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Beans: Sidestepping variety… to create varieties to combat drought, disease and pests

 Africa, Beans, Crop breeding, Genetics, Genomics, Legumes  No Responses »
Oct 302012
 
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BREAK-TIME AND BRAKE-TIME from beans for a bit: Steve Beebe takes a pause to strike a pose in a bean field.

“These [molecular breeding] techniques, combined with conventional methods, shorten the time it takes to breed improved varieties  that simultaneoulsy combine several traits.

And this means that we also get them out to farmers more quickly compared to phenotypic selection alone.”
– Steve Beebe

THE NEAR-PERFECT FOOD: Common beans (Phaseolus vulgaris L) comprise the world’s most important food legume, feeding about 200 million people in sub-Saharan Africa alone. Their nutritional value is so high, they have been termed ‘a near-perfect food’. They are also easy to grow, adapting readily to different cropping systems and maturing quickly.

That said, this otherwise versatile, adaptable and dapper dicotyledon does have some inherent drawbacks and ailments that crop science seeks to cure….

Rains are rapidly retreating, and drought doggedly advancing
Despite the crop’s widespread cultivation in Africa, “yields are low, stagnating at between 20 and 30 percent of their potential,” remarks Steve Beebe, GCP’s Product Delivery Coordinator for beans, and a researcher at the International Center for Tropical Agriculture (CIAT, by its Spanish acronym).

“The main problem is drought, brought about by climate change,” he says. “And it’s spreading – it already affects 70 percent of Africa’s major bean-producing regions.”  Drought decimates bean harvests in most of Eastern Africa, but is particularly severe in the mid-altitudes of Ethiopia, Kenya, Tanzania, Malawi and Zimbabwe, as well as in southern Africa as a whole.

A myriad of forms and hues: bean diversity eloquently speaks for itself in this riot of colours.

Drought, doubt and duality − Diversity a double-edged sword
“Common beans can tolerate drought to some extent, using various mechanisms that differ from variety to variety,” explains Steve. But breeding for drought resistance is complicated by the thousands of bean varieties that are available. They differ considerably according to growth habit, seed colour, shape, size and cooking qualities, and cultivation characteristics.

“A variety might be fantastic in resisting drought,” says Steve, ‘but if its plant type demands extra work, the farmers won’t grow it,” he explains. “Likewise, if consumers don’t like the seed colour, or the beans take too long to cook, then they won’t buy.”

Molecular breeding deals a hand, waves a wand, and weaves a band
This is where molecular breeding techniques come in handy, deftly dealing with the complexities of breeding drought-resistant beans that also meet farmer and consumer preferences. No guesswork about it: molecular breeding rapidly and precisely gets to the heart of the matter, and helps weave all these different ‘strands’ together.

The bean research team has developed ‘genetic stocks’, or strains of beans that are crossed with the varieties favoured by farmers and consumers. The ‘crosses’ are made so that the gene or genes with the desired trait are incorporated into the preferred varieties.

The resulting new varieties are then evaluated for their performance in different environments throughout eastern and southern Africa, with particular focus on Ethiopia, Kenya, Malawi and Zimbabwe which are the target countries of the Tropical Legumes I (TLI) project.

Propping up the plant protein: a veritable tapestry of terraces of climbing beans.

GCP supported this foundation work to develop these molecular markers. This type of breeding – known in breeder parlance as marker-assisted selection (MAS) – was also successfully used to combine and aggregate resistance to drought; to pests such as bean stem maggot (BSM); and to diseases such as bean common mosaic necrosis potyvirus (BCNMV) and to bruchid or common bacterial blight (CBB). The resulting ‘combinations’ laden with all this good stuff were then bred into commercial-type bean lines.

“These techniques, combined with conventional methods, shorten the time it takes to breed improved varieties that simultaneoulsy combine several traits,” comments Steve. “This means that we also get them out to farmers more quickly compared to phenotypic selection alone.”

Informed by history and reality
Breeding new useful varieties is greatly aided by first understanding the crop’s genetic diversity, and by always staying connected with the reality on the ground: earlier foundation work facilitated by GCP surfaced the diversity in the bean varieties that farmers grow, and how that diversity could then be broadened with genes to resist drought, pests and disease.

What next?
Over the remaining two years of Phase II of the Tropical Legumes I (TLI) project, the bean team will use the genetic tools and breeding populations to incorporate drought tolerance into farmer- and market-preferred varieties. “Hence, productivity levels on smallholder farms are expected to increase significantly,” says Steve.

