multiparent advanced generation intercross (MAGIC)

Genetic stocks: the secret to more productive and efficient crops

Crop breeding, Genetic resources, Genetics, Themes No Responses »

Oct 192015

Precious sorghum seed diversity.

Humans are a protective species. We like to hoard away our precious items in vaults and safes made of concrete and steel, safe from thieves and catastrophes.

One not-so-obvious precious item, which many people take for granted, is seed. Without seeds, farmers would not be able to grow the grains, legumes, vegetables and fruits we eat.

For centuries, farmers have harvested seeds to store and protect for planting the following year. Most of the time, farmers will only keep seeds harvested from plants that have excelled in their environment – that have produced high yields or have favourable qualities such as larger or tastier grain. This simple iterative process of selecting primarily for high yields means that many crops today are closely related genetically, which can make them more vulnerable to evolving diseases and pests.

Without diversity, a severe epidemic can completely wipe out a farmer’s crop — and even a whole region’s crop. One of the best-known historical examples of just such a disastrous crop failure is the Irish Potato Famine of the 19^th century, when potato blight disease caused extensive death, human suffering and social upheaval. A number of crops around the world are in similar danger today, including wheat, threatened by the Ug99 strain of stem rust disease, to which almost all the world’s wheat is susceptible, and cassava, menaced by African cassava mosaic virus (ACMV).

The solution – genetic diversity

Plant breeders are looking at ways to increase diversity among cultivated crops, mitigating the risks of pests and diseases and introducing genes that help plants thrive in their local environments. To do this they are looking for useful traits in traditional cultivars, related species and wild ancestors. Such traits may include tolerance to drought, heat, and poor soils as well as insect and disease resistance. Breeders cross these donor parents with high-yielding elite breeding lines. The resulting new varieties have all the preferred traits of their parents and none of the deficiencies.

The genetic diversity of crops and their wild relatives is held by gene banks. There are thousands of gene banks worldwide, which collect and store seeds from hundreds of thousands of varieties. Breeders and researchers submit seed and tissue of wild and cultivated varieties as well as of lines of new varieties they are trying to breed.

Staff hard at work in the medium-term storage room of the International Rice Genebank at IRRI.

“For years, gene banks were primarily repositories, but with genetics evolving, and its subsequent application in plant breeding growing over the past 10 years, breeders and geneticists are now mining gene banks for wild and exotic species that might have favourable genes for desired traits,” explains Ruaraidh Sackville Hamilton, evolutionary biologist and head of the International Rice Genebank maintained by the International Rice Research Institute (IRRI) at its headquarters in The Philippines.

Sifting through all these gene-bank collections for plants with desired traits is challenging for breeders, even for traits that are easy to select for through visual screening. For example, Ruaraidh says the rice collection held at the International Rice Genebank contains more than 117,000 different types of rice, or accessions.

In recognition of this challenge, the initial rationale of the CGIAR Generation Challenge Programme’s (GCP) genetic stocks activity was to make the diversity in gene banks more easily accessible and practical for the study – and application – of genetic diversity.

Taking stock of genetic stocks

The first step towards making diversity accessible to breeders was to develop reference sets, representing as much genetic diversity as possible within a small proportion of gene bank accessions, selected through pedigree and molecular marker information.

“Reference sets reduce the number of choices that breeders have to search through, from thousands down to a few hundred,” says Jean Christophe Glaszmann, a plant geneticist at France’s Centre de coopération internationale en recherche agronomique pour le développement (CIRAD; Agricultural Research for Development), who held a managing role at GCP between 2004 and 2010, overseeing much of the reference-set work as GCP’s Subprogramme Leader on Genetic Diversity during GCP’s Phase I.

“A reference set represents the whole diversity found in the collections. Breeders can then use this sample to make crosses with their preferred varieties to try and integrate specific genes from the reference-set lines into those varieties.”

During the first phase of GCP (2004–2008), the Programme focused on identifying and characterising reference sets, each of roughly 300 lines, for banana, barley, cassava, chickpea, coconut, common bean, cowpea, faba bean, finger millet, foxtail millet, groundnut, lentil, maize, pearl millet, pigeonpea, potato, rice, sorghum, sweetpotato, wheat and yam. For most crops phenotyping data – information about physical plant traits – were also being made available for the reference sets, helping researchers to select material of interest for breeding.

A trainee at the International Maize and Wheat Improvement Center (CIMMYT) shows off diverse wheat ears, a small sample of the thousands of different lines found in the centre’s gene bank.

A further aspect of the work was the development of data-kits, which included molecular markers used to genotype and verify the sets. These kits allow plant scientists to assess and compare the diversity of their own collections with that of the reference sets, thus facilitating the introduction of new diversity in their prebreeding programmes.

Jean Christophe says the reference sets and data-kits were pivotal to the success of GCP’s molecular-breeding projects as they allowed researchers in different institutes to simultaneously work on the same genetic materials. “The sets served as consistent reference material that everybody collaborating on the project could analyse,” he explains. “Some of these collaborations involved hundreds of researchers, particularly those projects seeking to map genomes and identify genes.”

During the second phase of GCP (2009–2014), the reference sets for GCP’s Phase II target crops (cassava, chickpea, common bean, cowpea, groundnut, maize, rice, sorghum and wheat) were thoroughly phenotyped under different environments, including biotic and abiotic stresses. Jean Christophe says this work helped to identify new alleles (alternative forms of a gene or genetic locus) associated with desired traits that could be used for breeding purposes. Reference sets have been used successfully to identify and use new plant material in breeding programmes to improve various traits, particularly disease resistance and even more complex traits such as drought tolerance in cassava, chickpea, cowpea, maize, sorghum and wheat.

Broadening groundnut’s genetic base to prevent disease

A farmer in Senegal shows off her groundnut crop, almost ripe for harvest.

Another objective of GCP’s genetic stocks activity was to create new diversity within domesticated cultivated crops that have narrow genetic diversity, such as groundnut.

“The groundnuts we grow today are not too dissimilar to the ones that were first created naturally five to six thousand years ago,” says David Bertioli, a plant geneticist at the University of Brasília, Brazil. “This means that they are genetically very similar and have a narrow genetic base – the narrowest of any cultivated crop.”

This genetic similarity means that all cultivated groundnuts are very susceptible to diseases, particularly leaf spot, requiring expensive agrochemicals, especially fungicides. Without agrochemicals, which smallholder farmers in Africa and Asia often cannot afford, yields can be very low.

David says groundnut breeders always recognised the need to increase diversity, but because cultivated groundnuts have had a narrow base for so long, they became radically different from their wild relatives, making it very difficult to successfully cross wild species with cultivated species.

New genetic diversity is created through recombination, that is, through crossing contrasting varieties to create novel lines. Researchers can study these recombinants to identify genes associated with desired traits or use them in further crosses to develop new varieties.

“One of our first jobs was to make wild-species recombinants to trace out the relatedness of the wild-species genomes,” says David. “Once we could see the relatedness, we could see which wild species we could cross with cultivated lines. We had to do a lot of these crosses, but we eventually started to broaden the genetic diversity of the cultivated lines.”

David says this painstaking work, carried out under GCP, also formed the platform for sequencing the groundnut genome for the first time.

“That gave us an even greater understanding of the genetic structure, which is laying the groundwork for new varieties with traits such as added disease resistance and drought tolerance,” says David.

An additional key outcome of the groundnut aspect of the Legumes Research Initiative was developing ‘wild × domesticated’ synthetic lines, which are being crossed with domesticated groundnut varieties in Malawi, Niger, Senegal and Tanzania to introduce higher drought tolerance.

Like many areas of Africa struck by climate change, this village in Tanzania is suffering the effects of drought, with temperature increases and increasingly unpredictable rainfall.

Genetic gain by exploiting genetic stocks

The genetic stocks activity has generated a large and diverse array of resources across GCP’s target crops, not just for groundnut.

Recombinant inbred lines (RILs) incorporating specific traits of interest – particularly drought tolerance – have been developed for cowpea, maize, rice, sorghum and wheat. RILs are stabilised genetic stocks, created over several years by crossing two inbred lines followed by repeated generations of sibling mating to produce inbred lines that are genetically identical. These can then be used to discover and verify the role of particular genes and groups of genes associated with desired traits.

