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Oct 262015
 

 

Photo: HK Tang/Flickr (Creative Commons)

An Indian patchwork of rice and maize fields.

“Once you’ve cloned a major gene in one crop, it is possible to find a counterpart gene that has the same function in another crop, and this is easier than finding useful genes from scratch” explains Leon Kochian, Professor in Plant Biology and Crop and Soil Sciences at Cornell University, USA, and Director of the Robert W Holley Center for Agriculture and Health, United States Department of Agriculture – Agricultural Research Service.

Leon was the Product Delivery Coordinator for the Comparative Genomics Research Initiative of the CGIAR Generation Challenge Programme (GCP). The Programme set out in 2004 to advance plant genetics in a bid to provide sustainable food-security solutions.

Between 2004 and 2014, GCP invested in projects to clone two genes and deploy them in elite local varieties. The first gene, SbMATE, encodes aluminium tolerance traits in sorghum; the work was a collaborative effort led by the Brazilian Corporation of Agricultural Research (EMBRAPA) and Cornell University, and gave rise to locally-adapted sorghum varieties released in South America and Africa. The second gene, PSTOL1, produces traits that improve phosphorus uptake in rice. This research was a collaboration between the Japan International Research Center for Agricultural Sciences (JIRCAS) and the International Rice Research Institute (IRRI). PSTOL1 has now been extensively deployed in Asian rice varieties.

Aluminium toxicity and low phosphorus levels in acid soils are major factors that hinder cereal productivity worldwide, particularly in sub-Saharan Africa, South America and Southeast Asia. Globally, acid soils are outranked only by drought when it comes to stresses that threaten food security.

Tolerance to high levels of aluminium and low phosphorus is conferred by major genes, which lend themselves to cloning. Major genes are genes that by themselves have a significant and evident effect in producing a particular trait; it’s therefore easier to find and deploy a major gene associated with a desired trait than having to find and clone several minor genes.

Photo: S Kilungu/CCAFS

Harvesting sorghum in Kenya.

Cloning major genes instrumental in hunt for resilient varieties

Locating a single gene within a plant’s DNA is like looking for a needle in a haystack. Instead of searching for a gene at random, geneticists need a plan for finding it.

The first step is to conduct prolonged phenotyping – that is, measuring and recording of plants’ observable characteristics in the field. By coupling and comparing this knowledge with genetic sequencing data, scientists can identify and locate quantitative trait loci (QTLs) – discrete genetic regions that contain genes associated with a desired trait, in this instance tolerance to aluminium or improved phosphorus uptake. They then dissect the QTL to single out the gene responsible for the desired trait. In the case of sorghum, researchers had identified the aluminium tolerance locus AltSB, and were looking for the gene responsible.

Once the gene has been identified, the next step is to clone it – that is, make copies of the stretch of DNA that makes up the gene. Geneticists need millions of copies of the same gene for their research: to gain information about the nucleotide sequence of the gene, create molecular markers to help identify the presence of the gene in plants and help compare versions of the gene from different species, and understand the mechanisms it controls and ways it interacts with other genes.

Photo: ICRISAT

Drying the sorghum harvest in India.

Sorghum was one of the simpler crops to work with, according to Claudia Guimarães.

“Sorghum has a smaller genome… with clear observable traits, which are often controlled by one major gene,” she says.

The first breakthrough was the identification and cloning of SbMATE, the aluminium tolerance gene in sorghum behind the AltSB locus. The next was finding a diagnostic marker for the gene so that it could be used in breeding.

Marking genes to quickly scan plants for desired traits

Photo: IRRI

Harvesting rice in The Philippines.

Once a desired gene is identified, a specific molecular marker must be found for it. This is a variation in the plant’s DNA, associated with a gene of interest, that scientists can use to flag up the gene’s presence. We can compare this process to using a text highlighter in a book, where the words represent the genes making up a genome. Each marker is like a coloured highlighter, marking sentences (genomic regions) containing particular keywords (genes) and making them easier to find.

In molecular breeding, scientists can use markers to quickly scan hundreds or thousands of DNA samples of breeding materials for a gene, or genes, that they want to incorporate into new plant varieties. This enables them to select parents for crosses more efficiently, and easily see which of the next generation have inherited the gene. This marker-assisted breeding method can save significant time and money in getting new varieties out into farmers’ fields.

Leon, who was also the Principal Investigator for various GCP-funded research projects, says that the cloning of SbMATE helped advance sorghum as a model for the further exploration of aluminium tolerance and the discovery of new molecular solutions for improving crop yields.

“This research also has environmental implications for badly needed increases in food production on marginal soils in developing countries,” says Leon. “For example, if we can increase food production on existing lands, it could limit agriculture’s encroachment into other areas.”

Photo: IRRI

Rice field trials in Tanzania.

Aluminium toxicity is the result of aluminum becoming more available to plants when the soil pH is lower, and affects 38 percent of farmland in Southeast Asia, 31 percent in South America and 20 percent in East Asia, sub-Saharan Africa and North America. Meanwhile phosphorus, the second most important inorganic plant nutrient after nitrogen, becomes less available to plants in acid soils because it binds with aluminium and iron oxides. Almost half of the ricelands across the globe are currently phosphorus deficient. The research therefore has the potential for significant impact across the world.

The GCP-funded scientists used markers to search rice and maize for genes equivalent to sorghum’s SbMATE. In maize they successfully identified a similar gene, ZmMATE1, which is now being validated in Brazil, Kenya and Mali. In rice the search continues, but will become easier now that markers for ZmMATE1 have been developed.

Similarly, having validated, cloned and developed markers for PSTOL1 gene in rice, researchers at IRRI and JIRCAS then worked with researchers at EMBRAPA and Cornell University to use PSTOL1 markers to search for comparable genes in sorghum and maize. In both crops, genes similar to PSTOL1 have been identified and shown to improve grain yields under low-phosphorus soil conditions, albeit through different mechanisms.

The GCP-funded discoveries are already being used in marker-assisted selection in national breeding programmes in Brazil, Kenya, Niger, Indonesia, Japan, The Philippines and USA in sorghum, maize and rice. They have led to the release of new, aluminium-tolerant sorghum varieties in Brazil, with more currently being developed, along with phosphorus-efficient rice varieties.