Partnerships
The work on beans is led by CIAT, working in partnership with Ethiopia’s South Agricultural Research Institute (SARI),  the Kenya Agricultural Research Institute (KARI),  Malawi’s Department of Agricultural Research and Technical Services (DARTS) and  Zimbabwe’s Crop Breeding Institute (CBI) of the Department of Research and Specialist Services (DR&SS).

Other close collaborators include the eastern, central and southern Africa regional bean research networks (ECABREN and SABRN, their acronyms) which are components of the Pan-African Bean Research Alliance (PABRA). Cornell University (USA) is also involved.

VIDEO: Steve talks about what has been achieved so far in bean research, and what remains to be done

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Banana genetics: (not-so-)Easy as ♫ABC, 123♫

 Bananas, Genetics, Genomics  No Responses »
Sep 202012
 
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Getting to the core of a world-favourite dessert by unravelling banana’s origin and genealogy

GCP has enabled us to lay a credible foundation, which gave us a leg-up in the intense competition that typifies the genome sequencing arena” – Angélique D’Hont, CIRAD researcher

‘A’ is also for Angélique, as you will see once you read on…

An ‘A’ to our banana team for ushering in a new era in banana genetics. But let soup precede dessert, and don’t let this worry you: stay with us because we’re still very much on the topic and focused on bananas, which offer the whole range from soup and starters, to main course and dessert, plus everything else in between, being central for the food security of more than 400 million people in the tropics: around a third each is produced in Africa, Asia-Pacific and Latin America, and the Caribbean. About 87  percent of all the bananas produced worldwide are grown by small-scale farmers.

Moving back then to soup for starters, we’re serving up our own unique blend of alphanumeric banana ‘soup’, spiced with ABCs, a pinch of 123s, plus a dash of alpha and omega. Curious about the ABCs? Look no further:‘C’ for getting to the core of ‘B’ for bananas, and an ‘A’ score for our ace genomics team that did it.

Read how GCP seeded … and succeeded, in helping open a new era in banana genetics. An achievement by itself, and an important milestone on the road to unlocking genetic diversity for the resource-poor, which is GCP’s raison d’être.

So get your travelling gear please, for time travel with a ‘midspace checkpoint’ in Malaysia.

We start in 2004, when GCP commissioned a survey of diversity with microsatellites (or SSRs, simple sequence repeats) for all mandate food crops in the CGIAR crop research Centres. The objective of that study was to make new genetic diversity from genebank accessions available to breeders.

The endpoint is opening new research avenues to incorporate genes for disease resistance, with the added bonus of an article published in Nature online on July 11 2012, entitled The banana (Musa acuminata) genome and the evolution of monocotyledonous plants.

It may not be quite as easy as the ABC and 123 that The Jacksons promise in song, but we promise you that the science is just as exciting, with practical implications for breeding hardy disease-resistant bananas. Onwards then to the first leg of this three-step journey!

(Prefer a shorter version of this story in pictures? We’ve got it! Choose your medium between Flickr and Facebook)

1) Let’s go Greek: the alpha and omega of it

Rewinding to the beginning

The proof of the pudding is in the eating: we imagine that Jean Christophe Glaszmann just has to be saying “Yummy!” as he samples this banana.

Start point, 2004: “At that time, several research groups had developed SSR markers for bananas, but there was no coordination and only sketchy germplasm studies,” recalls Jean Christophe Glaszmann (pictured), then the leader of what was GCP’s Subprogramme 1 (SP1) on Genetic Diversity on a joint appointment with CIRAD. He stepped down as SP1 Leader in March 2010, and is currently the Director of a multi-institutional research unit Genetic improvement and adaptation of Mediterranean and tropical plants (AGAP, by its French acronym) at France’s Centre de ccoopération internationale en recherche agronomique pour le développement (CIRAD) in Montpellier.

Jean Christophe continues, “The reference studies had been conducted with RFLP* markers, a very useful tool but far too cumbersome for undertaking large surveys. We mobilised Bioversity International, CIRAD and the International Institute of Tropical Agriculture for the project. The process took time, but delivered critical products.” [*RFLP stands for restriction fragmented length polymorphism]

Fastforward to 2012, and gets just a little geeky…

Eight years down the road in 2012, the list of achievements is impressive, as evidenced by a suite of published papers which provide the details of the analysis of SSR diversity and describe how the data enabled the researchers to unravel the origin and genealogy of the most important dessert bananas. The origin of the predominant variety – Cavendish – suggested by the markers, involves two rounds of spontaneous hybridisation between three markedly differentiated subspecies. This scheme has been marvellously corroborated by linguistic patterns found in banana variety names as revealed in a paper published in 2011 in the proceedings of USA’s National Academy of Sciences.