Near-isogenic lines (NILs) are RILs that possess identical genetic codes, except for differences at a few specific genetic loci. This enables researchers to evaluate particular genes and groups of genes that they may want to incorporate into breeding lines, particularly genes that have come from plants that otherwise do not perform well agronomically, such as wild relatives or older varieties. Sorghum NILs incorporating the Alt_SB locus for aluminium tolerance are being tested in Burkina Faso, Mali and Niger on problematic acid soils.

Multiparent advanced generation intercross (MAGIC) populations are a form of recombinants developed from crossing several parental lines from different genetic origins and, in some cases, exotic backgrounds to maximise the mix of genes from the parental lines in the offspring. MAGIC populations have been developed for chickpea, cowpea, rice and sorghum, and are being developed for common bean. Selected parental lines have been used to combine elite alleles for simple traits such as aluminium tolerance in sorghum and submergence tolerance in rice, as well as for complex traits such as drought or heat tolerance.

The further evaluation and use of the genetic stocks stemming from GCP-supported projects, as well as the generation of new genetic stocks, will continue beyond GCP through CGIAR’s Research Programs as well as through those institutes and national breeding programmes associated with GCP. There will be a continuing and evolving need to identify new genes associated with desired traits to improve cultivated germplasm.

Transplanting rice plants in Myanmar.

Sustaining genetic stocks into the future

Sustainability of genetic stocks has always been an issue, as stocks are generally not managed in a centralised way but are left under the direct responsibility of the scientists who developed them. These resources have therefore usually been handled in a highly ad hoc manner.

Because of high staff turnover in CGIAR Centers and breeding programmes in developing countries, and also because their management is neither centralised nor coordinated, these resources are also often lost as staff move from one organisation to another.

Although different genetic resources require different management protocols and storage timelines, the idea that gene bank curators take on the management of genetic stocks was proposed several years ago. For Centers such as IRRI, this is already a reality – for at least some of the genetic resources developed.

However, with the growing popularity of tapping into the rich diversity in gene banks that GCP’s genetic stocks activity has helped drive, gene bank supervisors such as Ruaraidh Sackville Hamilton are concerned about how genetic stocks will be sustained.

“The more popular molecular breeding and genetic stock become, the more funds we need to help us curate and disseminate them,” says Ruaraidh. He proposes to recover costs for managing genetic resources through a chargeback system on a two-tier scale, with non-profit organisations receiving stock at lower costs than commercial organisations. “Such a system would be sustainable and reduce the burden on gene bank institutes,” he says.

Still, the costs are of concern to institutes, particularly CGIAR Centers, which maintain most of the world’s plant crop gene banks.

CGIAR, a global partnership that unites 15 research Centres, including IRRI, is engaged in research for a food-secure future. CGIAR also created GCP. “CGIAR’s main priority is to conserve genetic resources for all humankind,” says Dave Hoisington, Senior Research Scientist and Program Director at the University of Georgia in the US. He was formerly Director of Research at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) and Director of the Genetic Resources Program and of the Applied Biotechnology Center at the International Maize and Wheat Improvement Center (CIMMYT) (both CGIAR Centers) and Chair of the GCP Consortium Committee.

“In both of the CGIAR Centers I worked in,” says Dave, “we always maintained the position that if the Center were to shut down, the last thing we’d do would be to turn out the lights of the gene bank. Even when we had funding cuts, we would never cut the budget for the gene bank.”

At work in the maize active collection in the gene bank at CIMMYT, which keeps maize and wheat diversity in trust for the world.

New programme to fund crop diversity

To alleviate some of the funding burden on CGIAR Centers and free up more money to use in research and development, CGIAR created a new CGIAR Research Program for Managing and Sustaining Crop Collections. The comprehensive five-year programme is managed by the Crop Trust (formerly Global Crop Diversity Trust).

“The Trust is a financial mechanism to raise an endowment, to ensure the conservation and availability of crop diversity,” says Charlotte Lusty, Genebank Programmes Coordinator at the Global Crop Diversity Trust. “The new programme is an extension of the Trust’s work. We aim to raise a USD 500 million endowment by 2016. The interest from this will be divided between the CGIAR Centers to cover all their long-term conservation operations.”

The new programme is also reviewing how gene banks within CGIAR are being managed, with a view to developing a quality management system, which it hopes will make gene banks run more efficiently. Charlotte says it is also encouraging stronger gene banks, such as IRRI and CIMMYT, to lend their expertise and experience to smaller gene banks so they can meet and build on their management quality.

Dave Hoisington believes that the new programme will provide CGIAR’s gene banks with greater capacity and make them even more attractive for researchers wanting to make use of their rich diversity.

A wide diversity of rice seed from the collection of the International Rice Genebank at IRRI.

Looking forward 30 years

Tapping into new diversity was really at the heart of GCP, and was a major, if not the primary, rationale for its establishment. Over its 10-year lifespan, has invested almost USD 28 million, or 18 percent of its budget, in developing genetic stocks, both reference sets and recombinants, for over 20 different crops.

Although these products don’t directly benefit farmers, they do indirectly help by significantly increasing breeding efficiency.

“All this research is fairly new and I am amazed, as a geneticist and plant breeder, by how far we’ve come since GCP started in 2004,” says David Bertioli.

“What we’ve been able to do in groundnut – that is, broaden the genetic base – hasn’t occurred naturally or through conventional breeding for thousands of years. And we’ve been able to do it in less than ten years.”

David recognises that the true value of the research will only be realised when new disease-resistant varieties are available for farmers to grow, which may be in five to seven years. “Only then will we be able to look back and consider the worth of all the hard work and cooperation that went into developing these precious varieties.”

GCP’s genetic stock activities have generated a large and diverse array of resources. These resources lay the foundation for further genetic stock development and will aid in researchers’ quests to tap into genetic diversity well into the future.

Hei Leung: rice man of MAGIC and gene discovery

Asia, Bananas, Comparative genomics in cereals, Phase I crops, Researchers, Rice No Responses »

Sep 242015

Hei Leung has always been passionate about diversity, especially genetic diversity, and that’s one reason why he leapt at the chance to get involved with the CGIAR Generation Challenge Programme (GCP) right from its inception more than a decade ago.

But GCP’s attraction for Hei wasn’t just about genetic diversity; it was also about working with diverse institutes and researchers. At the time, Hei had been working for the International Rice Research Institute (IRRI) for some 10 years, on and off, including a stint at Washington State University in the USA.

“The whole idea of the Challenge Programme was to bring people together from different places instead of an individual CGIAR Centre doing things,” he says.

Hei also saw the likely spin-offs from rice research to other crops such as wheat, maize and sorghum, which are also crucial to food security.

“Rice is a ‘model crop’ because of its small genome. This means researchers in major cereals like wheat and maize, which have much bigger genomes but share genes of similar functions, can benefit from our work with rice.”

From little pizzas great programmes grow!

It all began in 2003, over pizza, in Rome. Hei remembers that his commitment to GCP started when he met with a small group of people including Robert Zeigler, who was to become the first Director of GCP, and who is currently Director General of IRRI.

“Little did we know that pizza was so inspiring,” Hei says, recalling that it was during that meeting that they agreed on the name: the Generation Challenge Programme.

GCP was formally launched in 2004 in Brisbane, Australia, at the 4^th International Crop Science Congress.

Making the Programme ‘pro-poor’

Hei was initially involved with GCP as Subprogramme Leader for Comparative Genomics for Gene Discovery between 2004 and 2007, and later as a Principal Investigator for the Rice Research Initiative. Taking on his leadership role, Hei recognised from the start that many crops important to developing communities in Asia and Africa needed to become more drought-tolerant because of the increasing effects of climate change.

“We wanted to have a programme that is what we call ‘pro-poor’,” he says. “The majority of the world’s people depend on crops such as rice, wheat and maize for food.”

“I always feel that if you can solve eastern India’s problems, you can solve most of the problems in the world,” Hei adds. “If you travel in eastern India, you can see climate change happening day in, day out. You don’t have to wait 10 years or 50 years; it’s happening already. They either have too much or too little water. It’s a high-stress environment.”

Women at work threshing rice near Sangrur, Punjab, India.

Rice is the world’s most widely consumed cereal crop, and is particularly important as the staple food of 2.4 billion people in Asia. GCP recognised rice’s importance and invested almost USD 29.5 million in rice research and development.

Furthermore, the genetic breeding lessons learnt from rice can also be applied to other staple crops such as wheat, maize and sorghum.

Other GCP-supported researchers used comparative genetics to determine if the same or similar genes – for example, the phosphorus starvation tolerance (PSTOL1) protein kinase gene found in rice – was also present and operating in the same manner in sorghum and maize.

