31 July 2006

An Electronic Newsletter of Applied Plant Breeding
Sponsored by FAO and Cornell University

Clair H. Hershey, Editor

Archived issues available at: (NOTE: cut and paste link if it does not work directly)


1.01  Rising CO2 levels not as good for crops as thought
1.02  Two articles in Science of interest to plant breeders:
1.03  More on the Global Partnership Initiative for Plant Breeding Capacity Building
1.04  Brazil will share expertise in agriculture with Africa
1.05  Filipino scientists join effort to develop 'Golden Rice'
1.06  International collaboration helps CLIMA fight the negative effects of disease, drought, salinity, waterlogging and temperature on legume crops in Western Australia
1.07  In the battle against the devastating rice blast pathogen, USDA's Rice Core Collection proves a genetic treasure chest
1.08  The International Treaty on Plant Genetic Resources for Food and Agriculture - A real treaty
1.09  New research may reduce global need for nitrogen fertilizers
1.10  Gene controlling aphid resistance in soybean reported
1.11  Peru launches new kiwicha cultivar
1.12  IITA takes on banana virus with UV, juice help
1.13  New barley has higher yields, available phosphorous
1.14  Pinto bean lines developed to resist mold
1.15  Cloned oil palm making its way in Malaysia
1.16  UCSD biologists solve plant growth hormone enigma
1.17  Grass roots research will help develop new energy crops
1.18  Energy-rich portfolio of new genome sequencing targets for DOE JGI
1.19  Full-length switchgrass genes sequenced and genetic variation characterized
1.20  Plan to boost rice photosynthesis with inserted genes
1.21  Potato blight pathogenicity explained by genome plasticity
1.22  South Africa halts 'super sorghum' study
1.23  Biotechnology opens new opportunities for flavor and fragrance industry
1.24  How purple corn and RNA break genetic laws
1.25  Selections from Update 5-2006 of FAO-BiotechNews

(None submitted)

3.01  New search portal for IPK’s genebank (Gatersleben, Germany) is online

4.01  International Foundation for Science (IFS): Calls for applications

(None submitted)





1.01  Rising CO2 levels not as good for crops as thought

Scientists' predictions that rising levels of atmospheric carbon dioxide will boost crop yields have been too optimistic, according to a study published today (30 June) in Science.

It says the effect is likely to be only about half as strong as previously thought.

Researchers have long reported that most major crops grow faster and need less water when more carbon dioxide (CO2) is available.

It was thought that this 'fertilisation effect' might offset the negative effects on crops ­ such as increased temperature and reduced soil moisture ­ that climate change is expected to bring.

But the new study, led by Stephen Long of the University of Illinois at Urbana-Champaign, United States, points out that these conclusions are mostly based on research done in greenhouses or controlled-environment chambers in labs and fields.

Long's team surveyed results from a more realistic approach known as Free-Air Concentration Enrichment (FACE), which involves releasing CO2 just above the crops in open fields without interfering with other environmental conditions.

They concluded that the CO2 level expected by 2050 would only increase crop yields by about half what was predicted.

Long told SciDev.Net that the new results suggest that "the damaging effects of rising temperature and decreased soil moisture will not be offset by the fertilisation effect of rising CO2".

The researchers note that for some tropical crops such as maize and sorghum the fertilisation effect might not even apply because they do not use CO2 for growth in the same way that most other plants do.

Commenting on the research in the same issue of Science, David Schimel of the US National Center for Atmospheric Research says the findings "may move impacts on agriculture higher up on the list of pressing concerns about climate change".

Atmospheric CO2 concentrations have risen from 260 parts per million (ppm) 150 years ago to 380 ppm today, and are expected to rise to 550 ppm by 2050 because of human activities.