But what else happened in between the start- and end-point? We now get to the really ‘sweet’ part of this bonanza for banana breeding!

It is now possible to conduct research to identify and incorporate genes for disease resistance within fertile populations that are close to the early progenitors, and then inter-cross them to re-establish sterility and obtain vigorous, disease-resistant and seedless progenies.

 2) Of bits, bananas, breeding and breadcrumbs

Threading all these bits together for breeding better bananas is akin to following a trail of breadcrumbs, in which GCP played an important facilitating role: where in the germplasm to undertake genetic recombination is one key; and then, how to expedite incorporation of disease resistance and how to control sterility – so as to first suppress it, then re-establish it – is another set of keys that are necessary for proficient breeding.

Hei Leung in the lab at IRRI.

In 2005, Hei Leung (pictured), then Leader of GCP’s Subprogramme 2 on Comparative Genomics (until June 2007) on a dual appointment with the International Rice Research Institute (IRRI), recognised that with GCP’s main focus being drought tolerance in crops, Musa (the banana and plantain botanical genus) was somewhat on the fringe. However, it was still important that GCP support the emergence of banana genomics.

Hei is currently Programme Leader of Genetic Diversity and Gene Discovery at IRRI. He remembers, “We had a highly motivated group of researchers willing to devote their efforts to Musa. Nicolas Roux at Bioversity was a passionate advocate for the partnership. The GCP community could offer a framework for novel interactions among banana-related actors and players working on other crops, such as rice. The team led by Takuji Sasaki of Japan’s National Institute of Agrobiological Science, which had vast experience in rice genome sequencing, added the scientific power. So, living up to its name as a Challenge Programme, GCP decided to take the gamble on banana genomics and help it fly.”

Angélique D’Hont, CIRAD researcher and lead author of the article published in ‘Nature’.

Through several projects, GCP helped consolidate Musa genomic resources, contributed to the establishment of medium-throughput DArT markers as well as the construction of the first saturated genetic map. Additional contributions included the first round of sequencing of large chromosome segments (BAC clones) and its comparison with the rice sequence and a detailed analysis of resistance gene analogues. All these findings have now been published in peer-reviewed journals. And while publication takes time, it still remains a high-premium benchmark for quality and validation of results, and for efficient sharing of information. It reinforces the value of collaboration, builds capacity and gives visibility to all partners, thereby providing potential new avenues for funding.

Such was the case with bananas: using a collaborative partnership framework established with the Global Musa Genomics Consortium, animated by Nicolas Roux and now chaired by Chris Town, the community developed a case for sequencing the genome. With the mentorship of Francis Quétier, contacts were made with various major players in genomics, which in the end formalised a project between France’s CIRAD and CEA–Genoscope, funded by the Agence Nationale de la Recherche and led by Angélique D’Hont (pictured) and Patrick Wincker.

GCP contributed DArT analysis for anchoring the sequence to the genetic map. But, as stressed by Angélique, CIRAD researcher and lead author of the Nature paper: “Above all, GCP has enabled us to lay a credible foundation, which gave us a leg-up in the intense competition that typifies the genome sequencing arena. We were delighted that France rolled the dice in our favour by funding this work.”

3) Musa musings on the road to and from Malaysia checkpoint

Three years down the road, the team published a description of the genome of a wild banana from Malaysia.

Jean Christophe communes with a Musa plant, perhaps musing “What’s your family history and when will you be fully grown?”

Let’s drill down to some technical facts and figures here: the Musa genome has some 520 million nucleotides distributed across 11 chromosomes, revealing traces of past duplications and bearing some 36,000 genes. While most genes derived from duplication tend to lose their function, some develop novel functions that are essential for evolution; bananas seem to have an outstanding range of transcription factors that could be involved in fruit maturity.

And while the road ahead remains long, we now have a good understanding of banana’s genetic diversity, we have genomic templates for functional studies (a whole-gene repertoire) as well as for structural studies (the chromosome arrangement in one subspecies) aimed at unraveling the genomic translocations that could control sterility in the species complex.

It is now possible to conduct research to identify and incorporate genes for disease resistance within fertile populations that are close to the early progenitors, and then inter-cross them to re-establish sterility and obtain vigorous, disease-resistant and seedless progenies.