They found sorghum and maize varieties that contained genes, similar to rice’s PSTOL1, that also conferred tolerance to phosphorus-deficient soils by enhancing the plant’s root system. They were then able to develop molecular markers to help breeders in Brazil and Africa to identify lines with these genes, which can now be used in breeding and developed as varieties for farmers growing crops, particularly in acidic soils.

Seeing the potential for novel researcher interactions

Hei also recognised that crops that received less scientific attention but remained important as regional staple foods, such as bananas and plantains (of the genus Musa), could benefit from comparative genomics research.

“We had a highly motivated group of researchers willing to devote their efforts to Musa,” remembers Hei, who is currently IRRI Program Leader of Genetic Diversity and Gene Discovery.

“GCP’s community could offer a framework for novel interactions among banana-related actors and players working on other crops, such as rice. So, living up to its name as a Challenge Programme, GCP decided to take the gamble on banana genomics and help it fly.”

A banana farmer at work in the Philippines.

However, after four years, Hei found it difficult to maintain his GCP leadership role as well as keep on top of his IRRI work: “They said I was 50 percent with IRRI and 50 percent with GCP, but it is never like that in reality. I was always doing two jobs, or at least one-and-a-half jobs, and I didn’t think I was doing a good enough job for either. I thought it was time for other people to come into GCP.”

While Hei stepped down from a leadership role, he remained active working on GCP projects throughout the life of the Programme.

Hei says that during the last five years of GCP, a lot of technology to characterise genetic diversity evolved “to bring high-quality science to accelerate our mission to help the poor areas of Asia and Africa.”

A MAGIC affair

The development of MAGIC (multi-parent advanced generation intercross) populations is the project that Hei gets most excited about. From these populations, created by crossing different combinations of multiple parents, plant lines can be selected that have useful characteristics such as drought tolerance, salinity tolerance and the ability to produce better quality grain.

“Now many crop breeders are calling for MAGIC populations,” says Hei. “I feel proud that at GCP we decided to support this concept and activity. This is one of GCP’s most important legacies and it’s one of my most favourite things.”

Hei Leung looking relaxed in the lab at IRRI.

Honoured as a Fellow of the American Phytopathological Society (APS), Hei is recognised “for his leadership in the international community toward building and distributing rice genetic and genomic resources and creating capacity in plant pathology in the developing countries of Asia.”

Hei’s GCP leadership and research have clearly provided him with an important platform for taking on leadership and champion roles linking many individuals and organisations across Asia and Africa. His ASP profile concludes: “His promotion of collaborative research and his leadership in such programmes in the developing world have contributed to the building of a dynamic research community that promotes both basic knowledge and food security for Asia and the world.”

Making a difference to food security and farmer’s lives in developing countries is what GCP is all about. Such differences have been made possible through collaborative links that connect a diversity of organisations and people with the latest research in genetic diversity and breeding techniques.

A farmer transplants rice in the Philippines.

It’s amore!

Hei recalls his personal and professional journey with GCP with much affection: “I think that it has been a wonderful scientific journey in terms of knowing the science and opening up my mind to being more receptive to alternative ways of doing things.

“There have been so many friends I have met through networking with GCP. Sometimes you go through bumpy roads, but anything you do will have bumpy times. And it’s very unusual to have a programme so illuminating. We honoured our commitment to finish in 10 years. It is a programme that had a fresh start and a clean ending.

“Most importantly, GCP has enabled plant breeders to embrace cutting-edge science through partnerships that focused on improving crop yields in areas previously deemed unproductive,” he says. “GCP is unique, one-of-a-kind, and I love it!”

Chickpea’s promise: to be win-win for Africa and India

Africa, Asia, Capacity building, Chickpeas, Crop breeding, Genetics, Legumes No Responses »

Jun 012015

Crop science and collaboration help African farmers feed India’s appetite for chickpeas

Indian chickpea farmer with her harvest.

India loves chickpeas. With its largely vegetarian population, it has long been the world’s biggest producer and consumer of the nutritious legume. In recent years, however, India’s appetite for chickpea has outstripped production, and the country is also now the world’s biggest importer. With a ready market and new drought-tolerant varieties of chickpea, millions of smallholder African farmers are ready to make up India’s shortfall, improving livelihoods along the way and ensuring food security for some of the world’s most resource-poor countries.

GCP achieved real impacts in chickpea by catalysing and facilitating the deployment of advanced crop science, particularly molecular breeding, in the development of drought-tolerant varieties for both Africa and Asia. Over the course of its research, it also contributed to major advances in chickpea science and genomic knowledge.

Although India boasts the world’s biggest total chickpea harvest, productivity has been low in recent years with yields of less than one tonne per hectare, largely due to drought in the south of the country where much chickpea is grown. The country is relying increasingly on exports from producers in sub-Saharan Africa to supplement its domestic supply.

Drought has been hindering chickpea yields in Africa too, however, and this is a major concern not only for Africa but also for India. Ethiopia and Kenya are Africa’s largest chickpea producers, and both countries have been producing chickpea for export. However, their productivity has been limited, mainly because of heat stress and moisture loss, as well as by a lack of access to basic infrastructure and resources.

Indeed, drought has been the main constraint to chickpea productivity worldwide, and in countries such as Ethiopia and Kenya this is often made worse by crop disease, poor soil quality and limited farmer resources. While total global production of chickpea is around 8.6 million tonnes per year, drought causes losses of around 3.7 million tonnes worldwide.

A decade ago, chickpea researchers, supported by the CGIAR Generation Challenge Programme (GCP), started to consider the potential for developing new drought-tolerant varieties that could help boost the world’s production.

They posed this question: If struggling African farmers were armed with adequate resources, could they make up India’s shortfall by growing improved chickpea varieties for export? Empowering farmers to stimulate and sustain their own food production, it was proposed, would not only offer food security to millions of farmers, but could ultimately secure future chickpea exports to India.

An Ethiopian farmer harvests her chickpea crop.

In 2007, GCP kicked off a plan for a multiphased, multithemed Tropical Legumes I (TLI) project, which later became part of, and the largest project within, the GCP Legumes Research Initiative (RI; see box below) – the chickpea component of which would involve collaboration between researchers from India, Ethiopia and Kenya. The scope was not only to develop improved, drought-tolerant chickpeas that would thrive in semiarid conditions, but also to ensure that these varieties would be growing in farmers’ fields across Africa and South Asia within a decade.

“We knew our task would not be complete until we had improved varieties in the hands of farmers,” says GCP researcher Paul Kimurto from the Faculty of Agriculture, Egerton University, Kenya.

The success of GCP research in achieving these goals has opened up great opportunities for East African countries such as Ethiopia and Kenya, which are primed and ready to take advantage of a guaranteed chickpea market.

How drought affects chickpea

Chickpea is a pretty tough customer overall, being able to withstand and thrive on the most rugged and dry terrains, surviving with no irrigation – only the moisture left deep in the soil at the end of the rainy season.

Yet the legume does have one chink in its armour: if no rain falls at its critical maturing or ripening stage (otherwise known as the grain-filling period), crop yields will be seriously affected. The size and weight of chickpea legumes is determined by how successful this maturing stage is. Any stress, such as drought or disease, that occurs at this time will reduce the crop’s yield dramatically.

In India, this has been a particular problem for the past 40 years or so, as chickpea cropping areas have shifted from the cooler north to the warmer south.

“In the 1960s and 1970s when the agricultural Green Revolution introduced grain crops to northern India, chickpeas began to be replaced there by wheat or rice, and grown more in the south,” says Pooran Gaur from the International Crop Research Institute for the Semi-Arid Tropics (ICRISAT), headquartered in India. Pooran was an Activity Leader for the first phase of TLI and Product Delivery Coordinator for the chickpea component of the Legumes RI.

This shift meant the crop was no longer being grown in cooler, long-season environments, but in warmer, short-season environments where drought and diseases like Fusarium wilt have inhibited productivity.

“We have lost about four or five million hectares of chickpea growing area in northern India in the decades since that time,” says Pooran. “In the central and southern states, however, chickpea area more than doubled to nearly five million hectares.”

Escaping drought in India

“The solution we came up with was to develop varieties that were not only high yielding, but could also mature earlier and therefore have more chance of escaping terminal drought,” Pooran explains.

“Such varieties could also allow cereal farmers to produce a fast-growing crop in between the harvest and planting of their main higher yielding crops,” he says.