Link to full paper in Science
Reference: Science 312, 1918 (2006)

Source: SciDev.Net
30 June 2006

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1.02  Two articles in Science of interest to plant breeders:

Long, S., E. Ainswroth, A. Leakey, J. Noesberger, and D. Ort.  2006.  Food for thought:  Lower-than-expected crop yield stimulation with rising CO2 concentrations.  Science 312:1918-1921, 30 June 2006. (See overview in this edition of PBN-L)

And a commentary on the above article, in the same issue:
Schimel, D.  2006.  Climate change and crop yields:  Beyond Cassandra.  Science 312:1889-1890, 30 June 2006.

I encourage plant breeders to join AAAS, the professional society that publishes Science.  There is a AAAS Agriculture section, but it is small and needs more of us.   AAAS listens to its members.  If there are more agies in AAAS, we will have more influence on the programs and policies of what is a highly influential society.    At a minimum, it is another venue to work for increased understanding and  respect for our discipline.  Articles like the two cited above suggest that the time is ripe for this.    Alas, becoming an ag activist in AAAS is not free; annual dues are $142 ($75 for students). 

AAAS is not suggested as an alternative to our existing societies!  (e.g., CSSA, ASHS).  We should retain those memberships! -- because in those societies, we do determine programs and policies, and those societies work for us.  

Submitted by Ann Marie Thro

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1.03  More on the Global Partnership Initiative for Plant Breeding Capacity Building

(Follow-up on PBN-L Edition 168)

The article at the site below explains what the Global Partnership Initiative for Plant Breeding Capacity Building (GIPB) can do to work in partnership with your organization to strengthen national capacity to use plant genetic resources.

Contributed by Elcio Guimaraes

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1.04  Brazil will share expertise in agriculture with Africa

Carla Almeida
[RIO DE JANEIRO] African nations are set to benefit from Brazilian expertise in tropical agriculture thanks to an agreement between Brazil and Ghana.

Under the agreement signed this week (10 July), Ghana will host the first African branch of the Brazilian Agricultural Research Corporation (Embrapa).

The branch will act as a regional base for sharing Brazil's agricultural knowledge with the whole continent, and will be located at the Council of Scientific and Industrial Research in Accra.

Two staff will identify local research needs, plan studies that can be undertaken in Brazil, and seek international partners to cooperate in the agency's initiatives.

Research will be carried out in Brazil by Embrapa's 38 research units, which will send their findings back to Ghana.

Sotto Pacheco Costa, Embrapa's supervisor of bilateral cooperation, says the branch will also "train local technicians, in Brazil and in Africa, and offer technical assistance [on agricultural problems]".

The branch was decided upon after an increasing number of demands coming from Africa for Brazilian agricultural technology. The move comes as part of Brazil's commitment to South-South cooperation.

"This is a fascinating experience and a challenge to work with African countries", says Costa. "We are hoping to help resolve the problems in the agricultural sector and become closer partners."

14 July 2006

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1.05  Filipino scientists join effort to develop 'Golden Rice'

Manila, The Philippines
 By Carlos D. Marquez, Jr. (Correspondent), Business Mirror via SEAMEO SEARCA

Selected scientists from Germany, US, China, Vietnam and the Philippines are making rice nutrient -dense grain-food to save about 10 million children in poor countries from dying everyday due to malnutrition.

By 2015, as envisioned, a cup or 160 gram of what would be genetically engineered cooked rice can give the poor - who would often content themselves with rice alone for their diet - the combined nutrients from a slice of steak, a piece of prawn, a fried egg, some vegetables and fruits.

"The overall goal is to engineer rice with increased levels of provitamin E high quality protein, zinc and iron," explains the Golden Rice Project web site. The Golden Rice, notable for its yellowish color resulting from the high concentration of betacarotene in it, was first developed in 1999 by German scientist Peter Beyer of the University of Freiburg.

Now, the project ProVitamin A Rice Consortium, has been formed to fortify it further with protein, vitamin E, zinc and iron.

To achieve the goal, the consortium, funded by the Melinda and Bill Gates Foundation, gathered molecular biologists, biochemists and plant breeders from Albert-Ludwigs University, Freiburg, Germany, Michigan State University and Baylor College of Medicine in Houston, Texas, USA, the Chinese University of Hong Kong, the Cuu Long Delta Rice Research Institute and the Philippine Rice Research Institute (PhilRice) in Muñoz Science City, Philippines.