This is undoubtedly an inspiring challenge towards unlocking the genetic diversity in this crop, which is central to food security for more than 400 million people in the tropics.

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Breeding ‘sukses’ in Indonesia’s rice

 Asia, Crop breeding, Genetics, Genomics, Researchers, Rice  No Responses »
Sep 072012
 
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Joko infront of his office at ICABIOGRAD’s Molecular Biology Division.

Indonesian upland rice growers can expect to receive improved varieties that thrive in phosphorus-poor soils within a few years, thanks to the hard work of their national breeding programmes.

Joko Prasetiyono is a proud Indonesian researcher who loves rice.

“I don’t know why. I just love researching ways to improve it so it grows and yields better. I also I love to eat it,” says Joko with a laugh.

Having worked as a molecular breeder, concentrating solely on rice for 17 years at the Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development (ICABIOGRAD), one would expect a different reaction. But Joko says he’s as interested in the little white grain as much as when he started as an undergraduate with ICABIOGRAD.

And why wouldn’t he be when he and his team are contributing to research that has just been published in Nature and is set to reduce fertiliser application and improve rice yields in Indonesia and the world over by 20 percent!

Improving Indonesian varieties, no genetic modification

Farmers often use phosphate fertilisers to aid in growing rice in these areas, but this option is often too expensive for Indonesian upland growers.

The project has found plants that have a Pup1 locus (a collection of genes), with the specific gene PSTOL1, are able to tolerate phosphorus-deficient conditions and produce better yields than those not suited for the conditions. An Indian rice variety, Kasalath, was one such.

“We are breeding rice varieties that we know have a Pup1 locus and subsequent PSTOL1 gene in them with Indonesian varieties that are suited to Indonesia’s growing systems,” explains Joko.   

Partnering with the International Rice Research Institute (IRRI), ICABIOGRAD and their partner the Indonesian Center for Rice Research (ICRR) have improved the phosphorus tolerance of Indonesian rice varieties Dodokan, Situ Bagendit and Batur.

“The new plants we are creating are not genetically modified; just bred using smarter breeding techniques,” says Joko. “The aim is to breed varieties identical to those that farmers already know and trust, except that they will have the PSTOL1 gene and an improved ability to take up soil phosphorus.”

Joko says that these varieties are currently being tested in field trials and it will take another 2–3 years before Indonesian farmers will have a variety that will yield as well if not better, needing 30–50 percent less fertiliser.

Evolving Indonesian plant research 

ICABIOGRAD team selecting breeding material in 2010. L-R: Masdiar Bustamam, Tintin Suhartini and Ida Hanarida.

GCP is as much about its people and partnerships as its research and products. ICABIOGRAD benefited from a GCP capacity-building grant in mid-2007 to enhance the institute’s capacity in phenotyping and molecular analysis. The grant covered, among other areas, intensive residential staff training at IRRI; PhD student support; infrastructure such as a moist room, temperature-controlled centrifuge apparatus, computers and appropriate specialised software; and  a blast innoculation room. These capacity-building activities were coordinated by Masdiar Bustamam who has since retired, but was then a Senior Scientist at ICABIOGARD.

But coming back to Joko and the PSTOL1 work, Joko started on this project in 2005 as a GCP-funded PhD student at Bogor Agriculture University, Indonesia. He is grateful to be part of a transnational project, which has offered him technical support that he would not otherwise have been able to receive through ICABIOGRAD alone.

IRRI visits ICABIOGRAD in 2009. L-R: Matthias Wissuwa, Sigrid Heuer (both IRRI), Masdiar Bustaman (ICABIOGRAD) and Joong Hyoun Chin

Joko believes the experience of working with IRRI, as a joint partner on this project, will leave an important, and lasting, legacy for researchers at ICABIOGRAD and ICRR. The partnership has also challenged the two local institutes to broaden their horizons past their borders.

“IRRI is teaching us how to use marker-assisted selection and we [ICABIOGRAD and ICRR] are just as busy identifying phosphorus-deficient hotspots in upland areas, choosing the best Indonesian recipient rice varieties for the gene, conducting the breeding and phenotyping testing,” he clarifies.

Breeding for sustainability

The ultimate goal of this project is to help Indonesian growers use marginal land.

Over half the world rice lands are deficient of ‘plant-available’ phosphorus, and Indonesia is no different. Joko explains that while there is plenty of phosphorus in the soil, plants are not able to access it.

“Other minerals in the soil like aluminum, calcium and iron are bound to phosphorus, shielding it from plants roots so they can only absorb a fraction of it.”