New short-duration varieties are expected to play a key role in expanding chickpea area into new niches where the available crop-growing seasons are shorter.

“In southern India now we are already seeing these varieties growing well, and their yield is very high,” says Pooran. “In fact, productivity has increased in the south by about seven to eight times in the last 10–12 years.”

The southern state of Andhra Pradesh, once considered unfavourable for chickpea cultivation, today has the highest chickpea yields (averaging 1.4 tonnes/hectare) in India, producing almost as much chickpea as Australia, Canada, Mexico and Myanmar combined.

Indian chickpea farmer with her harvest.

Developing new varieties: Tropical Legumes I in action

GCP-supported drought-tolerance breeding activities in chickpea created hugely valuable breeding materials and tools during the Programme’s decade of existence, focussing not only in India but African partner countries of Ethiopia and Kenya too. A key first step in Phase I of TLI was to create and phenotype – i.e. measure and record the observable characteristics of – a chickpea reference set. This provided the raw information on physical traits needed to make connections between phenotype and genotype, and allowed breeders to identify materials likely to contain drought tolerance genes. This enabled the creation in Phase II of breeding populations with superior genotypes, and so the development of new drought-tolerant prebreeding lines to feed into TLII.

A significant number of markers and other genomic resources were identified and made available during this time, including simple sequence repeats (SSRs), single nucleotide polymorphisms (SNPs) and Diversity Array Technologies (DArT) arrays. The combination of genetic maps with phenotypic information led to the identification of an important ‘hot spot’ region containing quantitative trait loci (QTLs) for several drought-related traits.

Two of the most important molecular-breeding approaches, marker-assisted backcrossing (MABC) and marker-assisted recurrent selection (MARS), were then employed extensively in the selection of breeding materials and introgression of these drought-tolerance QTLs and other desired traits into elite chickpea varieties.

Developing chickpea pods

Markers – DNA sequences with known locations on a chromosome – are like flags on the genetic code. Using them in molecular breeding involves several steps. Scientists must first discover a large number of markers, of which only a small number are likely to be polymorphic, i.e. to have different variants. These are then mapped and compared with phenotypic information, in the hope that just one or two might be associated with a useful trait. When this is the case, breeders can test large quantities of breeding materials to find out which have genes for, say, drought tolerance without having to grow plants to maturity.

The implementation of techniques such as MABC and MARS has become ever more effective over the course of GCP’s work in chickpea, thanks to the emergence and development of increasingly cost-effective types of markers such as SNPs, which can be discovered and explored in large numbers relatively cheaply. The integration of SNPs into chickpea genetic maps significantly accelerated molecular breeding.

The outcome of all these molecular-breeding efforts has been the development and release of locally adapted, drought-tolerant chickpea varieties in each of the target countries – Ethiopia, Kenya and India – where they are already changing lives with their significantly higher yields. Further varieties are in the pipeline and due for imminent release, and it is anticipated that, with partner organisations adopting the use of molecular markers as a routine part of their breeding programmes, many more will be developed over the coming years.

Molecular breeding in TLI was done in conjunction with target-country partners, with at least one cross carried out in each country. ICRISAT also backed up MABC activities with additional crosses. The elite lines that were developed underwent multilocation phenotyping in the three target countries and the best-adapted, most drought-tolerant lines were promoted in TLII.

The project placed heavy emphasis on capacity building for the target-country partners. Efforts were made, for instance, to help researchers and breeders at Egerton University in Kenya and the Ethiopian Institute of Agricultural Research (EIAR) in Ethiopia to undertake molecular breeding activities. At least one PhD and two Master’s students each from Kenya, Ethiopia and India were supported throughout this capacity-building process.

The magic of genetic diversity

One of the important advances in chickpea science supported by GCP, as part of TLI and its mission to develop drought-tolerant chickpea genotypes, was the development of the first ever chickpea multiparent advanced generation intercross (MAGIC) population.

It was created using eight well-adapted and drought-tolerant desi chickpea cultivars and elite lines from different genetic origins and backgrounds, including material from Ethiopia, Kenya, India and Tanzania. These were drawn from the chickpea reference set that GCP had previously developed and phenotyped, allowing an effective strategic selection of parental lines. The population was created by crossing these over several generations in such a way as to maximise the mix of genes in the offspring and ensure varied combinations.

MAGIC populations like these are a valuable genetic resource that makes trait mapping and gene discovery much easier, helping scientists identify useful genes and create varieties with enhanced genetic diversity. They can also be directly used as source material in breeding programmes; already, phenotyping a subset of the chickpea MAGIC population has led to the identification of valuable chickpea breeding lines that had favourable alleles for drought tolerance.

Through links with future molecular-breeding projects, it is expected that the investment in the development of MAGIC populations will benefit both African and South Asian chickpea production. GCP was also involved in developing MAGIC populations for cowpea, rice and sorghum, which were used to combine elite alleles for both simple traits, such as aluminium tolerance in sorghum and submergence tolerance in rice, and complex traits, such as drought or heat tolerance.

Decoding the chickpea genome

Chickpea seed

In 2013, GCP scientists, working with other research organisations around the world, announced the successful sequencing of the chickpea genome. This major breakthrough is expected to lead to the development of even more superior varieties that will transform chickpea production in semiarid environments.

A collaboration of 20 international research organisations under the banner of the International Chickpea Genome Sequencing Consortium (ICGSC), led by ICRISAT, identified more than 28,000 genes and several million genetic markers. These are expected to illuminate important genetic traits that may enhance new varieties.

“The value of this new resource for chickpea improvement cannot be overstated,” says Doug Cook from the University of California, Davis (UC Davis), United States. “It will provide the basis for a wide range of studies, from accelerated breeding, to identifying the molecular basis of a range of key agronomic traits, to basic studies of chickpea biology.”

Doug was one of three lead authors on the publication of the chickpea genome, along with Rajeev Varshney of ICRISAT, who was Principal Investigator for the chickpea work in GCP’s Legumes RI, and Jun Wang, Director of the Beijing Genomics Institute (BGI) of China.

“Making the chickpea genome available to the global research community is an important milestone in bringing chickpea improvement into the 21st century, to address the nutritional security of the poor – especially the rural poor in South Asia and Africa,” he says.

Increased food security will mean higher incomes and a better standard of living for farmers across sub-Saharan Africa.

For Pooran Gaur, GCP played the role of catalyst in this revolution in genomic resource development. “GCP got things started; it set the foundation. Now we are in a position to do further molecular breeding in chickpea.”

The chickpea genome-sequencing project was partly funded by GCP. Other collaborators included UC Davis and BGI-Shenzhen, with key involvement of national partners in India, Canada, Spain, Australia, Germany and the Czech Republic.

In September 2014, ICRISAT received a grant from the Indian Government for a three-year project to further develop chickpea genomic resources, by utilising the genome-sequence information to improve chickpea.

Indian women roast fresh green chickpeas for an evening snack in Andhra Pradesh, India.

Chickpea success in Africa: new varieties already changing lives

With high-yielding, drought tolerant chickpea varieties emerging from the research efforts in molecular breeding, GCP’s partners also needed to reach out to farmers. Teaching African farmers about the advantages of growing chickpeas, either as a main crop or a rotation crop between cereals, has brought about a great uptake in chickpea production in recent years.

A key focus during the second phase of TLI, and onward into TLII, was on enhancing the knowledge, skills and resources of local breeders who have direct links to farmers, especially in Ethiopia and Kenya, and so also build the capacity of farmers themselves.

“We’ve held open days where farmers can interact with and learn from breeders,” says Asnake Fikre, Crop Research Director for EIAR and former TLI country coordinator of the chickpea work in Ethiopia.

“Farmers are now enrolled in farmer training schools at agricultural training centres, and there are also farmer participatory trials.

“This has given them the opportunity to participate in varietal selection with breeders, share their own knowledge and have their say in which varieties they prefer and know will give better harvest, in the conditions they know best.”

EIAR has also been helping train farmers to improve their farm practices to boost production and to become seed producers of these high-yielding chickpea varieties.

“Our goal was to have varieties that would go to farmers’ fields and make a clearly discernible difference,” says Asnake. “Now we are starting to make that kind of impact in my country.”

In fields across Ethiopia, the introduction of new, drought-tolerant varieties has already brought a dramatic increase in productivity, with yields doubling in recent years. This has transformed Ethiopia’s chickpea from simple subsistence crop to one of great commercial significance.