This current research, which aims to fuse vital nutrients and achieve a balanced composition of the needed amino acids, is part of the Grand Challenges in Global Health Program of the Bill and Melinda Gates Foundation in collaboration with plant breeding and crop protection multinational Syngenta.

The consortium is led by German scientist Peter Beyer, the acknowledged "principal investigator" of the Golden Rice project. Each of the consortium members has an assigned task in completing the rice project.

The University of Freiburg and Michigan State University are in charge of the multigene stacking and for transformations; Baylor College of Medicine with Michigan State University identifies quantitative trait loci (QTLs) for iron bioavailability and assess bioavailability in model systems as well as the human iron acceptability studies; Chinese University of Hong Kong enhances the protein quality and lysine content of rice; CLRRI and PhilRice do the introgression of the needed nutrient into their respective local varieties; while IRRI takes charge of the latter task in the rice varieties in other Southeast Asian countries.

"Hopefully, we can develop one single line per country containing all the essential micronutrients," said Dr. Rhodora R. Aldemita, chief science research specialist of PhilRice and a genetic engineering expert. She is the PhilRice principal scientist for the Golden Rice project.

Aldemita had her postdoctoral fellowship at the Albert-Ludwigs University Freiburg, Germany, from June 2003 to December 2005 and PhD in Botany from Purdue University, in Indiana, USA, in 1996. She obtained her Ms in Agronomy from the University of the Philippines-Los Baños, Laguna.

Aldemita conducts breeding studies to incorporate the provitamin A genes into PSBRc 82 and Mabango 1together with Dr. Antonio A. Alfonso, a molecular plant breeder and geneticist who heads PhilRice's Plant Breeding and Biotechnology Division.

Antonio is crossing the female parent of the two Philippine rice varieties, selected for their popularity, taste and other attributes with the male parent donor SGR1, or the Syngenta Golden Rice 1, which contains around 8 mg per gram of beta-carotene.

After producing an F1, or the resulting progeny, it will then be crossed again with the two recurrent parents PSBRc82 and Mabango 1. The process, Antonio adds, will be done repeatedly until a uniform line, with the same agronomic characteristics of the parent is obtained.

Another study deals with the incorporation of the Golden Rice characteristics into the locally adapted tungro-and bacterial blight-resistant varieties.

"PhilRice already has conventionally bred varieties which contain these disease-resistant traits and adding vitamin A through conventional breeding and backcrossing is a very important endeavor. The product will become a new variety with all the desired genes in it," Aldemita said.

SGR1 contains the important genes to convert the precursor geranyl-geranyl pyrophosphate present in the rice endosperm into beta-carotene. The daffodil gene phytoene synthase, and the phytoene desaturase from a common soil bacterium Erwinia uredovora were introduced into the variety Cocodrie through Agrobacterium tumefaciens - mediated transformation. This led to the production of high amounts of beta-carotene in the endosperm which is available for food.

In the latter course of the five-year project, Aldemita will introduce multinutrient constructs to include genes for vitamin A, E, high lysine, and possibly iron zinc into rice through genetic engineering. "Achieving this will be the realization of an ultimate goal, that of improving the nutrient and protein quality of the staple rice," she confided.

"Golden Rice and other engineered rice lines with stacked traits will be incorporated into ongoing breeding and seed delivery programs for developing countries," said the Golden rice web site. When fully developed, the engineered variety will be made available to farmers.

28 June 2006

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1.06  International collaboration helps CLIMA fight the negative effects of disease, drought, salinity, waterlogging and temperature on legume crops in Western Australia

Nedlands, Perth, Western Australia
Agricultural scientists from Iran, Egypt, Pakistan and China, along with their Australian allies, are fighting the negative effects of disease, drought, salinity, waterlogging and temperature on legume crops in Western Australia and their countries.

