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Temperate matters in agriculture

By | Blog, Future Directions, GPC Community

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Most of the world’s food is produced in temperate zones. The Global Food Security program’s Evangelia Kougioumoutzi reports on the TempAg network.

Agricultural production in temperate regions is highly productive with a significant proportion of global output originating from temperate (i.e. non-tropical) countries – 21% of global meat production and 20% of global cereal production [link opens PDF] originate from Europe alone. This proportion is very likely to increase in light of climate change.

Temperature zones

Little fluffy clouds: temperate zones are well suited to agricultural production. Image credit: connect11/Thinkstock

TempAg is an international research collaboration network that was established to increase the impact of agricultural research and inform policy making in the world’s temperate regions. Its work does not solely focus on research, but also provides insights into current thinking through mapping existing scientific findings and outstanding knowledge gaps. In this way, the network aspires to become a platform for the alignment of national agricultural research and food partnership programs (such as Global Food Security) that will enable the development of more effective agricultural policies with a long-term vision.

Since its official inauguration in Paris in April 2015, TempAg has been leading a series of on-going workstreams around:

  • Boosting resilience of agricultural production systems at multiple scales and levels
  • Optimising land management for ecosystem services and food production
  • Improving sustainability of food productivity in the farms & enterprise level

You can read more about these themes on the TempAg website: http://tempag.net/themes/.

Future foresights

After 18 months of existence, TempAg held a foresight workshop in London on 5–7 October to determine its future priorities.

Forty delegates took part in the workshop, coming from the 14 different countries in the temperate region, and from academia, policy, industry, and professionals at the science–policy interface. Through a series of presentations and interactive sessions, participants were invited to consider what the current and future challenges are in temperate agriculture, taking into account the needs of policy makers and industry in helping them to improve sustainable agriculture practices.

 

Temperate zones

Temperate zones cover much of the world’s major food-growing areas. Image from Wikipedia/CIA-Factbook

 

To tackle sustainability in temperate agriculture, there is a need to better manage risks and stresses (both biotic and abiotic), as well as finding ways to manage the restoration of natural capital, ecosystem services, and soils. During the workshop, it was noted that utilizing the diversity within different agricultural systems, via identifying the best practice and using the appropriate technological mix, may be a way forward in making production systems more sustainable.

Participants stressed the importance of taking a holistic view of the sustainability agenda within agriculture, without just focusing on environmental aspects. This means also taking into consideration socioeconomic factors, such as making food value chains (like turning milk into cheese), more equitable by identifying who gets the equity from the food commodities’ prices, or identifying what the optimum legal framework for sharing data might be.

The group also considered sustainable agriculture issues from a policy and industry needs angle. It was interesting to see that dealing with shocks (environmental, socioeconomic, and technological) featured highly in this discussion as well. It was suggested that increasing resilience to these shocks could be facilitated via the widespread diffusion of existing technologies. Engaging with farmers during this time would be necessary to identify technology uptake barriers.

Forward moves

Future-proofing agricultural resilience and enhancing the capacity to respond to shocks was deemed an urgent priority, so the development of a comprehensive map identifying the multiple shocks that could impact on farm resilience in temperate zones might be a future workstream for TempAg. Work in this area could help develop models to assess the flexibility within agricultural production systems.

 

What we eat is largely based on the types of food we produce. Therefore, healthy diets are intrinsically linked with our production systems. Another area of interest for TempAg could be to explore what the nutritional value of crops should be for better health, and what a nutritional diet will look like for sustainable temperate agriculture. Developing frameworks in this area could further inform future farming practices in temperate areas.

Since TempAg’s initiation, two major global policy agendas have been adopted by the international community: the Sustainable Development Goals and the Paris COP21 agreement. Identifying what types of data and scientific evidence policy makers will need to achieve the agriculture-relevant targets was another area where TempAg could focus its activity moving forward.

Finally, delegates highlighted areas of work that could help to build more effective policies with a longer-term vision. These included developing economic tools for valuing natural capital and ecosystem services, as well as integrated assessment tools to monitor the performance and impact (environmental cost) of existing policies.

This article is cross-posted with the Global Food Security blog.


About Evangelia Kougioumoutzi

Evangelia is International Coordinator & Programme Manager for the Global Food Security program (GFS). Before joining GFS, Evangelia worked as an Innovation Manager for GFS partners BBSRC. She holds a PhD in plant development and genetics from the University of Oxford.

 

Farming Futures: integrating plant research and industry in the agri-food supply chain

By | Blog, Interviews

This week we speak to Tim Williams, the Business Manager of Farming Futures and Research Fund Development Manager at Aberystwyth University, UK.

Could you give a brief introduction to Farming Futures and its mission?

Farming Futures is an independent, UK-based, inclusive agri-food supply chains alliance. Our mission is to work with researchers and industry to share knowledge, with the aim of improving the sustainability and productive efficiency of agriculture, all within the context of healthy, high-quality food.

 

What is the history of the organization?

Farming Futures started with an idea by Professor Wayne Powell in 2009 (then the director of the Institute of Biological, Environmental and Rural Sciences (IBERS) at Aberystwyth) in discussion with Mark Price, who was the Managing Director of British supermarket chain Waitrose. It was launched in 2010, starting out as the Centre of Excellence for UK Farming (CEUKF). Waitrose seed-funded Farming Futures, and since then we have received support from the Agriculture and Horticulture Development Board (AHDB) and Innovate UK.

