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Oct 192015
 

IBP-logoBy 2050, the global demand for food will nearly double, numbers of farmers are predicted to decrease and the amount of suitable farmland is not expected to expand. To meet these challenges, farmers will rely on plant breeders becoming more efficient at producing crop varieties that are higher yielding and more resilient.

The Integrated Breeding Platform (IBP), established by the CGIAR Generation Challenge Programme (GCP), provides plant breeders with state-of-the-art, modern breeding tools and management techniques to increase agricultural productivity and breeding efficiency. Its work democratises and facilitates the adoption of these tools and techniques across world regions and economies, from emerging national programmes to well-established companies. In particular, it is helping to bridge the technological and scientific gap prevailing in developing countries by providing purpose-built informatics, capacity-building opportunities and crop-specific expertise to support the adoption of best practice by breeders, including the use of molecular technologies. This will help reduce the time and resources required to develop improved varieties for farmers.

IBP is certainly a winner for maize breeder Thanda Dhliwayo of the International Maize and Wheat Improvement Center (CIMMYT): “IBP is the only publicly available integrated breeding data-management system. I see a lot of potential in increasing efficiency and genetic gain of public breeding programmes,” he says.

For Graham McLaren, who was GCP’s Bioinformatics and Crop Information Sub-Programme Leader, an informatics system is vital for advancing the adoption of modern breeding strategies and the use of molecular technologies.

“One of the biggest constraints to the successful deployment of molecular technologies in public plant breeding, especially in the developing world, is a lack of access to informatics tools to track samples, manage breeding logistics and data, and analyse and support breeding decisions,” says Graham, who is now IBP Deployment Manager for Eastern and Southern Africa.

This is why IBP was set up, explains Graham: “We want to put informatics tools in the hands of breeders – be they in the public or private sector, including small- and medium-scale enterprises – because we know they can make a huge difference.”

Breeders access IBP's services through its Web Portal.

Breeders access IBP’s services through its Web Portal.

Handling big data

Knowledge is power, making data are almost a crucial a raw material for plant breeding as seeds. To make good choices about which plants to use, breeders need information from thousands of plant lines about a wide range plant of characteristics, usually collected during field trials or greenhouse experiments, in a process known as phenotyping. Effective information management is therefore critical in the success of a breeding programme. IBP tackles these crucial information management issues, and many of its current users are finding it invaluable for handling their phenotypic data. IBP also aims to facilitate the use of molecular-breeding techniques, which require genetic as well as phenotypic information (see box), and support users in integrating these into their breeding process.

Marker-assisted selection – highlighting genes that control desired traits This technique involves using molecular markers (also known as DNA markers) to flag the presence of specific genes associated with desired traits and trace their descent from one generation to the next. These markers are themselves fragments of DNA that highlight particular genes or genetic regions by binding near them. To use an analogy, think of a story as the plant’s genome: its words are its genes, and a molecular marker works as a text highlighter. Molecular markers are not precise enough to highlight specific words (genes), but they can highlight sentences (genomic regions) that contain them. Plant breeders can generally use molecular markers early in the breeding process to determine whether plants they are developing will have the desired trait.

The advent and implementation of molecular breeding has increased breeders’ efficiency and capacity to generate new varieties – although the inclusion of genetic data has also added to the amount of information that breeders need to handle.

Photo: HarvestPlus

An abundant harvest of nutrient-enriched cassava in Nigeria.

“Prior to molecular breeding, we would record our observations of how plants performed in the field [phenotypic data] in a paper field book; we would either file the book away or re-enter the data into an Excel spreadsheet,” says Adeyemi (Yemi) Olojede, Assistant Director and Coordinator in charge of the Cassava Research Programme at the National Root Crops Research Institute (NRCRI) in Nigeria and Crop Database Manager for NRCRI’s GCP-funded projects.

“We still need to phenotype, but molecular-breeding techniques allow us to select for plant characteristics early in the breeding process by analysing the plant’s genotype to see if it has genes associated with desirable traits,” says Yemi. Groundwork is needed in order to make this possible: “This means we need to analyse the data of each plant’s genetic make-up as well as the phenotypic data so we can verify whether certain genes are responsible for the traits we observe.”

By using molecular markers to make certain which plants have useful genes right from the start  – simply by testing a tiny bit of seed or seedling tissue – breeders and agronomists like Yemi can carefully select which ‘parent’ plants to use. These are then crossed in just the same way as in conventional breeding, but using only the most promising parents makes each generation is a much bigger step forward. Another advantage for breeders is that they do not necessarily have to grow all of the progeny from each set of crosses – usually thousands – all the way to maturity to see which plants have inherited the traits they are interested in.

The IBP Breeding Management System makes it much easier for breeders to manage their data and make good use of both phenotypic and genotypic information. The Crossing Manager function facilitates the planning and tracking of crosses.

The IBP Breeding Management System makes it much easier for breeders to manage their data and make good use of both phenotypic and genotypic information. The Crossing Manager function facilitates the planning and tracking of crosses.

All of this makes breeding more efficient, reducing the time and cost associated with field trials and cutting the cumulative time it takes to breed new varieties by half or more. The end result is that farmers get the new crop varieties they need more quickly.

Keeping track of masses of information has always been a headache for breeders. However, the increased burden of data management that molecular breeding brings – together with the need to be able to carry out specialised genotypic analysis (study of the genetic make-up of an organism) – has proved to be a limitation for many public national breeding programmes such as NRCRI. These have consequently struggled to adopt molecular-breeding techniques as readily as the private sector.

Wanting to overcome this limitation as part of its mission to advance plant science and improve crops for greater food security in the developing world, in 2009 GCP gave Graham McLaren the momentous task of overseeing the development of the Integrated Breeding Platform.

Clearing the bottleneck

The IBP Web Portal provides information and access to services and crop-specific community spaces. These help breeders design and carry out integrated breeding projects, using conventional breeding methods combined with and enhanced by marker-assisted selection methods. The Portal also provides access to downloadable informatics tools, particularly the Breeding Management System (BMS).

While there are multiple analytical and data-management systems on the market for plant breeders, what sets the BMS apart is its availability to breeders in developing countries and its integrated approach. Within a single software suite, breeders are able to manage all their activities, from choosing which plants to cross to setting up field trials.

Graham explains that IBP has brought together all the basic tools that a breeder needs to carry out day-to-day logistics, data management and analysis, and decision support. “We’ve worked with different breeders to develop a whole suite of tools – the BMS – that can be configured to support their various needs,” explains Graham. “Having all the tools in one place allows breeders to move from one tool to the next during their breeding activities, without complex data manipulation. We’ve also set up the system for others to develop and share their tools, so that it can continue to grow with new innovative ideas.”

The IBP Breeding Management System has a complete range of interconnected tools. The Germplasm Lists Manager supports breeders in managing their sets of breeding materials.

The IBP Breeding Management System has a complete range of interconnected tools. The Germplasm Lists Manager supports breeders in managing their sets of breeding materials.

Another feature of the Platform is that it provides breeders with access to genotyping services to allow them to do marker-assisted breeding. This is particularly useful for breeders in developing countries, who often don’t have the capacity to do this work. “It’s about giving all breeders the opportunity to enhance the way they do their job, without breaking the budget,” says Graham.

A unique and holistic component of IBP is the Platform’s community-focused tools. “IBP is as much about sharing knowledge as it is about managing data,” says Graham. “We’ve integrated social media to allow anybody with an interest in breeding, say, cowpeas, to join the cowpea community. They needn’t necessarily be a collaborator; they just have to have an interest in breeding cowpeas. They could read about what’s going on, contact people in the community and say ‘I’ve seen results for your trial. Could you send me some seed because I think it will do well in my region?’ or ‘Could you please further explain the breeding method you used?’ That’s what we hope to inspire with those communities.”

Graham concedes that this aspiration for the Platform has not yet been fully realised. However, he is hopeful that by providing training, coupled with the support from several key institutes and breeders, these communities will help to increase adoption of IBP and its tools.

“We are well aware that this Platform will be a big step for a lot of breeders out there, and they will need to invest time and patience into learning how to adapt it to their circumstances,” says Graham. “However, this short-term investment will save them time and money in the long term by making their process a lot more efficient.”

