Jan 082015
 

Welcome to Brazil! Journey by road six hours northwest from Rio de Janeiro and you’ll arrive to Sete Lagoas,  a city whose name means ‘Seven Lagoons’ in Portuguese. Although cloistered in farmlands, the city is largely a commercial centre, but also the seat of Embrapa Milho e Sorgo, the nerve centre of EMBRAPA’s maize and sorghum research, and so could pass for the ‘sede’ (Portuguese for headquarters) of the these two cereals. EMBRAPA is the Portuguese acronym for Empresa Brasileira de Pesquisa Agropecuária; the Brazilian Agricultural Research Corporation. EMBRAPA is a GCP Consortium member, and contributed to the proposal that founded GCP.

Photo provided by J MagalhãesJurandir Magalhães (pictured), or Jura, as he likes to be referred to in informal settings such as our story today, is a cereal molecular geneticist who has been working at the Embrapa Milho e Sorgo centre since 2002. “The centre develops projects and research to produce, adapt and diffuse knowledge and technologies in maize and sorghum production by the efficient and rational use of natural resources,” Jura explains.

Such qualities are exactly what appeal to GCP, which has supported Jura as a Principal Investigator since 2004. Beyond science and on to governance and advisory issues, Jura is also EMBRAPA’s representative on the GCP Consortium Committee.

Home and away, on a journey of discovery in sorghum
Hailing from Belo Horizonte, Minas Gerais State, where he was born, Jura attended the Federal University of Viçosa in his home state. Upon completing his Master’s degree at the university in 1995, he proceeded to USA’s Cornell University in 1998 for his PhD, under the watchful eye of Leon Kochian, another GCP Principal Investigator.

Sorghum rainbow_A Borrell

No, it’s not photo-shopped. This Australian sorghum-and-double-rainbows shot is from Supa Snappa, Andy Borrell, also a GCP sorghum Principal Investigator. See http://bit.ly/1tBAOMW

At Cornell, Jura worked with Leon on identifying the genes associated with aluminium tolerance in sorghum. “At the time, genes associated with aluminium tolerance were known for cereals in the Triticeae family (wheat, barley and rye). But the same genes were not found in the Poaceae family (sorghum, rice and maize). This suggested that there were different aluminium-tolerance genes at play, so it was a really pioneering project.” Continuing with the Cornell team after his PhD, Jura worked with Leon to  map the location of a major aluminium-tolerance genetic ‘hotspot’ in sorghum, which the project team contracted to  AltSB  for short (aluminium-tolerance gene or locus in Sorghum bicolor). The mapping also marked the next chapter  of what was to be a long-term professional relationship for the pair.

Brazil beckons, joining GCP, leadership and enduring partnerships
But in between, Brazil broke in and beckoned her native son home. And so it was that in 2002, Jura packed his bags and accepted a position with EMBRAPA’s maize and sorghum research centre. And despite the geographical distance, it wasn’t long before he and Leon teamed up again. “When I left Cornell, Leon and I had finished mapping AltSB and we were keen to clone it so we could then develop aluminium-tolerant sorghum varieties more efficiently,” says Jura.

Two years after his return to Brazil,  Leon and Jura – in 2004 – submitted a joint proposal for a competitive grant for their first GCP project on aluminium tolerance in cereals, premised on AltSB. This project contributed to GCP’s foundation work on sorghum in this and other projects, the common goal being a bid to provide farmers in the developing world with sorghum crops that would be able to tolerate harsh soils. But the project contributed much more with a deep taproot in pre-history, as that which we today call ‘sorghum’, ‘maize’ and ‘rice’ were once one millions of ‘Jurassic’ years ago. More on that interesting side-story.

And since this first project, EMBRAPA and Cornell University have collaborated with several other research institutes around the world, particularly in Africa.

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

Left to right (foreground): Leon, Jura and Sam Gudu (Moi University) examine crosses between Kenyan and Brazilian maize, at the Kenya Agricultural Research Institute (KARI), Kitale, in May 2010.

