Seeds are the start and end point for the vast majority of human agriculture. The annual global seed trade is currently valued at over £34 billion, and the production and sale of high quality seeds which germinate uniformly and rapidly underpin this industry. Seeds experience a range of stresses in the field prior to crop establishment. These include low water stress and mechanical impedance from compact soils. Seed vigour refers to the ability of seed to germinate and establish seedlings across a wide range of environmental conditions, and defines the success of crop establishment in the field. This is a key determinant of yield as the absence of a plant leads to no end product to harvest. Improving this trait in crops is a primary goal of the agricultural industry, however the underlying mechanisms of vigour remain poorly understood. The growth of plant cells is a mechanical process driven by internal turgor pressure pushing against the surrounding cell wall. Cells get bigger when the surrounding cell wall is weakened and yields in response to internal turgor. Genes which encode proteins that are secreted to the cell wall and modify its structural composition and strength have been identified. Once such protein is named expansin, and acts to loosen cell wall structures, permitting cell growth. The seed to seedling transition is driven exclusively through cell expansion in the absence of cell divisions. The ability to generate of mechanical force sufficient to counteract external stresses defines the ability of a seedling to establish across a wide range of environmental conditions, and hence be vigorous. Increasing the expression of expansin enables seedling establishment under stress conditions which normally limit this process. Seed vigour may therefore be considered a mechanically driven agronomic trait and the control of expansin expression a target. This project takes an interdisciplinary approach to uncover the genetic factors and mechanical basis of the seed to seedling transition, and seed vigour. We previously identified proteins which represent high confidence candidate regulators of expansin gene expression. Increasing expansin gene expression can increase seed vigour making these genetic targets to enhance seed vigour. These genes will be explored in the model plant system Arabidopsis. These findings will be extended to enhance seed vigour in the crop species Brassica oleracea. Mutations within newly characterized vigour genes will be identified in different Brassica plants. Together with industrial partner Syngenta, the vigour of these new Brassica seeds will be characterized. This will lead to the identification of varieties which can be used directly in breeding programs to enhance seedling establishment, field crop performance and yield. We have previously shown that the size, shape and arrangement of cells can influence the early stages of seed germination in response to growth-promoting gene expression, such as expansin. This observation highlighted the presence of mechanical constraints on plant growth. How these constraints affect the growth of seedlings however remains unknown. Understanding the mechanical basis of the seed to seedling transition is of central importance to understanding the establishment of crops in the field and seed vigour. Using a combination of 3D image analysis and mechanical modelling, the relationship between growth promoting gene expression and seedling growth will be established. In this way the mechanical basis of seedling establishment and seed vigour will be uncovered. Enhancing Brassica seed vigour will increase both crop yields and food security during this period of rapid climate change. The findings in this project may in turn may in turn be extended to other crop species.

Food security is critical to the effective functioning of human society and plant protection products (PPPs) such as herbicides, insecticides and fungicides, play a vital role supporting this endeavour by maintaining crop yields through the reduction of pests. However, there is always a risk that by releasing chemicals inherently designed to be toxic to some target pest or disease, that unacceptable effects on the wider environment may also result. As such, environmental risk assessment (ERA) plays an essential role in the regulation of PPPs in the UK and European Union as well as globally. Current ERA methods require a comparison of predicted exposure following the use of a product to a known effect concentration of that product. Exposure has been predicted using mechanistic fate models for two decades, whilst determining effects endpoints (e.g. LD50, the concentration of a product that results in mortality of 50% of organisms) has consistently required animal testing under simplistic exposure regimes. The problem with this approach is that exposure is dynamic and simple assumptions of constant exposure in the laboratory tests are therefore not realistic. Furthermore, the effects of a product are identified on an individual organism (e.g. the effect on the number of eggs an organism lays), however, we are often more interested in what the effects on a whole population are and protecting a certain level of ecosystem functioning that maintains all the services humans enjoy from their environment (e.g. food security in agriculture, wildlife ecotourism). As such, this project looks to explore the link between individuals and populations using ecological models to address issues with the current risk assessment methodology and unnecessary / excessive animal testing. Two groups of species will be studied: bats and mayflies. Our current understanding of the risk to bats is lacking, as it is not known whether they are active when agricultural products are being applied, nor how they may come into contact with chemical residue after application (e.g. though foraging and drinking). Field surveys will be performed to assess the presence / absence of bats in agricultural landscapes throughout the growing season and to observe the links between chemical exposure (direct spraying and residues) and food items within these landscapes. Ecological models will then be used to explore how exposure on individual bats leads to changes in bat populations. Mayflies meanwhile are indicators of good water health as they are sensitive to changes in the environment and also to exposure to many chemicals. However, they are difficult to culture in the laboratory and provide variable results in experimental tests on chemical effects. In this project we will establish a laboratory culture of mayflies by exploring environmental cues that induce synchronised swarming. Once established, experimental studies will be performed to investigate how changes in the environment result in changes in growth, reproduction and survival. The results will be used to parameterise an ecological model that can then explore the effects of chemicals on populations of mayflies. The species selected for this project are of significant interest with regards to environmental health and knowledge of population-level responses to chemical exposure will allow appropriate mitigation of risk to be considered in the registering of plant protection in the future, all whilst further reducing animal testing.