“Targeted farmers are now planting up to half their land with chickpea,” Asnake says. “This has not only improved the fertility of their soil but has had direct benefits for their income and diets.”

Varieties like the large-seeded and high-valued kabuli have presented new opportunities for farmers to earn extra income through the export industry, and indeed chickpea exports from eastern Africa have substantially increased since 2001.

“The high yields of the drought-tolerant and pest-resistant chickpea, and the market value, meant that I am no longer seen as a poor widow but a successful farmer,” says Ethiopian farmer Temegnush Dabi.

“Ultimately, by making wealth out of chickpea and chickpea technologies in this country, people are starting to change their lives,” says Asnake. “They are educating their children to the university level and constructing better houses, even in towns. This will have a massive impact on the next generation.”

A similar success story is unfolding in Kenya, where GCP efforts during TLI led to the release of six new varieties of chickpea in the five years prior to GCP’s close at the end of 2014; more are expected to be ready within the next three years.

While chickpea is a relatively new crop in Kenya it has been steadily gaining popularity, especially in the drylands, which make up over 80 percent of Kenya’s total land surface and support nearly 10 million Kenyans – about 34 percent of the country’s population.

Drought tolerance experiments in chickpea at Egerton University, Njoro, Kenya.

“It wasn’t until my university went into close collaboration with ICRISAT during TLII and gained more resources and training options – facilitated by GCP – that chickpea research gained leverage in Kenya,” Paul Kimurto explains. “Through GCP and ICRISAT, we had more opportunities to promote the crop in Kenya. It is still on a small scale here, but it is spreading into more and more areas.”

Kenyan farmers are now discovering the benefits of chickpea as a rotational or ‘relay’ crop, he says, due to its ability to enhance soil fertility. In the highlands where fields are normally left dry and nothing is planted from around November to February, chickpea is a very good option to plant instead of letting fields stay fallow until the next season.

“By fixing nitrogen and adding organic matter to the soil, chickpeas can minimise, even eliminate, the need for costly fertilisers,” says Paul. “This is certainly enough incentive for cereal farmers to switch to pulse crops such as chickpea that can be managed without such costs.”

Households in the drylands have often been faced with hunger due to frequent crop failure of main staples, such as maize and beans, on account of climate change, Paul explains. With access to improved varieties, however, farmers can now produce a fast-growing chickpea crop between the harvest and planting of their main cereals. In the drylands they are now growing chickpeas after wheat and maize harvests during the short rains, when the land would otherwise lie fallow.

“Already, improved chickpeas have increased the food security and nutritional status of more than 27,000 households across the Baringo, Koibatek, Kerio Valley and Bomet areas of Kenya,” Paul says.

It is a trend he hopes will continue right across sub-Saharan Africa in the years to come, attracting more and more resource-poor farmers to grow chickpea.

Chickpea’s promise meeting future challenges

Beyond the end of GCP and the funding it provided, chickpea researchers are hopeful they will be able to continue working directly with farmers in the field, to ensure that their interests and needs are being addressed.

“To sustain integrated breeding practices post-2014, GCP has established Communities of Practice (CoPs) that are discipline- and commodity-oriented,” says Ndeye Ndack Diop, GCP’s Capacity Building Leader and TLI Project Manager. “The ultimate goal of the CoPs is to provide a platform for community problem solving, idea generation and information sharing.”

Ndeye Ndack has been impressed with the way the chickpea community has embraced the CoP concept, noting that Pooran has played an important part in this and the TLI projects. “Pooran was able to bring developing-country partners outside of TLI into the CoP and have them work on TLI-related activities. Being part of the community means they have been able to source breeding material and learn from others. In so doing, we are seeing these partners in Kenya and Ethiopia develop their own germplasm.

“Furthermore, much of this new germplasm has been developed by Master’s and PhD students, which is great for the future of these breeding programmes.”

“GCP played a catalytic role in this regard,” explains Rajeev Varshney. “GCP provided a community environment in ways that very few other organisations can, and in ways that made the best use of resources,” he says. “It brought together people from all kinds of scientific disciplines: from genomics, bioinformatics, biology, molecular biology and so on. Such a pooling of complementary expertise and resources made great achievements possible.”

An Ethiopian farmer loads his bounteous chickpea harvest onto his donkey.

For Rajeev, the challenge facing chickpea research beyond GCP’s sunset is whether an adequate framework will be there to continue bringing this kind of community together.

“But that’s what we’re trying to do in the next phase of the Tropical Legumes Project (Tropical Legumes III, or TLIII), which kicks off in 2015,” explains Rajeev, who will be TLIII’s Principal Investigator. TLIII is to be led by ICRISAT.

“We will continue to work with the major partners as we did during GCP, which will involve, first of all, upscaling the activities we are doing now,” he says. “India currently has the capacity, the resources, to do this.”

Rajeev is hopeful that the relatively smaller national partners from Ethiopia and Kenya, and associated partners such as Egerton University, EIAR and maybe others, will have similar opportunities. “We hope they can also start working with their governments, or with agencies like USAID, and be successful at convincing them to fund these projects into the future, as GCP has been doing,” he says.

“The process is like a jigsaw puzzle: we have the borders done, and a good idea of what the picture is and where the rest of the pieces will fit,” he says.

Certainly for Paul Kimurto, the picture is clear for the future of chickpea breeding in Kenya.

“Improvements in chickpea resources cannot end now that new varieties have started entering farmers’ fields,” he says. “We’ve managed to develop a good, solid breeding programme here at Egerton University. The infrastructure is in place, the facilities are here – we are indeed equipped to maintain the life and legacy of GCP well beyond 2015.”

This can only be good news for lovers of the legume in India. With millions of smallholder farmers in Kenya and Ethiopia poised to exploit a ready market for new varieties that will change their families’ lives, chickpea’s potential for ensuring food security across the developing world seems more promising than ever.

Rice research reaps a rich harvest of products, people and partners

Asia, Comparative genomics in cereals, Crop breeding, Genetics, Partnerships, Rice No Responses »

Mar 172015

Harvesting rice by hand in The Philippines.

Rice plays a key role in global food security, particularly in Asia, where 90 percent of the world’s rice is grown and eaten. By 2050, Asia’s population is estimated to grow by one billion to 5.2 billion people, who will continue to depend on rice as their major staple food.

But with rising demand for rice has also come increasing salinity, droughts and other stresses, along with decreasing areas of land available for farming the crop.

And that’s why the CGIAR Generation Challenge Programme (GCP) placed a major focus on rice throughout its 10 years of existence.

Key ingredient in the rice research fest was GCP’s relationship with the International Rice Research Institute (IRRI), headquartered in The Philippines. GCP supported IRRI in its endeavours to use the latest molecular plant-breeding techniques, along with traditional plant-breeding tools, to develop rice crops better able to cope with various stresses and still be productive.

“These ‘super’ crops will revolutionise rice farming,” says IRRI Director General Robert Zeigler, who was also the first Director of GCP.

For more on GCP’s rice research see our Sunset Story ‘The power of rice unlocked’.

Rice that can survive increasingly salty water

Climate change is one of the major threats facing rice production. As sea levels rise, salt water enters further up rivers with the high tides and affects rice production areas.

Each year in Bangladesh, during the boro rice season from November to May, salinity is so high that a white film of salt covers the country’s coastal paddy fields. For Bangladeshi farmers, this white colour is a warning sign that their land is ‘sick’. Around the world, Bangladesh, India, Myanmar and parts of Africa are most affected by increasing salinity.

Right from the beginning of GCP, salinity was a problem firmly on the rice research agenda.

Highly saline soils in India (left), and a close-up showing a surface crust of salt on afflicted soil (right).

Leading this research was IRRI plant physiologist Abdelbagi Ismail, who dreamed of the ‘super’ rice crop that could “tolerate salinity, drought and submergence”.

Abdelbagi has managed and overseen most of the progress made during the discovery of a major genetic region, or quantitative trait locus (QTL), associated with salinity tolerance and named Saltol.

Abdelbagi Ismail examines rice plants in the field in Bangladesh.

Its insertion into well-known rice varieties used by farmers in Bangladesh, Indonesia and The Philippines is part of the revolution taking place in rice research.

Abdelbagi says Saltol was mapped and markers were developed for its use in breeding more salt-tolerant rice varieties. Its salt-tolerance code is now being transferred into several varieties evaluated with IRRI partners in South and Southeast Asia.

“These projects also provided opportunities for both degree training and non-degree training to several of our partners in the countries involved,” he adds.