Jura leads several EMBRAPA and GCP collaborative projects across three continents (Africa, Asia and the Americas). The partnerships forged by and through these projects go well beyond project life and frame, and will therefore continue after GCP’s sunset. Jura is both team leader and team player. And a couple of GCP projects in which Jura is part of the project team will run on in 2015 (see page 10), after GCP’s closure in December 2014.

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Jul 232014
 

 

DNA spiral

DNA spiral

Crop researchers including plant breeders across five continents are collaborating on several GCP projects to develop local varieties of sorghum, maize and rice, which can withstand phosphorus deficiency and aluminium toxicity – two of the most widespread constraints leading to poor crop productivity in acidic soils. These soils account for nearly half the world’s arable soils, with the problem particularly pronounced in the tropics, where few smallholder farmers can afford the costly farm inputs to mitigate the problems. Fortunately, science has a solution, working with nature and the plants’ own defences, and capitalising on cereal ‘family history’ from 65 million years ago. Read on in this riveting story related by scientists, that will carry you from USA to Africa and Asia with a critical stopover in Brazil and back again, so ….

… welcome to Brazil, where there is more going than the 2014 football World Cup! Turning from sports to matters cerebral and science, drive six hours northwest from Rio de Janeiro and you’ll arrive in Sete Lagoas, nerve centre of the EMBRAPA Maize and Sorghum Research Centre. EMBRAPA stands for Empresa Brasileira de Pesquisa Agropecuária  ‒  in  English, the Brazilian Agricultural Research Corporation.

Jura_w

Jurandir Magalhães

Jurandir Magalhães (pictured), or Jura as he prefers to be called, is a cereal molecular geneticist and principal scientist who’s been at EMBRAPA since 2002.

“EMBRAPA develops projects and research to produce, adapt and diffuse knowledge and technologies in maize and sorghum production by the efficient and rational use of natural resources,” Jura explains.

Such business is also GCP’s bread and butter. So when in 2004, Jura and his former PhD supervisor at Cornell University, Leon Kochian, submitted their first GCP project proposal to clone a major aluminium tolerance gene in sorghum they had been searching for, GCP approved the proposal.

“We were already in the process of cloning the AltSB gene,” remembers Jura, “So when this opportunity came along from GCP, we thought it would provide us with the appropriate conditions to carry this out and complete the work.”

Cloning the AltSB gene would prove to be one of the first steps in GCP’s foundation sorghum and maize projects, both of which seek to provide farmers in the developing world with crops that will not only survive but thrive in the acidic soils that make up more than half of the world’s arable soils (see map below).

More than half of world’s potentially arable soils are highly acidic.

More than half of world’s potentially arable soils are highly acidic.

… identifying the AltSB gene was a significant achievement which brought the project closer to their final objective, which is to breed aluminium-tolerant crops that will improve yields in harsh environments, in turn improving the quality of life for farmers.”

A star is born: identifying and cloning AltSB
For 30 years, Leon Kochian (pictured below) has combined lecturing and supervising duties at Cornell University and the United States Department of Agriculture, with his quest to understand the genetic and physiological mechanisms behind the ability of some cereals to withstand acidic soils. Leon is also the Product Delivery Coordinator for GCP’s Comparative Genomics Research Initiative.

Leon Kochian

Leon Kochian

Aluminium toxicity is associated with acidic soils and 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 ions damage roots and impair their growth and function. This results in reduced nutrient and water uptake, which in turn depresses yield.

“These effects can be limited by applying lime to increase the soil’s pH. However, this isn’t a viable option for farmers in developing countries,” says Leon, who was the Principal Investigator for the premier AltSB project and is currently involved in several off-shoot projects.

Working on the understanding that grasses like barley and wheat use membrane transporters to insulate themselves against subsoil aluminium, Leon and Jura searched for a similar transporter in 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 Leon. “The organic acid binds with the aluminium ion, preventing it from entering the root. We found that in certain sorghum varieties, AltSB is the gene that encodes a specialised organic acid transport protein – SbMATE*  –  which mediates the release of citric acid. From cloning the gene, we found it is highly expressed in aluminium-tolerant sorghum varieties. We also found that the expression increases the longer the plant is exposed to high levels of aluminium.”