 

Farming Futures

The inauguration meeting of Farming Futures in 2009, then known as the Centre of Excellence for UK Farming. Left-Right: Tim Williams, Wayne Powell, Heather Jenkins, David Davies, Philip Morgan, Jamie Newbold.

 

How has plant and crop research been integrated into the recommendations presented by Farming Futures?

Plant science is the fundamental driver for agri-food development. We work closely with industry, as well as the AHDB and other farm advisory bodies across the UK to inform them about new developments. Accelerated, directed breeding programs using genomic and phenomic technologies are helping us to develop new varieties that offer more productive, more resilient, environmentally friendly plants – not just as food crops, but also for soil quality, nutrient retention, flood reduction, energy biomass, renewable chemistry, and a host of other desirable characteristics.

Historically, to paraphrase a fellow botanist, we have bred ‘needy, greedy plants’ that deplete resources and need lots of nasty chemicals to keep them growing. Now scientists are mining the genomes of crop ancestors to rediscover the genetic traits we unwittingly threw away on the route to increased yield.

 

What roles do research partners such as universities play?

We work together in a pre-competitive way to enable research, and to represent farming within agri-food policy – researchers from different organizations can collaborate thanks to our partners’ trusting relationships with each other. Collaborations in science are vital because the problems our global society faces are multi-factorial, non-linear and multi-disciplinary. They are far too complex for the typical university research team, working alone, to address efficiently. We need the equivalent of the CERN Large Hadron Collider project for agri-food.

In addition to helping researchers to bring in millions of pounds worth of applied research projects (at least £12 million, but it is notoriously difficult to find out what industry is funding), Farming Futures helped to establish the government-funded Agri-Food Tech Centres of Innovation for a total of around £90 million, bringing in industry to co-fund and support three of the four: the Agrimetrics Centre, Agri-Epi-Centre and Centre of Innovation Excellence in Livestock. In time, these Centres will catalyze a lot of collaborative research and will help stimulate innovation and technology uptake by industry.

 

What climate change challenges will farmers face? Are there any specific challenges that Farming Futures can address?

Farming Futures and its network brings together scientists from different disciplines to discuss these problems and potential solutions. For instance, people from the UK’s national weather service (the Met Office) and some of the biggest food retailers and processors in the world come together at our conferences and workshops to think through scenarios and solutions. These solutions include breeding crops for increased resilience, not just peak yield. We are running out of fungicides that work efficiently, in the same way that we are running out of antibiotics; however, some very clever scientists have worked out some potential solutions that are more environmentally sound, so I am an optimist.

This problem solving is best done at the supply-chain level as it brings in a wider expertise. As I repeat often, a colleague once said to the board of one of the world’s biggest brewers, “No barley = no beer = no business”, inferring the question, “What are you doing to ensure that barley growers are going to be able to supply you in the future?”

 

Your website has an interesting study from 2011 highlighting six potential jobs of the future, including geoengineer, energy farming, web 3.0 farm host, pharmer, etc. How can students direct their skill development to meet the needs of the future?

There are many emerging jobs and skills, but each of these named jobs from 2011 are actually in practice now. The web 3.0 has now become web 4.0, which is the “internet of things”, with data collection from lots of devices including drones for precision agriculture and robots for weeding and picking crops.

The future of agri-food is in big data, including consumer behavior, weather forecasting, genomics, phenomics, and real-time analysis of the growth progress of plants and animals on-farm. We need more electronic and mechanical engineers with an understanding of biology, as well as more biologists who work within the agri-food industries and in government policy development.

 

Farming Future exhibition

The Farming Futures exhibition stand at the Livestock Event, NEC Birmingham, 2012.

 

What are you currently working on?

We are currently working with partners on a number of projects across the Agri-Food Tech Centres and trying to form more research collaborations. One of our big projects is The National Library for Agri-Food. I am currently working with web developers and experts from Jisc and the British Library to scope the requirements and to build a demonstration web site.

Finally, I would just like to add that we are open to collaborations across agri-food supply chains and will work to foster them, either openly or privately as appropriate.

 


In addition to IBERS, Farming Futures has four founding members (Northern Ireland’s Agri-Food and Biosciences Institute (AFBI), Harper Adams University (HAU), NIAB with East Malling Research (NIAB-EMR), and Scotland’s Rural College (SRUC)) and an influential Steering Board, chaired by Lord Curry of Kirkharle, who is very well known and respected in UK government and farming.

 

Cassava brown streak: lessons from the field

By | Blog, GPC Community

This week’s post was written by Katie Tomlinson, a PhD student at the University of Bristol, UK, who spent three months as an intern at the National Crops Resource Research Institute in Uganda. She fills us in on the important research underway at the Institute, and how they communicate their important results to local farmers and benefit rural communities.  

Over the summer, I had a great time at the National Crops Resources Research Institute (NaCRRI) in Uganda. I’m currently in the second year of my PhD at the University of Bristol, UK, where I’m researching how the cassava brown streak disease (CBSD) viruses are able to cause symptoms, replicate and move inside plants. I was lucky enough to be given a placement at NaCRRI as part of the South West Doctoral Training Partnership Professional Internship for PhD Students (PIPS) scheme, to experience the problem for myself, see the disease in the field, meet the farmers affected and investigate the possible solutions.

