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The Bioscience behind: References BBSRC invests around £78m a year in plant and crop science research at universities and institutes across the UK. Through partnerships with the EU and other international partners, it also supports research that is helping to improve crop yields in developing countries across the world. John Innes Centre Rothamsted Research www.jic.ac.uk www.rothamsted.ac.uk www.bbsrc.ac.uk Professor Caroline Dean, John Innes Centre with University of South California Mikhail Semenov and colleagues, Rothamsted Research Rothamsted Research Professor John Snape, John Innes Centre, with colleagues at the University of Nottingham Professor Keith Edwards, University of Bristol, and Professor Peter Shewry at Rothamsted Research Dr John Foulkes and colleagues, University of Nottingham with John Innes Centre and Rothamsted Research Dr Dave Laurie, John Innes Centre Professor Graham Moore, John Innes Centre Professor Michael Holdsworth and Dr John Foulkes, University of Nottingham with Professor John Snape, John Innes Centre Dr Dimah Habash and Dr Martin Parry, Rothamsted Research Dr Mikhail Semenov and colleagues, Rothamsted Research with Crop and Food Research, New Zealand Professor Peter Horton, University of Sheffield Dr Adam Price, University of Aberdeen, with Dr Richard Whalley and colleagues, Rothamsted Research Professor Wayne Powell, Institute of Biological, Environmental and Rural Sciences with NIAB and IRRI, Phillipines Dr Ratan Yadav, Institute of Biological, Environmental with colleagues in Rural Sciences, ICRISAT, India and University of Cape Coast, Ghana Professor Andrew Meharg, University of Aberdeen, with Dr Fangjie Zhao and colleagues, Rothamsted Research Professor William Davies, Lancaster University Dr Nash Nashaat, Rothamsted Research Dr Graham King and colleagues, Rothamsted Research Professor Keith Lindsey, University of Durham with Warwick HRI Richard Hayes and colleagues, Institute of Biological, Environmental and Rural Sciences Dr Eric Ober, Broom’s Barn Professor Chris Gilligan, University of Cambridge Professor Brian Kerry, Rothamsted Research Dr Richard Gutteridge and colleagues, Rothamsted Research Frank Van Den Bosch, Rothamsted Research and Professor Chris Gilligan, University of Cambridge Professor Chris Gilligan, University of Cambridge Professor Bruce Fitt and colleagues, Rothamsted Research Dr Ratan Yadav, Institute of Biological, Environmental and Rural Sciences with John Innes Centre Dr Nash Nashaat, Rothamsted Research Professor John Turner, University of East Anglia Professor Jim Beynon, Warwick HRI Professor Matthew Dickinson, University of Nottingham Dr Paul Hand, Warwick HRI with CSL, CABI and KARI, Kenya Professor Lin Field and colleagues, Rothamsted Research Dr Graham Moores, Rothamsted Research, New South Wales Agriculture, Endura SpA, Italy Dr Kim Hammond-Kosack and colleagues, Rothamsted Research Professor David Rice, University of Sheffield Professor John Pickett, Rothamsted Research secure harvests T he world’s population is growing inexorably and harvests worldwide are threatened by climate change. Grain stores must be sufficient to protect against price volatility and speculation – particularly in poor, developing countries. Within a lifetime, regions near the equator could face agricultural losses of up to over a third. BBSRC January 2009 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15. 16. 17. 18. 19. 20. 21. 22. 23. 24. 25. 26. 27. 28. 29. 30. 31. 32. 33. 34. 35. 36. 37. 38. 39. Crop productivity increased dramatically throughout the 20th Century, but further increases are not automatic. The scientific challenges in ensuring adequate food supplies are considerable. We need to focus on where production gains are most readily and sustainably achievable. This means identifying and selecting crop traits and production systems that can increase yields in particular soils and climatic conditions, and reducing losses to pests and diseases. To do this requires knowledge of how plants grow and of the factors that limit productivity, as well as knowledge of how they interact with other organisms and environmental factors. The following examples illustrate some of the ways that scientific research supported by the BBSRC and other funders including Defra, DFID, EU and BBRO are meeting these challenges. Global food security depends ultimately on growing enough crops. Economic, political and social factors are important, but sufficiency and sustainability of harvests are the primary needs. Harnessing natural diversity Plant science research reveals how plants function. It explains, for example, why leaves and plants are the shape they are, why plants flower when they do, and why some are better than others at converting energy into seeds or growing in poor soils. It also reveals how plants respond to stresses such as drought (or flooding) and attack by pests and diseases. These are important characteristics in crop breeding and agronomy, and the underlying mechanisms can be harnessed to improve crops. P lants vary greatly in shape and size, and grow across the world under vastly different climatic