouse studies will be integrated in ecological, evolutionary and management models with the ultimate aim to design novel management to prevent, delay or mitigate the evolution of herbicide resistance. Finally, the environmental and economic impacts of novel management will be explored. The project therefore has the primary goal of using state of the art approaches spanning molecular biology, weed science, modeling and agronomy to provide new resistance control measures within the life of the programme. The project is divided into 5 integrated work packages which will address the following questions 1. What are the molecular mechanisms that underpin the evolution of metabolic herbicide resistance? 2. What is the extent of the herbicide resistance problem in UK black-grass populations and what impacts is resistance having on black-grass populations and crop yields? 3. What are the genetic, ecological and agronomic factors that promote and constrain the emergence of herbicide resistance? 4. How can applied evolutionary models be used to manage herbicide resistance? 5. What are the economic and environmental consequences of novel weed and resistance management strategies? The major outputs will be: 1. A rapid diagnostic toolkit for the on-farm characterisation of herbicide resistance. 2. A resistance audit for the extent and distribution of resistance to the major herbicide modes of action in black-grass. 3. A suite of models to address key questions in the emergence and management of resistance. 4. Management recommendations, together with an analysis of their impacts.