“Partnerships are crucial for us to build the capacity of the researchers in these countries and to ensure our outputs and outcomes reach the farmers that need them.

“All our partners benefitted from salt-tolerant varieties developed conventionally through this project, and they also provided pipelines for uptake and dissemination by farmers.”

Having developed new lines following the discovery of the Saltol QTL, Abdelbagi’s GCP-supported team trained plant breeders in country programmes to successfully breed for salt tolerance and other stresses.

In this way, Abdelbagi says, they are improving the capacity of researchers in developing countries to take up new breeding techniques, such as the use of molecular markers. “This can reduce the time it takes to breed new varieties, from six to ten years at the moment, down to two or three years,” he says.

This means that benefits to smallholder rice farmers struggling with salinity will happen sooner rather than later. And Abdelbagi credits GCP’s partnership approach, working directly with the countries in need, for the success so far.

“The salt-tolerant varieties are now being widely distributed,” he says. “Some of these varieties have doubled farmers’ productivity in affected areas.

“The work developed technologies of value to our needy farmers.

“We do believe this is the start of a second Green Revolution, especially for those who farm in less favourable areas and that missed this opportunity during the first Green Revolution.”

Partnership approach key to new rice gene for uptake of phosphorus

More than 60 percent of rainfed lowland rice is produced on poor and problem soils, including those that are naturally low in phosphorus. This is an essential for nutrient growing crops, but providing phosphorus through fertilisers is costly and unfeasible for many smallholder rice growers.

IRRI’s Sheryl Catausan prepares the roots of a rice plant for scanning as part of the work of the PSTOL1, phosphorus uptake research team at IRRI.

This problem was the focus of GCP’s rice phosphorus-uptake project led by IRRI molecular biologist Sigrid Heuer.

The project was enormously successful, with its discovery of the PSTOL1 (‘phosphorus starvation tolerance 1’) gene within the Pup1 locus, which was published in the prestigious journal Nature.

“We wanted it in Nature for a couple of reasons,” she says. “To raise awareness about phosphorus deficiency and phosphorus being a limited resource, especially in poorer countries; and to draw attention to how we do molecular breeding these days, which is a speedier, easier and more cost-effective approach to developing crops that have the potential to alleviate such problems.”

Following the PSTOL1 discovery, researchers are now working with developing-country researchers and extension agencies to help them understand how to breed local varieties of rice that can be grown in phosphorus-deficient soils. They are also collaborating with other crop breeders looking to breed similar maize, sorghum and wheat varieties.

Tobias Kretzschmar, a molecular biologist with IRRI, says that GCP’s partnership approach was the key to the project having an impact on the rice farmers who needed it most.

“For me, the collaborations that were forged through these inter-institutional projects made the difference,” he says.

Sigrid agrees: “GCP was always there supporting us and giving us confidence, even when we were not sure.”

Solving the insoluble: a gene for drought tolerance

Rice is a crop that not only needs water, but loves water. So developing a drought-tolerant rice variety is a quest to find a seemingly impossible gene.

However, GCP-supported researchers did just that: they solved the insoluble.

“They were very successful in terms of getting drought tolerance,” says Hei Leung of IRRI, who was GCP Subprogramme Leader for the Comparative Genomics Research Initiative between 2004 and 2007, and also a Principal Investigator for the Rice Research Initiative. “They’re now getting a 1.5 tonne rice yield advantage under water stress. I mean, that’s unheard of! This is a crop that needs water.

“This is one of GCP’s big success stories; that you can actually get drought tolerance is a seemingly impossible task for a water-loving rice plant.”

As Subprogramme Leader, Hei played a critical role in the creation, management, delivery and communication of a wide portfolio of research projects. He credits the nature of how GCP was set up for accelerating the breeding programme for drought-tolerant rice.

“The advantage of GCP is that it is run by a small group of people who can make fast decisions,” he says. “This means they can respond to the needs of researchers: ‘Okay, we are going to invest on that. We’re going to have a meeting on this’.

“The real advantage of GCP is its agility. Usually with other organisations you have new ideas and then have to slave away for a year to get the funding to implement them. But GCP was quick.”

Hei Leung (right) explains rice screening processes to a visiting scholar at IRRI.

IRRI and GCP deliver genetic resources to those who need them most

Tobias says one of the main objectives of GCP and IRRI is to make genetic stocks available to breeders, particularly in developing countries.

“Without that, IRRI would fail in its central mission to reduce hunger and poverty,” he says. “In order to achieve this mission, tight collaboration with our agricultural and extension partners in other countries is the key.”

In fact, this idea of protecting the future through genetic material was influential in the choice of GCP as a CGIAR Challenge Program name. Hei, who was involved from the start with GCP, talks about the meeting in a Rome pizzeria where participants came up with the name: “When we talk about ‘generation’, we are really talking about the work we do with genetic diversity; it is about the future generation,” he says.

Part of that future generation is about sharing genetic resources or stocks, but first the genetic diversity of such stocks needs to be characterised. Hei remembers that one of the first GCP projects in 2004 brought together researchers in various countries to characterise the genetic diversity of various crops, including rice.

“But everyone was using different genotyping platforms and markers, and the technology back then was not what we have now,” he recalls.

“So we spent a lot of resources getting poor quality data. In a sense, it was a failure. On the other hand, it was also a success because we alerted people to the importance of characterising diversity in every single crop. The whole concept of getting all the national partners doing genetic resource characterisation is a good one.

“We have evolved the technology together over the last 10 years of GCP. Now the country partners feel enabled. They are not scared of the technology.”

Abdelbagi agrees that characterising genetic diversity is essential, and adds that making such genetic stocks readily available to breeders is also vital.

“This has not been an issue before,” he explains. “With the new regulations of germplasm control and intellectual property issues, it became extremely difficult to exchange germplasm with some countries. One important lesson we learnt was to engage in direct discussion with our partners in efforts to influence their policies and guidelines to allow essential exchange of genetic stocks and breeding material, at least at the regional level.”

Abdelbagi adds that another big challenge has been to provide country partners with materials and DNA markers for marker-assisted selection programmes and to make sure these were properly used in breeding programmes.

“We solved this by hosting a workshop at IRRI and with continued visits with GCP collaborators,” he says.

Rice terraces in Ifugao Province in The Philippines.

‘Super’ crops: something ‘magic’ happens

Hei says that the GCP project he’s most passionate about, and one that leaves a lasting legacy, is the development of multiparent advanced generation intercross (MAGIC) populations, which will potentially yield lines that are tolerant to environmental stresses, grow well in poor soils and produce better quality grain.

“MAGIC populations will leave behind a very good resource towards improving different crop species,” says Hei. “I’m sure that they will expand on their own.”

GCP funded the development of four kinds of rice populations, including indica MAGIC, which is the most advanced of the MAGIC populations developed so far. These populations contain multiple desirable traits, including: blast and bacterial blight-resistance, salinity and submergence tolerance and grain quality.

New generation of researchers working on a new rice revolution

Rice farmer in her field in Rwanda.

Robert Zeigler’s dream of a new rice Green Revolution with ‘super crops’ is coming true, thanks in part to GCP’s focus on combining cutting-edge molecular plant-breeding techniques with conventional plant breeding.

“With all this going for us, the second Green Revolution means we can meet the great challenges ahead with unprecedented efforts that will result in unparalleled impacts,” he says. “This will range from mining the rice genomes for needed traits to developing climate change-ready rice.”

IRRI researchers like Abdelbagi agree that new plant-breeding techniques, such as those fostered by GCP, are making ‘super’ crops more likely: “I’m committed to understand how plants can be manipulated to adapt to, and better tolerate, extreme environmental stresses, which seems more feasible today than it has ever been before.

“GCP-supported work has provided mechanisms for developing varieties with multiple stress tolerances, besides the improvements in yield and quality.”

And for Hei, GCP’s 10-year legacy is not just about the technology but also about the people.

“Over ten years you have three generations of PhD students,” he says. “Many people became a ‘new generation’ scientist through this programme. Many people have benefitted. GCP is one of a kind. I’m just in love with it.”

The power of rice unlocked

Africa, Asia, Comparative genomics in cereals, Crop breeding, Genomics, Rice, Women in science No Responses »

Mar 042015

A woman harvests rice in Ifugao, The Philippines.

Plant geneticist Sigrid Heuer remembers very clearly entering the transgenic greenhouse in Manila to see her postdoctoral student holding up a rice plant with ‘monster’ roots.