and soil conditions. But at a fundamental level they are remarkably similar. As a result, adaptations, which have evolved over many thousands of years to enable plants to tolerate particular stresses or combat pests and diseases, also exist in relatives of our crop species and can be incorporated into modern varieties. Information gained from one species, including the small weed Arabidopsis (the ‘laboratory mouse’ of plant science) is often directly applicable to complex crops such as oilseed rape, wheat, rice and maize. Manipulating plants for food stretches back over thousands of years. The weedy wild relatives of some crops are virtually unrecognisable from today’s high yielding varieties. Familiar crops such as broccoli, Brussels sprouts and cabbage have all arisen by selection and breeding from a common ancestral gene pool. Flowering time Plant breeders are able to alter traits such as height and shape; the rate of growth and the time of flowering; as well as sensitivity to pests and disease. But plant genetics is often complex; involving the concerted action of many different genes, which are influenced by seasonal and environmental factors. Many plants survive winter by suppressing flowering until temperatures rise. They need a spell of cold weather to trigger flowering. But the amount of cold needed for different plants depends on the conditions in which they live. Changes to the length or severity of winters threaten this delicate balance; and increase the risk of crops failing to flower or flowering too early. Long term sustainability is an increasingly important factor. High yields have to be achieved predictably year after year in ways that sustain soil fertility for future crops, keeping the agricultural ecosystem working, without harming the environment. The FLC gene plays a key role in delaying flowering over winter. Subtly different forms of the gene exist in ‘varieties’ of Arabidopsis from the Arctic Circle to near the Equator, determining how the plants control flowering as winter progresses. In UK ‘varieties’, for example, a four-week cold snap is enough to switch off FLC and trigger flowering, but in Swedish ‘varieties’ 14 weeks are needed. Using variants of corresponding FLC genes in crops could help breeders to time flowering in line with changing weather patterns.[1] Arabidopsis Genome analysis of this small weed provides a guide to the role of corresponding genes in major crops. Increasing crop yields Crop yield is determined by a complex mix of genetic and environmental factors. Ultimately, it depends on how much energy the plant captures from sunlight and how efficiently this is converted into a harvestable product (e.g. grain or leaf). Wheat: W heat is genetically complex, making it difficult for breeders to identify and select combinations of genes to improve performance. The bread-making species Triticum aestivum, for example, has three sets of chromosomes. Nonetheless, researchers are mapping the wheat genome, and have found combinations of genes that have general effects on wheat yield and some with very specific effects. These include some that influence a plant’s reserves of stem soluble carbohydrate. The higher the reserves the higher the yield can be.[4] O ptimising crop yield involves trade-offs. The height of a plant and the size, shape and angle of its leaves affect how much sunlight it can capture. A big leaf canopy at the top of a tall plant captures this energy very efficiently and blocks the light from reaching the base, so stopping weeds from growing there. A fastgrowing canopy also stops early-season rain from penetrating the crop and so reduces the risk of fungal spores splashing up from the ground. And rapid stem growth in tall crops quickly moves the upper leaves away from lower ones that can harbour these spores. By identifying the linkage between genes for easily observed ‘marker’ traits and those that affect crop performance, scientists have compiled libraries of DNA sequences of wheat and other crops that are used in the crop improvement programmes of major international breeding companies. This approach is helping to identify markers for processing traits such as flour quality. A new pan-European analysis of the composition of grain from over 150 cereal varieties provides the first clues about how they rank in terms of the beneficial compounds they contain, enabling breeders to combine high yield with good milling qualities and health benefits.[5] But all these benefits of tall, fast growing crops must be weighed against the cost of less productive lower leaves, the greater risk that plants will fall over in wet and windy conditions, and the fact that they put proportionately less of their energy into grain than shorter plants. Scientists at Rothamsted Research (RRes) have developed computer models that show the complex interactions of factors such as weather, cropping, sprays, fertilisers and machinery on yield and environmental impact. These help farmers to optimise systems, for example by making the best possible use of nutrients in the soil, whilst retaining soil fertility for future crops.