For Guoyou Ye, a senior scientist with the International Rice Research Institute (IRRI), participating in IBP meant that he has gained a lot more understanding about the needs of breeders in developing countries for user-friendly tools.

“I started to spend time doing something for the resource-poor breeders. This has resulted in many invitations by breeding programmes in different countries to conduct training, and has given me a chance to establish a network for future work. I also had the chance to work with internationally well-known scientists and informatics specialists,” he says.

Photo: N Palmer/CIAT

Freshly threshed rice in India.

Providing help where it is needed

Yemi Olojede is another person who has been championing IBP, and his focus has been in Nigeria and other African countries. He spent time at GCP’s headquarters in Mexico in 2012 to sharpen his data-management skills and provide user insights on the cassava database. “I enjoy working with the IBP team,” says Yemi. “They pay attention to what we [agronomists and breeders] want and are determined to resolve the issues we raise.”

Yemi has also helped the IBP team run workshops for plant breeders throughout Africa.

He recounts that attendees were always fascinated by IBP and the BMS, but cautious about the effort required to learn how to use it. They were pleased, though, when they received step-by-step ‘how to’ manuals to help them train other breeders in their institutes, with additional support to be provided by IBP or Yemi’s team in Nigeria.

“We told them if they had any challenges, they could call us and we would help them,” says Yemi. “I feel this extra support is a good thing for the future of this project, as it will build confidence in the people we teach. They can then go back to their research institutes and train their colleagues, who are more likely to listen and learn from them than from someone else.”

IBP is continuing to run these training courses, through newly established regional hubs in Africa and Asia.

Breeders and researchers rate the Integrated Breeding Platform (IBP) “IBP is an important tool in current and future enhancement of national breeding programmes.” –– Hesham Agrama, Soybean Breeder, International Institute of Tropical Agriculture, Zambia “The tools being developed with IBP will form the basis of crop information management at the Semiarid Prairie Agricultural Research Centre [SPARC] and other Agriculture and Agri-Food Canada research centres.” –– Shawn Yates, Quantitative Genetics Technician, SPARC, Canada  “We have successfully integrated IBP with our lentil programme and also included IBP in the training that we conduct regularly for the benefit of our partners in national agricultural research systems.” –– Shiv Agrawal, lentil breeder, International Center for Agricultural Research in the Dry Areas, Syria “Our institute has embraced use of the Breeding Management System and IBP, and we are already seeing results in improved data management within the Seed Co group research function.” –– Lennin Musundire, senior maize breeder, Seed Co Ltd, Zimbabwe

Mark Sawkins, IBP Deployment Manager for West and Central Africa, is helping to coordinate the formation and integration of the regional hubs within key agricultural institutes, including the Africa Rice Center in Benin, Biosciences Eastern and Central Africa (BecA) in Kenya, Centre d’étude régional pour l’amélioration de l’adaptation à la sécheresse (CERAAS) in Senegal, the Chinese Academy of Agricultural Sciences (CAAS) in China, the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) in India, the International Institute of Tropical Agriculture (IITA) in Nigeria, and the National Center for Genetic Engineering and Biotechnology (BIOTEC) in Thailand. Several further hubs are planned in additional countries, including in Latin America.

He says the hubs provide localised support in the use of IBP tools: “Their role is to champion IBP in their region,” says Mark. “They can take advantage of their established relationships and skills to help new users adopt the Platform. This includes providing education and training, technical support for IBP tools, and encouraging users to build their networks through the crop communities.”

IBP Regional Hubs worldwide.

IBP Regional Hubs worldwide.

Breeding rice and maize more efficiently using IBP

For Mounirou El-Hassimi Sow, a rice breeder from the Africa Rice Center, IBP is more than just a tool that helps him manage his data: “I’m seeing the whole world of rice breeders as a small village where I can talk to everyone,” he says.

“Through IBP, I have access to this great network of people, who I would never have met, who I can refer to when I have some challenges.”

Social networking tools are a novel feature incorporated into IBP to further develop the capacity of breeders like Mounirou. IBP hosts a number of crop-based and technical Communities of Practice that were established by GCP. These have nurtured relationships between breeders across different countries and organisations, encouraging knowledge sharing and support for young scientists.

Another way GCP has promoted and developed capacity to use IBP and molecular-breeding techniques is through training. Starting in April 2012, the Integrated Breeding Multiyear Course (IB–MYC) trained 150 plant breeders and technicians from Africa and Asia. The participants attended three two-week intensive face-to-face training workshops spread over three years, with assignments and ongoing support between sessions.

Photo: V Boire/IBP

Roland Bocco (Africa Rice center, Benin), Dinesh K. Agarwal (ICAR, India) and Susheel K. Sarkar (ICAR, India) work together on a statistics assignment during their final workshop of the Integrated Breeding Multiyear Course (IB–MYC).

Mounirou participated in the course and says it provided him with the opportunity to learn more about molecular breeding and practice using the associated management and data analysis tools. “I had learnt about the tools in university and seen them on the Internet, but I did not know how to use them,” says Mounirou. “During the first year, we learnt about the theory and how the tools work. During the second and third years, we were comfortable enough with the tools to use our own data and troubleshoot this with the tutors. This was great and provided me with confirmation that these tools were applicable and useful for my work.”

Mounirou says he is now sharing what he learnt during the course with his co-workers and other plant breeders in Africa. “Since the Africa Rice Center became a regional hub for IBP, I’ve volunteered to help train rice breeders. It’s great to be able to share what I learnt and help them realise how this tool will help make their work so much easier.”

Photo: CIMMYT

A maize farmer and community-based seed producer in Kenya.

Another IB–MYC trainee, Murenga Geoffrey Mwimali, a maize breeder from the Kenya Agriculture and Livestock Research Organisation (KALRO), is also helping his networks to benefit from IBP. “When I returned from the training, I took the initiative to demonstrate the Platform to the management of my organisation, to show them that it is what we need to implement at the institute level. They were overwhelmingly positive, and we are working on running a training course for other researchers in the organisation to learn how to use the Platform.”

Jean-Marcel Ribaut, GCP and IBP Director, says these championing efforts are exactly what GCP and IBP were hoping IB–MYC would initiate. “By providing this initial intensive training to these selected participants, we felt this groundswell of capacity would slowly grow once they built their confidence,” says Jean-Marcel. “That young researchers like these feel they are competent and obligated to share what they learnt is a true credit to the product and the participants.”

From the GCP nest to world-scale deployment

IBP has been the single largest GCP investment. From 2009 to 2014, GCP allocated USD 22 million to the initiative, with financial support from the Bill & Melinda Gates Foundation, the European Commission, the UK Department for International Development, CGIAR and the Swiss Agency for Development and Cooperation. This represented 15 percent of GCP’s entire budget.

Following GCP’s close in December 2014, IBP will continue to develop and improve over the next five years, with funding primarily originating from the Bill & Melinda Gates Foundation. While the priority has been on informatics and service development in Phase I, the main focus of Phase II will be to concentrate on deployment and adoption. In the long term, the Platform is seeking further ongoing funding, and also looking into implementing some form of user-contribution for specialised or consulting services.

“We wanted to develop a tool to provide developing countries with access to modern breeding technologies, breeding materials and related information in a centralised and practical manner, which would help them adopt molecular-breeding approaches and improve their plant-breeding efficiency,” says Jean-Marcel. “I believe we have achieved this and at the same time built a tool that will prove very useful for commercial companies too. If we want the tool to continue to be affordable and sustainable for developing countries, then we have to look at ways of finding new sources of funding and of making revenue to offset the costs.”

Stewart Andrews, IBP Business Manager, is helping to make this happen.

“What we are looking at is a tiered membership system in the private sector, where enterprises would pay more the larger they are,” explains Stewart. “This would also be dependent on where in the world they are, with enterprises in Europe and North America contributing proportionately more financially than those in developing countries. This will help us to continue investing in our solutions while keeping them accessible to national programmes and universities in developing countries at little to no fee.”

For Jean-Marcel, creating a commercial stream for IBP services is a win for all parties. “If we are able to generate revenue we can not only provide sustainable support and offset the cost for poorer institutes, we can also continue to develop and improve the BMS software suite so that it becomes the tool of choice all over the world. In terms of social responsibility, the corporate world can play an essential role in this not only as donors but even more effectively as clients and users – adopting the BMS makes good business sense.”