Photo: S Kilungu/CCAFS

Showing off freshly harvested sorghum in Kenya.

Cloning a worthwhile investment

Gene cloning was a relatively small cost in GCP’s research budget – about five percent (approximately USD 7 million) of a total research budget of USD 150 million spread over 10 years.

The gene-cloning component nonetheless yielded important genes for aluminium tolerance and phosphorus-uptake efficiency, within and across genomes. The molecular markers that have been developed are helping plant breeders across the world produce improved crop varieties.

Jean-Marcel Ribaut, Director of GCP, concludes: “The new markers developed for major genes in rice, sorghum and maize will have a significant impact on plant-breeding efficiency in developing countries.

“Breeders will be able to identify aluminium-tolerance and phosphorus-efficiency traits quicker, which, in time, will enable them to develop new varieties that will survive and thrive in the acid soils that make up more than half of the world’s arable soils.”

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Photo: CSISA

A rice farmer in Bihar, India.

Sep 282015
 

 

Photo: Agência BrasíliaSorghum is already a drought-hardy crop, and is a critical food source across Africa’s harsh, semi-arid regions where water-intensive crops simply cannot survive. Now, as rainfall patterns become increasingly erratic and variable worldwide, scientists warn of the need to improve sorghum’s broad adaptability to drought.

Crop researchers across the world are now on the verge of doing just that. Through support from the CGIAR Generation Challenge Programme (GCP), advanced breeding methods are enhancing the capacity of African sorghum breeders to deliver more robust varieties that will help struggling farmers and feed millions of poor people across sub-Saharan Africa.

Photo: ICRISAT

A farmer in her sorghum field in Tanzania.

Sorghum at home in Africa

From Sudanese savannah to the Sahara’s desert fringes, sorghum thrives in a diverse range of environments. First domesticated in East Africa some 6000 years ago, it is well adapted to hot, dry climates and low soil fertility, although still depends on receiving some rainfall to grow and is very sensitive to flooding.

In developed countries such as Australia, sorghum is grown almost exclusively to make feed for cattle, pigs and poultry, but in many African countries millions of poor rural people directly depend on the crop in their day-to-day lives.

Photo: ICRISAT

A Malian woman and her child eating sorghum.

In countries like Mali sorghum is an important staple crop. It is eaten in many forms such as couscous or (a kind of thick porridge), it is used for making local beer, and its straw is a vital source of feed for livestock.

While the demand for, and total production of, sorghum has doubled in West Africa in the last 20 years, yields have generally remained low due to a number of causes, from drought and problematic soils, to pests and diseases.

“In Mali, for instance, the average grain yield for traditional varieties of sorghum has been less than one tonne per hectare,” says Eva Weltzein-Rattunde, Principal Scientist for Mali’s sorghum breeding programme at the International Crops Research Institute for the Semi-Arid-Tropics (ICRISAT).

In a continued quest to integrate ways to increase productivity, GCP launched its Sorghum Research Initiative (RI) in 2010. This aimed to investigate and apply the approaches by which genetics and molecular breeding could be used to improve sorghum yields through better adaptability, particularly in the drylands of West Africa where cropping areas are large and rainfall is becoming increasingly rare.

Kick starting the work was a GCP-funded collaboration between project Principal Investigator Niaba Témé, plant breeder at Mali’s Institut d’économie rurale (IER) and the RI’s Product Delivery Coordinator Jean-François Rami of the Centre de coopération internationale en recherche agronomique pour le développement (CIRAD; Agricultural Research for Development), France, with additional support from the Syngenta Foundation for Sustainable Agriculture in Switzerland.

The collaboration aimed to develop ways to improve sorghum’s productivity and adaptation in the Sudano-Sahelian zone, starting with Mali in West Africa, and expanding later across the continent to encompass Burkina Faso, Ethiopia, Kenya, Niger and Sudan.

Photo: F Noy/UN Photo

A farmer harvest sorghum in Sudan.

Sorghum gains from molecular research

Since 2008, with the help of CIRAD and Syngenta, Niaba and his team at IER have been learning how to use molecular markers to develop improved sorghum germplasm through identifying parental lines that are more tolerant and better adapted to the arid and volatile environments of Mali.

The two breeding methods used in the collaboration are known as marker-assisted recurrent selection (MARS) and backcross nested association mapping (BCNAM).

MARS

Photo: N Palmer/CIAT“MARS identifies regions of the genome that control important traits,” explains Jean-François. “It uses molecular markers to explore more combinations in the plant populations, and thus increases breeding efficiency.”

Syngenta, he explains, became involved through its long experience in implementing MARS in maize.

“Syngenta advised the team on how to conduct MARS and ways we could avoid critical pitfalls,” he says. “They gave us access to using the software they have developed for the analysis of data, and this enabled us to start the programme immediately.”

With the help of the IER team, two bi-parental populations from elite local varieties were developed, targeting two different environments found in sorghum cropping areas in Mali. “We were then able to use molecular markers through MARS to identify and monitor key regions of the genome in consecutive breeding generations,” says Jean-François.

“When we have identified the genome regions on which to focus, we cross the progenies and monitor the resulting new progenies,” he says. “The improved varieties subsequently go to plant breeders in Mali’s national research program, which will later release varieties to farmers.”

Jean-François is pleased with the success of the MARS project so far. “The development of MARS addressed a large range of breeding targets for sorghum in Mali, including adaptation to the environment and grain productivity, as well as grain quality, plant morphology and response to diseases,” he says. “It proved to be efficient in elucidating the complex relationships between the large number of traits that the breeder has to deal with, and translating this into target genetic ideotypes that can be constructed using molecular markers.”

Jean-François says several MARS breeding lines have already shown superior and stable performance in farm testing as compared to current elite lines, and these will be available to breeders in Mali in 2015 to develop new varieties.

Photo: ICRISAT

Eva Weltzein-Rattunde examines sorghum plants with farmers in Mali.

BCNAM

Like MARS, the BCNAM approach shows promise for being able to quickly gain improvements in sorghum yield and adaptability to drought, explains Niaba, who is Principal Investigator of the BCNAM project. BCNAM may be particularly effective, he says, in developing varieties that have the grain quality preferences of Malian farmers, as well as the drought tolerance that has until now been unavailable.