[2] Hereward, a modern short-strawed wheat variety (foreground) and an old variety, Squrehead’s Master. The former has smaller, more erect upper leaves that let light pass lower down, so increasing yield from lower leaves but allowing more weed growth.[3] Yields of UK winter wheat are currently limited by the number of grains in the ‘ear’. However, yield can be increased in plants that (a) grow faster before flowering and then produce more grains, and (b) have higher reserves of stem soluble carbohydrate from which to fill the grains. Researchers at Nottingham, in collaboration with the International Maize and Wheat Improvement Center (CIMMYT), have developed lines of wheat by crossing a ‘large ear’ wheat, developed at CIMMYT in Mexico, and a UK elite wheat, with the aim of incorporating ‘longer ears’ into UK adapted varieties. The lines have two to three more spikelets than conventional wheat. The team is working with a plant breeding company to understand the physiology and genetics of the large-ear variety, and to increase grain production in elite varieties. Predictable and stable quality of harvested materials is very important commercially. In collaboration with wheat breeders, the HGCA and downstream industries, researchers at the John Innes Centre (JIC), the University of Nottingham, RRes and Harper Adams University College, are investigating the factors controlling Hagberg Falling Number (HFN), a key determinant of wheat grain quality. The findings will help in identifying ‘smart screens’ that breeders can use to improve HFN, as well as identifying key combinations of genes.[6] In traditional cool, wet UK summers, lateflowering crops have an advantage because they fully utilise the long growing period. But to cope with much hotter and drier summers, we will need wheat varieties like those of Southern Europe that flower and amass yield earlier, but which are otherwise suited to UK conditions and markets. A gene in barley could hold the answer. It controls the plant’s response to the length of daylight. Different varieties of wheat and barley have slightly different forms of the gene and flower at different times. Understanding this natural variation will help breeders to optimise flowering time to UK climate.[7] Rice and other tropical crops Increasing crop yields Getting novel traits into wheat P lants need sunlight but they also need to be able to dissipate potentially damaging levels of energy if they are to resist enviromental stress. This is a particular problem in parts of South America, Africa and Asia. By studying how some variants of Arabidopsis can survive under conditions of excess light intensity, scientists discovered that changes in xanthophyll pigments bound to the lightharvesting complexes found in plant cells increases the extent of stress tolerence. Some of wheat’s wild relatives have potentially useful traits such as drought-tolerance and diseaseresistance. But these cannot be bred into commercial varieties because of a mechanism in wheat that prevents its chromosomes from swapping genes, except with other wheat plants. With EU-funding and BBSRC-DfID support respectively, these researchers have collaborated with local research institutions to explore whether genes for similar protective mechanisms can be used to improve productivity of bean crops in South Africa, and rice in the Philippines.[12] Scientists at the JIC have found that a gene called Ph1 senses when parental wheat chromosomes match and allows them to cross. They are identifying ways to block Ph1 temporarily so that breeders can cross wheat varieties with wild relatives to obtain hybrids with new traits. Once a useful gene is incorporated, Ph1 would be switched on again, fixing the new gene in subsequent generations of the crop.[8] A round 30% of the two million hectares of winter wheat produced annually in the UK is grown on droughtprone soils. But research suggests that, by 2050, heat-stress may be a much bigger problem than drought. For early-flowering wheat varieties, such as Avalon, higher temperatures would bring forward maturation and wetter winters would provide the water they need. But later flowering varieties would be adversely affected. Crop trials by scientists at the JIC and the University of Nottingham show that a long-lasting green flagleaf area is by far the most important determinant of high yield in winter wheat during the late season drought. These researchers have identified, and located on wheat chromosomes, genes that could offer new sources of drought-tolerance for breeders.[9] Around the Mediterranean basin the situation is very different, with water shortages severely reducing wheat yields. As part of a European project coordinated by RRes scientists, the search is on for combinations of genes that control how pasta-making varieties sense and respond to drought, and which traits are needed for stable high yield. This involves correlating data about gene activity under different conditions with physiological changes in crop performance.[10] Having the most appropriate crop varieties is only the start. Growers need to know how to manage crops in terms of sowing and harvesting times, soil conditions, and fertiliser and pesticide interventions. Predictive computer models that assess the likely impact of climate change on grain yield, yield variability and geographical distribution are helping farmers to optimise land use in a changing climate.