Stewart says a sustainable income is vital for providing training and assistance. “We currently have about 7,000 researchers in the developing world who get this software for free, and each week we get 20–25 requests for help, assistance and training. This support costs money but is indispensable, particularly for those in the developing world who are trying to implement molecular breeding for the first time. You have to remember that this software is all part of a revolution in terms of plant breeding, so we need to provide as much assistance as we can if these breeders are going to buy into molecular breeding and all of its benefits.”

The IBP team is convinced that rolling out IBP will have a significant impact on plant breeding in developing countries.

Indeed, so far there have been more than 1,300 unique downloads of the BMS, with at least 250 early adopters worldwide using the software suite across their day-to-day breeding activities. The Platform’s strategy now builds on three regional teams (West and Central Africa, Eastern and Southern Africa, and South and South East Asia), each including experienced breeders and data managers. With the help of local representatives at seven well-established Regional Hubs to date (with more Hubs in development), this strategy has thus far yielded commitments from six African countries at the national level; from 24 Institutes spanning 58 breeding programmes at different stages of the adoption process; from 14 Universities where faculty members are using and/or teaching the BMS, partially or entirely; and from 134 “champions” engaged in the deployment plans and in supporting their peers.

“Because IBP has a very wide application, it will speed up crop improvement in many parts of the world and in many different environments. What this means is that new crop varieties will be developed in a more rapid and therefore more efficient manner,” concludes Graham.

More links

Jun 192015
 
Photo: N Palmer/CIAT

Bean Market in Kampala, Uganda.

Common beans are the world’s most important food legume, particularly for subsistence and smallholder farmers in East and Southern Africa. They are a crucial source of protein, are easy to grow, are very adaptable to different cropping systems, and mature quickly.

To some, beans are ‘a near-perfect food’ because of their high protein and fibre content plus their complex carbohydrates and other nutrients. One cup of beans provides at least half the recommended daily allowance of folate, or folic acid – a B vitamin that is especially important for pregnant women to prevent birth defects. One cup also supplies 25–30 percent of the daily requirement of iron, 25 percent of that of magnesium and copper, and 15 percent of the potassium and zinc requirement.

Unfortunately, yields in Africa are well below their potential – between 20 and 30 percent below. The main culprit is drought, which affects 70 percent of Africa’s major bean-producing regions. Drought is especially severe in the mid-altitudes of Ethiopia, Kenya, Malawi and Zimbabwe, as well as across Southern Africa.

“For the past seven or eight years, rains have been very unreliable in central and northern Malawi,” says Virginia Chisale, a bean breeder with Malawi’s Department of Agricultural Research and Technical Services.

“In the past, rains used to be very reliable and people were able to know the right time to plant to meet the rains in critical conditions,” she says. “Now these primary agriculture regions are either not receiving rain for long periods of time, or rains are not falling at the right time.”

Virginia recounts that during the 2011/12 cropping season there were no rains soon after planting, when it is important that beans receive moisture. Such instances can cut bean yields by half.

Photo: N Palmer/CIAT

Steve Beebe in the field.

“Drought is a recurrent problem of rainfed agriculture throughout the world,” says Steve Beebe, a leading bean breeder with the International Center for Tropical Agriculture (CIAT). “Since over 80 percent of the world’s cultivated lands are rainfed, drought stress has major implications for global economy and trade.”

Steve was the Product Delivery Coordinator for the beans component of the Legumes Research Initiative (RI), part of Phase II of the CGIAR Generation Challenge Programme (GCP). The RI incorporated several projects, the biggest of which was Tropical Legumes I (TLI) (see box). The main objective of the work on beans within TLI was to identify and develop drought-tolerant varieties using marker-assisted breeding techniques. The resulting new varieties were then evaluated for their performance in Ethiopia, Kenya, Malawi and Zimbabwe.

“It’s vital that we develop high-yielding drought-tolerant varieties so as to help farmers, particularly in developing countries, adapt to drought and produce sustained yields for their families and local economies,” says Steve.

The Tropical Legumes I project (TLI) was initiated by GCP in 2007 and subsequently incorporated into the Programme’s Legumes Research Initiative (RI). The goal of the RI was to improve the productivity of four legumes – beans, chickpeas, cowpeas and groundnuts – that are important in food security and poverty reduction in developing countries, by providing solutions to overcome drought, poor soils, pests and diseases. TLI was led by GCP and focussed on Africa. Work on beans within TLI was coordinated by the International Center for Tropical Agriculture (CIAT). The partners in the four target countries were Ethiopia’s South Agricultural Research Institute (SARI), the Kenya Agricultural Research Institute (now known as the Kenya Agricultural and Livestock Research Organization, KALRO), Malawi’s Department of Agricultural Research and Technical Services (DARTS) and Zimbabwe’s Crop Breeding Institute (CBI) of the Department of Research and Specialist Services (DR&SS). Cornell University in the USA was also a partner. Tropical Legumes II (TLII) was a sister project to TLI, led by the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) on behalf of the International Institute of Tropical Agriculture (IITA) and CIAT. It focussed on large-scale breeding, seed multiplication and distribution primarily in sub-Saharan Africa and South Asia, thus applying the ‘upstream’ research results from TLI and translating them into breeding materials for the ultimate benefit of resource-poor farmers. Many partners in TLI also worked on projects in TLII.

For an overview of the work on beans from the perspectives of four different partners, watch our video below, “The ABCs of bean breeding”.

What makes a plant drought tolerant?

The question of what makes a plant drought tolerant is one that breeders have debated for centuries. No single plant characteristic or trait can be fully responsible for protecting the plant from the stress of intense heat and reduced access to water.

“It’s a difficult question to answer for any plant, including beans,” says Steve. “Once you do isolate a trait genetically, it can often be difficult to identify this trait in a plant in the field, for example, identifying the architecture and length of a plant’s roots.”

Phenotyping is an important process in conventional plant breeding. It involves identifying and measuring the presence of physical traits such as seed colour, pod size, stem thickness or root length. Gathering data about a range of such characteristics across a number of different plant lines helps breeders decide which plants to use as parents in crosses and which of the progeny have inherited useful traits.

Root length has long been thought of as a drought-tolerance trait: the longer the root, the more chance it has of tapping into moisture stored deeper in the soil profile.

Given, however, that it is difficult to inspect root length in the field, researchers at CIAT have been exploring other more accessible drought-tolerance traits they can more easily identify and measure. One of these is measuring the weight of the plants’ seeds.

Photo: N Palmer/CIAT

Comparison between varieties in trials of drought tolerant beans at CIAT’s headquarters in Colombia.

Fat beans indicate plants coping with drought stress

“We measure seed weight because we are discovering that under drought stress, drought-tolerant bean varieties will divert sugars from their leaves, stems and pods to their seed,” says Steve. “We call this trait ‘pod filling’, and for us it is the most important drought-tolerance trait to be found over the last several years.”

Finding bean plants with larger, heavier seeds when growing under drought conditions indicates that the plants are coping well, and means farmers’ yields are maintained.

As part of GCP’s Legumes RI, African partners like Virginia have been measuring the seed weight of several advanced breeding lines, which can be used as parents to develop new varieties. These breeding lines have been bred by CIAT and demonstrate this pod-filling process and consequent tolerance of drought.

Although this measurement is relatively cheap and easy for breeders all over the world to do, Steve and his team are interested in finding an even more efficient way to spot plants that maintain full pods under drought.

“We are trying to understand which genes control this trait so we can use molecular-assisted breeding techniques to determine when the trait is present,” says Steve. Having identified several regions of genes related to pod filling, he and his team have developed molecular markers to help breeders identify which plants have these desired genes. “The use of molecular markers in selection significantly reduces the time and cost of the breeding process, making it more efficient. This means that we get improved varieties out to farmers more quickly.”

Photo: N Palmer/CIAT

Bean farmer in Rwanda.

Molecular markers (also known as DNA markers) are used by researchers as ‘flags’ to identify particular genes within a plant’s genome (DNA) that control desired traits, such as drought tolerance. These markers are themselves fragments of DNA that highlight particular genes or regions of genes by binding near them.