Field test of Pup1 lines at Taman Bogo , Indonesia.

In most countries, farmers apply phosphate fertilisers to their crops to combat this deficiency. For Joko this is not a sustainable approach for a lot of Indonesia’s farmers because the fertilisers are expensive and costs will continue to rise as phosphate supplies dwindle.

“Our approach is a lot more sustainable and cost-effective than applying fertiliser. We’ll breed these new plants for phosphorus-poor soils to produce more roots so they can find more phosphorus. The more phosphorus they find, the more of it they can absorb.”

Joko hopes these new plants will help farmers on marginal lands to obtain decent yields without having to spend money on expensive phosphate fertilisers.

“It’s great that our work has been recognised by Nature for publication, but what we really want is to help rice growers here in Indonesia and around the world.”

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♫We’ll rock your world!♫

 Comparative genomics in cereals, Crop breeding, Genomics, Researchers, Rice  No Responses »
Sep 072012
 
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“It is very rare that scientists can take their projects wherever they go. I’ve been very lucky to be able to do this, and much of this has to do with the support I’ve received from GCP.” – Matthias Wissuwa

In the world of phosphorus, Matthias (pictured) is somewhat of a ‘rock star, not that he would admit to it. We don’t understand why not, since to borrow his words, the project he’s involved has becoming something of a ‘celebrity project’ in the scientific community.

For  a decade-and-a-half, he has searched tirelessly for a rice gene that could improve the crop’s yield in phosphorus-deficient soils –which make up half of the world’s soils. Last month, his transnational team published in Nature that their 15-year quest had ended, having finally found the elusive gene – Pup1.

We celebrate this happy ending, especially as we had the added pleasure of talking to Matthias recently: it was delightful in listening to the modest German recount the long journey which has taken him from his home town of Hamburg, to USA, Japan, The Philippines and back to Japan, all this while,  faithfully ‘carrying’ Pup1 with him as he switched employers. As you’ve seen, Japan scores a double strike, so our ‘rock star’ is also ‘big on Japan’! 

Talking to Matthias, we could sense the achievement was only just sinking in – that he and his team’s years of laboratory work was becoming a practical reality that will aid rice-growing farmers from Africa to Asia,  and hopefully other grain growers in years to come. Here’s what Matthias had to say…

You started this project back in 1997. Tell us how you became interested in phosphorus deficiency and rice.

After completing my PhD in the United States, I accepted a postdoc position in Tsukuba, Japan, with the National Institute of Agro-Environmental Sciences (NIAES). It was an easy decision because my wife is Japanese.

My postdoc host, Dr Ae was interested in phosphorus, particularly in legumes. I originally started work on tolerance to phosphorus deficiency in groundnuts, but soon changed to rice to take advantage of the molecular tools available for rice.

Tsukuba is a very new city. It’s called The Science City in Japan because the Japanese government built it to house all the national research institutes. This was great for me as I became interested in QTL mapping, which was pioneered by scientists in Tsukuba. I got talking to people in the rice research community in Tsukuba and was introduced to Dr Yano, who was developing mapping populations for rice at the National Institute of Agrobiological Sciences. He kindly gave me his populations and that’s how I started to map QTL for phosphorus-deficiency tolerance in rice.

Dr Ae was perplexed by my decision, believing that studying legumes was far more challenging than rice. He always told me: “Rice is boring. They just make long, fine roots to capture phosphorus.” That was 15 years ago and he turned out to be right. Long roots are the secret for phosphorus uptake in rice, particular in Kasalath and varieties like that.

Field trials for phosporus-efficient rice in The Philippines.

Did you share Dr Ae’s hypothesis that longer roots were the secret to some rice varieties being able to tolerate phosphorus-deficient soils?

For a long time, I was not sure if it was just long roots. It was a real chicken-and-egg scenario – does strong phosphorus uptake spur root growth, or the other way around?

As it turns out, it is the latter – plants growing longer roots help with the uptake of more phosphorus – and Pup1 is responsible for this.

We have now shifted our aim and are looking for varieties of rice tolerant to phosphorus-deficient soils that either:

  • release organic acids, phosphatases or some other compound that makes phosphorus more readily available for the plant to absorb, or
  • manipulate soil microorganisms to favour those that can aid in making phosphorus more soluble, or
  • very efficiently utilise phosphorus once it is taken up.

All three mechanisms are found in legumes, so there is reason to believe that they exist in rice and we are now working on finding them.