[11] Climate change poses a risk to rice production, the staple crop for over two billion people. At the University of Aberdeen, researchers are identifying the basis of how varieties of rice differ in drought-tolerance. Marker assisted selection is also being used to develop drought-tolerant varieties. In particular, and with scientists at Rothamsted Research, work is underway to identify genetic markers that reflect the ability of rice varieties to penetrate hard soils – a key feature of drought tolerance.[13] Irrigation Irrigation waters accumulate salts that can damage plants. We need to know more about the mechanisms by which plants protect themselves, as a step to developing more resistant crops. Using Arabidopsis as a model species, research at the University of Glasgow shows that some protease enzymes are critical in protecting plants, and that varieties with high levels of proteases are much more tolerant of high salt levels. Arsenic contamination of groundwater is a problem in some irrigated rice fields in South East Asia. The search is on to improve local varieties of rice by breeding-in genes from varieties that export only low levels of inorganic arsenic to protect human health.[16] A BBSRC-DfID funded project is using new techniques to identify rice genes that confer tolerance to extremes of climate and attack by disease, with a view to developing new rice varieties for Africa and Asia.[14] A partnership between scientists in Wales, India and Ghana is exploring the genetic make-up needed to increase the drought tolerance of pearl millet (below), a crop that provides food security to around 500 million people in Africa and Asia.[15] Increasing crop yields Increasing crop yields UK grasses Cotton When plants are at risk of drying-out their roots send signals to the leaves to close leaf pores and conserve water. Research at Lancaster University shows that Partial Root Drying (PRD), in which alternately some roots are watered and others are not, slows leaf growth but enables plants to maintain themselves on low levels of water. An EC-funded study in Turkey showed that cotton plants grown with PRD used half the water and could be harvested three weeks earlier than those irrigated conventionally.[17] Oilseeds Y ield is not the only factor in determining grass quality as a forage crop. Levels of water-soluble carbohydrate play a crucial role in improving digestibility and the quality of silage made from grass, as well as in improving the efficiency of nitrogen-use and reducing pollution from excreted nitrogen. Working with British Seed Houses (part of Germinal Holdings Ltd), and with support from BBSRC and Defra, researchers have developed a perennial ryegrass variety, AberMagic (above), that combines several key attributes including: high digestibility, high dry matter yield and good persistency, high quality silage and good nitrogenuse efficiency.[21] I ndia is the world’s largest grower of oilseeds, but at yields below half of those obtained in developed countries. The main problems are drought, poor soils, low inputs and losses to pests and diseases. Collaborative research between RRes and Indian scientists has led to the development of droughttolerant breeding lines of rapeseed-mustard, and has shown that varieties can be bred successfully for use on rice-fallow land, which otherwise would be left uncultivated.[18] New research between RRes and the University of Delhi, Pant University of Agriculture and Technology and Krishida Seeds Ltd is using a common brassica genome sequence to identify options for increasing oilseed productivity and disease resistance.[19] Researchers in the UK are (i) identifying genes that regulate oil production in embryonic Arabidopsis with a view to targeting equivalent genes in crop species such as oilseed rape, and (ii) exploring options for blocking enzymes that breakdown stored oils in oilseed species. Both approaches offer breeders the prospect of being able to increase yields significantly.[20] UK Sugar beet The sugar-beet crop in the UK is grown in the dry east, where drought is an increasing risk. With industrial funding, scientists at Broom’s Barn are assessing a wide range of genetic material to identify varieties that can grow well under drought conditions and still produce good yields of sugar in their roots. They have found some useful markers, such as green crop canopy size, which plant breeders can use to predict drought-tolerance, and are working with an international seed company to accelerate selection of new drought-tolerant varieties.