To use an analogy, think of a story as the plant’s genome: its words are the plant’s genes, and a molecular marker works like a text highlighter. Molecular markers are not precise enough to highlight specific words (genes), but they can highlight sentences (genomic regions) that contain these words (genes), making it easier and quicker to identify whether or not they are present.

Photo: J D'Amour/HarvestPlus

Beans from Rwanda.

Plant breeders can use molecular markers from early on in the breeding process to choose parents for their crosses and determine whether progeny they have produced have the desired trait, based on testing only a small amount of seed or seedling tissue.

“If the genes are present, we grow the progeny and conduct the appropriate phenotyping; if not, we throw the progeny away,” explains Steve. “This saves us resources and time because we need to grow and phenotype only the few hundred progeny which we know have the desired genes, instead of a few thousand progeny, most of which would not possess the gene.”

Outsourcing genotyping to the UK Steve says a significant contribution made by GCP was facilitating a deal with a private UK company (LGC Genomics, formerly KBioscience) that is able to quickly and cheaply genotype leaf samples sent to them by African breeders. The company then forwards the data to the International Center for Tropical Agriculture (CIAT), who analyse it and let the breeders in Africa know which progeny contain the desired genes and are suitable for breeding, and which ones to throw away.  “The whole process takes roughly four weeks, but saves the breeders the time and effort to grow all progeny,” says Steve. “This system works well for countries that don’t have the capacity or know-how to do the molecular work,” says Darshna Vyas, a plant genetics specialist with LGC Genomics. “Genotyping has advanced to a point where even larger labs around the world choose to outsource their genotyping work, as it is cheaper and quicker than if they were to equip their lab and do it themselves. We do hundreds of thousands of genotyping samples a day – day in, day out. It’s our business.”

GCP has supported this foundation work, building on the extensive bean research already done by CIAT dating back to the 1970s, to develop molecular markers not only for drought-tolerance traits such as pod filling, but also for traits associated with resistance to important insect and disease menaces.

“Under drought conditions, plants become more susceptible to pests and diseases, so it was important that we also try to identify and include resistance traits in the drought-tolerant progeny,” says Steve.

Drought is but one plant stressor – diseases and pests wreak havoc too

Photo: W Arinaitwe/CIAT/PABRA

Common bacterial blight on bean.

The bean diseases that farmers in Ethiopia, Kenya, Malawi and Zimbabwe continually confront are angular leaf spot, bean common mosaic virus, common bacterial blight and rust. Key insect pests are bean stem maggot and aphids.

“We’ve had reports of bean stem maggot and bean common mosaic virus wiping out a whole field of beans,” says Virginia. “Although angular leaf spot and common bacterial blight are not as damaging, they can still reduce yields by over 50 percent.”

Virginia says this is devastating for farmers in Malawi, many of whom only have enough land and money to grow beans to feed their families and sell what little excess there is at market to purchase other necessities.

“This is why we are excited by the prospect of developing not just drought-tolerant varieties, but drought-tolerant varieties with disease and pest resistance as well,” says Virginia.

Virginia’s team in Malawi – along with other breeders in Ethiopia, Kenya and Zimbabwe – are currently using over 200 Mesoamerican and Andean bean breeding lines supplied by CIAT to help breed for drought tolerance and disease and pest resistance. Although many do not yet have the capacity to do molecular breeding in their countries, thanks to advances in plant science it is becoming more feasible and cheaper to outsource molecular breeding stages of the process (see box above).

“With help from GCP and CIAT, we have successfully crossed a line from CIAT with some local varieties to produce plants that are high yielding and resistant to most common bean diseases,” Virginia says.

Photo: ILRI

Malawian farmer Jinny Lemson grows beans to feed her livestock.

Ethiopia’s new bean breeders

Photo: ILRI

Young women sorting beans after a harvest in Ethiopia.

One man who has been helping build this new breeding capacity is Bodo Raatz, a molecular geneticist who joined CIAT and GCP’s Legumes RI in late 2011.

“We’ve [CIAT] hosted several African PhD students here in Colombia and have conducted several workshops in Colombia and Africa too,” says Bodo.

“At the workshops we teach local breeders and technicians how to use genetic tools and markers for advanced breeding methods, phenotyping and data management. The more people there are who can do this work, the quicker new varieties will filter through to farmers.”

Bodo says he has found delivering the training both personally and professionally rewarding, especially “seeing the participants understand the concepts and start using the tools and techniques to develop new lines [of bean varieties] and contribute to the project.”

One national breeder whom Bodo has seen advance from the training is Daniel Ambachew, then a bean breeder at the Southern Agricultural Research Institute (SARI) in Ethiopia.

Daniel started as a GCP-funded Master’s student enrolled at Haramaya University, Ethiopia, evaluating bean varieties with both tolerance to drought and resistance to bean stem maggot. He eventually became the Ethiopian project leader for beans within GCP’s Legumes RI.

“Daniel is currently one of only a handful of bean breeders in Ethiopia who are using molecular-assisted breeding techniques to breed new varieties,” says Bodo. “It’s quite an achievement, especially now that he has taken on the lead role in Ethiopia.”

Photo: N Palmer/CIAT

Buying and selling at a bean market in Kampala, Uganda.

For Daniel, learning about and using the new molecular-breeding techniques has been an exciting new challenge. “The most interesting part of the technology is that it helps us understand what is going on in the plant at a molecular level and lets us know if the crosses we are making are successful and the genes we want are present,” says Daniel. “All this helps improve our efficiency and speeds up the time it takes us to breed and release new varieties for farmers.”

By the end of 2014, Daniel and his team had finished the third year of trials and had several drought-tolerant lines ready for national trials in 2015 and eventual release in 2016.

Between 2012 and 2014, Daniel, and two other breeders from SARI, attended GCP’s three-year Integrated Breeding Multiyear Course, learning how to design molecular-assisted breeding trials; collect, analyse and interpret genotypic and phenotypic data from the trials; and manage data using the GCP’s Integrated Breeding Platform (IBP), particularly its Breeding Management System (BMS).

“The IBP is a really fantastic tool,” says Daniel. “During the course we learnt about the importance of recording clear and consistent phenotypic data, and the IBP helps us to do this as well as store it in a database. It makes it easier to refer to and learn from the past. I’m now trying to pass on the knowledge I’ve learnt as well as create and implement a data-management policy for all plant breeders and technicians in our institute.”

Bodo agrees with Daniel about the importance of IBP and believes it will be a true legacy of GCP beyond the Programme’s end in 2014. “The Platform has been designed to be the main data-management platform for plant breeders. It allows breeders to talk the same language and will reduce the need for learning new systems.”

Daniel says the challenge for his institute now is to build further capacity among staff – and to retain it. “At the moment we only have two bean breeders,” says Daniel. “It’s hard to retain research staff in Ethiopia as salaries are very low, so people move on to new, higher paying positions when they get the chance. It’s not unique to Ethiopia, but true of all Africa.”

Photo: O Thiong'o/CIAT/PABRA

Bean trials at KALRO in Kenya.

Kenya chasing higher bean yields

Across the border, Kenya has also been facing staffing issues.

“We are behind Ethiopia, Malawi and Zimbabwe in terms of our capacity and our trials,” says David Karanja, a bean breeder and project leader at the Kenya Agricultural and Livestock Research Organisation (KALRO, formerly the Kenya Agricultural Research Institute, or KARI). “At the start of the project, we didn’t have a breeder to lead the project for almost two years. However, we are now rapidly catching up with the others.”

And it’s a good thing too, as the country is in need of higher yielding beans to accommodate its population’s insatiable appetite for the crop. Out of the four target African countries, Kenya is the largest bean producer and consumer. As such, the country relies on beans imports from Ethiopia, Malawi, Tanzania and Uganda.

“A lot of families eat beans every day,” says David. “On average, the population eats 14–16 kilograms per person each year, but in western Kenya the average is over 60 kilograms.”

Photo: CIMMYT

Githeri, a Kenyan staple food made with maize and beans.

Kenyans consume an average total of 400,000 tonnes of beans each year, consistently more than the country produces. Projected trends in population growth indicate that this demand for beans will continue to increase by three to four percent annually.