Western Australian and Iranian researchers, for example, are pooling resources to find drought tolerant chickpea genotypes to benefit drought affected Iranian and Australian farming systems.

Associate Professor Nasser Majnoun Hosseini, of the University of Tehran, is in West Australia for six months to help develop agronomic and genetic strategies to increase yields during drought.

Speaking at the Centre for Legumes in Mediterranean Agriculture (CLIMA) at the University of West Australia (UWA), he explained that Iran’s farming systems have similarities to Western Australia.

“Iran has arid regions, with low annual rainfall, where chickpea is grown although current varieties give poor emergence and establishment under limited moisture conditions.

“There is a need for chickpea varieties that can emerge early, with limited soil moisture and then withstand cold and dry winter conditions, hence we are screening for suitable genotypes under simulated conditions in the glasshouse at CSIRO,” Professor Hosseini said.

Three other scientists, from Egypt, Pakistan and China, are collaborating with local scientists at UWA, CSIRO and the Department of Agriculture and Food (DAFWA).

Visiting Western Australia on an Australian Government Endeavour Fellowship, Dr Magdi Abdelhamid, of the National Research Centre, Cairo, is working with CLIMA to improve water use efficiency in faba beans and studying how they fix nitrogen when moisture stressed.

“Drought is extremely stressful for crops and understanding how they grow at that time will allow us to define drought resistant traits and ultimately breed cultivars better able to withstand stress and produce respectable yields,” Dr Abdelhamid said.

At the opposite end of the rainfall spectrum, Asia Gulnaz of the Nuclear Institute for Agriculture and Biology (NIAB), Pakistan Atomic Energy Commission, is exploring the interactions between waterlogging and salinity and their effects on legumes.

Funded by the International Atomic Energy Agency (IAEA), her study, using radio-isotope techniques, will help legume breeders develop and select salt and waterlogging tolerant cultivars.

 “Salinity and transient waterlogging are important production constraints in Pakistan and Australia,” she said.

Western Australia will also benefit from the genomic researching skills of Dr Ruiming Lin of the Chinese Academy of Agricultural Science, Beijing.

He is collaborating with UWA and DAFWA to identify a marker in lupin to create an anthracnose resistant plant using the Microsatellite anchored Fragment Length Polymorphisms (MFLP) technique.

Developed by CLIMA, MFLP shows DNA patterns and produces genetic markers.

Dr Lin will use the MFLP technique he learns in Western Australia to develop a yellow rust resistant wheat variety when he returns to China.

CLIMA Director, Professor Kadambot Siddique described international collaboration as a very important CLIMA activity, which enhances research capacity in Western Australia.

“Simultaneously hosting such high achieving scientists from four countries reflects CLIMA’s standing in the global legume science community and augers well for the future of Western Australian legume growers, the ultimate beneficiaries of such collaboration.”

19 July 2006

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1.07  In the battle against the devastating rice blast pathogen, USDA's Rice Core Collection proves a genetic treasure chest

Agricultural Research Service scientists have discovered a few good rice plants--and are taking them to the bank.

The researchers, in their hunt for rice genes to guard against the devastating rice blast pathogen Magnaporthe grisea, recently tapped the country’s most diverse collection of rice. This genebank--the U.S. Department of Agriculture’s (USDA) Rice Core Collection--contains more than 1,700 rice plant accessions from more than 100 countries.

The ARS scientists, working at the Dale Bumpers National Rice Research Center in Stuttgart, Ark., evaluated the hundreds of accessions by growing and testing each one in the laboratory and field.

Led by ARS geneticist Wengui Yan, the scientists discovered new rice genes resistant to blast. This destructive disease impacts about 30 percent of the world’s rice plants each year.

Finding new genes to counter disease, pests and other threats is central to the longevity of all crops. But rice, which helps feed more than two-thirds of the world’s population, especially benefits from continuous access to new genetic material, or germplasm.

That’s because the crop’s nemesis, rice blast, has growers and breeders engaged in a never-ending, tug-of-war battle. Farmers plant rice that’s expected to stand up to the blast-causing fungus. But in just a short period of time, the pathogen finds a new way to overcome its weary host.