 

Cassava brown streak disease

Cassava brown streak disease symptoms on tubers. Image credit: Katie Tomlinson.

 

Cassava is a staple food crop for approximately 300 million people in Africa. It is resilient to seasonal drought, can be grown on poor soils and harvested when needed. However, cassava production is seriously threatened by CBSD, which causes yellow patches (chlorosis) to form on leaves and areas of tubers to die (necrosis), rot and become inedible.

Despite being identified in coastal Tanzania 80 years ago, CBSD has only been a serious problem for Uganda in the last 10 years, where it was the most important crop disease in 2014–2015. The disease has since spread across East Africa and threatens the food security of millions of people.

NaCRRI is a government institute, which carries out research to protect and improve the production of key crops, including cassava. The focus is on involving farmers in this process so that the best possible crop varieties and practices are available to them. Communication between researchers and farmers is therefore vital, and it was this that I wanted to assist with.

 

Scoring cassava brown streak disease

Scoring cassava plants for Cassava brown streak symptoms. Image credit: Katie Tomlinson.

 

When I arrived I was welcomed warmly into the root crop team by the team leader Dr Titus Alicai, who came up with a whole series of activities to give me a real insight into CBSD. I was invited to field sites across Uganda, where I got to see CBSD symptoms in the flesh! I helped to collect data for the 5CP project, which is screening different cassava varieties from five East and Southern African countries for CBSD and cassava mosaic disease (CMD) resistance. I helped to score plants for symptoms and was fascinated by the variability of disease severity in different varieties. The main insight I gained is that the situation is both complex and dynamic, with some plants appearing to be disease-free while others were heavily infected. There are also different viral strains found across different areas, and viral populations are also continually adapting. The symptoms also depend on environmental conditions, which are unpredictable.

I also got to see super-abundant whiteflies, which transmit viruses, and understand how their populations are affected by environmental conditions. These vectors are also complex; they are expanding into new areas and responding to changing environmental conditions.

It has been fascinating to learn how NaCRRI is tackling the CBSD problem through screening different varieties in the 5CP project, breeding new varieties in the NEXTGEN cassava project, providing clean planting material and developing GM cassava.

 

Tagging cassava plants

Tagging cassava plants free from Cassava brown streak disease for breeding. Image credit: Katie Tomlinson.

 

And there’s the human element…

In each of these projects, communication with local farmers is crucial. I’ve had the opportunity to meet farmers directly affected, some of whom have all but given up on growing cassava.

 

Challenging communications

Communicating has not been easy, as there are over 40 local languages. I had to adapt and learn from those around me. For example, in the UK we have a habit of emailing everything, whereas in Uganda I had to talk to people to hear about what was going on. This is all part of the experience and something I’ll definitely be brining back to the UK! I’ve had some funny moments too… during harvesting the Ugandans couldn’t believe how weak I was; I couldn’t even cut one cassava open!

 

Real world reflections

I’m going to treasure my experiences at NaCRRI. The insights into CBSD are already helping me to plan experiments, with more real-world applications. I can now see how all the different elements (plant–virus–vector–environment–human) interact, which is something you can’t learn from reading papers alone!

Working with the NaCRRI team has given me the desire and confidence to collaborate with an international team. I’ve formed some very strong connections and hope to have discussions about CBSD with them throughout my PhD and beyond. It’s really helped to strengthen collaborations between our lab work in Bristol and researchers working in the field on the disease frontline. This will help our research to be relevant to the current situation and what is happening in the field.

 

Some of the NaCRRI team

Saying goodbye to new friends: Dr. Titus Alicai (NaCRRI root crops team leader), Phillip Abidrabo (CBSD MSc student) and Dr. Esuma Williams (cassava breeder). Image credit: Katie Tomlinson.

 

Plantwise – promoting and supporting plant health for the Sustainable Development Goals

By | Blog, Global Change, GPC Community
Andrea Powell

Andrea Powell, CABI

Promoting and supporting plant health will be an important part of how we achieve the United Nations’ Sustainable Development Goals (SDGs). Andrea Powell, Chief Information Officer of the Centre for Agriculture and Biosciences International (CABI) looks at how the CABI-led Plantwise programme is helping to make a difference.

By Andrea Powell

 

On 26th and 27th July 2016, CABI held its 19th Review Conference. This important milestone in the CABI calendar saw our 48 member countries come together to agree a new medium-term strategy. As always, plant health was a key focus to our discussions, cutting across many of CABI’s objectives. For CABI, with 100 years of experience working in plant health, it has become one of our most important issues, upon which our flagship food security program, Plantwise, has been built.

Plant health can, quite simply, change the lives and livelihoods of millions of people living in rural communities, like smallholder farmers. Human and animal health make headlines, while plant health often falls under the radar, yet, it is crucial to tackling serious global challenges like food security. Promoting and supporting plant health will be an important way to achieve the Sustainable Development Goals (SDGs).

Plant health and the SDGs

Take, for example, SDG 1, which calls for ‘no poverty’. The UN states that one in five people in developing regions still lives on less than $1.25 a day. We know that many of these people are smallholder farmers. By breaking down the barriers to accessing plant health knowledge, millions of people in rural communities can learn how to grow produce to sell to profitable domestic, regional and international markets.