Even though the area planted to beans has been increasing, David says farmers and breeders need to work together to improve productivity, which is well below where it should be. “The national average yield is 100 kilograms per hectare, which can range from 50 kilograms up to 700 kilograms, depending on whether we experience a drought, or a pest or disease epidemic,” explains David. “The minimum target we should be aiming for is 1,200 kilograms per hectare.”

Such a figure may seem impossible, but David believes that new breeding techniques and the varieties KALRO are producing with the help of CIAT are providing hope that farmers can reach these lofty goals.

“We have several bean lines that are showing good potential to produce higher yields under drought conditions and also have resistance to diseases like rust and mosaic virus,” says David. “They are currently under national trials, and we are confident these will be released to farmers in 2015.”

Photo: O Thiong'o/CIAT/PABRA

Varieties fare differently in KALRO bean trials in Kenya.

Commercialising beans

Photo: CIAT

Maturing bean pods.

“Many subsistence farmers have limited access to good quality bean seeds; they lack knowledge of good crop, pest and disease management; and they have poor post-harvest storage facilities,” says Godwill Makunde, who was previously a breeder at Zimbabwe’s Crop Breeding Institute (CBI) and leader of GCP’s Legumes RI bean project in Zimbabwe.

TLI’s sister project, Tropical Legumes II (TLII, see box above), led by the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), provided the route by which the upstream work of TLI would have impact in helping these farmers, seeking to deliver the new varieties developed under TLI into their hands. As part of TLII, Godwill, his successor Bruce Mutari, and other African partners worked on developing sustainable seed systems.

“Because beans are self-pollinating, which means each crop is capable of producing seed exactly as it was sown, farmers tend to propagate seed on farm,” says Godwill. “While this can be cost effective, it can reduce farmers’ access to higher yielding, tolerant lines, like the ones we are currently producing.”

In none of the partner countries of TLI and TLII are there formal systems for producing and disseminating bean seeds. Godwill and other partners are working with seed companies on developing a sustainable model where both farmers and seed companies can benefit.

Success built on a solid foundation

Photo: N Palmer/CIAT

Field workers tend beans in Rwanda.

A key to the success of the beans component of GCP’s Legumes RI, according to Ndeye Ndack Diop, GCP’s Capacity Building Theme Leader and TLI Project Manager, has been partners’ existing relationships with each other.

“Many of the partners are part of a very strong network of bean breeders: the Bean Coordinated Agricultural Project [BeanCAP],” explains Ndeye Ndack, adding that the TLI and BeanCAP networks benefited each other.

BeanCAP released more than 1,500 molecular markers to TLI researchers, which have helped broaden the genetic tools available to developing-country bean breeders.

TLI was also able to leverage and advance previous BeanCAP work and networks. For example, it was through this collaboration that GCP was introduced to LGC Genomics, a company it then worked with on many other crop projects.

To sustain integrated breeding practices beyond the Programme’s close in 2014, GCP established Communities of Practice (CoPs) that are discipline- and commodity-oriented.

“GCP’s CoP for beans has also helped to broaden both the TLI and BeanCAP networks too,” says Ndeye Ndack. “The ultimate goal of the CoPs is to provide a platform for community problem solving, idea generation and information sharing.”

Developing physical capacity

Besides developing human capacity, GCP has also invested in developing infrastructure in Ethiopia, Kenya and Zimbabwe.

SARI now has an irrigation system to enable them to conduct drought trials year round. “We have 12.5 hectares of irrigation now, which we use to increase our efficiency and secure our research,” says Daniel. “We can also increase seed with this irrigation during the off-season and develop early generation seeds for seed producers.”

In Zimbabwe, CBI received specialised equipment that enables them to extract DNA and send it for genotyping in the UK.

Both SARI and CBI also received automatic weather stations from GCP for high-precision climatic data capture, with automated data loading and sharing with other partners in the network.

Delivering the right beans to farmers

Back in Malawi, Virginia says another important facet of the TLII project is that researchers understand what qualities farmers want in their beans. “It’s no use developing higher yielding beans if the farmer doesn’t like the colour, or they don’t taste nice,” she says. “For example, consumers in central Malawi prefer khaki or ‘sugar beans’, which are tan with brown, black or red speckles. While those in southern Malawi tend to prefer red beans. Farmers know this and will grow beans that they know consumers will want.”

Photo: N Palmer/CIAT

Diversity at bean market in Masaka, Uganda.

Breeders in all four countries have been conducting workshops and small trials with farmers to find out this information. In Kenya, David finds farmer participation a great way to promote the work they are doing and show the impact the new drought-tolerant and disease-resistant lines can have.

“Farmers are excited and want to grow these varieties immediately when they see for themselves the difference in yield these new varieties can produce compared to their regular varieties,” says David. “They understand the pressure on them to produce more yields and are grateful that these varieties are becoming more readily available as well as tailored to their needs.”

For Steve, such anecdotes provide him and his collaborators with incentives to continue their quest to discover more molecular markers associated with drought tolerance, post-GCP.

“It’s a testament to everyone involved that we have been able to develop these advanced lines with pod-filling traits using molecular techniques, and make them available to farmers in six years instead of ten,” says Steve.

More links

Mar 262015
 

 

Photo: R Cheung/Flickr

Wheat growing in China.

For as long as peoples and countries have traded wheat, drought has continually played a part in dictating its availability and price. Developed countries have become more able to accommodate the bad years by using intensive agricultural practices to grow and store more wheat during more favourable years. However, farmers, traders and consumers are still at the mercy of drought when it comes to wheat availability and prices.

A recent example where drought in just one country inflated the world’s wheat prices was in the People’s Republic of China during 2010–11.

For almost six months, eight provinces in the north of China received little to no rain. Known as the breadbasket of China, these eight provinces grow more than 80 percent of the country’s total wheat and collectively produce more wheat than anywhere else in the world.

It was the worst drought to hit the provinces in 60 years.

With over 1.3 billion mouths to feed, China’s demand for wheat is high and ever increasing. When this demand was coupled with the reduced wheat yield caused by the severe 2010–11 drought, wheat prices around the world rose. While this price rise was beneficial for wheat growers in other countries, it made wheat unaffordable for many consumers and traders in developing nations.

Although this was a one-in-60-year event, previous droughts had already made locals question the sustainability of wheat production in this naturally dry region of China, where water consumption has increased in the past 50 years due to intensive agriculture, industry and a growing and increasingly urbanised population.

Wheat growers and breeders know they need to find wheat varieties and apply practices that will help them adapt to and tolerate drier conditions and still produce sustainable yields.

Luckily, they have help from a community of breeders around the world.

Photo: E Zotov/Flickr

An Uyghur baker displays his bread in Kashi, Xinjiang, China.

Sharing knowledge to improve breeding efficiency and sustainability

In March 2009, 70 international plant breeding leaders and experts from the public and private sector converged in Montpellier, France, as part of a CGIAR Generation Challenge Programme (GCP) initiative to draw up roadmaps to improve plant-breeding efficiency in developing countries.

Richard Trethowan, professor in plant breeding at the University of Sydney, Australia, remembers the meeting distinctly. “We all got together and thought how we could use what we had learnt during the first phase of GCP [2004–2009] – all the genetics and molecular-breeding work – to deliver new varieties of crops, particularly in countries where it will have the greatest impact.”

The resulting roadmap for wheat became the GCP Wheat Research Initiative (RI), with Richard as Product Delivery Coordinator. It had two very clear destinations in mind: China and India.

Richard explains why China and India were targeted – as the world’s two wheat-production giants – in the video below.


Wheat Research Initiative developed capacity and infrastructure in China and India The Wheat RI aimed to integrate genetic diversity for water-use efficiency and heat tolerance into Chinese and Indian breeding programmes. Some aspects of the RI sprang from work led by Francis Ogbonnaya of the International Center for Agricultural Research in the Dry Areas (ICARDA) and by Peter Langridge of the Australian Centre for Plant Functional Genomics (ACPFG). Jean-Marcel Ribaut, GCP Director, says of the work: “The GCP’s RI approach was not about large impacts in the short term. Rather, what GCP demonstrated was definitive proof-of-concept of the power of molecular breeding to increase crop productivity, thereby improving food security. Other agencies are now able to upscale and outscale the proven concept at the national, or even at the regional level.”