The blast resistance genes the Stuttgart researchers discovered should give rice plants a needed boost. These findings are different from any resistance genes currently available to the U.S. rice industry.

The USDA Rice Core Collection is part of the ARS-coordinated National Plant Germplasm System, a cooperative effort by public and private organizations to preserve crops’ genetic diversity. This collection is referred to as “core” because it captures the essential genetic diversity contained in an even larger USDA rice collection of 18,000 accessions. Working with a smaller core collection streamlines breeders’ efforts to uncover valuable genes.

Read more about the research in the July 2006 issue of Agricultural Research magazine, available online at:

Washington, DC
ARS News Service
Agricultural Research Service, USDA
Erin Peabody
ARS is the USDA’s chief scientific research agency.

12 July 2006

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1.08  The International Treaty on Plant Genetic Resources for Food and Agriculture - A real treaty

Rome, Italy
The International Treaty on Plant Genetic Resources for Food and Agriculture may still have a few sharp edges. It’s not the prettiest creature. And those who worked on it over the years have certainly lost a lot of their hair. But, the Treaty is now decidedly REAL.

Efforts to achieve an international treaty addressing the conservation and exchange of plant genetic resources date to the late 1970s. Reaching consensus on a binding instrument proved impossible before the new millennium.

The absence of an agreed international framework for acquisition of genetic resources stifled exchange and perpetuated mistrust without providing any off-setting benefits. Accusations swirled. New words, such as “biopiracy,” entered the lexicon. Collecting for conservation purposes decreased – countries were leery of what might be lost, stolen or misappropriated. Exchanges declined, undermining breeding programs.

Some assumed genetic resources could be sold sample-by-sample and that the marketplace would thus provide an incentive for conservation. It didn’t happen. There was no market, little access, and zero benefits. Everyone lost.

Because seeds are so easy to multiply and transport, genetic resources defy attempts at commercialization. For 500 years, they have foiled all attempts.

In economists’ terms they are a “public good.” The marketplace provides little, if any, economic incentive to entrepreneurs to conserve crop diversity in order to sell it. And yet, it is in society’s interest that crop diversity be conserved.

It has been wryly observed that governments always do the right thing…but only when all other options have been exhausted. The challenge countries faced in the Treaty negotiations was how to regulate the exchange of genetic resources so as to promote both access and the rewards that flow from access (e.g., food security).

For political reasons, negotiators also needed to find a mechanism for generating additional benefits, benefits they could manage and dispense. If selling genetic resources were unworkable, providing access with no regulation or recompense was unthinkable, and not providing access was slowly suicidal.

New International Legal Framework
Following seven years of formal negotiations, the International Treaty on Plant Genetic Resources for Food and Agriculture debuted in 2002. Featuring a Multilateral System for the access and benefit-sharing of crop diversity, it lacked the detailed provisions needed to implement the system.

The tough nuts-and-bolts decisions were bequeathed to the first meeting of the Treaty’s Governing Body, the 104 countries that had formally ratified the Treaty when the Governing Body convened in June in Madrid.

Confounding most observers who thought the issues too technically and politically intractable to resolve, the Governing Body:

Agreed on the terms of a standard Material Transfer Agreement (sMTA) through which all crop diversity covered by the Treaty’s Multilateral System (covering more than 35 of the world’s most important crops, plus a number of forages) will be accessed and used. The sMTA calls for a royalty of 1.1% of sales to be paid into a fund when (a.) genetic material is accessed from the Treaty’s multilateral system, (b.) it is incorporated into a product that is a plant genetic resource, such as a new crop variety, (c.) the product is commercialized, and (c.) there are restrictions, such as patent protection, that limit use of the product for further plant breeding and research. Users can opt for a lower royalty rate (0.5%) if they apply it to all products of a particular crop regardless of whether there are restrictions to further use and regardless of whether multilateral system materials were used in making them. The Treaty’s Governing Body will control and dispense funds raised, using them to support crop diversity related programs.