Plantwise ReportSDG 2 focuses on achieving ‘zero hunger’. Almost one billion people go hungry and are left malnourished every day – and many are children. Subsistence farmers, who grow food for their families to eat, can be left with nothing when their crops fail. Access to plant health knowledge can help prevent devastating crop losses and put food on the table.

Interestingly, SDG 17 considers ‘partnerships for the goals’ and is critical to the way in which we can harness and share plant health knowledge more widely to help address issues like hunger and poverty. By themselves, individual organizations cannot easily resolve the complicated and interconnected challenges the world faces today. This is why partnership is at the heart of CABI’s flagship plant health programme: Plantwise.

What is Plantwise?

Plantwise Report 2015

Since its launch in 2011, the goal of Plantwise has been to deliver plant health knowledge to smallholder farmers, ensuring they lose less of what they grow. This, in turn, provides food for their families and improves living conditions in rural communities. Plantwise provides support to governments, helping to make national plant health systems more effective for the farmers who depend on them. Already, Plantwise has reached nearly five million farmers. With additional funding, and by developing new partnerships, we aim to bring relevant plant health information to 30 million farmers by 2020, safeguarding food security for generations to come.

Plantwise ‘plant clinics’ are an important part of the fight against crop losses. Established in much the same way as clinics for human health, farmers visit the clinics with samples of their sick crops. Plant doctors diagnose the problem, making science-based recommendations on ways to manage it. The clinics are owned and operated by over 200 national partner organizations in over 30 countries. At the end of 2015, nearly five thousand plant doctors had been trained.

Plantwise

A Plantwise plant clinic in action. Credit: Plantwise

Harnessing technology for plant health

The Plantwise Knowledge Bank reinforces the plant clinics. Available in over 80 languages, it is an online and offline gateway to plant health information, providing the plant doctors with actionable information. It also collects data about the farmers, their crops and plant health problems. This enables in-country partner organizations to monitor the quality of plant doctor recommendations; to identify new plant health problems – often emerging due to trade or climate change issues; and develop new best-practice guidelines for managing crop losses.

Plantwise

The first ever e-plant clinic, held in Embu Market, Kenya. Credit: Plantwise

The Plantwise flow of information improves knowledge and helps the users involved: farmers can receive crop management advice, and researchers and governments can access data from the field. With a new strategy for 2017–19 agreed, CABI will continue to focus on building strong plant health systems. We are certain that plant health is of central importance to achieving the SDGs and, together in partnership, we look forward to growing the Plantwise program and making a concrete difference to the lives of smallholder farmers.

“A few years ago, I would make ZMW 5000 per year. Last year I got 15 000. I have never missed any plant clinic session. I’ve been very committed, very faithful, because I have seen the benefits.”––Kenny Mwansa, Farmer, Rufunsa District, Zambia.

Take a look at Plantwise in action in Zambia (YouTube):

Plantwise in Zambia

Meet Linda, a Zambian plant doctor

Meet Kenny, a Zambian farmer

 

Learn more about Plantwise at www.plantwise.org.

Uncovering the secrets of ancient barley

By | Blog, Interviews

This week we speak to Dr Nils Stein, Group Leader of the Genomics of Genetic Resources group at the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK). We discuss his recent work on the genomes of 6000-year-old cultivated barley grains, published in Nature Genetics, which made the headlines around the world.

Nils Stein

Dr Nils Stein, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)

Could you describe your work with the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)?

The major research focuses of my group, the Genomics of Genetic Resources, are to continue sequencing the genomes of barley and wheat, perform comparative genomics on the Triticeae tribe, isolate genes of agronomic interest, and investigate the genomics of wild barley relatives.

We are currently leading the work to generate the barley reference genome, and we are also partners in several wheat genome sequencing projects. We are genotyping-by-sequencing (GBS) all 20 000 barley accessions in the IPK Genebank, as well as 10 000 pepper accessions as part of a Horizon 2020 project (G2P-SOL) investigating the Solanaceae crop species.
Your recent collaborative paper on the genomic analysis of 6,000-year-old barley grains made headlines around the world. What did this study involve?

This was an interdisciplinary study to sequence the DNA of 6000-year-old barley grains. The grains were excavated by a team of Israeli archaeologists and archaeobotanists led by Prof. Ehud Weiss, Bar-Ilan University, the DNA was extracted and sequenced by ancient DNA specialists Prof. Johannes Krause and Dr. Verena Schünemann in Germany, and the data were analyzed by Dr. Martin Mascher in the context of our comprehensive barley genome diversity information. This allowed the resulting sequence information to be put into a population genetic and ecogeographic context.

Ancient barley

Preserved remains of rope, seeds, reeds and pellets (left), and a desiccated barley grain (right) found at Yoram Cave in the Judean Desert. Credit: Uri Davidovich and Ehud Weiss.

What led you to the realization that barley domestication occurred very early in our agricultural history?

The genome of the analyzed ancient samples was highly conserved with extant barley landraces of the Levant region, which look very similar to today’s high-yielding barley varieties. Although suggestive and tendentious, this told us that the barley crop 6000 years ago looked very similar to extant material. The physical appearance and the archaeobotanical characters of the analyzed seeds also very much resembled modern barley.