GCP has been interested in the project since 2004 as its outcome aligns with GCP’s goals to improve crop yields and security in developing countries… It has become something of a ‘celebrity project’ in the scientific community, attracting researchers to work on the project or collaborate with us.

In 2002 you left NIAES and accepted a position with the International Rice Research Institute (IRRI), and were encouraged to continue your work on Pup1. When you moved back to Tsukuba in 2005 to accept the position you currently hold with the Japan International Research Center for Agricultural Sciences (JIRCAS), you were again encouraged to continue your Pup1 project, collaborating with your successor at IRRI, Dr Sigrid Heuer. How important has it been to you and the project to have the support of your institutes?

It is very rare that scientists can take their projects wherever they go. I’ve been very lucky to be able to do this, and much of this has to do with the support I’ve received from GCP. They’ve been interested in the project since 2004 as its outcome aligns with GCP’s goals to improve crop yields and security in developing countries.

When I left IRRI, Sigrid was just starting and was more or less free to take on the project, so I asked her if she’d be interested in continuing my work with Pup1 at IRRI and collaborate with me in Japan. She was actually the perfect person for the project because her background in molecular biology complemented my background as a plant breeder.

Over the past seven years, we have worked together very well, and with the addition of Rico Gamuyao, a PhD student supervised by Sigrid, things have recently progressed quite quickly to the point that we were able to pinpoint Pup1.

So GCP has played a major role along your journey?

Yes, definitely. The support from GCP on the Pup1 project, now in its 8th year, was instrumental at getting this project to where it is.

Quite simply, the funding from GCP allowed us to hire Rico as well as Juan Pariasca-Tanaka, a project scientist with me at JIRCAS. Neither Sigrid nor myself had the time to do all the hands-on work so having both Rico and Juan has been hugely helpful.

How important has the collaboration between IRRI and JIRCAS been for the project?

Are they playing with mud? Not at all! Working. Matthias (L) and Rico (R) have zipped up their boots and gone back to their bee…er…. we mean, roots, mucking mud here as they do some fieldwork related to the search for PSTOL1.

Tremendously important. Sigrid’s group at IRRI is relatively small as is mine in Japan, so we rely on each other’s complementary expertise when working on complicated projects.

We have also been fortunate to have constant interest in the project from the scientific community. It has become something of a ‘celebrity project’, and as such, attracted researchers to work on the project or collaborate with us.

For example, we are working with two US groups at Cornell University and Penn State, that are also funded by GCP, trying to track down Pup1 in other crops and identifying genes that control root architecture, and how different architectures may affect P uptake.

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

It really has been a team effort and we wouldn’t have got to where we are now without all the help of everyone involved

You’ve been described as the Godfather and Guru of Pup1. How do compliments like this make you feel?

It makes me laugh but of course it’s a very well-meant comment, and to some extent, considering I’ve worked on it for 15 years, you could say that there is some truth to it.

I’ve done all the original work, but Sigrid has been just as instrumental. She did the part where my expertise was no longer adequate – the molecular side, looking at genes and thinking about the function of a gene and testing for its function.

It really has been a team effort and we wouldn’t have got to where we are now without all the help of everyone involved, which also includes the support of Dr Yano over the years.

…phosphorus deficiency is a worldwide problem that has recently gained public attention because of how expensive phosphate fertilisers have become…Farmers are always interested in saving money and improving yields and we believe this discovery will help with both.

Have you been surprised by the attention this project has received?

As I said, the project has always been in the scientific spotlight because it was the first to map a major QTL for phosphorus uptake.

We knew from the Sub1 story – the submergence tolerance gene, which was published in Nature 4–5 years ago – that the media would probably be interested in this similar discovery. I’m still very surprised that this unsexy story has caused such interest.

You have to remember though, phosphorus deficiency is a worldwide problem that has recently gained public attention because of how expensive phosphate fertilisers have become. About four years ago, the price almost tripled and continues to stay high.

Farmers are always interested in saving money and improving yields and we believe this discovery will help with both.

Phosphorus deficiency is probably even more critical in Africa than it is in Asia… This means Pup1 may have its biggest impact in Africa.

How will the research continue?

Having focused so much on the basic research, we now want to turn our attention to the application. IRRI and JIRCAS will train national breeding programmes to use marker-assisted selection and help them breed their own rice varieties with Pup1.

Sigrid and IRRI are mainly working with Asian national breeding programmes and we at JIRCAS focus more on African programmes such as the Africa Rice Center. Phosphorus deficiency is probably even more critical in Africa than it is in Asia, as phosphate fertilisers aren’t used nearly as much as they are in Asia. This means Pup1 may have its biggest impact in Africa.