[*Editor’s note: different from the gene with the same name, hence not in italics]

Leon says identifying the AltSB gene and then cloning it was a significant achievement and it brought the project closer to their final objective, which he says is “to breed aluminium-tolerant crops that will improve yields in harsh environments, in turn improving the quality of life for farmers.”

This research was long and intensive, but it set a firm foundation for the work in GCP Phase II, which seeks to use what we have learnt in the laboratory and apply it to breed crops that are tolerant to biotic or abiotic stress such as aluminium toxicity and phosphorus deficiency.”

Comparative genomics: finding similar genes in different crops
Wheat, maize, sorghum and rice are all part of the Poaceae (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 a 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 is a fundamental research theme for GCP research as part of its second phase.

rajeev-varshney_1332450938

Rajeev Varshney

“The objective during GCP Phase I was to study the genomes of important crops and identify genes conferring resistance or tolerance to biotic or abiotic stresses,” says Rajeev Varshney (pictured), Director, Center of Excellence in Genomics and Principal Scientist in applied 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 Phase II, which seeks to use what we have learnt in the laboratory and apply it to breed crops that are tolerant to biotic or abiotic stress such as aluminium toxicity and phosphorus deficiency.”

Until August 2013, Rajeev had oversight on GCP’s comparative genomics research projects on aluminium tolerance and phosphorus deficiency is sorghum, maize and rice, as part of his GCP role as Leader of the Comparative and Applied Genomics Theme.

“Phosphorus deficiency and aluminium toxicity are soil problems that typically coincide in acidic soils,” says Rajeev. “They are two of the most critical constraints responsible for low crop productivity on acid soils worldwide. These projects are combining the aluminium tolerance work done by EMBRAPA and Cornell University with the phosphorus efficiency work done by IRRI [International Rice Research Institute] and JIRCAS [Japan International Research Centre for Agricultural Sciences] to first identify and validate similar aluminium-tolerance and phosphorus-efficient genes in sorghum, maize and rice, and then, secondly, breed crops with these combined improvements.”

These collaborations are really exciting! They make it possible to answer questions that we could not answer ourselves, or that we would have overlooked, were it not for the partnerships.”

When AltSB met Pup1
Having spent more than a decade identifying and cloning AltSB, Jura and Leon have recently turned their attention to identifying and cloning the genes responsible for phosphorus efficiency in sorghum. Luckily, they weren’t starting from scratch this time, as another GCP project on the other side of the world was well on the way to identifying a phosphorus-efficiency gene in rice.

Led by Matthias Wissuwa at JIRCAS and Sigrid Heuer at IRRI, the Asian base GCP project had identified a gene locus, which encoded a particular protein kinase that allowed varieties with this gene to grow successfully in low-phosphorous conditions. They termed the region of the rice genome where this gene resides as ‘phosphorus uptake 1’ or Pup1 as it is commonly referred to in short.

“In phosphorus-poor soils, this protein kinase instructs the plant to grow larger, longer roots, which are able to forage through more soil to absorb and store more nutrients,” explains Sigrid. “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!”

Read more about the mechanics of Pup-1 and the evolution of the project.

Jura and Leon are working on the same theory as IRRI and JIRCAS, that larger and longer roots enhance phosphorus efficiency. They are identifying sorghum with these traits, using comparative genomics to identify a locus similar to Pup1 in these low-phosphorus-tolerant varieties, and then verify whether the genes at this locus are responsible for the trait.

“So far, the results are promising and we have evidence that Pup1 homologues may underlie a major QTL for phosphorous uptake in sorghum,” says Jura who is leading the project to identify and validate Pup1 and other phosphorus-efficiency QTLs in sorghum.  QTL stands for ‘quantitative trait locus’ which refers to stretches of DNA containing ‒ or linked to ‒ the genes responsible for a quantitative trait  “What we have to do now is to see if this carries over in the field, leading to enhanced phosphorus uptake and grain yield in low-phosphorus soils,” he adds.

Jura and Leon are also returning the favour to IRRI and JIRCAS and are collaborating with both institutes to identify and clone in rice similar genes to the AltSB gene in sorghum.

“These collaborations are really exciting! They make it possible to answer questions that we could not answer ourselves, or that we would have overlooked, were it not for the partnerships,” says Sigrid.