 

These barley grains contain the oldest plant genomes reconstructed to date. Did you find any differences between the samples that might give us an insight into the traits that were first selected in the early domestication of the crop?

We have only scratched the surface so far. The major domestication genes controlling dehiscence, brittleness or row-type of the main inflorescence had the same alleles in the ancient samples that are found in extant barley, confirming that these traits were selected for early in domestication. Additional analyses on other genes controlling different traits in barley are still ongoing – bear in mind that many of the genes controlling major traits in barley are still unknown, which complicates the selection of targets for analysis.

Modern barley

Modern barley cultivar. Credit: Christian Scheja. Used under license: CC BY 2.0.

 Do these grains have any genetic variation that we lack at key loci in modern barley lines, for example in stress or disease resistance?

This is matter of ongoing analysis. So far it is obvious that the most genetically similar extant landraces from the Levant region have accumulated natural mutations over the last 6000 years, resulting in additional variation that we don’t find in the ancient sample.

 

What can we expect from the barley genome projects in the future?

The International Barley Genome Sequencing Consortium is preparing a manuscript on the reference sequence of barley. This will allow further analysis of the ancient DNA data with a more complete, genome-wide view, including the consideration of a more complete gene set than has been available so far. Our Israeli collaborators (Professor Ehud Weiss and Professor Tzion Fahima) have more ancient samples of similar quality. We hope we will be able to generate a more comprehensive view of the ancient population genomics of barley in the future, to better address the question of novel ancient alleles and lost genetic diversity.

The Barley Pan-Genome analysis will soon give us a better understanding of the structural variation in the barley genome. Putting the ancient DNA information into this more comprehensive genomic context will be very exciting. We also hope to be able to compare a variety of ancient samples of different ages to more precisely date the event of barley domestication.


You can read the paper here: Genomic analysis of 6000-year-old cultivated grain illuminates the domestication history of barley ($).

Protecting plants, protecting people

By | Blog, GPC Community
Professor Sophien Kamoun

Professor Sophien Kamoun (The Sainsbury Lab, UK)

This week on the blog, Professor Sophien Kamoun describes his work on plant–pathogen interactions at The Sainsbury Lab, UK, and discusses the future of plant disease.

Could you begin by describing the focus of your research on plant pathogens?

We study several aspects of plant–pathogen interactions, ranging from genome-level analyses to mechanistic investigations focused on individual proteins. Our projects are driven by some of the major questions in the field: how do plant pathogens evolve? How do they adapt and specialize to their hosts? How do plant pathogen effectors co-opt host processes?

One personal aim is to narrow the gap between research on the mechanisms and evolution of these processes. We hope to demonstrate how mechanistic research benefits from a robust phylogenetic framework to test specific hypotheses about how evolution has shaped molecular mechanisms of pathogenicity and immunity.

 

Phytophtora ramorum

Sudden oak death is caused by the oomycete Phytophthora ramorum. Image from Nichols, 2014. PLOS Biology.

Tree diseases such as sudden oak death, ash dieback and olive quick decline syndrome have been making the news a lot recently. Are diseases like these becoming more common, and if so, why?

It’s well documented that the scale and frequency of emerging plant diseases has increased. There are many factors to blame. Increased global trade is one. Climate change is another. There is no question that we need to increase our surveillance and diagnostics efforts. We’re nowhere near having coordinated responses to new disease outbreaks in plant pathology, especially when it comes to deploying the latest genomics methods. We really need to remedy this.

 

The wheat blast fungus recently hit Bangladesh. Could you briefly outline how it is being tackled by plant pathologists?

Wheat blast has just emerged this last February in Bangladesh – its first report in Asia. It could spread to neighboring countries and become a major threat to wheat production in South Asia. Thus, we had to act fast. We used an Open Science approach to mobilize collaborators in Bangladesh and the wider blast fungus community, and managed to identify the pathogen strain in just a few weeks. It turned out that the Bangladeshi outbreak was caused by a clone related to the South American lineage of the pathogen. Now that we know the enemy, we can proceed to put in place an informed response plan. It’s challenging but at least we know the nature of the pathogen – a first step in any response plan to a disease outbreak.

 

Which emerging diseases do you foresee having a large impact on food security in the future?

Obviously, any disease outbreak in the major food crops would be of immediate concern, but we shouldn’t neglect the smaller crops, which are so critical to agriculture in the developing world. This is one of the challenges of plant pathology: how to handle the numerous plants and their many pathogens.

European Corn Borer

European corn boreer. Image from Cornell University. Used under license CC BY 2.0.

As far as new problems, I view insect pests as being a particular challenge. Our basic understanding of insect–plant interactions is not as well developed as it is for microbial pathogens, and research has somewhat neglected the impact of plant immunity. The range of many insect pests is expanding because of climate change, and we are moving to ban many of the widely used insecticides. This is an area of research I would recommend for an early career scientist.

 

What advice would you give to a young researcher in this area?

Ask the right questions and look beyond the current trends. Think big. Be ambitious. Don’t shy away from embracing the latest technologies and methods. It’s important to work on real world systems. Thanks to technological advances, genomics, genome editing etc., the advantages of working on model systems are not as obvious as they were in the past.

 

How can we mitigate the risks to crops from plant diseases in the future?