“BCNAM involves using an elite recurrent parent that is already adapted to local drought conditions, then crossing it with several different specific or donor parents to build up larger breeding populations,” he explains. “The benefit of this approach is it can lead to detecting elite varieties much faster.”

Eva and her team at ICRISAT have also been collaborating with researchers at IER and CIRAD on the BCNAM project. The approach, she says, has the potential to halve the time it takes to develop local sorghum varieties with improved yield and adaptability to poor soil fertility conditions.

“We don’t have these types of molecular-breeding resources available in Mali, so it’s really exciting to be a part of this project,” she says. “Overall, we feel the experience is enhancing our capacity here, and that we are closer to delivering more robust sorghum varieties which will help farmers and feed the ever-growing population in West Africa.”

Indeed, during field testing in Mali, BCNAM lines derived from the elite parent variety Grinkan have produced more than twice the yields of Grinkan itself. As they are rolled out in the form of new varieties, the team anticipates that they will have a huge positive impact on farmers’ livelihoods.

Photo: E Weltzein-Rattunde/ICRISAT

Malian sorghum farmers.

Mali and Queensland similar problem, different soil

In Mali and the wider Sahel region within West Africa, cropping conditions are ideal for sorghum. The climate is harsh, with daily temperatures on the dry, sun-scorched lower plains rarely falling below 30°C. With no major river system, the threat of drought is ever-present, and communities are entirely dependent on the 500 millimetres of rain that falls during the July and August wet season.

“All the planting and harvesting is done during the rainy season,” says Niaba. “We have lakes that are fed by the rain, but when these lakes start to dry up farmers rely mostly on the moisture remaining in the soil.”

Over 17 thousand kilometres to the east of Mali, in north-eastern Australia’s dryland cropping region, situated mainly in the state of Queensland, sorghum is the main summer crop, and is considered a good rotational crop as it performs well under heat and moisture stress. The environment here is similar to Mali’s, with extreme drought a big problem.

Average yields for sorghum in Queensland are double those in Mali—around two tonnes per hectare—yet growers still consider them low, directly limited by the crop’s predominantly water-stressed production environment in Australia.

One of the differentiating factors is soil. “Queensland has a much deeper and more fertile soil compared to Mali, where the soil is shallow, with no mulch or organic matter,” says Niaba. “Also, there is no management at the farm level in Mali, so when rain comes, if the soil cannot take it, we lose it.”

Photo: Bart Sedgwick/Flickr (Creative Commons)

Sorghum in Queensland, Australia.

Making sorghum stay green, longer

Another key reason for the difference in yields between Queensland and Mali is that growers in Queensland are sowing a sorghum variety of with a genetic trait that makes it more tolerant to drought.

This trait is called ‘stay-green’, and over the last two decades it has proven valuable in increasing sorghum yields, using less water, in north-eastern Australia and the southern United States.

Stay-green allows sorghum plants to stay alive and maintain green leaves for longer during post-flowering drought—that is, drought that occurs after the plant has flowered. This means the plants can keep growing and produce more grain in drier conditions.

“We’ve found that stay-green can improve yields by up to 30 percent in drought conditions with very little downside during a good year,” says Andrew Borrell from the Queensland Alliance for Agriculture and Food Innovation (QAAFI) at the University of Queensland (UQ) in Australia.

“Plant breeders have known about stay-green for some 30 years,” he says. “They’d walk their fields and see that the leaves of certain plants would remain green while others didn’t. They knew it was correlated with high yield under drought conditions, but didn’t know why.”

Stay-green’s potential in Mali

With their almost 20 years working on understanding how stay-green works, Andrew and his colleagues at UQ were invited by GCP in 2012 to take part in the IER/CIRAD collaborative project, to evaluate the potential for introducing stay-green into Mali’s local sorghum varieties and enriching Malian pre-breeding material for the trait.

A pivotal stage in this new alliance was a 12-month visit to Australia by Niaba and his IER colleague Sidi Coulibaly, to work with Andrew and his team to understand how stay-green drought resistance works in tall Malian sorghum varieties.

“African sorghum is very tall and sensitive to variation in day length,” explains Andrew. “We have been looking to investigate if the stay-green mechanism operates in tall African sorghums (around four metres tall) in the same way that it does in short Australian sorghum (one metre tall).”

Having just completed a series of experiments at the end of 2014, the UQ team consider their data as preliminary at this stage. “But it looks like we can get a correlation between stay-green and the size and yield of these Malian lines,” says Andrew. “We think it’s got great potential.”

Photo: S Sridharan/ICRISAT

Sorhum growing in Mozambique.

Sharing knowledge as well as germplasm

Eva Weltzein-Rattunde has played more of an on-the-ground capacity development role in Mali since accepting her position at ICRISAT in 1998. She says “the key challenges have been improving the infrastructure of the national research facilities [in Mali] to do the research as well as increasing the technical training for local agronomists and researchers.”

Photo: ICRISAT

A Malian farmer harvests Sorghum.

A large part of GCP’s focus is building just such capacity among developing country partners to carry out crop research and breeding independently in future, so they can continue developing new varieties with drought adaptation relevant to their own environmental conditions.

A key objective of the IER team’s Australian visit was to receive training in the methods for improving yields and drought resistance in sorghum breeding lines from both Australia and Mali.

“We learnt about association mapping, population genetics and diversity, molecular breeding, crop modelling using climate forecasts, and sorghum physiology, plus a lot more,” says Niaba. This training complemented previous training Niaba and IER researchers had from CIRAD and ICRISAT through the MARS and BCNAM projects.

“We [CIRAD] have a long collaboration in sorghum research in Mali and training young scientists has always been part of our mission,” says Jean-François. “We’ve hosted several IER students here in France and we are always interacting with our colleagues in Mali either over the phone or travelling to Mali to give technical workshops in molecular breeding.”

Photo: Rita Willaert/Flickr (Creative Commons)

Harvested sorghum in Sudan.

Working together to implement MARS in the sorghum breeding program in Mali represented many operational challenges, Jean-François explains. “The approach requires a very tight integration of different and complementary skills, including a strong conventional breeding capacity, accurate breeders’ knowledge, efficient genotyping technologies, and skills for efficient genetic analyses,” he says.