To make a difference in rural development, to truly contribute to improved food security through crop improvement and incomes for poor farmers, we knew that capacity development had to be a continuing cornerstone in our strategy.”

Building capacity in Africa
In GCP Phase II which is more application oriented, projects must have objectives that deliver products and build capacity in developing-world breeding programmes.

Jean-Marcel Ribaut

Jean-Marcel Ribaut

“The thought behind the latter requirement is that GCP is not going to be around after 2014 so we need to facilitate these country breeding programmes to take ownership of the science and products so they can continue it locally,” says Jean-Marcel Ribaut, GCP Director (pictured). “To make a difference in rural development, to truly contribute to improved food security through crop improvement and incomes for poor farmers, we knew that capacity development had to be a continuing cornerstone in our strategy.”

Back to Brazil: Jura says this requirement is not uncommon for EMBRAPA projects as the Brazilian government seeks to become a world leader in science and agriculture. “Before GCP started, we had been working with African partners for five to six years through the McKnight Project. It was great when GCP came along as we were able to continue these collaborations.”

Samuel Gudu

Samuel Gudu

One collaboration Jura was most pleased to continue was with his colleague and friend, Sam Gudu (pictured), from Moi University, Kenya. Sam has been collaborating with Jura and Leon on several GCP projects and is the only African Principal Investigator in the Comparative Genomics Research Initiative.

“Our relationship with EMBRAPA and Cornell University has been very fruitful,” says Sam. “We wouldn’t have been able to do as much as we have done without these collaborations or without our other international collaborators at IRRI, JIRCAS, ICRISAT or Niger’s National Institute of Agricultural Research [INRAN].”

Sam is currently working on several projects with these partners looking at validating the genes underlying major aluminium-tolerance and phosphorus-efficiency traits in local sorghum and maize varieties in Kenya, as well as establishing a molecular breeding programme.

“The molecular-marker work has been very interesting. We have selected the best phosphorus-efficient lines from Brazil and Kenya, and have crossed them with local varieties to produce several really good hybrids which we are currently field-testing in Kenya,” explains Sam. “Learning and using these new breeding techniques will enable us to select for and breed new varieties faster.”

Sam is also grateful to both EMBRAPA and Cornell University for hosting several PhD students as part of the project. “This has been a significant outcome as these PhD students are returning to Kenya with a far greater understanding of molecular breeding which they are sharing with us to advance our national breeding programme.”

We’ve used the knowledge that Jura’s and Leon’s AltSB projects have produced to discover and validate similar genes in maize…We identified Kenyan lines carrying the superior allele of ZmMATE …This work will also improve our understanding of what other mechanisms may be working in the Brazilian lines too.” 

‘Everyone’ benefits! Applying the AltSB gene to maize
Claudia Guimarães (pictured) is a maize geneticist at EMBRAPA. But unlike Jura, her interest lies in maize.

Claudia

Claudia Guimarães

Working on the same comparative genomics principle used to identify Pup1 in sorghum, Claudia has been leading a GCP project replicating the sorghum aluminium tolerance work in maize.

“We’ve used the knowledge that Jura’s and Leon’s AltSBprojects have produced to discover and validate similar genes in maize,” explains Claudia. “From our mapping work we identified ZmMATE as the gene underlying a major aluminium tolerance QTL in maize. It has a similar sequence as the gene found in sorghum and it encodes a similar protein membrane transporter that is responsible for citrate extradition.”

A maize field at EMBRAPA. Maize on the left is aluminum-tolerant while the maize on the right is not.

A maize field at EMBRAPA. Maize on the left is aluminium-tolerant while the maize on the right is not.

Using molecular markers, Claudia and her team of researchers from EMBRAPA, Cornell University and Moi University have developed near-isogenic lines from Brazilian and Kenyan maize varieties that show aluminium tolerance, with ZmMATE present. From preliminary field tests, the Brazilian lines have had improved yields in acidic soils.

“We identified a few Kenyan lines carrying the superior allele of ZmMATE that can be used as donors to develop maize varieties with improved aluminium tolerance,” says Claudia.  “This work will also improve our understanding of what other mechanisms may be working in the Brazilian lines too.”