My general take is to be suspicious of silver bullets. I like to say “Don’t bet against the pathogen”. I believe that for truly sustainable solutions, we need to continuously alter the control methods, for example by regularly releasing new resistant crop varieties. Only then we can keep up with rapidly evolving pathogens. One analogy would be the flu jab, which has a different formulation every year depending on the make-up of the flu virus population.

 

Blight Potato

Potato with blight, caused by the oomycete Phytophthora infestans. Image credit: USDA. Used under license CC BY-ND 2.0.

Is there anything else you’d like to add?

I read that public and private funding of plant science is less than one tenth of biomedical research. Not a great state of affairs when one considers that we will add another two billion people to the planet in the next 30 years. As one of my colleagues once said: “medicine might save you one day; but plants keep you alive everyday”.

 

Underutilized crops and insects replace fishmeal in aquaculture feed

By | Blog, Future Directions, GPC Community

Farmed fish are often fed with fishmeal, produced from the dried tissues of caught marine fish. In 2012, a total of 16.3 million metric tons of fish were caught to produce fishmeal and fish oil, 73% of which was used in aquaculture. This practice is unsustainable, and as the global human population is expected to rise to 9 over billion by 2050, capture fisheries will not be able to satisfy the demand for fish protein.

Barramundi

Barramundi fish

In recent decades there has been extensive research into ingredients to replace fishmeal, but this has focused mainly on sources of plant carbohydrate and protein such as maize and soy, which also serve as human foods. While these crops are now used in some commercial aquaculture feeds, they are not suitable for many species and have had less than optimal results. In addition, many countries do not grow these mainstream crops and are left in the undesirable position of having to import fishmeal alternatives, which can be cost prohibitive, and increase carbon emissions.

An alternative to fishmeal

Insect based feed

Insect based fish feed

The Crops for the Future (CFF) team in Malaysia is working with the University of Nottingham, UK, to investigate insect-based aquaculture feed as a replacement to fishmeal use in fisheries. Both organizations recognize that current rates of wild fish depletion are unsustainable and will not meet future demand for fishmeal under a ‘business as usual’ scenario. With support from the Newton-Ungku Omar Fund Institutional Linkages Programme, they have shown that the quality of insect larvae as an aquafeed ingredient is affected by the substrate on which the insects feed.

The CFF ‘FishPLUS’ program has revealed that black soldier fly (BSF; Hermetia illucens) larvae fed with underutilized crops can be used to produce insectmeal and replace up to 50% of fishmeal in formulated aquaculture. These crops are not used for human food and can be grown on marginal land close to areas of aquaculture production in tropical climates, increasing the sustainability of the process.

Producing insectmeal with underutilized crops

Ground Sesbiana

Ground Sesbania is used to feed the black soldier fly larvae

Over a year, the researchers worked with a private sector supplier to develop laboratory-scale BSF breeding pods in which different substrate combinations of underutilized crops could be trialed. BSF feeding trials were conducted using five separate or combined underutilized crops as substrate, i.e. Sesbania (Sesbania sp.); 90% Sesbania with 10% Moringa (Moringa oleifera); Bambara groundnut (Vigna subterranea) leaf; Bambara groundnut flour; and Moringa leaf.

The best results were obtained by feeding the larvae on Sesbiana, a nitrogen-fixing legume that grows well in marginal tropical landscapes and is not a human food crop. Overall, nutrient analyses indicated that the amino acid profile for insectmeal is encouraging and closely resembles fishmeal.

Successful feeding trials

Black soldier fly larvae

Black soldier fly larvae

Fish feeding trials using the BSF insectmeal were undertaken in Malaysia at the CFF Field Research Centre. The trial fish, barramundi, accepted a formulated feed with up to 50% replacement of fishmeal with Sesbania-fed BSF insectmeal. The feed conversion ratio, mortality rate and biomass growth rate were all comparable to control trials with commercial fishmeal aquaculture feed. Back in the UK, complementary antinutritional studies at the University of Nottingham contributed essential information to guide the development of an optimal aquaculture feed formulation in the future.

Waste not, want not

Amaranth alternative fertilizer

Amaranth growing with either commercial fertilizer (right) or FishPLUS substrate compost (left)

This project also embraces the use of undigested material from the insect feeding as compost for crops like okra and amaranth. For example, 10kg of Sesbania leaves produces 1kg of BSF pre-pupae and 9kg of undigested waste material. When used as a soil conditioner in our agronomy trial, this waste material improve the crop growth at a comparable level to commercial fertilizer. This could be used by terrestrial crop farmers to reduce their fertilizer bill.

The findings of this project are of importance to world food security. As leaders in this field of research, the UK and Malaysian partners are well placed to leverage these preliminary results and explore scalability and options for commercialization of benefit to both economies.


CFF is the world’s first and only organization dedicated to research on underutilized crops. Professor M.S. Swaminathan, World Food Prize Laureate and Father of the Asian Green Revolution, described CFF as `the need of the hour.’

You can see more about the FishPLUS project from Crops for the Future in the video below:



This article was written by FishPLUS Team, for Crops for the Future.