We are also looking for new sources of tolerance to phosphorus-deficiency. One very exciting project involves West African rice (Oryza glaberrima) the father of the Nerica ™ (New Rice for Africa) varieties.

So far, we have found that this rice is very tolerant to phosphorus-deficient soils. It does have Pup1, but in addition harbours novel genes that also enhance performance on phosphorus-deficient soils.

We hope to discover a Pup2 in the years to come.

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Rooting for the key to more phosphorus for rice

 Comparative genomics in cereals, Crop breeding, Genetics, Genomics, Rice  3 Responses »
Sep 072012
 
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Preparing rice root samples (Photo: IRRI)ALL IN THE ROOTS: A plant’s roots are a marvellously multitalented organ. They act as fingers and mouths helping plants forage and absorb water and nutrients. They act like arms and legs offering a sturdy base of support so a plant doesn’t keel over. They help store food and water, like our stomach and fat cells. And in some plants, can spawn new life – we leave that to your imagination!

That is why it is of little surprise that this multitalented organ was the key to discovering why some rice lines yield better in phosphorus-poor soils, a puzzle whose answer has eluded farmers and researchers… until now.  And even better, the findings hold promise for sorghum, maize and wheat too. Please read on!

 In search of the key – The Gene Trackers
In 1999, Dr Matthias Wissuwa, now with the Japan International Research Centre for Agricultural Sciences (JIRCAS), deduced that Kasalath, a northern Indian rice variety, contained one or more genes that allowed it to grow successfully in low-phosphorus conditions.

For years, Matthias made it his mission to find these genes, only to find it was as easy as finding a needle in a genetic haystack. He teamed up with the International Rice Research Institute (IRRI), and with GCP’s support, the gene trackers were able to narrow the search down to five genes of interest.

“We had started with 68 genes and within three years, we had narrowed in on these five candidate genes. And then, one-by-one, we checked whether they were related to phosphorous uptake,” recollects Dr Sigrid Heuer, senior scientist at IRRI and leader of the team that published the discovery in Nature in August 2012.

Sigrid Heuer at a rice phosphorus uptake demonstration field in The Philippines.

“In the end we found that if a certain protein kinase gene was turned on in tolerant plants like Kasalath, then those plants would perform better in phosphorus-deficient soils.”

They named this protein kinase gene PSTOL1, which stands for Phosphorus Starvation Tolerance. “When we put this gene into intolerant rice varieties that did not have this gene, they performed better in phosphorus-deficient soils.”

The importance of phosphorus
Rice, like all plants, needs phosphorus to survive and thrive. It’s a key element in plant metabolism, root growth, maturity and yield. Plants deficient in phosphorus are often stunted.

Sigrid explains that whereas phosphorus is abundant in most soils, it is however not always easily accessible by plants. “Many soil types bond tightly to phosphorus, surrendering only a tiny amount to plant roots. This is why more than half of the world’s rice lands are phosphorus-deficient.”

Farmers can get around this by applying phosphate fertilisers. However this is a very expensive exercise and is not an option for the majority of the world’s rice growers, especially the poorer ones –the price of rock phosphate has more than doubled since 2007. The practice is also not sustainable since it is a finite resource.

By selecting for rice varieties with PSTOL1, growers will be less reliant on phosphate fertilisers.

How it works: unravelling PSTOL1 mechanics
In phosphorus-poor soils, PSTOL1 switches on during the early stage of root development. The gene tells the plant to grow larger longer roots, which are able to forage through more soil to absorb and store more nutrients.

“By having a larger root surface area, plants can explore a greater area in the soil and find more phosphorus than usual,” says Sigrid. “It’s like having a larger sponge to absorb more water.”

A rice variety — IR-74 — with Pup1 (left) and without Pup1 (right).

Although the researchers focussed on this one key nutrient, they found the extra root growth helped with other vital elements like nitrogen and potassium.

Another by-chance discovery was that phosphorus uptake 1 (Pup1), the collection of genes (locus) where PSTOL1 is found, is present within a large group of rice varieties.

“We found that in upland rice varieties – those bred for drought-prone environments – most have Pup1,” says Sigrid. “So the breeders in these regions have, without knowing it, been selecting for phosphorus tolerance.”

“When thinking about it, it makes sense as phosphorus is very immobile in dry soils, therefore these plants would have had to adapt to grow longer roots to reach water deeper in the soil and this, at the same time, helps to access more reservoirs of phosphorous .”