Because of this requirement, he adds, there are very few reported experiences of the successful implementation of MARS.  It is also the reason why these kinds of projects would normally not be undertaken in a developing country like Mali, but for the support of GCP and the dedicated mentorship of Jean-François.

sorghum quote 2“GCP provided the perfect environment to develop the MARS approach,” says Jean-François. “It brought together people with complementary skills, developed the Integrated Breeding Platform (IPB), and provided tools and services to support the programme.”

In addition to developing capacity, Jean-François says one of the great successes of both the MARS and the BCNAM projects was how they brought together Mali’s sorghum research groups working at IER and ICRISAT in a common effort to develop new genetic resources for sorghum breeding.

“This work has strengthened the IER and ICRISAT partnerships around a common resource. The large multiparent populations that have been developed are analysed collectively to decipher the genetic control of important traits for sorghum breeding in Mali,” says Jean-François. “This community development is another major achievement of the Sorghum Research Initiative.” The major challenge, he adds, will be whether this community can be kept together beyond GCP.

Considering the numerous ‘non-GCP’ activities that have already been initiated in Africa as a result of the partnerships forged through GCP research, Jean-François sees a clear indication that these connections will endure well beyond GCP’s time frame.

GCP’s sunset is Mali’s sunrise

Photo: S Sridharan/ICRISAT

Sorghum at sunset in Mozambique.

Among the new activities Jean-François lists are both regional and national projects aimed at building on what has already been achieved through GCP and linking national partners together. These include the West African Agricultural Productivity Program (WAAPP), the West Africa Platform being launched by CIRAD as a continuation of the MARS innovation, and another MARS project in Senegal and Niger through the Feed the Future Innovation Lab for Collaborative Research on Sorghum and Millet at Kansas State University.

“These are all activities which will help maintain the networks we’ve built,” Jean-François says. “I think it is very important that these networks of people with common objectives stick together.”

sorghum quoteFor Niaba, GCP provided the initial boost needed for these networks to emerge and thrive. “We had some contacts before, but we didn’t have the funds to really get into a collaboration. This has been made possible by GCP. Now we’re motivated and are making connections with other people on how we can continue working with the material we have developed.”

“I can’t talk enough of the positive stories from GCP,” he adds. “GCP initiated something, and the benefits for me and my country I cannot measure. Right now, GCP has reached its sunset; but for me it is a sunrise, because what we have been left with is so important.”

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Photo: ICRISAT

A sorghum farmer in her field in Tanzania.

Mar 102015
 

 

Niaba Témé

Niaba Témé

“I can’t talk enough about the positive stories from the Generation Challenge Programme [GCP]. It initiated something new. I cannot measure its benefits for my country, for myself and for the sorghum-breeding and -producer communities. Right now, GCP has reached its sunset; but for me it is a sunrise, because what we have been left with is so very important.”

Growing up in a farming community in Mali, on the southern edge of the Sahara Desert, plant breeder Niaba Témé knows the ups and downs of farming in the harsh, volatile semiarid regions of Africa.

“I used to love harvesting the millet and helping my mother with her groundnut crops,” he remembers fondly. “We grew other dryland crops too, like sorghum, cowpeas, Bambara nuts, sesame and dah.”

Niaba’s village of Yendouma-Sogol is one of many villages balanced along the edge of the Bandiagara escarpment – 150 kilometres of sandstone cliffs soaring hundreds of metres above the sandy plains below. The region is considered one of the most challenging places in the world to be a farmer. The climate is harsh, with the average daily temperature on the dry, sun-scorched plains rarely falling below 30°C and often exceeding 40°C during the hottest months of the year. With no major water source available for drinking, cropping and livestock husbandry, the threat of drought is ever-present here, as it is across much of Africa’s semiarid landscape.

While much of Mali’s irrigated agriculture relies on water from the River Niger, villages like Niaba’s depend entirely on the 500 or so millimetres of rainfall they receive during the July–August wet season. In the years that the rains didn’t come, Niaba’s family were unable to harvest anything at all. The repeated failure of his parents’ crops – coupled with a natural interest in science – inspired Niaba to embark on a career where he could help farming families like his own defend themselves against the risks of drought and extreme temperatures.

Photo: F Fiondella/CCAFS

Farmland in Diouna, Mali. Farmers here must contend with the Sahel’s dry, sandy soil and whatever limited rainfall the clouds bring to grow sorghum, millet, maize, and other crops.

Niaba’s journey

Niaba’s first big step along the research road was when he enrolled to study agronomy at Mali’s Institut Polytechnique Rural de Formation et de Recherche Appliquée in Eastern Bamako. Within two years he was offered a scholarship to study plant breeding at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) in Hyderabad, India. He then worked at the Cinzana Research Station in Mali.

Niaba later spent 11 years in the USA completing a bachelor’s degree, master’s degree and finally PhD in agronomy at Texas Tech University before returning home to Mali in 2007, where he was soon recruited by Mali’s Institut d’Économie Rurale (IER) to take charge of their new biotechnology lab at the Centre Régional de Recherche Agronomique.

His journey with the Generation Challenge Programme began in 2010 when IER received GCP funding to carry out sorghum research in Africa as part of GCP’s Sorghum Research Initiative (RI) launched that same year. The project was a collaboration with ICRISAT and France’s Centre de coopération internationale en recherche agronomique pour le développement (Agropolis–CIRAD; Agricultural Research for Development). With an initial focus on Mali, the project’s results would expand to encompass five other countries in the Sudano-Sahelian region: Burkina Faso, Ethiopia, Kenya, Niger and Sudan.

Sorghum the survivor gets even tougher

Photo: ICRISAT

Hand milling of sorghum grains – an arduous task, mostly carried out by poor women in the drylands of Africa.

Drought-hardy crops such as sorghum are ideal for Mali’s conditions, where more water-intensive crops such as maize simply cannot survive. Millions of poor rural people across Africa depend on sorghum in their day-to-day lives: it is eaten in many forms, used to make alcoholic beverages and as animal fodder, and is converted into biofuel for cooking.