Newton-IUCAP workshop

Newton-IUCAP workshop

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Plant Artificial Chromosome Technology

By | Blog, Future Directions

Established GM technologies are far from perfect

The first genetically modified (GM) crops were approved for commercial use in 1994, and GM crops are now grown on over 180 million hectares across 29 countries. The most used forms of genetic modification are systems that result in herbicide resistance or expression of the Bt toxin in maize and cotton to provide protection against pests such as the European corn borer. These systems both require few novel genes to be introduced to the plant, and allow more efficient use of herbicides and pesticides, both of which are harmful to the environment and human health. Current systems of genetic modification usually involve

Agrobacterium tumefaciens is used to genetically engineer plants in the lab. In nature this bacteria uses its ability to alter plant DNA to cause tumours.

Agrobacterium tumefaciens is used to genetically engineer plants in the lab. In nature this bacteria uses its ability to alter plant DNA to cause tumours. Image by Jacinta Lluch Valero used under Creative Commons 2.0.

the use of Agrobacterium vectors, direct transformation by DNA uptake into the plant protoplast, or bombardment with gold particles covered in DNA. However, current systems of transformation are far from perfect. Many beneficial traits such as disease resistance require stacking of multiple genes, something that is difficult with current transformation systems. Furthermore, it is essential that transgenes are positioned correctly within the host genome. Current systems of genetic modification can insert genes into the ‘wrong’ place, disrupting function of endogenous genes or having implications for down or upstream processes. An additional problem is that transfer of transgenes from one line to another requires several generations of backcrossing. However, the past two decades have seen great developments in microbiology. Many new tools and resources are now available that could greatly enhance the biotechnology of the future.

 

New technologies

Many new and emerging technologies are now available that could transform plant genetic engineering. For example, high throughput sequencing and the wide availability of bioinformatics tools now make identifying target genes and traits easier than ever. Technologies such as site-specific recombination (SSR) and genome editing allow specific regions of the genome to be precisely targeted in order to add or remove genes. Artificial chromosome technology is also part of this emerging group that could be of benefit to plant science. Synthetic chromosomes have already been used in yeast, and widely studied in mammalian systems due to their potential use in gene therapy. Although there have so far been no definitive examples in plants, work has been done in maize that shows the potential of the technology for use in GM crops.

 

Building an artificial chromosome

A minichromosomes is a small, synthetic chromosome with no genes of its own. It can be programmed to express any desirable DNA sequence that could encode for one, or a number, of genes. An ideal minichromosome would be small and only contain essential elements such as a centromere, telomeres and origin of replication. Once introduced into the plant the minichromosomes should be designed such that interference with host growth and development is minimal. A key requirement is that the chromosome is stable during both meiosis and mitosis. This would ensure introduced genes do not become disrupted or mutated during cell division and reproduction. Gene expression would therefore remain the same for many generations. Finally, the DNA sequence on the minichromosomes could be designed such that it is amenable to SSR or gene editing systems. This would allow re-design and addition of new traits further down the line.

 

Potential advantages of artificial chromosomes

Plant artificial chromosomes (PACs) have many advantages over traditional transformation systems. For example, to confer complex traits such as disease resistance and tolerance to abiotic stresses such as heat and drought, multiple genes are required. This is not easy with current methods of modification.

PACs could offer a new way to introduce beneficial traits to our crops plants and feed a growing population.

PACs could offer a new way to introduce beneficial traits to our crops plants and feed a growing population.Image by Seattle.Romer. Used under Creative Commons 2.0.

However, PACs allow an almost unlimited number of genes to be integrated into the host system. A further possibility that comes from being able to add multiple genes is the addition of new metabolic pathways into the plant. This could allow us to change the nutrients produced by a plant to benefit our diets. Additionally, in a contained environment, plants could be used as a cheap, sustainable way to produce pharmaceuticals. A second major benefit of PACs is that they avoid linkage drag. This is when a desirable gene is closely linked to a deleterious gene that acts to reduce plant fitness. Where this linkage is very tight even repeated backcrossing cannot separate out the genes. Design of new DNA sequences completely avoids this problem, and could allow us to select out detrimental traits from out crop plants.

 

Regulations for novel biotechnology

Emerging technologies pose new questions to policy makers regarding GM regulation. For example, the use of genome editing, whereby specific sites in the genome are targeted and modified, produces an end product with a phenotype almost identical to one that could be achieved through conventional breeding. This sets genome-edited crops apart from other transgene-containing GM material. For this reason many now argue that genome-edited crops ought not to come under current GM regulations. Much of this argument centres on whether or not to regulate the scientific technique used to produce a crop, or to regulate the end product in the field. For more information on genome editing including current regulations and consensus, see the links at the end of this article.

 

PACs pose a different set of problems entirely. Minichromosomes would be foreign bodies in the plant, and gene stacking within these introduces even more foreign genes than is possible with current technologies. This would require extensive assessment of both environmental and health effects prior to commercialization. Currently regulatory approval costs around $1-15 million per insertion into the genome. These heavy charges may discourage the further development of minichromosomes technology. However, with PACs it is possible that a particular package of genes could be assessed once, and then transferred into numerous cultivars. This would eliminate the requirement to individually engineer and test every cultivar, so perhaps saving time and money in the long term.

 

More information on genome editing:

Sense about science genome editing Q & A

The regulatory status of genome-edited crops

The Guardian article on genome editing regulation

A proposed regulatory network for genome edited crops in Nature

A recent workshop on the CRISPR-CAS system of genome editing was held in September 2015 by GARNet and OpenPlant at the John Innes Centre in Norwich, UK. You can read the full meeting report here.