Breeding for phosphorus tolerance, and going beyond rice
Using conventional breeding methods, Sigrid says that her team introduced PSTOL1 into two irrigated rice varieties and three Indonesian upland varieties, and found that this increased yields by up to 20 percent.

“In our pot experiments,” she added, “when we use soil that is really low in phosphorus, we see yield increases of 60 percent and more. This will mean growers of upland rice varieties will probably benefit the most from these new lines, which is pleasing given they are among the poorest rice growers in the world.”

Read how Indonesian researchers are developing their own breeds of upland rice with the PSTOL1 gene

Sigrid also sheds light on broadening the research to other crop varieties: “The project team is currently looking at Pup1 in sorghum and maize and we are just about to start on wheat.”

Building capacity and ensuring impact
Like all GCP projects, this one invests as much time in building capacity for country breeding programmes as on research.

Sigrid and her team are currently conducting the first Pup1 workshop to train researchers from Bangladesh, India, Indonesia, Nepal, Philippines, Thailand and Vietnam. They will share molecular markers that indicate the presence of PSTOL1, techniques to select for the gene, as well as for new phosphorus-efficient varieties.

Breeding for phosphorus-efficient rice in the Philippines.

“The aim of these workshops is to take these important tools to where they are most needed and allow them to evolve according to the needs and requirements of each country,” says Dr Rajeev Varshney, GCP’s Comparative and Applied Genomics Leader. “Breeders will be able to breed new rice varieties faster and more easily, and with 100 percent certainty that their rice plants will have the gene. Within three to five years, each country will be able to breed varieties identical to those that growers know and trust except that they will now have the Pup1 gene and an improved ability to unlock and take up soil phosphorus.”

Joining hands in collaboration
This IRRI-led project was conducted in collaboration with JIRCAS and the Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development (ICABIOGRAD) working with the Indonesian Centre for Rice Research. Other partners included: Italy’s University of Milano, Germany’s Max Planck Institute in Golm, the University of The Philippines at Los Baños, USA’s Cornell University and University of California (Davis and Riverside), Brazil’s EMBRAPA, Africa Rice Center, Iran’s Agricultural Biotechnology Research Institute, Australia’s Commonwealth Scientific and Industrial Research Organisation (CSIRO) and University of Dhaka in Bangladesh.

Links

Sigrid’s presentation at the GCP General Research Meeting 2011

Extract from a ‘genomicist’s’ diary: Excited in Seattle!

 Genomics, Integrated Breeding Platform  No Responses »
Aug 222012
 
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Which we promise you is a much greater thriller than ‘Sleepless in Seattle’. We’d like to share with you an exciting day in the life of our Comparative Genomics Leader, Rajeev Varshney (pictured). And yes, we just made up the word ‘genomicist’ featuring in this blogpost’s title: if those who study economics are ‘economists’, then it’s logical that those who study genomics are…’genomicists’ of course!

Rewind to early July, and here’s the extract from Rajeev’s jottings in his diary on that day…

10 July 2012 – I had a wonderful day in Seattle today: I delivered a presentation on Genomics and informatics for digitalisation of crop breeding in the brainstorming session on A digital revolution in agriculture at the Bill & Melinda Gates Foundation.

The meeting was chaired by Bill Gates and attended by his former and present associates (high-level business executives, entrepreneurs, philanthropists) and selected officials from the Gates Foundation. Discussions centred on four main topics – architecture, genomics, ecological intensification and ICT for a digital revolution in agriculture.

I was privileged to be invited to the meeting as one of three specialists in genomics (the other two being Jun Wang, Executive Director of BGI [Beijing Genomics Institute in Shenzhen China]; and Bob Reiter, VP at Monsanto). In total, there were 10 external experts from all four core areas in the meeting. I never thought that I would have the opportunity to spend a day with such a group of eminent personalities!”

GCP’s work on the Integrated Breeding Platform and on crop ontology were of relevance at the meeting.

A couple of snapshots from that meeting follow, and do look at the links below the photos…

 

Rajeev (standing left) gives his presentation during the meeting

Rajeev on the left, and guess who’s on the right?….That’s right! Bill Gates!

 

 

 

 

 

 

 

 

Links: Rajeev’s profile | Comparative and Applied Genomics Theme | Comparative Genomics Research Initiative | Integrated Breeding Platform | Crop ontology (click on crop of interest from the menu along the top, then follow the ‘crop ontology’ link from the links in the box on the left)

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