Like China, India is an extremely water-stressed country, with the water table in many places falling at an alarming rate. In North Gujarat alone, an established wheat district in western India, the water table is reported to be dropping by as much as six metres per year.

Delivering wheat varieties that have improved water-use efficiency and higher tolerance to drought will have the greatest impact in these countries, given they are the two largest producers of wheat worldwide.

“Even though the Initiative is set to conclude in 2015, the outcomes have already been absolutely phenomenal for such a short time-bound project, given that wheat is such a complex plant to work with,” exclaims Richard. “While we are still a few years away from releasing new drought-tolerant varieties, we have been able to develop systems and build capacity to reduce the time it takes to develop and release these varieties.”

Tapping into genetic diversity to enhance wheat’s drought and heat tolerance

Photo: Rasbak/Wikimedia Commons

Spikes of emmer wheat.

One project that impressed Richard was that led by Satish Misra, GCP Principal Investigator and senior wheat breeder at Agharkar Research Institute, Pune, India.

In a collaboration with the University of Sydney, Australia, and the International Maize and Wheat Improvement Center (CIMMYT), the project identified novel genes associated with drought- and heat-tolerance traits in ancestral wheat lines (of emmer wheat).

Emmer wheat is a minor crop grown mainly in marginal lands, where farmers can produce a small harvest but nowhere near the yield of more elite cultivated lines. Satish explains that emmer wheat lines are very useful for breeders because they have a larger diversity of novel genes than more popular wheat types, such as durum or bread wheat.

Photo: X Fonseca/CIMMYT

Durum wheat spike.

“Durum lines are more commonly used by breeders because of their high yield and hard grain, which is used to make bread wheat and pasta,” Satish says. “However, because of their popularity and continual use in breeding, durum wheat lines have become less and less diverse with years of cultivation.”

The first task was to identify emmer lines that might have genes for drought and heat tolerance. Satish says that CIMMYT played an important part in this process. “They gave us access to their gene bank, which contains almost 2,000 emmer lines. More importantly, they helped us develop a reference set that encapsulated all the diversity found in the emmer lines they had.”

A reference set reduces the number of choices that breeders have to search through, from thousands down to a few hundred – in this case, 300 emmer lines.

“CIMMYT also developed 30 synthetic emmer wheat lines by crossing wild emmer wheat species with domesticated wheat species,” says Satish. “The synthetic lines contain the novel drought- and heat-tolerance genes.”

Satish and Richard’s teams crossed these synthetic lines with durum wheat lines and identified 41 resulting lines with high levels of stress tolerance. These are undergoing further evaluation in India and Australia.

“What Satish has been able to do in five years is amazing and is currently having a big impact in wheat breeding in India and Australia,” says Richard. “We’ve had local breeding companies here in Australia come to us requesting the lines we developed. The same is happening in India, too.”

Reaping existing skills  For Richard, the preliminary success of the Wheat RI is due, at least in part, to the speed with which national breeding programmes in both China and India are learning and incorporating new molecular-breeding techniques. “This was another reason why we chose to focus on China and India: they had the infrastructure and human capacity to start doing this almost immediately,” says Richard. “In other countries where GCP is investing, more time is going into teaching breeders the basics of molecular breeding and genetics. In China and India, they already have that basic understanding and are able to quickly incorporate it into their current programmes.”

Reaping existing skills

Photo: R Pamnani/Flickr

A baker butters naan bread in Hyderabad, India.

For Richard, the preliminary success of the Wheat RI is due, at least in part, to the speed with which national breeding programmes in both China and India are learning and incorporating new molecular-breeding techniques.

“This was another reason why we chose to focus on China and India: they had the infrastructure and human capacity to start doing this almost immediately,” says Richard. “In other countries where GCP is investing, more time is going into teaching breeders the basics of molecular breeding and genetics. In China and India, they already have that basic understanding and are able to quickly incorporate it into their current programmes.”

This does not mean, however, that the work is not focused on building capacity, given that molecular breeding is still a relatively new concept for many breeders around the world.

Ruilian Jing says the China project is continually working to educate and train wheat breeders in molecular-breeding techniques.

“When we started the project, we found that most institutions that focus on wheat breeding in China had the equipment to do marker-assisted breeding but were unsure how to use it,” says Ruilian, professor in plant breeding at the Chinese Academy of Agricultural Sciences (CAAS) and Principal Investigator for the Wheat RI’s drought-tolerant wheat project in China.

Much of Ruilian’s work in China has been in educating these breeders so they can start achieving outcomes.

Younger researchers taking a lead

Ruilian explains that those leading the charge to become educated in molecular-breeding techniques are young researchers, including seven PhD students and one Master’s student supported by the project in China.

One such researcher who is enthusiastically applying these new approaches is Yonggui Xiao, a molecular plant breeder at the Institute of Crop Science, CAAS.

“Working as part of this GCP project gave me my first opportunity to practice using molecular-breeding techniques to improve the quality and yield of wheat under drought conditions,” says Yonggui.

“We have so far successfully used several molecular markers to produce an advanced variety, with higher yield and preferred qualities [taste, grain colour] under water stress, and this will be released to farmers [in 2015].”

Photo: R Saltori/Flickr

Women of the Nakhi people harvest wheat in Songzanlinsi, Yunnan, China.

Yonggui is now expanding the application of the technology to develop varieties with resistance to powdery mildew, a fungal disease that can reduce wheat yields and quality during non-drought years. “Overall, we have been impressed by how these new techniques complement our conventional breeding techniques to improve selection efficiency, in turn reducing the time and costs of producing advanced varieties,” says Yonggui.

Success stories like these make Ruilian’s job easier as she tries to encourage more and more plant breeders to experiment with these new breeding techniques.

At the same time, she is impressed by this new generation of molecular wheat breeders who will ensure that these techniques benefit wheat research in many years to come: “This form of capacity, the human capacity, which we are building, is what will leave the largest legacy in China and help this technology spread from generation to generation and crop to crop.”

Overcoming complex traits, genes and wary breeders

Photo: CCAFS

Wheat farmer in India.

Across the Himalayas, Ruilian’s Indian counterpart, Vinod Prabhu, is just as pleased with the progress and results his team are producing.

“Over the last five years, we have discovered several water-use efficiency traits and their related genes, bred new lines to incorporate the genes and traits and run national trials, all of which would be unheard of using only conventional breeding practices,” says Vinod, Head of the Genetics Division at the Indian Agricultural Research Institute in New Delhi and the Principal Investigator for the Wheat RI’s drought-tolerant wheat project in India.

By the end of the projects in November 2015, partners in China and India will deliver 15–20 new wheat lines with drought and heat tolerance, adapted to each country’s conditions. An additional target for both China and India is to produce four wheat varieties with improved water-use efficiency and higher heat tolerance. These varieties will have the potential to cover about 24 million hectares and minimise yield loss from heat or drought, or both, by up to 20–50 percent.

Vinod confides that all these outcomes are far more than what he initially expected they would achieve: “When we started, we had a lot of reservations about the complexity of breeding for drought tolerance in wheat as well as the acceptance and uptake of these new breeding techniques by conventional breeders.”

Vinod’s primary role has been to coordinate the Indian centres working on the project (see box at end). But he has also been working to convince Indian plant breeders that these unconventional, new breeding techniques will improve their efficiency and aid in their quest to breed for heat- and drought-tolerant wheat varieties.

“Many world-leading wheat breeders were wary at first, but they have definitely started to see the merit in using the technology to enhance their conventional methods as we edge closer towards releasing new varieties in such a short time,” says Vinod.

Photo: N Palmer/CIAT

Wheat seed ready for planting in Punjab, India.

Incorporating conventional methods

An aspect of the Wheat RI that Ruilian and Vinod have been continually promoting is the importance of conventional breeding methods. “These new molecular-breeding techniques are only a small part of the whole breeding process,” says Ruilian. “Yes, they provide a big impact, but in the grand scheme of things they need to be viewed as one tool in a breeder’s tool box.”