“They were enormous,” she recalls. “This is when I knew we had the right gene. It confirmed years of work. That was our eureka moment.

So massive was the effect of that gene that I knew we had the right one.”

This genetic discovery – described in more detail a little later – is one of the shining lights of the 10-year-long CGIAR Generation Challenge Programme (GCP) established in 2004.

GCP-supported researchers aimed high: they wanted to contribute to food security in the developing world by using the latest advances in crop science and plant breeding.

And with the lives of half of the world’s population directly reliant on their own agriculture, there is a lot at stake. Land degradation, salinity, pollution and excessive fertiliser use are just some of the challenges.

Rice is one of the most critical crops worldwide

Amelia Henry, drought physiology group leader at the International Rice Research Institute (IRRI), explains why rice was such a critical crop for GCP research. She says rice is grown in a diverse set of environmental settings, often characterised by severe flooding, poor soils and disease.

Cycling through rice fields in Odisha, India.

In Asia, 40 percent of rice is produced in rainfed systems with little or no water control or protection from floods and droughts – meaning rice plants are usually faced with too much or too little water, and rarely get just enough. In addition, 60 percent (29 million hectares) of the rainfed lowland rice is produced on poor and problem soils, including those that are naturally low in phosphorus.

Phosphorus deficiency and aluminium toxicity are two of the most widespread environmental causes of poor crop productivity in acidic soils, where high acid levels upset the balance of available nutrients. And drought makes these problems even worse.

Phosphorus is essential for growing crops. Its commercial use in fertilisers is due to the need to replace the phosphorus that plants have extracted from the soil as they grow. Soils lacking phosphorus are an especially big problem in Africa, and the continent is a major user of phosphate fertilisers. However, inappropriate use of fertilisers can, ironically, acidify soil further, since excess nitrogen fertiliser decreases soil pH.

Meanwhile, high levels of aluminium in soil cause damage to roots and impair crop growth, reducing their uptake both of nutrients like phosphorus and of water – making plants more vulnerable to drought. Aluminium toxicity is a major limitation on crop production for more than 30 percent of farmland in Southeast Asia and South America and approximately 20 percent in East Asia, sub-Saharan Africa and North America.

The challenge today is to tap into the genetic codes of key crops such as rice and wheat to feed a growing global population. Science plays a crucial role in identifying genes for traits that help plants tolerate more difficult environmental conditions, and producing crop varieties that contain these genes.

Plant biologists are already developing new rice lines that produce higher yields in the face of reduced water, increasingly scant fertiliser as costs rise, and unproductive soils. However, ‘super’ crops are needed that can combine these qualities and withstand climate changes such as increasing temperatures and reduced rainfall in a century when the world’s population is estimated to reach nearly 10 billion people by 2050.

Bringing the best scientific minds to improve rice varieties

Ambitious in concept, the GCP research focussed on bringing together experts to work on these critical problems of rice production for some of the world’s poorest farmers.

The programme was rolled out in two phases that sought to explore the genetic diversity of key crops and use the most important genes for valuable traits, such as Sigrid’s discovery made in a rice variety that is tolerant of phosphorus-poor soils. Each phase involved dedicated teams in partner countries.

GCP Principal Investigator Hei Leung, from IRRI, says GCP is unique, one of kind: “I love it.” He says GCP has enabled rice researchers and breeders to embrace cutting-edge science through partnerships focussed on improving crop yields in areas previously deemed unproductive.

Hei says GCP wanted to target research during its second phase on those crops that most poor people depend upon. “We wanted to have a programme that is what we call ‘pro-poor’, meaning the majority of the world’s people depends on those crops,” he says.

Rice is the ‘chosen one’ of GCP’s cereal crop research and development, with the biggest slice of GCP’s research activities dedicated to this, the most widely consumed staple food.

It is crucial to increase rice supplies by applying research and development such as that carried out by GCP researchers over the past 10 years, Hei says.

For more on the relationship between GCP and IRRI – and an extra sprinkling of salt on your rice (fields) – see our Sunset Story ‘Rice research reaps a rich harvest of products, people and partners’.

Relying on rice’s small genome in the hunt for drought-tolerance genes

Researchers had been trying to map the genomes of key cereal crops for over two decades. Rice’s genome was mapped in 2004, just as GCP started.

Rice has a relatively small genome, one-sixth the size of the maize genome and 40 times smaller than the wheat genome. This makes it a useful ‘model’ crop for researchers to compare with other crops.

“People like to compare with rice because wheat and maize have very big genomes, and they don’t have the resources,” explains Hei.

After the rice genome had been sequenced, the next step was to focus down to a more detailed level: the individual genes that give rice plants traits such as drought tolerance. Identifying useful genes, and markers that act as genetic ‘tags’ to point them out, gives scientists an efficient way to choose which plants to use in breeding.

One of GCP’s Principal Investigators for rice was Marie-Noëlle Ndjiondjop, a senior molecular scientist with the Africa Rice Center.

“Rice is becoming a very important crop in Africa,” she says. “Production has been reduced by a lot of constraints, and drought is one of the most important constraints that we face in Africa.”

Meet Marie-Noëlle below (or on YouTube), in our series of Q&A videos on rice research in Africa.

Marie-Noëlle’s team recognised that drought tolerance was likely to be a complex trait in rice, involving many genes, due to the mix of physiological, genetic and environmental components that affect how well a plant can tolerate drought conditions. To help discover the rice varieties likely to have improved drought tolerance, Marie-Noëlle’s team used an innovative approach known as bi-parental marker-assisted recurrent selection (MARS).

“With such a complex trait, you really need to have all the tools and infrastructure necessary; through GCP we were able to buy the necessary equipment and put in the infrastructure needed to find and test the drought trait in rice lines.

“By using the MARS approach we identified the genetic regions associated with drought and are moving towards developing new rice lines that the African breeder and farmer will be using in the next decade to grow crops that are better able to withstand drought conditions.”

Likewise, Amelia Henry’s IRRI team also developed drought-tolerant lines, particularly for drought-prone areas of South Asia. She says many of the promising deep-rooted or generally drought-tolerant varieties identified in the early decades after IRRI’s foundation in 1960 are still used today as ‘drought donors’.

“Since the strength of our project was the compilation of results from many different sites, this work couldn’t have been done without the GCP partners,” she says. “They taught me a lot about how rice grows in different countries and what problems rice farmers face.”

Hei agrees that GCP partnerships have been crucial, including in the successful breeding of rice with drought tolerance: “They’re getting a 1.5-tonne rice yield advantage under water stress. I mean, that’s unheard of! This is a crop that needs water.”

A rice farmer in Rwanda.

But the researchers could not rest with just one of rice’s problems solved.

Hei says GCP’s initial focus on drought was a good one but then, “I remember saying, ‘We cannot just go for drought. Rice, like all crops, needs packages of traits’.”

He knows that drought is just one problem facing rice farmers, noting “this broadened our research portfolio to include seeking to breed rice varieties with traits of tolerance to aluminium toxicity, salt and poor soils.”

The scope widens: phosphorus-hungry rice and a huge success

Sigrid Heuer was in The Philippines working for IRRI when she became involved in the ground-breaking phosphorus-uptake project for rice.

She took over the project being headed by Matthias Wissuwa. Much earlier, Matthias had noted that Kasalath – a traditional northern Indian rice variety that grew successfully in low-phosphorus soil – must contain advantageous genes. His postdoctoral supervisor, Noriharu Ae, thought that longer roots were likely to be the secret to some rice varieties being able to tolerate phosphorus-deficient soils.

Matthias, now a senior scientist in the Crop, Livestock and Environment Division at the Japan International Research Center for Agricultural Sciences (JIRCAS), says that for a long time he was not sure if it was just long roots: “It was a real chicken-and-egg scenario – does strong phosphorus uptake spur root growth, or is it the other way around?”

Screening for phosphorus-efficient rice, able to make the best of low levels of available phosphorus, on an IRRI experimental plot in The Philippines. Some types of rice have visibly done much better than others.

Sigrid Heuer used her background in molecular breeding to take up the challenge with GCP to find the genes responsible for the Kasalath variety’s long roots.

“I spent years looking for the gene,” Sigrid says. “It was like trying to find a needle in a haystack; the genomic region where the gene is located is very complex.

“We had little biogenomics support at the time and I had three jobs and two kids; I was spending all my nights trying to find this gene.”

Sigrid Heuer in the field at IRRI.