But even sorghum has its limits. While the demand for it has doubled in West Africa in the last 20 years, productivity has generally remained low, with an average yield of only one tonne per hectare for traditional varieties in Mali. This is mostly due to post-flowering drought, poor soils and farming conditions, and limited access to quality, high-yielding seed. As rainfall patterns become increasingly erratic and variable across the world, scientists warn of the need to improve sorghum’s broad adaptability to drought, to ensure future food security in Africa.

The GCP Sorghum RI, with Niaba’s help, aimed to support the development of new breeds of sorghum that could survive better on less water in drought-stricken parts of Africa. It sought to improve sorghum yield and quality for African farmers and, in turn, improve the livelihoods and food security of communities across sub-Saharan Africa.

In 2012, Niaba found himself travelling once again, this time to Australia with IER colleague Sidi B Coulibaly. They spent three weeks working alongside, and training with, Andrew Borrell and his sorghum research team at the Queensland Government Department of Agriculture, Fisheries and Forestry’s (DAFF) Hermitage Research Facility in Warwick.

“We have been collaborating with researchers at DAFF and The University of Queensland since 2009, to introduce what is called the ‘stay-green’ drought-resistant gene into our local sorghum varieties,” says Niaba.

Photo provided by A Borrell

Left to right: Niaba Témé with David Jordan (Australia), Sidi B Coulibaly (Mali) and Andrew Borrell (Australia), visiting an experiment at Hermitage Research Facility in Queensland, Australia.

Niaba’s no longer green when it comes to using stay-green

Stay-green is a drought adaptation trait that allows sorghum plants to stay alive and maintain green leaves for longer during post-flowering drought. This means the plants can keep growing and produce more grain in drier conditions. It has contributed significantly to an increase in sorghum yields, using less water, in north-eastern Australia and southern USA for the last two decades.

GCP’s stay-green project aimed to evaluate the potential for introducing stay-green into Mali’s local sorghum varieties, enriching Malian pre-breeding material for the trait, and training African sorghum researchers, such as Niaba, in the methods of improving yields and drought resistance in sorghum breeding lines from both Australia and Mali.

Photo provided by E Weltzein-Rattunde

A sorghum farmer in Mali.

“In Australia we learnt about association mapping, population genetics and diversity, molecular breeding, crop modelling using climate forecasts, and sorghum physiology,” says Niaba.

Learning to use molecular markers was particularly exciting, he says, “because molecular markers make it easier to see if the plant being bred has the gene related to drought tolerance, without having to go through the lengthy process of growing the plant to maturity and risk missing the trait through visual inspection.”

Niaba says the molecular training he received in Australia complemented previous training he had received through a collaborative GCP-funded project with Agropolis–CIRAD and Syngenta Foundation for Sustainable Agriculture, in which he learnt to use molecular markers to identify and monitor key regions of sorghum’s genome in consecutive breeding generations through a process called marker-assisted recurrent selection (MARS).

A large part of GCP’s focus is building such capacity among developing country partners to carry out crop research and breeding independently in the future, so they can continue developing new varieties with drought adaptation relevant to their own environmental conditions.

“Our time in Australia was an intense but rewarding experience, more so for the fact that between the efforts of Australia and Mali, we have now developed new drought-tolerant crops which will enhance food security for my country,” says Niaba. “Similarly with the help of Agropolis–CIRAD and Syngenta, we are using molecular markers to improve breeding efficiency of sorghum varieties more adapted to the variable environment of Mali.”

Photo provided by A Borrell

Niaba (foreground) examining a sorghum panicle at trials in Mali in 2009.

Sorghum sunrise in Mali

On the back of the MARS project, Niaba successfully obtained GCP funding in 2010 to carry out similar research with Agropolis–CIRAD and collaborators in Africa at ICRISAT.

“In that project, we were trying to enhance sorghum grain yield and quality for the Sudano-Sahelian zone of West Africa using the backcross nested association mapping (BCNAM) approach,” explains Niaba. “This involved using an elite recurrent parent that is already adapted to local drought conditions. The benefit of this approach is that it can lead to detecting elite varieties much faster.”

The approach has the potential to halve the time it takes to develop local sorghum varieties with improved yield and adaptability to drought. The project developed 100 lines for 50 populations from backcrosses carried out with 30 recurrent parents. The lines are now being validated in Mali.

Photo: P St-Jacques/DFATD-MAECD

Agronomists inspect a field of sorghum in Mali.

Niaba says such successful collaborations and capacity development opportunities have been made possible only through GCP support.

“We had some contacts before, but we didn’t have the funds or skills to really get into a collaboration. Now we’re motivated and are making connections with other people so we can continue working with the material we have developed.

“GCP’s time may be ending, but it very much represents a new day – a sunrise for the work we are doing with sorghum here in Mali.”

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Photo: N Palmer/CIAT

Sorghum for sale.

Dec 052014
 

It’s a cruel feature of some of the most populous areas of the world, particularly in the tropics and subtropics: acid soils. They cover a third of the world’s total land area – including significant swathes of Africa, Asia and Latin America – and 60 percent of land we could use for growing food. Today around 30 percent of all arable land reaches levels of acidity that are toxic to crops.

Soil acidity occurs naturally in higher rainfall areas and varies according to the landscape and soil. But we also make the problem worse through intensive agricultural practices. The main cause of soil acidification is the overuse of nitrogen fertilisers, which farmers apply to crops to increase production. Ironically, the inefficient use of nitrogen fertiliser can instead make matters worse by decreasing the soil pH.

60 percent of the world’s potential crop-growing land is highly acidic. Map courtesy of Leon Kochian.

60 percent of the world’s potential crop-growing land is highly acidic. Map courtesy of Leon Kochian.

Acidity prevents crops from accessing the right balance of nutrients in the soil, limiting farmers’ yields. Its negative effect on world yield is second only to drought and is particularly hard felt by subsistent and smallholder farmers who cannot afford to correct soil pH using calcium-rich lime. As a result, these farmers are forced to grow less profitable, acid-tolerant crops like millet, or suffer huge yield losses when growing more popular cereal crops like wheat, rice or maize.