What has pleased Jura and other Principal Investigators the most is the leadership that African partners have taken in GCP projects.

Cherry on the cereal cake
With GCP coming to an end in December 2014, Jura is hopeful that his and other offshoot projects dealing with aluminium tolerance and phosphorus efficiency will deliver on what they set out to do.

“For me, the cherry on the cake for the aluminium-tolerance projects would be if we show that AltSB improves tolerance in acidic soils in Africa. If everything goes well, I think this will be possible as we have already developed molecular markers for AltSB.”

What has pleased Jura and other Principal Investigators the most is the leadership that African partners have taken in GCP projects.

“This has been a credit to them and all those involved to help build their capacity and encourage them to take the lead. I feel this will help sustain the projects into the future and one day help these developing countries produce varieties of sorghum and maize for their farmers that are able to yield just as well in acidic soils as they do in non-acidic soils.”

In the foreground, left to right, Leon, Jura and Sam in a maize field in Kenya.

In the foreground, left to right, Leon, Jura and Sam in a maize field at the Kenya Agricultural Research Institute (KARI), Kitale, in May 2010. They are examining crosses between Kenyan and Brazilian maize germplasm.

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Mar 312014
 
Vincent Vadez

Vincent Vadez

Today, we travel to yet another sun-kissed spot, leaving California behind but keeping it legumes. We land in Africa for some ground truths on groundnuts with Vincent Vadez (pictured), groundnut research leader for the Tropical Legumes I (TLI) Project. Vincent fills us in on facts and figures on groundnuts and Africa – a tale of ups and downs, triumphs and trials, but also of  ‘family’ alliances not feuds, and of problems, yes,  but also their present or potential solutions. On to the story then! Read on to find out why groundnuts are…

….A very mixed bag in Africa
Groundnuts (Arachis hypogaea L), also called peanuts, are a significant subsistence and food crop in sub-Saharan Africa. There, groundnuts are grown in practically every country, with the continent accounting for roughly a quarter of the world’s production. Despite this rosy African statistic, problems abound: for example, nearly half (40 percent) of the of the world’s total acreage for groundnuts is in Africa, which dramatically dims the 25 percent global production quota.

In Africa, groundnuts are typically cultivated in moderate rainfall areas across the continent, usually by women.

In Africa, groundnuts are typically cultivated in moderate rainfall areas across the continent, usually by women. (See editorial note* at the end of the story)

Clearly then, Africa’s yields are low, borne out by telling statistics which show African production at 950 kilos per hectare, in acute contrast to 1.8 tonnes per hectare in Asia.

…every year, yields worth about USD 500 million are lost”

What ails Africa’s production?
The main constraints hampering higher yields and quality in Africa are intermittent drought due to erratic rainfall, as well as terminal drought during maturation. And that is not all, because foliar (leaf) diseases such as the late leaf spot (LLS) or groundnut rosette are also taking their toll.  Economically speaking, every year, yields worth about USD 500 million are lost to drought, diseases and pests. Plus, the seeding rates for predominantly bushy groundnut types are low, and therefore insufficient to achieve optimal ground cover. Thus, genetic limitations meet and mingle with major agronomic shortcomings in the cultivation of groundnuts, making it…

…. A tough nut to crack
Groundnuts are mostly cultivated by impoverished farmers living in the semi-arid tropics where rainfall is both low and erratic.

Tough it may be for crop scientists, but clearly not too tough for these two youngsters shelling groundnuts at Mhperembe Market, Malawi.

. Tough it may be for crop scientists, but clearly not too tough for these two youngsters shelling groundnuts at Mhperembe Market, Malawi.

“To help double the productivity of this crop over the next 10 years, we need to improve groundnuts’ ability to resist drought and diseases without farmers needing to purchase costly agricultural inputs,” says Vincent.

But the crop’s genetic structure is complex, plus, for resistance to these stresses, its genetic diversity is narrow. “Groundnuts are therefore difficult and slow to breed using conventional methods,” says Vincent. And yet, as we shall see later, groundnuts are distinctly disadvantaged when it comes to molecular breeding. But first, the good news!