Conventional vs marker-assisted breeding To conventionally breed a new wheat variety, two wheat plants are sexually crossed. The aim is to combine the favourable traits from both parent plants and exclude their unwanted traits in a new and better plant variety. This is achieved by selecting the best plants from among the progeny over several generations. Marker-assisted breeding allows breeders to be much more efficient and targeted in their activities. It still requires breeders to sexually cross plants, but they can use genetic information to tell them which plants have particular genes for useful traits, which helps them to choose which parent plants to cross, and then to confirm which of the progeny have inherited the desired gene without necessarily growing and phenotyping all of them under conditions that would express that trait.

For more information on conventional versus molecular breeding, or marker-assisted breeding, see our quick guide here on the Sunset Blog.

Phenotyping: How to manage a subjective process

One of the most important processes of the Wheat RI, and plant breeding in general, is phenotyping: measuring and recording observable characteristics of the plant such as drought tolerance or susceptibility to pests and diseases. Breeders phenotype the plants they have developed to see which ones have the traits they are interested in and also – for molecular breeding to be possible – to establish links between specific genes and specific traits.

Unfortunately, phenotyping has caused a bit of trouble for both Chinese and Indian partners. The challenge stems from the fact that one person’s observations about a plant’s phenotype or characteristics may not be the same as another person’s.

“This is always a challenge for any collaborative plant-breeding project,” says Vinod. “Unless all trials are inspected by one person, there will always be a risk of inconsistent observations.

Photo: CIMMYT

Scientists from South Asia learn phenotyping on a training course at CIMMYT.

To help overcome this inconsistency, one of the first activities of the Wheat RI was to develop phenotyping protocols that allowed researchers in different research institutes and countries to collect comparable data. GCP enlisted Matthew Reynolds, a wheat physiologist at CIMMYT, to help with this.

“Each breeder has their own ways to do things, so it’s important to develop standardised protocols, particularly for a transnational project like this,” explains Matthew. “We developed a few standardised phenotyping manuals and travelled to China to give some intensive hands-on training.”

This problem is not unique to China and India. Another GCP wheat project is providing promising results to help overcome the risk of inconsistency and increase the efficiency and accuracy of phenotyping. Led by Fernanda Dreccer, based at Australia’s Commonwealth Scientific and Industrial Research Organisation (CSIRO), in collaboration with the International Center for Agricultural Research in the Dry Areas (ICARDA), the project is developing a reliable phenotyping approach to detect drought-adaptive traits in wheat crops using cheap and simple tools.

“For example, using just a camera you can analyse crop cover, which is an important trait for shading the crop and/or trapping heat,” says Fernanda. “The idea was to test different non-invasive, low-cost tools and compare them to find something that would provide accurate and useful data related to identifying drought-tolerance traits.”

Another important aspect of phenotyping that Fernanda’s project is helping with is constant and consistent analysis of a crop’s surroundings. “It’s just as important to measure the environment of the crop as it is [to measure] the crop itself to make a correlation between an environmental impact and a plant’s reaction,” says Fernanda.

Since the static nature of single observations can give a misleading or incomplete picture, Fernanda’s team is integrating live crop, weather and soil data through mobile sensors in the field with the aim of producing constant phenotypic information. “This will provide new insights into the interaction between the genotype and the environment. This in turn will help to accelerate the detection of wheat genotypes better suited to cope with drought.”

Photo: R Martin/CIMMYT

A young farmer in her wheat field in India.

Managing the tsunami of phenotyping data

Although a plant breeder’s work should be simplified and made more efficient by combining molecular-breeding technologies with advanced phenotyping techniques and protocols, the reality is not necessarily so easy.

There are many steps to the plant-breeding puzzle, all of which produce data. The more advanced the techniques and – in the case of wheat – the more complex the plant’s genome, the more pieces of data breeders need to sift through to find solutions.

Before the Wheat RI started, Richard saw that this impending tsunami of data was going to be a problem in both China and India: “Both countries had the skills to carry out these advanced techniques, but they didn’t have in place a strong culture of data management.”

This problem is by no means unique to China and India, Richard says: “Most of the time, plant breeders keep a log of all their data in a book or Excel sheet. However, these data often get lost once a project is completed.”

GCP recognised this problem before the RIs began and has, since 2009, been developing the Breeding Management System (BMS) – a suite of interconnected software designed to manage the mass of data – as part of its Integrated Breeding Platform (IBP).

“The BMS is the first tool that can help breeders record and collate their data in a coordinated way,” says Richard. “This is vital in a project like this, which has several institutes across three countries working towards a similar product.”

Vinod agrees with Richard, adding that the BMS was relatively easy for his Indian partners to learn and use: “The BMS is great as we have no way of losing data.”

Rolling out the BMS in China, though, has been more difficult due to the language barrier. Ruilian explains: “We are now working towards translating the IBP, but it will be an ongoing challenge as the platform continually changes and is updated.”

Ruilian is optimistic that a translated BMS will become a viable tool for Chinese breeders in the future. “The more that we collaborate with other countries, the more a tool like this becomes important to have.”

Watch Richard on adoption of IBP tools in the video below.

Friendly competition helping inspire India’s wheat breeders

Vinod credits two things for the successful development of new wheat varieties and integration of new breeding techniques and data-management systems: a clear, logical plan and friendly competition between China and India to breed the first new drought-tolerant varieties.

“The initial plan, which Richard helped develop in Montpellier, was logical and well thought out. Although we initially thought it was overambitious in its objectives, we have been able to meet them so far, which is a great credit to the team and their enthusiasm to try these new technologies and see for themselves the benefits first hand.

“What has also helped is our competitive spirit, as we would like to achieve the objectives before the Chinese breeders do. Our breeders are always asking me for updates on how China is progressing!” Vinod adds, with a chuckle.

Ruilian agrees with Vinod’s assessment, adding: “The project would not have been as successful if it was solely national. It needed the international collaboration and friendly competition to help build confidence and drive.”

For Richard this international collaboration, between two very different and proud cultures, allowed the project to broaden its scope and troubleshoot quicker than usual.

“They [the Chinese and Indian researchers] think about problems in different ways. When you get a group of people in a room from different backgrounds, you can come up with great integrated plans, things you would never have come up with within just a national team,” says Richard.

Watch Richard on the beauty of diversity in research partnerships in the video below.

Securing wheat production into the future

With the project concluding in 2015, both the Chinese and Indian researchers are working towards completing national trials and releasing their new, advanced drought-tolerant varieties to farmers and other breeders. However, for Richard, the impact of the Wheat RI may not be fully recognised for 10–20 years.

“The initial new varieties that both China and India develop will help farmers in the short term. However, as both countries become more advanced in using the technology, future varieties are sure to be more and more robust. What’s more, these techniques and tools are sure to filter through to other national wheat-breeding programmes, as well as to other crops.”

In the case of wheat, new drought-tolerant varieties will help secure both China’s and India’s wheat industries, helping to stabilise wheat yields, and consequently prices, the world over. These new varieties may not be the silver bullet for eliminating the risks of drought, but they will go a long way to mitigating its impact.

Photo: Rosino/Flickr

Donkeys bring home the wheat harvest in Qinghai, China.

The GCP Wheat Research Initiative involved 10 institutes from China, India and Australia: China – Chinese Academy of Agricultural Sciences (Institute of Crop Science; National Key Facility for Crop Gene Resources and Genetic Improvement) Hebei Academy of Agricultural Sciences Shanxi Academy of Agricultural Sciences  Xinjiang Academy of Agricultural Sciences India – Indian Agricultural Research Institute Punjab Agricultural University Agharkar Research Institute  National Research Centre on Plant Biotechnology Jawaharlal Nehru Krishi Vishwa Vidyalaya Australia – Plant Breeding Institute, University of Sydney The Wheat RI built on several previous GCP projects conducted by the International Maize and Wheat Improvement Center (CIMMYT) and International Center for Agricultural Research in the Dry Areas (ICARDA).

More links

Jan 302015
 

“Little had been done to advance the genetic diversity of lentils.” This was the picture back in 2005, recalls Aladdin Hamwieh, a scientist at the International Center for Agricultural Research in the Dry Areas (ICARDA) based in Lebanon.