“In Kenya, acidic soils cover almost 90 percent of the maize-growing areas and can reduce yields by almost 60 percent,” says Samuel Gudu, Professor and Deputy Vice-Chancellor (Planning & Development) at Moi University in Kenya. “Farmers know that the soil affects their yields, but they still grow maize because it is so popular.”

As is true in many other sub-Saharan countries, maize is a staple of the Kenyan diet: the average Kenyan consumes 98 kilograms of it each year. But maize prices in Kenya are among the highest in Africa, which directly affects the poorest quarter of the population, who spend 28 percent of their income on the crop.

“Yield losses play a big part in this economic imbalance and are why we need affordable agronomic options to help our farmers improve yields,” says Samuel, who was a Principal Investigator of a GCP comparative genomics project which sought to provide some of these options.

A Kenyan farmer prepares her maize plot for planting. Acid soils cover almost 90 percent of Kenya’s maize-growing area, and can more than halve yields.

A Kenyan farmer prepares her maize plot for planting. Acid soils cover almost 90 percent of Kenya’s maize-growing area, and can more than halve yields.

Aluminium toxicity and phosphorus deficiency: Public enemies number one and two in the fight against acidic soils

Between 2004 and 2014, crop researchers and plant breeders across five continents collaborated on several GCP projects to develop local varieties of maize, rice and sorghum that can withstand phosphorus deficiency and aluminium toxicity – two of the most widespread constraints leading to poor crop productivity in acidic soils.

Aluminium toxicity is the primary limitation on crop production for more than 30 percent of farmland in Southeast Asia and Latin America and approximately 20 percent in East Asia, sub-Saharan Africa and North America. Aluminium becomes more soluble in acid souls, creating a toxic glut of aluminium ions that damage roots and impair their growth and function. This results in reduced nutrient and water uptake, which in turn depresses yield.

Phosphorus deficiency is the next biggest soil deficiency after nitrogen to limit plant production. In acid soils, phosphorus is stuck (fixed) in forms that plants cannot take up. All plants need phosphorus to survive and thrive; it is a key element in plant metabolism, root growth, maturity and yield. Plants deficient in phosphorus are often stunted.

In a double whammy, the damage that aluminium toxicity causes to roots means that plants cannot efficiently access native soil phosphorus or even added phosphorus fertiliser – and adding phosphorus is an option that is rapidly becoming less viable.

“The world is running out of phosphorus as quickly as it is running out of oil,” says Leon Kochian, a Professor in the Departments of Plant Biology and Crop and Soil Science at Cornell University in the USA. “This is making its application a more expensive and less sustainable option for all farmers wanting to improve yields on acidic soils.” Indeed, the price of rock phosphate has more than doubled since 2007.

For 30 years, Leon has combined lecturing and supervising duties at Cornell University and the United States Department of Agriculture with his scientific quest to understand the genetic and physiological mechanisms that allow some cereals to tolerate acidic soils while others wither. And for the last 10 years, he has played an important leading role in GCP’s effort to develop new, higher yielding varieties of maize, rice and sorghum that tolerate acidic soils.

GCP builds on past crop breeding successes

The rationale behind GCP’s efforts stems from two independent and concurrent projects, which had been flourishing on different sides of the Pacific well before GCP was created.

One of those projects was co-led by Leon at Cornell University in collaboration with a previous PhD student of his, Jurandir Magalhães, at the Brazilian Corporation of Agricultural Research (EMBRAPA) Maize & Sorghum research centre.

Working on the understanding that the cells in grasses like barley and wheat use ‘membrane transporters’ to insulate themselves against excessive subsoil aluminium, Leon and Jurandir searched for a similar transporter in the cells of sorghum varieties that were known to tolerate aluminium.

“In wheat, when aluminium levels are high, these membrane transporters prompt organic acid release from the tip of the root,” explains Jurandir. “The organic acid binds with the aluminium ion, preventing it from entering the root.” Jurandir’s team found that in certain sorghum varieties, the gene SbMATE encodes a specialised organic acid transport protein, which stimulates the release of citric acid. They cloned the gene and found it was very active in aluminium-tolerant sorghum varieties. They also discovered that the activity of SbMATE increases the longer the plant is exposed to high levels of aluminium.

The rice variety on the left (IR-74) has the the gene locus Pup1, conferring phosphorus-efficient longer roots, while the rice on the right does not.

The rice variety on the left (IR-74) has the the gene locus Pup1, conferring phosphorus-efficient longer roots, while that on the right does not.

The other project, co-led by Matthias Wissuwa at Japan International Research Centre for Agricultural Sciences (JIRCAS) and Sigrid Heur at the International Rice Research Institute (IRRI) in The Philippines, was looking for genes that could improve rice yields in phosphorus-deficient soils. They had already identified a gene locus (a section of the genome containing a collection of genes) that produced a protein which allowed rice varieties with to grow successfully in low-phosphorous conditions. The locus was termed ‘phosphorus uptake 1’ or Pup1 for short. With GCP support, the team were able to make the breakthrough of discovering the protein kinase gene responsible, PSTOL1 (‘phosphorus starvation tolerance 1’), and understanding its mechanism.

“In phosphorus-poor soils, this protein instructs the plant to grow larger, longer roots, which are able to forage through more soil to absorb and store more nutrients,” explains Sigrid, a plant geneticist at IRRI and a GCP Principal Investigator. “By having a larger root surface area, plants can explore a greater area in the soil and find more phosphorus than usual. It’s like having a larger sponge to absorb more water.”

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

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

Leon clarifies that both projects were fairly advanced before they became part of the GCP fold. “Our team had already identified the gene SbMATE and were in the process of cloning it for breeding purposes. The IRRI and JIRCAS team had also identified Pup1 and were in the process of identifying and cloning the gene.”

The purpose of cloning these genes was to create molecular markers to help breeders identify whether the genes were present in the varieties they were working with. As an analogy, think of ‘reading’ a plant’s genome as you would read a story: the story’s words are the plant’s genes, and a molecular marker works as a text highlighter. Different markers can highlight or tag different keywords in the story. Tagging the location of beneficial genes in the DNA of plant genomes allows scientists to see which of the plants or seeds they are interested in – perhaps only a few out of hundreds or thousands – contain these genes. This forms the basis of marker-assisted breeding, which can help plant breeders halve the time it takes them to breed new high-yielding varieties for acidic soil conditions.