 

 

 

 

 

 

 

 

 

 

 

Integrated Pest Management Systems

By | Blog, Future Directions

Herbivorous pests can devastate crops, with huge economic and social impacts that threaten global food security. In 2011 scientists warned that biological threats, including pests and pathogens, account for a 40% loss in global production and have the potential for even higher losses in the future.

A farmer sprays pesticides on her crop

A farmer sprays pesticides on her crop. From IFPRI – IMAGES. Used under Creative Commons 2.0.

In the 1950s and 1960s huge amounts of pesticides were being used in agriculture, with negative effects on both humans and ecology. Pests and pathogens were developing resistance to pesticides, and to counteract this chemical companies were developing ever stronger, more expensive chemicals.

Perry Adkisson and Ray Smith, both entomologists, noted the harmful effects on the economy and environment of the overuse of synthetic pesticides. Working together they identified practical approaches to pest control that minimized pesticide use. They developed and popularized integrated pest management (IPM) systems, for which they won the World Food prize in 1997.

 

“Integrated Pest Management (IPM) means the careful consideration of all available pest control techniques and subsequent integration of appropriate measures that discourage the development of pest populations and keep pesticides and other interventions to levels that are economically justified and reduce or minimize risks to human health and the environment. IPM emphasizes the growth of a healthy crop with the least possible disruption to agro-ecosystems and encourages natural pest control mechanisms.” FAO definition

 

What is IPM?

IPM is an approach to crop production that considers the whole ecosystem, integrating a number of management techniques, rather than focusing all resources on a single practice such as pesticide use. Adkisson and Smith identified a number of principals around which successful IPM should be based:

Firstly, crop varieties should be selected that are appropriate to the culture and local environment. This would ensure the crop species is already adapted to local conditions, and may have some defense mechanisms to protect itself from biotic and abiotic stresses.

Secondly, IPM is based around pest control rather than complete eradication. Therefore, maximum tolerable levels of the pest that still enable good crop yields should be identified and the pests should be allowed to survive at this threshold level, although allowing a number of pests to exist within the crop requires continual monitoring. Good knowledge of pest behavior and lifecycle enables the prediction of where more or less controls are required.

Finally, when choosing a method of control, both mechanical methods, such as traps or barriers, or appropriate biological control are preferential. However, pesticides can be integrated into the plan if necessary, providing use is responsible and not in excess of requirements. Some really cool practices are now emerging that can be used as part of an IPM system around the world.

 

Enhancing biological control

Simply reducing pesticide use can actually lead to increased yields, as farmers in Vietnam discovered when scientists convinced them to try it for themselves. Their nemesis, the brown planthopper (Nilaparvata lugens), is increasingly resistant to insecticides, with devastating outbreaks becoming more common. Rice farmers found that by stopping their typical regular insecticide sprays, the planthopper’s natural predators such as frogs, spiders, wasps and dragonflies were able to survive and remove the pests, giving farmers a 10% increase in harvest income. This improved biological control is a key component of IPM.

Brown Planthopper

The Brown Planthopper (Nilaparvata lumens) on a rice stem. From IRRI photos. Used under Creative Commons 2.0.

 

Push-pull technology

Push-pull agriculture has been very successful in Kenya, where stemborer moths can cause vast yield losses in maize with estimated economic impacts of up to US$ 40.8 million per year. Push-pull technology uses selected species as intercrops between the main crops of interest. Intercrops work in two ways, by pushing pests away from the economically valuable crop, and pulling them towards a less valuable intercrop. The stemborer moth push-pull system uses Desmodium (Desmodium uncinatum) to repel stemborer moths. Desmodium species are small flowering plants that produce secondary metabolites that repel insects. Moths are then attracted to the surrounding napier grass instead.

Aside from controlling the stemborer moth, this system has a number of additional benefits. Desmodium suppresses the growth of Striga grass (a devastating weed that you can read about here) via a number of mechanisms, primarily through interfering with root growth. Additionally, the intercrop species can be used for animal fodder and improve soil fertility. The multiple benefits and success of this system has meant push pull has now been adopted by over 80,000 small-holdings in Kenya and is being rolled out to Uganda, Tanzania and Ethiopia.

 

Stem borer larva feeding on a maize stem.

Stem borer larva feeding on a maize stem. From International Institute of Tropical Agriculture. Used under Creative Commons 2.0.

Abrasive weeding

Abrasive weeding is a relatively new technique that involves firing air-propelled grit at a crop to physically kill any weeds growing between crop rows. One issue with this method is that it indiscriminately damages the stem and leaf tissue of both crops and weeds, but grit applicator nozzles are available to more directly target the base of the stem to minimize collateral damage. A recent study found abrasive weed control reduced weed density by up to 80% in tomato and pepper fields, with 33-44% increases in yield.

Maize cob or walnut shells are currently the most frequently used grits, but the technique offers the exciting possibility of combining fertilization and weed control in one step, which could reduce time and cost to the farmer. For example, soybean meal is able to destroy plant tissues when fired from the gun, and has high nitrogen content that is released slowly into the soil over a period of at least three months, making it an ideal source of fertilizer.

 

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