…wild relatives have genes for resisting the stresses… molecular markers can play a critical role”

Why blood is thicker than water, and family black sheep are valued
Kith and kin are key in groundnut science. Vincent points out that groundnuts have several wild relatives that carry the necessary genes for resisting the stresses – especially leaf diseases – to which the crop is susceptible. These genes can be transferred from the wild cousins to the cultivated crop by blending conventional and molecular breeding techniques. But that is easier said than done, because cultivated groundnuts can’t cross naturally with their wild relatives owing to chromosomic differences.

Groundnut flower

Groundnut flower

“In modern breeding, molecular markers can play a critical role,” says Vincent. “Using markers, one can know the locations of genes of interest from an agronomic perspective, and we can then transfer these genes from the wild relatives into the groundnut varieties preferred by farmers and their markets.”

[The] ‘variegated’ partnership has been essential for unlocking wild groundnut diversity…”

Partnerships in and out of Africa, core capacities
“Partners are key to this work,” says Vincent. The groundnut work is led by the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), with collaborators in the target countries, which are Malawi (Chitedze Agricultural Research Centre), Senegal (Institut sénégalais de recherches agricoles ‒ ISRA) and Tanzania (Agricultural Research Institute, Naliendele), Moving forward together, continuous capacity building for partners in Africa is part and parcel of the project. To this end, there have been several training workshops in core areas such as molecular breeding and phenotyping, farmer field days in the context of participatory varietal selection, as well as longer-term training on more complex topics such as drought, in addition to equipping the partners with the critical infrastructure needed for effective phenotyping.

Freshly dug-up groundnuts.

Freshly dug-up groundnuts.

Further afield out of Africa, Vincent’s team also collaborates with the Brazilian Agricultural Research Corporation (EMBRAPA), France’s Centre de coopération internationale en recherche agronomique pour le développement ‒ CIRAD, and USA’s University of Georgia.

This ‘variegated’ partnership has been essential for unlocking the wild groundnut diversity when about 12 years ago the EMBRAPA team successfully generated a number of ‘synthetic’ groundnuts from their wild relatives. Unlike the wild groundnuts, these synthetic groundnuts can be crossed to the cultivated type, bringing with them treasure troves of beneficial genes pertaining to the wild that would be otherwise unreachable for the cultivated varieties. Taking this one step further, the CIRAD‒ISRA team, in a close North‒South partnership, has used one of the synthetics from the Brazilian programme to generate new genetic diversity in the groundnut cultivar Fleur11. They are using additional synthetics from ICRISAT to further enlarge this genetic diversity in cultivated groundnuts.

These techniques and tools provide signposts on the genome of varieties for characteristics of importance”

A world first for an ‘orphan’, goals achieved, and what next
Among other goals, the team notably achieved a world first: “To produce the first SSR-based genetic linkage map for cultivated groundnuts!” declares Vincent. SSR stands for simple sequence repeat. The map was published in 2009,  followed later on by a groundnut consensus map in 2012.

Youngster bearing fresh groundnuts along River Gambia in Senegal.

Youngster bearing fresh groundnuts along River Gambia in Senegal.

But what do these maps and their publication mean for groundnut production? Vincent explains: “These techniques and tools provide signposts on the genome of varieties for characteristics of importance ‒ for instance, resistance to a disease ‒ and these are used in combination to speed up the development of groundnut varieties that are more resistant to the stresses found in the harsh environments where most of the tropical world’s poor farmers live. Accelerating development means quicker delivery to farmers who are at high risk of going hungry. TLI Phase I produced synthetic groundnuts with new genes for disease resistance.”

In Phase II of the TLI Project which terminates in mid-2014, the team has continued to identify new genetic and genomic resources, for instance new sources of drought resistance from the germplasm and which are currently being used in the development of new breeding stocks. What is significant about this is that groundnuts ‒ like most other members of the legume family ‒ do not have much in the way of genomic and molecular-genetic resources, and are in fact consequently referred to in some circles as ‘orphans’ of the genome revolution. The focus has also been on resistance to rust, early and late leaf spot, and rosette – all economically critical diseases – by tapping the resilience of GBPD4, a cultivar resistant to rust and leaf spot, and introducing its dual resistance to fortify the most popular varieties against these diseases. The team also hopes to scale up these promising examples.