Leon says that GCP provided both projects with the opportunity to validate their discoveries and to use what they had found to develop new aluminium-tolerant sorghum varieties and phosphorus-efficient rice varieties for farmers. But it’s what happened next that made this GCP initiative unique.

Finding the best genes within the crop family

Sorghum, rice, maize and wheat are all part of the Poaceae (true grasses) family, evolving from a common grass ancestor 65 million years ago. Over this time, they have become very different from each other. However, at the genetic level they still have a lot in common.

Over the last 20 years, genetic researchers all over the world have been mapping these cereals’ genomes. These maps are now being used by geneticists and plant breeders to identify similarities and differences between the genes of different cereal species. This process is termed ‘comparative genomics’ and was a fundamental research theme for GCP during its second phase (2008–2014).

“The objective during GCP Phase I (2004-2007) was to study the genomes of important crops and identify genes conferring resistance or tolerance to various stresses, such as drought,” says Rajeev Varshney, Director of the Center of Excellence in Genomics at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT). “This research was long and intensive, but it set a firm foundation for the work in GCP’s second phase, which sought to use what we have learnt in the laboratory and apply it to breed better varieties of crops.”

Rajeev oversaw GCP’s comparative genomics research projects on aluminium tolerance and phosphorus deficiency in sorghum, maize and rice, as part of his GCP role as Leader of the Comparative and Applied Genomics Research Theme.

“The idea behind the sorghum, maize and rice initiative was to use the discoveries we had independently made in sorghum and rice to see if we could find the same genes in the other crop,” explains Rajeev. “In other words, we wanted to see if we could find PSTOL1 in sorghum and SbMATE in rice.”

Working together through a number of comparative genomics projects, the researchers were highly successful in reaching this goal, discovering valuable sister genes and beginning to introduce them into new improved crop varieties for farmers.

Extending research in sorghum and rice to maize

Researchers at Cornell and EMBRAPA had already been using similar comparative techniques to look for SbMATE in maize because of its close familial connection to sorghum. This research was overseen by Leon and another EMBRAPA researcher, Claudia Guimarães.

“We used the knowledge that Jurandir and Leon’s SbMATE project produced to prove that we had a major aluminium-tolerance gene,” reflects Claudia.

The SbMATE gene in sorghum explains about 80 percent of its aluminium tolerance, but Claudia says that in maize it explains only about 20 per cent, making it harder for researchers to find without a little help knowing what to look for. “So we had to dig a little deeper for other similar genes that confer aluminium tolerance, and we found ZmMATE.”

Maize trials in the field at EMBRAPA. The maize plants on the left are aluminium-tolerant while those on the right are not.

Maize trials in the field at EMBRAPA. The maize plants on the left are aluminium-tolerant while those on the right are not.

ZmMATE1 has a similar genetic sequence to SbMATE and encodes a similar protein membrane transporter that releases citric acid from the roots. Just as in sorghum, citric acid binds to aluminium in the soil, making it difficult for it to enter plant roots. The team have also discovered related gene ZmMATE2, which also encodes a transporter protein, but appears to confer aluminium tolerance via a different mechanism, as yet unclear.

Claudia has developed a number of molecular markers for ZmMATE, which have been successfully used by breeders at EMBRAPA as well as by African partners in Niger and Kenya, such as Samuel Gudu, to identify maize breeding lines that have the gene.

“We used aluminium-tolerant maize varieties sourced locally and from Brazil to develop a range of potential new varieties,” says Samuel. “The goal is to develop varieties that are suited to our environment and not too dissimilar to varieties that Kenyan farmers like to grow, except they have a higher tolerance to aluminium toxicity.”

Left to right (foreground): Leon Kochian, Jurandir Magalhães and Samuel Gudu examine crosses between Kenyan and Brazilian maize, at the Kenya Agricultural Research Institute (KARI), Kitale, in May 2010.

Left to right (foreground): Leon Kochian, Jurandir Magalhães and Samuel Gudu examine crosses between Kenyan and Brazilian maize, at the Kenya Agricultural Research Institute (KARI), Kitale, in May 2010.

Involving farmers in the crop breeding process is an important part of such programs being successful, explains Samuel. “They help us identify maize varieties that they have observed have higher tolerance to acidic soils. We also try to incorporate other features that they want, such as disease resistance and higher yield. By incorporating their feedback into the breeding process they are more likely to grow any new varieties, as they have played a part in their development.”

Samuel says they have developed some local aluminium-tolerant varieties, which rank among the best for aluminium tolerance. Interestingly, these varieties seem to have a different aluminium-tolerance mechanism to the Brazilian varieties.

“From the work Samuel has done, we’ve possibly identified a novel source of aluminium tolerance in Kenyan maize varieties,” says Claudia. “We are now working together with Leon to identify the genes that are conferring this tolerance so we can develop markers to help Kenyan maize breeders also identify these varieties more efficiently.”

To help in the process, Samuel and his team are developing single-cross hybrids with a combination of both the novel Kenyan sources of aluminium tolerance and ZmMATE from Brazil, which will be even more tolerant to acidic soils.

Breeding for multiple stresses is a step-by-step process

Suradiyo, a farmer from Bojong Village near Yogyakarta, Indonesia, harvests rice.

Suradiyo, a farmer from Bojong Village near Yogyakarta, Indonesia, harvests rice.

In Asia, about 60 percent of rainfed rice is grown on soils that are affected by multiple stresses. These typically include phosphorus deficiency as well as aluminium toxicity, salinity and drought.

These stresses are particularly hard felt in Indonesia, which is the world’s third-largest rice producer. Joko Prasetiyono is a molecular rice breeder at the Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development (ICABIOGRAD). His team have been collaborating with IRRI and JIRCAS for many years and contributed to validating the effect of Pup1 by embedding it into three popular local rice varieties – Dodokan, Situ Bagendit and Batur – which were then able to tolerate phosphorus-deficient conditions.

“The aim [with GCP research] was to breed varieties identical to those that farmers already know and trust, except that they have PSTOL1 and an improved ability to take up soil phosphorus,” says Joko.

Joko says that these varieties – which will be available in one to two years – will yield as well as, if not better than, traditional varieties, and will need 30–50 percent less fertiliser.