“Lentil has a narrow genetic base, meaning not too many varieties are used in production,” he explains.

Photo: ICARDA

A small sample of the lentil diversity available in the ICARDA gene bank.

It was on this premise that Aladdin joined a three-year global effort to capture and understand the genetic diversity of the world’s lentil varieties – a protein-rich crop that plays an integral part in the lives of many people in Central and West Asia and North Africa (CWANA), South Asia and North America.

He was funded by the CGIAR Generation Challenge Programme (GCP) to develop a refined set of genetic reference materials for lentils so that plant breeders across the globe could access the best gene pool available to be able to improve food security in developing countries.

“Essentially, the genetic make-up of lentil was repeatedly filtered until 15 percent of ICARDA’s gene bank was collected,” says Aladdin.

ICARDA has the largest collection of lentil genes in the world. Some work had been done on improving the genetics of lentils to withstand harsh, dry conditions. But it was not enough to prepare for the challenge the world is now facing – feeding almost 10 billion people by 2050 and climate conditions that mean longer dry periods and more erratic rainfall.

ICARDA has a global mandate for research on lentil improvement. As such, ICARDA houses the world’s collection of lentils, held in trust as a global public good. It includes 8,789 different types of seed of cultivated lentils from 70 countries, 1,146 breeding lines and 574 new seed samples from 4 wild lentil species representing 23 countries. From this, a collection of 1,000 plants was identified for use as GCP reference materials, consisting of traditional farmer varieties, wild relatives and elite varieties and cultivars. Individual plants of each were planted in 2005 so that seed could be collected at the end of the growing season.

The reference set captures the existing genetic diversity of lentils and makes it easier for scientists to search for genes that can help overcome the challenges to lentil production. It consists of about 150 accessions, or 15 per cent of the global collection studied (see box).

Creating the reference set immediately helped researchers to understand more about lentils. “The major outcome was that different gene pools were identified where accessions from Europe and America were clearly separated from Asia and Africa,” Aladdin says. “Accessions from India, Afghanistan and Pakistan were also separated from accessions from the Middle East and North Africa.”

A common resource for lentil breeders

International cooperation and knowledge sharing are hallmarks of GCP, with one of the Programme’s key goals being to facilitate collaboration between scientists from across the globe in breeding new varieties of crops that can not only tolerate drought, but also resist diseases and tolerate poor soils. Ashutosh Sarker, a former lentil breeder and currently Coordinator and Food Legume Breeder for ICARDA’s South Asia and China Regional Program, says production challenges for lentils vary from country to country. While demand is rising globally, he says, some developing countries are having trouble meeting their own need for this staple food.

Photo: P Casier/CGIAR

A woman farmer with lentils in Bihar, India.

This was where the GCP work came in; its purpose, according to Aladdin, was to “develop a diverse reference set that is small and easy to handle. This way, it can be sent around the world for scientists to simultaneously screen for desirable or undesirable traits. This has important implications for developing countries.”

The reference collection serves as a common resource for all lentil breeders interested in the same crop.

“These materials can be accessed to achieve farming goals – to produce tough plants suitable for local environments. In doing this, farmers have a greater likelihood of success, which ultimately improves the wider population’s food security.”

When Aladdin’s team studied the reference collection, they were able to identify favourable genes.

“This enables us to look at the genes of plants and highlight those traits that best suit certain environments,” he says, “and then breed plants to be better adapted.”

Lentils – with a protein content ranging from 22 to 35 percent – are an important source of dietary protein in both human and animal diets, second only to soya beans as a source of usable protein. Lentils are currently grown on 3.8 million hectares worldwide, with a total annual production of over 3.5 million tonnes. The major producers of lentils are countries the South Asia and CWANA regions, and Canada, Australia and the USA. Productivity is low in developing countries, largely because the crop is grown on marginal lands in semiarid environments, without irrigation, weeding or pest control.

Diversity is key to searching for valuable breeding traits

Shiv Kumar Agrawal, who joined ICARDA in 2009, uses the reference set developed for GCP to identify and create markers for drought-tolerant and early-maturing traits for key lentil-producing countries, including Bangladesh, Ethiopia and India.

“Developing more markers will help mitigate lentil’s barriers to production,” says Shiv, pointing to climate change and rising temperatures in production zones as adversely affecting lentil yields.

Markers are like genetic ‘tags’ that indicate which plants or seeds have particular genes, so markers related to relevant genes – for traits such as heat tolerance, for example – can help breeders choose which plant materials to use when developing a new variety.

“Breeding for this should be a priority,” he continues. “Developing heat-tolerant lentil plants would help to expand the area of legume cultivation, stabilise yield in areas prone to heat stress and mitigate impacts of global climate change in the future.”

This is the same for other traits, he says, which would improve food security in developing countries: “Developing extra-early breeds of lentils has great scope in diversifying cropping methods and gives more flexibility for farmers.”

Photo: T Wolday/Bioversity International

Farmers in Ethiopia winnow orange lentils.

Karthika Rajendran, a postdoctoral student working with Shiv at ICARDA, uses both conventional and molecular-breeding approaches to develop heat-tolerant lentil cultivars that mature early. The products of GCP, she says, are “helpful to identify the source of genetic diversity and molecular markers for the traits identified under each research targets.”

Like Shiv, Karthika stresses the value of heat-tolerant varieties for heat-stressed areas and in reducing the impacts of climate change, and adds that improving other traits alongside also has significant impacts: “The development of machine-harvestable lentils reduces the production cost, increases the farm profit, reduces the drudgery of women and improves the nutritional and food security of smallholder farmers in developing countries.”

Photo: E Huttner/ACIAR

Farmer Minto with lentils in his field in Bangladesh.

While achieving such lentil varieties may be some way down the track, Shiv and Karthika offer a small glimpse of what the future holds and the promise of making even more from GCP’s genetic reference set than what has been achieved so far.

Preserving genetic resources

Aladdin Hamwieh is also looking to the future: “We don’t know what tomorrow brings, so people need to understand the value of such genetic reference material.”

He reflects on the reality of how civil unrest in developing countries often means local agriculture is disrupted and crops destroyed, which can mean the loss of traditional varieties.

“We could lose interesting genes from these,” says Aladdin. “We must therefore maintain and protect the ICARDA database, because it stores important information that the next generation won’t be able to study in nature.”

Aladdin is adamant that this is important not only for developing countries but for the whole world. “We can’t make genes in future so this one we cannot lose,” he stresses.

A ‘backup’ duplicate copy of ICARDA’s lentil collection is stored in the Arctic Circle at the Svalbard Global Seed Vault.

Groundwork on lentils ‘gave orientation to future breeding efforts’

Although GCP’s genetic research work on lentils came to an end in 2007, scientists all over the world can still access the materials – and are reaping other benefits from GCP’s work too. For example, ICARDA is using GCP’s Integrated Breeding Platform (IBP) – particularly the Breeding Management System (BMS) – for its lentil-breeding programme.

Reflecting GCP’s collaborative spirit, Shiv explains that his team have not only successfully integrated use of BMS within their own programme, but have also included it in regular training programmes for developing country partners.

Karthika says, “We use the BMS to store historical data of crossing blocks and germplasm collections and to create fieldbooks, field maps and labels of yield trials. We use the crossing manager to build up the list of the crossing blocks, and the breeding manager to maintain the pedigree of the breeding programme.”

She explains that within the BMS, “the breeding view demonstrated a great potential to analyse the phenotypic and genotypic data for single and multienvironmental conditions,” and notes that “the Molecular Breeding Design Tool would be useful in the process of marker-assisted selection.”

ICARDA plans to implement the BMS to develop fieldbooks for Lentil International Elite Nurseries, using the IBFieldbook tool, and to distribute the books to developing country partners for data collection.

“Once the database is centralised, it will facilitate rapid access to breeding material and easy sharing of knowledge and technology to the developing country partners,” says Karthika.

Such ongoing advances in breeding technologies since the outset of GCP mean the refining process can continue.

“We should not stop,” says Aladdin, encouraging other lentil breeders and researchers to continue their work.

Photo: Bill & Melinda Gates Foundation

A female farmer in India helps to harvest lentils by sifting them after fellow workers have beaten the stalks to remove the seeds from their pods.