We believe this team is firmly on the way to fulfilling their two-fold project objectives which were: (1) to develop genomic resources and produce the first molecular-breeding products of the crop by injecting  disease resistance (from TLI Phase I work) into farmer- and market-preferred varieties; and, (2)  to lay the foundation for future marker-assisted recurrent selection (MARS) breeding by tapping on newly identified sources of drought tolerance.

 the genetic stocks that hold the most promise to overcome leaf disease are found in the wild relatives… A thorough reflection is needed to combine good genetics with sound agronomic management”

The future
But the team is not resting on their laurels, as the work will not stop with the fulfillment of project objectives. In many ways, their achievements are in fact just the beginning. The new breeding stocks developed during TLI Phase II need to be evaluated further for their drought tolerance and disease resistance prior to their deployment in breeding programmes, and this activity ‒ among others ‒ is included for the next phase of the work in the proposed Tropical Legumes III project. In particular, the genetic stocks that hold the most promise to overcome leaf disease are found in the wild relatives. Thus, the existing materials need to be fully exploited and more need to be produced to cover the full breadth of potential stresses. Vincent adds “Of course an increasing part of the efforts will be about assuring quality evaluation data, meaning we must continue to significantly enhance the capacity ‒ both human and physical ‒ of our partners in target countries. Last but not least, the good wheat and rice cultivars that directly arose from the green revolution would have been nothing without nitrogen fertiliser and irrigation.” Vincent adds that the same applies to groundnuts: they are cultivated in infertile soil, at seeding rates that are unlikely to optimise productivity.

Groundnut drawing

Groundnut drawing

For this reason, and others explained above, “A thorough reflection is needed to combine good genetics with sound agronomic management,” Vincent concludes, stressing the importance of what he terms as ‘looking beyond  the fence’. Vincent’s parting shot, as our conversation draws to close: “In fact, I have grown increasingly convinced over the past year that we probably overlook those agronomic aspects in our genetic improvements at our peril, and we clearly need a re-think of how to better combine genetic improvement with the  most suitable and farmer-acceptable agronomic management of the crop.”

Much food for thought there! And probably the beginnings of an animated conversation to which a groundnut crop model, on which Vincent and team are currently working, could soon yield some interesting answers on the most suitable genetic-by-management packages, and therefore guide the most adequate targets for crop improvement.

Links

*Editorial note: Erratum – Photo changed on April 8 2014, as the previous one depicted chickpeas, not groundnuts. We  apologise to our readers for the error.

Jun 262012
 

It’s all about water and weakness  or strength. The Greek legend has it that Achilles was dipped into River Styx by his mother, Thetis, in order to make him invulnerable. His heel wasn’t covered by the water and he later died of the wound from an arrow that struck his heel.

In our times, this analogy can be applied to chickpeas, where this streetwise tough customer in the crop kingdom that thrives on the most rugged terrains is hamstrung if there is no rain at the critical grain-filling period – its sole Achilles’ heel, when it cannot take the searing heat in the drylands it otherwise thrives in.

But before you read on about the latter-day borrowing of this ancient legend, and science’s quest to heal the hit from heat and to cure the crop’s fatal flaw on water, first, an important aside…

Who’s now calling the shots in chickpea research?

Molecular breeding in Phase I was led by ICRISAT, with country partners in a supporting role. In Phase II, activities are being led by country partners, which also assures sustainability and continuity of the work. ICRISAT is now in a facilitating role, providing training and data, while the research work is now in the hands of country partners.” – Pooran Gaur, Principal Scientist: Chickpea Breeding,  ICRISAT.

The facts
Chickpeas are an ancient crop that was first domesticated in central and western Asia. Today, this crop is cultivated in 40 countries and is second only to common beans as the food legume most widely grown by smallholders. The two main types of chickpeas – desi and kabuli – are valuable for both subsistence and cash.

Even for the hardy, times are tough
“Chickpeas are well-known to be drought-tolerant,” says Rajeev K Varshney, Principal Investigator of the project to improve chickpeas work in the Tropical Legumes I Project (TLI). He explains, “The plants are very efficient in using water and possess roots that seek out residual moisture in deeper soil layers.” However, he points out that, with changing climatic conditions, especially in drier areas, terminal drought – when rain does not fall during grain-filling – is the crop’s Achilles’ heel, and principal production constraint.