[22] Reducing the impact of pests and diseases Around 25% of the world’s crops are lost to pests or diseases. In some circumstances, climate change will make this worse for some pests and diseases as the environment has more effect on their development. For instance, milder winters enable aphids to survive and so damage crops earlier in the growing season. There are also ongoing challenges from pests and disease-causing organisms that have evolved to overcome pesticides, and from the restriction or banning of some effective control agents because of concerns about environmental impact. Soils R esearch is providing several options for improved control of pests and disease including: Efficient disease control requires an understanding of the interactions between soils, crops and pests and pathogens in the soil. For example, work at RRes is characterising how populations of microbes in the soil may be used to help suppress fungi that attack roots and nematodes. Research supported by the EU and DfID has led to a novel biological control agent, based on a strain of a natural soil fungus that is a particularly effective parasite of nematodes.[24] better preventative, diagnostic and pre-emptive strategies development of naturally resistant crops strategies to prolong the effectiveness and sustainable use of existing pesticides development of novel control agents (chemical and biological) The knowledge required for such strategies includes understanding the mechanisms by which organisms infect plants, and how these might be blocked; as well as understanding the ways plants respond to attack, and how these defences might be strengthened. It also includes understanding how pests and diseases build up and spread between crops, as well as how they, in turn, evolve to counter to plants’ natural defences and the use of pesticides. Research at RRes has also shown that maintaining levels of phosphate in the soil can help to protect against take-all disease in wheat. Using grass leys in rotation also delays the risk of epidemics starting in subsequent wheat crops.[25] Computer modelling has helped growers in Africa and Asia to improve yields of their staple crop cassava by controlling Cassava Mosaic Virus Disease (CMVD), which is spread by whitefly. The models, generated from experimental data, revealed that frequent removal of infected plants is by far the most effective way of limiting CMVD infections. Growing resistant varieties, on the other hand, can prevent disease spread only when whitefly density is low; although combined use of resistant varieties and frequent removal of infected plants can prevent the start of an epidemic in many cases. The models also showed that some control strategies can inadvertently select strains of the virus that grow faster in plants and so counteract control.[26] Predicting and minimising attacks P redictive modelling of how diseases spread, and the probable impact of different control methods can identify when and where farmers should intervene. This helps to eliminate unnecessary spraying and to optimise dosage. But it can be counter-intuitive. For example, research at the University of Cambridge shows that, when deploying limited resources to treat disease in two interconnected regions, it is more effective to treat the one with the lower level of infection first, rather than trying to equalise the level of infection in each region.[23] Robert Brook/Science Photo Library Rhizomania is a serious disease of sugar beet, caused by a soil-borne virus that is spread by farm machinery. By the time symptoms appear the disease has spread, making containment difficult. Field scale control fails to halt the disease but farm scale response, i.e. responding to the arrival of symptoms on the next-nearest neighbouring farm is effective.[27] Research on the life cycle and biology of pests and diseasecausing organisms underpins several online forecasting services that provide growers with frequent updates on when a significant percentage of crops is likely to be infected in their regions. This enables them to prepare controls in advance against diseases such as light leaf spot, which causes an estimated £30m annual loss in winter oilseed rape in the UK, and phoma stem canker that can cause losses of £100m in epidemic years and is predicted to increase in severity with climate change.[28] Reducing the impact of pests and diseases Disease-resistant crops A round 500 million people worldwide depend on the grain crop pearl millet. Downy mildew disease can reduce crop yields by up to 80%. Collaborative research with scientists in India has led to the breeding of a new variety that is resistant to attack by the causative pathogen.[29] Work led by RRes scientists in India has helped to develop disease-resistant oilseed brassicas. This involved 5,000 farmers in training programmes at 73 sites and has led to increased self-sufficiency in vegetable oils and enabled short-duration oilseed production in rotation with rice where land was previously left fallow. This has included identifying breeding lines of Indian mustard and oilseed rape-Ghobi sarson resistant to multiple strains of the downy mildew and white rust pathogens, and lines of oliseed rape-Ghobi sarson that are tolerant to Alternaria blight and stem rot under Indian field conditions.