But the work is only partly finished for Joko and his Asian partners. They are now building on previous work done at Cornell and EMBRAPA to include the SbMATE gene in their varieties. “Higher yields will only be possible if the plant can also tolerate excess aluminium, which severely inhibits root growth and thereby water and nutrient uptake,” explains Joko. “We are also looking at incorporating salt-tolerance and drought-tolerance genes. It’s a step-by-step process where we hope to build tolerance to the multiple stresses that afflict most rice-growing areas throughout Asia and the world.”

Introducing PSTOL1 into maize and sorghum

At EMBRAPA, Claudia is also interested in building up tolerance to multiple stresses and was involved in the project to look for genes similar to PSTOL1 in maize. “As soon as IRRI and JIRCAS had cloned the gene and created markers, we started using the markers to search for the gene in maize, as Jurandir did in sorghum,” she says.

Women farmers in India bring home their sorghum harvest.

Women farmers in India bring home their sorghum harvest.

Finding genes that confer phosphorus-efficiency traits in maize and sorghum has been a more challenging project, according to Leon. “From the rice work, we knew a big part of phosphorus efficiency was to do with root architecture – you want to have shallow horizontal roots instead of roots that grow down, which is often the case in maize and sorghum,” he explains. “This is because there is less accessible phosphorus further down the soil profile.”

Observing root architecture is difficult in ordinary soil, so the team had to develop new ways to visualise the plants’ roots. They grew plants in a transparent nutrient gel, which they then photographed to create three-dimensional images of the root structure.

The team found sorghum and maize varieties that contained genes similar to PSTOL1 in rice, but which also have longer root systems that radiated outwards rather than downwards in gels with higher concentration of aluminium. “These observations helped validate multiple PSTOL1 regions in sorghum and maize, which we’ve been able to develop markers for to help breeders identify these traits more easily,” says Leon.

These markers have successfully been used by sorghum breeders in Brazil and Africa to identify phosphorus-efficient varieties. Maize breeders in both Brazil and Africa are expected to use similar markers to validate their varieties in 2015.

New sorghum varieties prove their worth in the field

Eva Weltzien is one Africa-based sorghum breeder who has benefited from these PSTOL1 and SbMATE markers. Based in Mali at ICRISAT, Eva and her team have been using the markers to select for aluminium-tolerant and phosphorus-efficient varieties and validating their performance in field trials across 29 environments in three countries in West Africa.

She says the markers have helped evolve the way they do their breeding. “Using molecular markers, we are able to identify whether the lines we are breeding have genes that confer the traits that we want,” explains Eva. “It has really revolutionised our breeding program and helped it make great progress in the past three to four years.”

In Mali, sorghum is an important staple crop. It is used to make (a thick porridge), couscous, and local beers. Part of its popularity is its adaptability to various climates – in Mali it is grown in very dry environments as well as in forest/rainforest zones. However, it is widely affected by acidic soils.

Sorghum farmers at work in the field in Mali.

Sorghum farmers at work in the field in Mali.

“Low phosphorus availability is a key problem for farmers on the coast of West Africa, and breeding phosphorus-efficient crops to cope with these conditions has been a main objective of ICRISAT in West Africa for some time,” says Eva.

“We’ve had good results in terms of field trials. We have at least 20 lines we are field testing at the moment, which we selected from 1,100 lines that we tested under high and low phosphorous conditions.” Eva says that some of these lines could be released as new varieties as early as next year.

“Overall, we feel the GCP partnership with EMBRAPA and Cornell is enhancing our capacity here in Mali, and that we are closer to delivering more robust sorghum varieties that will help farmers and feed the ever-growing population in West Africa.”

Leon notes that the work by Eva in Mali and by other African partners in Niger and Kenya is imperative for the research. “Just because plants have these genes, doesn’t mean they will all display aluminium tolerance or phosphorus efficiency. You still need to test and observe for these traits in the field and determine what other factors might affect plants grown in acidic soils.”

One surprising observation that has Leon intrigued is a local sorghum variety with a phosphorus-efficiency gene that is close to where the SbMATE gene resides in the sorghum genome. “This suggests that SbMATE, which aids with aluminium tolerance, may also improve phosphorus efficiency. This means we could use SbMATE markers to look for both phosphorus efficiency and aluminium tolerance,” he says. Leon and Jurandir will continue to validate this result post-GCP.

Working together to improve food security worldwide

GCP’s comparative genomics projects have laid a significant foundation for further research into and breeding for tolerance to multiple plant stresses.

A Kenyan farmer in her maize field.

A Kenyan farmer in her maize field.

“We’re in a golden age of biology where we are learning more and more about the complexities and commonalities of plants, which is allowing us to manipulate them ever so slightly to help them tolerate multiple environmental stresses,” says Leon. “As a geneticist, I am extremely proud to be part of this, particularly seeing the potential impact that the basic research we do in the laboratory can have on crop improvement and the lives of people in poorer countries.”

Although not all projects produced new and improved varieties ready for release, they are well and truly in the pipeline. Each partner institute is committed to work together and source new funding to continue on their quest to produce further products.

“GCP has really installed in us a spirit to see this work through and expand on it,” says Leon. “I mean, we are now working with other countries and institutes to share what we have learnt with them and help them make the discoveries that we have. It’s a credit to GCP for bringing us all together; that was a key to the success of the project. Each partner has brought their expertise to the table – genomics, molecular biology, plant breeding – and it has been great to see the impact filter into Africa and Asia.”

In Kenya, Samuel agrees with Leon’s assessment. “GCP gave us an opportunity to build our expertise and start interacting with the rest of the world,” he says. “But more importantly, it means that we’re contributing to food security in Kenya, and that makes us really proud.”

Although the sun is setting on GCP, work on comparative genomics projects is still in progress, with all parties still working towards delivering important new acid-beating varieties to farmers.

A boy rides his bicycle next to a rice field in the Philippines. With acid soils affecting half the world’s current arable land, acid-beating crop varieties will help farmers feed their families – and the world – into the future.

A boy rides his bicycle next to a rice field in the Philippines. With acid soils affecting half the world’s current arable land, acid-beating crop varieties will help farmers feed their families – and the world – into the future.

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