“Chickpeas are such tough plants that, even for conditions of terminal drought, yields can be increased by improving root characteristics and water-use efficiency,” says Rajeev. The research team has identified several lines with superior traits such as drought tolerance, after screening a set of 300 diverse lines selected based on molecular diversity of large germplasm collections.

VIDEO CLIP: Recipe for chickpea success

Enhancing the genetic makeup to beat the heat
The team went on to develop genomic resources such as molecular markers. With these markers, the team developed a high-density genetic map, and identified a genomic region containing several quantitative trait loci (QTLs), conferring drought tolerance. “QTLs help pinpoint, more specifically, the location of genes that govern particular traits like root length” explains Rajeev.

Longer roots will naturally give the plants a deeper reach into the water table. Root length is the difference between survival and perishing, which is why trees will be left standing on a landscape otherwise laid bare by prolonged drought.

Q for ‘quick’: QTLs speed things along from lab to field, and running with the winners
The discovery of QTLs makes identifying tolerant plants not only easier, but also cheaper and faster. “This means that better-adapted varieties will reach farmers faster, improving food security,” says Rajeev.

Pooran Gaur, GCP’s Product Delivery Coordinator for chickpeas, Principal Scientist for Chickpea Breeding at ICRISAT, and an important collaborator on the TLI project, adds, “We began marker-assisted selection backcrossing (MABC) in Phase I. By 2011, lines were already being evaluated in Ethiopia, India and Kenya. We are now at the stage of singling out the most promising lines.”

Putting chickpeas to the test: Rajeev Varshney (left) and Pooran Gaur (right) inspecting a chickpea field trial.

What was achieved in Phase I, and what outcomes are expected?
Phase I run from mid-2007 to mid-2010, during which time 10 superior lines for improved drought tolerance and insect resistance were identified for Ethiopia, Kenya and India. As well, a total of 1,600 SSR markers and 768 SNPs on GoldenGate assays were developed, along with an expanded DArT array with more than 15,000 features. A high-density reference genetic map and two intraspecific genetic maps were developed.

“We now have materials from marker-assisted backcrossing by using the genomic resources we produced in Phase I. These materials were sent to partners last year [2011]. And because in most cases we have the same people working in TLI as in TLII, this material is being simultaneously evaluated across six to seven locations by all TLI and TLII partners,” says Pooran.

“Preliminary analysis of data is quite encouraging and it seems that we will have drought-tolerant lines soon,” adds Rajeev.

Future work, and who’s now calling the shots in the field
In Phase II, 1,500 SNPs on cost-effective KASPar assays have been developed that have been useful to develop a denser genetic map. In collaboration with University of California–Davis (USA) and the National Institute of Plant Genome Research (India), a physical map has been developed that will help to isolate the genes underlying the QTL region for drought tolerance. A novel molecular breeding approach called marker-assisted recurrent selection (MARS) has been adopted. Over the remaining two years of Phase II, the chickpea work will focus on developing chickpea populations with superior genotypes for drought tolerance through MABC and MARS.

Pooran adds, “Molecular breeding in Phase I was led by ICRISAT, with country partners in a supporting role. In Phase II, activities are being led by country partners, which also assures sustainability and continuity of the work. ICRISAT is now in a facilitating role, providing training and data, while the MABC and MARS aspects are both in the hands of country partners.”

“Another important activity in Phase II is development of multi-parents advanced generation intercross (MAGIC) population that will help generation of genetic populations with enhanced genetic diversity,” says Rajeev.

Partnerships
The chickpea work is led by the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), working with partners at the Ethiopian Institute of Agricultural Research, Egerton University in Kenya, and the Indian Agricultural Research Institute. Additional collaborators in Phase I included the University of California–Davis (USA), the National Center for Genome Resources (USA) and DArT P/L (Australia).

For more information on the overall work in chickpeas, please contact Rajeev K Varshney, Principal Investigator of the chickpea work.

Video: Featuring Rajeev and partners Fikre Asnake (Ethiopia) and Paul Kimurto (Kenya)

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