[30] Healthier coconut palms Working with the Oil Palm Research Institute in Ghana, scientists at the University of Nottingham are searching genetic varieties of coconut palm to find types that can resist the lethal yellowing-type disease called Cape St Paul wilt, which is devastating plantations in coastal tropical Africa. Arabidopsis clues to disease resistance Scientists at the University of East Anglia have identified genes in Arabidopsis that protect the plant against a wide range of powdery mildew diseases. They also showed that when transferred into laboratory tobacco plants, the genes again provided this protection. In current research these genes are being tested for their ability to provide disease resistance in squash – genetically modified forms of which are widely grown in the USA.[31] A major programme at Warwick HRI is identifying genes in Arabidopsis that trigger plants to defend themselves against downy mildew. These researchers are also studying the genes in the pathogen that suppress the plant’s response. Information about the mechanisms of this ‘arms race’ between the plant and the pathogen will inform new strategies for breeding durable resistance into crops and reveal new targets for attack.[32] The disease is caused by a phytoplasma bacterium. As well as finding resistant forms of palms, the scientists are also exploring how infection spreads from palm to palm, so that replanting may be managed to reduce further losses in future. Transmission by seed is one possible explanation being investigated.[33] In related work, the Nottingham team is investigating the molecular basis of phytoplasma infection using Catharanthus rosea (Madagascar periwinkle) as a model system. ...and kale and cabbages B lack rot is a bacterial disease caused by Xanthomonas campestris. It can devastate vegetable crops in warm climates, such as East Africa, and often destroys entire crops grown by smallholders. Control of this seed-borne disease is difficult as there is no effective chemical treatment. UK geneticists and pathologists are working with crop scientists in Kenya, using the latest genomic tools in brassicas and Arabidopsis, to identify genes that confer broad-spectrum resistance to black rot. This will enable more rapid breeding of resistance into local varieties. the large-ear variety, and to increase grain production in elite varieties.[34] Reducing the impact of pests and diseases Reducing the impact of pests and diseases Overcoming resistant pests New forms of control C otton boll weevil, whitefly and diamondback moth are among the major crop pests that are becoming increasingly difficult to control. This is because exposure to pesticides has driven the selection of resistance, for example individuals that produce much higher levels of enzymes that deactivate pesticides. P lants use chemical signals to repel pest species and to attract beneficial insects that they need for pollination. By planting companion species with crops this ‘push-pull’ effect can be harnessed for pest control. Research is identifying the biochemical and molecular basis of pesticide resistance, as well as the conditions that result in the selection and spread of resistance in insect populations. From this, scientists have developed rapid diagnostics for detecting resistance and methods for predicting, and therefore counteracting, its development.[35] Working with maize growers in East Africa, scientists at RRes used inter-crop lines of Desmodium to repel stem borers from A novel approach, developed by scientists at RRes and New South Wales Agriculture in Australia, can restore the effectiveness of conventional pesticides to which pests have become resistant. In partnership with Italian company Endura SpA, they have developed a product that first inhibits the pesticide-degrading enzymes and then delivers a dose of pesticide. In field trials in Spain, this approach achieved 100% control of whitefly that were previously resistant to the pesticide.[36] Cotton boll weevil (top, photo by Pest and Diseases Image Library) and diamondback moth. New targets for fungicides and herbicides H eadblight or ‘scab’ in wheat costs millions of pounds worldwide each year, in terms of lost yield and reduced quality as a result of fungal toxins making the grain unusable in food or animal feed. There are no varieties with high levels of resistance and current fungicides provide only partial control. By using high throughput screening of the metabolic compounds produced by the fungus as it causes infection, scientists at RRes are finding new targets for novel pesticides.[37] Scientists at the University of Sheffield and the agrochemical company Syngenta are combining the academics’ structural biology expertise with the company’s identification of new chemicals that have potential as new generation herbicides. The partnership advances understanding of how molecular structure determines the activity of herbicides, and offers industry the opportunity of novel targeted compounds capable of killing weeds that have become resistant to conventional herbicides.[38] The active site of a novel herbicide target (imidazoleglycerol phosphate dehyrdatase), which binds its substrate between two manganese ions. within the crop and a peripheral crop of attractive Napier grass to ‘lure’ them away from the maize. This dramatically increased yields, and as a bonus the intercrop suppressed the parasitic weed Striga, and the border crop provided forage to rear calves.[39]