But one day, Sigrid’s postdoctoral student Rico Gamuyao excitedly called her downstairs to the transgenic greenhouses. “Rico had used transgenic plants to see whether this gene had any effect. He was digging out plants from experimental pods.”

Sigrid says that moment in the Manila labs was the turning point for the project’s researchers.

Matthias’ team had previously identified a genomic region, or locus, named Pup1 (‘phosphorus uptake 1’) that was linked to phosphorus uptake in lines of traditional rice growing in poor soils. However, its functional mechanism remained elusive until the breakthrough GCP-funded project sequenced the locus, showing the presence of a Pup1-specific protein kinase gene, which was named PSTOL1 (‘phosphorus starvation tolerance 1’). The discovery was reported in the prestigious scientific journal Nature on 23 August 2012 and picked up by media around the world.

The gene instructs the plant to grow larger and longer roots, increasing its surface area – which Sigrid compares to having a bigger sponge to absorb more water and nutrients in the soil.

“Plants growing longer roots have more uptake of phosphorus – and PSTOL1 is responsible for this.

“GCP was always there, supporting us and giving us confidence, even when we weren’t sure we were going to succeed,” she recalls. “They really wanted us to succeed, so, financially and from a motivational point of view, this gave us more enthusiasm.”

She adds, jokingly, “With so many people having expectations about the project, it was better not to disappoint.”

For some insight straight from the source, listen to Matthias in our podcosts below. In these two bitesized chunks of wisdom he discusses the importance of phosphorus deficiency and of incorporating PSTOL1 into national breeding programmes; his work in Africa and the possibility of uncovering an African ‘Pup2’; what the PSTOL1 discovery has meant for him; and the essential contribution of international partnerships and GCP’s support.

Members of the IRRI PSTOL1, phosphorus uptake research team chat in the field in 2012. From left to right they are are: Sigrid Heuer, Cheryl Dalid, Rico Gamuyao, Matthias Wissuwa and Joong Hyoun Chin.

Phosphorus-uptake gene not all it seemed – an imposter?

But PSTOL1 was definitely not what it seemed. “It was identified under phosphorus-deficient conditions and the original screen was set up for that,” says Sigrid.

Researchers eventually discovered that Pup1 and the PSTOL1 gene within it were not really all about phosphorus at all: “It turns out it is actually a root-growth gene, which just happens to enhance uptake of phosphorus and other nutrients such as nitrogen and potassium.

“The result is big root growth and maintenance of that growth under stress. If you have improved root growth, there is more access to soil resources, as a plant can explore more soil area with more root fingers.”

Her team showed that overexpression of PSTOL1 gene significantly improves grain yield in varieties growing in phosphorus-deficient soil – by up to 60 percent compared to rice varieties that did not have the gene.

In field tests in Indonesia and The Philippines, rice with the PSTOL1 gene produced about 20 percent more grain than rice without the gene. This is important in countries where rice is grown in poor soils.

A farmer harvests rice in South Sulawesi, Indonesia.

Sigrid, now based in Adelaide at the Australian Centre for Plant Functional Genomics, says the introduction of the new gene into locally adapted rice varieties in different locations across Asia and Africa is expected to boost productivity under low-phosphorus conditions.

“The ultimate measure for these kinds of projects is whether a gene works in different environments. I think we have a lot of evidence that says it does,” she says.

The discovery of PSTOL1 promises to improve the food security of rice farmers on phosphorus-deficient land though assisting them to grow more rice and earn more.

Titbits of further research successes: aluminium tolerance and MAGIC genes

Drought, low-phosphorus soils, aluminium toxicity, diseases, acid soils, climate change… the list seems never-ending for challenges to growing rice. Apart from the successes with drought and phosphorus that GCP scientists achieved, there was to be much more in the works from other GCP researchers.

During GCP Phase I, a team led by Leon Kochian of Cornell University, USA, with colleagues at the Brazilian Corporation of Agricultural Research (EMBRAPA), JIRCAS and Moi University, Kenya, successfully identified and cloned a major sorghum aluminium-tolerance gene.

In Phase II, they worked towards breeding aluminium-tolerant sorghum lines for sub-Saharan Africa, as well as applying what they learnt to discover similar genes in rice and maize.

Hei Leung says GCP leaves a lasting legacy in the development of multiparent advanced generation intercross (MAGIC) populations. These help breeders to identify valuable genes, and from among the populations they can also select lines to use in breeding that have favourable traits, such as being tolerant to environmental stresses, having an ability to grow well in poor soils or being able to produce better quality grain.

“MAGIC populations will leave behind a very good resource towards improving different crop species,” says Hei. “I’m sure that they will expand on their own.”

GCP funded the development of four different MAGIC populations for rice, including both indica and japonica types. And the idea of developing MAGIC populations has spread to other crops, including chickpeas, cowpeas and sorghum.

For more on MAGIC see our Sunset Story ‘Rice research reaps a rich harvest of products, people and partners’.

A farmer harvests rice in Nepal.

Meeting the challenges and delivering outcomes to farmers

But with success come the frustrations of getting there, according to Nourollah Ahmadi, GCP Product Delivery Coordinator for rice across Africa. “This is because things are not always going as well as you want.”

Nourollah, from Centre de coopération internationale en recherche agronomique pour le développement (Agropolis–CIRAD; Agricultural Research for Development), says sometimes he felt overwhelmed coordinating GCP’s rice projects because “the challenges were perhaps too big.”

Project Delivery Coordinators monitor projects first-hand, conducting on-site visits, advising project leaders and partners and helping them implement delivery plans.

“One of the problems was the overall level of basic education of people who were involved in the project,” Nourollah says.

Rice cultivation in Mali is on the rise.

His work with GCP has opened up new prospects for some of the poorest farmers in the world: “For five years, I have been coordinating one of the rice initiatives implemented by the Africa Rice Center and involving three African countries.” These are Burkina Faso, Mali and Nigeria.

He says GCP has brought much-needed expertise and technical skills to countries which can now use genetic insights to produce improved crops tolerant of drought conditions and poor soils and resistant to diseases. Using new molecular-breeding techniques has provided a more effective way to move forward, still firmly focussed on helping the world’s poorest farmers achieve food security.

“We don’t change direction, we change tools – sometimes you have a bicycle, sometimes you have a car,” Nourollah says.

Hei agrees there have been challenges: “It’s been a bumpy road to get to this point. But the whole concept of getting all the national partners doing genetic resource characterisation is a very good one.

Right now they are enabled; they are not scared about the technology. They can apply it.”

Sigrid says applied research is judged on two scales: “One is the publications and science you’re doing. The other is whether the work has any impact in the field, whether it works in the field. Bringing these two together is sometimes a challenge.”

GCP has managed to meet both challenges. New crop varieties have been released to farmers, and more than 450 scientifically reviewed papers have been published since 2004.

Building on the rice success story and leaving a lasting legacy

The work that GCP-supported researchers have done for rice is also being used in other crops. For example, researchers used comparative genomics to determine if genes the same as or similar to those found in rice are present and operating in the same manner in sorghum and maize.

The GCP team found sorghum and maize varieties that contained genes, similar to rice’s PSTOL1, that also confer tolerance of phosphorus-deficient soil with an enhanced root system. They were then able to develop markers to help breeders in Brazil and Africa identify phosphorus-efficient lines.

The knowledge that GCP-supported rice researchers have generated is shared through communities of practice, through websites, publications, research meetings and the Integrated Breeding Platform.

As Amelia Henry notes, GCP’s achievements will be defined by “the spirit of dedication to openness with research data, results and germplasm and giving credit and support to partners in developing countries.” The work in rice in many ways exemplifies GCP’s collaborative approach, commitment to capacity building and deeply held belief that together we can go so much further in helping farmers.

Unlocking genetic diversity in crops for the resource-poor was at the heart of GCP’s mission, which in 2003 promised ‘a new, unique public platform for accessing and developing new genetic resources using new molecular technologies and traditional means’.

Certainly for poor rice farmers in Asia and Africa, the work that GCP has supported in applying the latest molecular-breeding techniques will lead to rice varieties that will help them produce better crops on poor soils in a changing climate.

Rice farmers in Indonesia.

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Bringing the best scientific minds to improve rice varieties

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The scope widens: phosphorus-hungry rice and a huge success

Phosphorus-uptake gene not all it seemed – an imposter?

Titbits of further research successes: aluminium tolerance and MAGIC genes

Meeting the challenges and delivering outcomes to farmers

Building on the rice success story and leaving a lasting legacy

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