The evolution of insect resistance to insecticides represents a growing threat to the sustainable control of many important insect crop pests and disease vectors, threatening global food security and human health. To effectively combat resistance, it is critically important to understand its underlying genomic architecture, including the genetic variants underpinning resistance and their affect on phenotype. Advances in genome sequencing technology over the last two decades have greatly facilitated investigation of the genetic basis of insecticide resistance. However, key knowledge gaps remain on the type and number of genetic variants affecting resistance and their relative contribution to phenotype. Many of these deficits in understanding relate to the current paradigm of using a single reference genome as the starting point for most genomic analyses. This approach means that certain types of genetic variation not present in the reference typically remain undiscovered. This problem is particularly acute for structural variation (SV) encompassing presence-absence variation (PAV), copy number variation (CNV) and chromosomal rearrangements, which, as a consequence, have been referred to as the 'dark matter' of the genome. The failure to effectively characterise SV is important, as in humans SVs have been shown to affect more of the genome per nucleotide change than any other class of sequence variant. Furthermore, research by ourselves and others has provided clear evidence that SV can be a key source of genetic variation in the evolution of insecticide resistance. The overarching objective of this project is to develop a new paradigm for the genomic analysis of adaptive traits such as insecticide resistance in pest insects. We will leverage recent advances in sequencing technology, in combination with an exceptional biological resource comprising a living library of globally sampled clones of the damaging aphid crop pest Myzus persicae, to assemble the pangenome, the collection of all the DNA sequences that occur in a species, of this pest. This unprecedented resource will allow us to characterise the complete spectrum of genetic variation in a global crop pest species for the first time, and address multiple key knowledge gaps on the insect pangenome and the role of SV in adaptive evolution. These include understanding the percentage of the pangenome that is structurally variant in pest populations and how this differs across different SV types, how often and how many SVs lead to changes in gene function or expression, and crucially, their overall relevance and contribution to key phenotypic traits such as insecticide resistance. Our analyses will focus on three types of SV that have been frequently implicated in insecticide resistance, comprising CNV, PAV and chromosomal rearrangements. We will then test for association between the full spectrum of genetic variation identified in our aphid clone library and insecticide resistance. Finally, we will examine the impact of different types of SVs on gene expression and gene function, and validate the role of a selection of candidate SVs in resistance using functional approaches. Together, these analyses will allow us to fundamentally and systematically interrogate the genetic determinants of insecticide resistance in a way that has never been previously possible. The knowledge and tools generated in this project will provide both fundamental advances in our understanding of the genetic variation that provides the substrate for natural selection in insects, and powerful resources to develop strategies for the sustainable control of highly damaging, globally distributed crop pests.

The virus called turnip mosaic virus (TuMV) is an important pathogen infecting many crop plant types, reducing yields and making them unmarketable. In order to reproduce, the virus has to use certain proteins in plants. Without these proteins it cannot reproduce. One such plant protein is called the eukaryotic initiation factor iso4E [eIF(iso)4E]. We have shown that in Chinese cabbage (Brassica rapa sub-species pekinensis) which has three copies of eIF(iso)4E, if one of the copies is missing, the virus cannot reproduce, but the plant is unaffected. Chinese cabbage varieties with this resistance (that was identified and characterised at the University of Warwick) are currently being developed by an international seed company (Syngenta). Chinese cabbage is the most important vegetable brassica crop worldwide. We have been unable to identify any resistance to TuMV in the related and important plant species Brassica oleracea, which includes broccoli, cabbage, cauliflower, kale, Brussels sprouts etc. In collaboration between the Elizabeth Creak Horticultural Technology Centre and the Plant Virology Group at the University of Warwick, NIAB and the commercial plant breeding company Syngenta, we aim to knock out the copy of eIF(iso)4E that TuMV needs in order to reproduce in B. oleracea utilising gene editing technology, thereby establishing a technique to rapidly develop virus-resistant varieties of the different B. oleracea types. In collaboration with the commercial seed company Syngenta, we also aim to move the copy of eIF(iso)4E that the virus cannot use from Chinese cabbage into B. oleracea by conventional crossing, in order to develop virus-resistant plants by this alternative route.

Wireworms are major pests of cereal crops and root vegetables in Europe and also in North America. Seed treatments and other contact insecticides are used to protect crops from larval feeding damage. However, current chemical options are being withdrawn in Europe and it is very questionable when and if at all a new soil insecticide could be registered for wireworm management. Semiochemicals (naturally occurring development- and behaviour-modifying chemicals, such as different volatiles) are not harmful to the environment at the level they are required and can provide a "green" alternative for soil pest management. Similar to aboveground insects, soil-dwelling arthropods are also attracted to or repelled by root volatiles that occur in the gas phase and diffuse in soil pores. Whereas carbon dioxide is a universal attractant, root-emitted volatiles are more specific, mid-range signals that help soil pests to track and find their host plant. We have identified from crop roots and created synthetic volatile blends that attract wireworms in laboratory behavioural studies. We now aim to test if they retain their attractive properties in more realistic setups, i.e. crop fields. The main aim of this project is to thus carry out field trials with these synthetic blends (lures) to check if they are able to attract large numbers of wireworms into traps, containing germinating seeds, that we will build during the project. Such traps with and without the lures will be sunk in the soil in agricultural fields and checked regularly for captured wireworms. On the one hand, we want to see if traps with lures catch more wireworms then those without lures, which will indicate that they are suitable for precise pest monitoring before seed sowing. On the other hand, we will test lured traps to see if they can catch enough wireworms to reduce crop damage, and we will compare their performance with pesticide treatments. This will tell us if traps with lures can replace pesticides and provide growers with an alternative wireworm management tool. The proposed study is an important step in the development of monitoring and attract-and-kill strategies for wireworm management, which could also be extended to the management of other soil-dwelling pests.