Agreed on a financial strategy for implementation of the Treaty and Rules of Procedure for the Governing Body.

-Approved the text of agreements bringing collections held by the CGIAR under the terms of the Treaty. These collections contain much of the diversity of the world’s major crops and are the most widely used collections in the world.

-Expressed in the final report of the meeting its “unanimous support” for the Global Crop Diversity Trust and approved and signed a Relationship Agreement with the Trust recognizing, uniquely, the Trust’s role as an “essential element” of the Treaty’s funding strategy in regards to ex situ conservation and availability of plant genetic resources.

In short, the Treaty became Real in Madrid.

The Treaty removes the uncertainty of access and the fear of exploitation that prevailed in the 1990s – uncertainty and fear that choked off exchanges of crop diversity and undercut conservation and plant breeding efforts.

By promoting cooperation and the sharing of genetic resources, will the Treaty reduce the impulse of countries to take an “every man for himself” approach to conservation? We’ll see. It should, because through cooperation based on the Treaty, a rational, efficient, effective and sustainable system can now be created for conserving crop diversity and making it available to all. This can be done without incurring large costs, and it can be done without diminishing any country’s access to the crop diversity it needs.
The International Treaty on Plant Genetic Resources for Food and Agriculture

A legal framework is in place. Now it is time for thinking to shift and for attitudes to catch up to the new reality. By normalizing transactions, the Treaty should help create a new climate of trust and cooperation among custodians and users of crop diversity. If it does, it will be the Treaty’s greatest achievement. This may take a little time. By then we may all be a little loose in the joints and shabby, but it won’t matter. The new global system will be Real.

Learn more about the topic
Explanatory Guide to the International Treaty on Plant Genetic Resources for Food and Agriculture, by G. Moore and W. Tymowski.
Summary of the First Session of the Governing Body of the International Treaty on Plant Genetic Resources for Food and Agriculture

Source: The Global Crop Diversity Trust via
21 July 2006

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1.09  New research may reduce global need for nitrogen fertilizers

Research published June 29 in the journal Nature reveals how scientists at the John Innes Centre (JIC), Norwich and Washington State University, USA have managed to trigger nodulation in legumes, a key element of the nitrogen fixing process, without the bacteria normally necessary. This is an important step towards transferring nodulation, and possibly nitrogen fixation, to non-legume crops which could reduce the need for inorganic fertilizers.

The researchers, funded by the Biotechnology and Biological Sciences Research Council (BBSRC), the Royal Society and the US National Science Foundation, have used a key gene that legumes require to establish the interaction with the nitrogen-fixing bacteria to trigger the growth of root nodules, even in the absence of the bacteria.

The fixation of nitrogen by some plants is critical to maintaining the health of soil as it converts the inert atmospheric form of nitrogen into compounds usable by plants. Legumes, as used in this study, are an important group of plants as they have the ability to fix nitrogen – which they owe to a symbiotic relationship with nitrogen-fixing bacteria in root nodules. Legumes are often used as a rotation crop to naturally enhance the nitrogen content of soils. Scientists have been working for a number of years to understand the symbiosis between legumes and rhizobial bacteria, with the hope that one day they can transfer this trait to crop plants, the majority of which cannot fix nitrogen themselves.

Intensive crop agriculture depends heavily on inorganic fertilisers that are often used to provide nutrients particularly nitrogen that are critical for plant growth. The production of nitrogen fertilisers requires a large amount of energy and is estimated to constitute approximately 50 per cent of the fossil fuel usage of the modern agricultural process. Inorganic fertilizers also cause environmental problems associated with leeching into our water systems.

Dr Giles Oldroyd is the research leader at JIC. He said: "We now have a good understanding of the processes required to activate nodule development. The nodule is an essential component of this nitrogen fixing interaction as it provides the conditions required for the bacteria. Nodules are normally only formed when the plant perceives the presence of the bacteria. The fact that we can induce the formation of nodules in the plant in the absence of the bacteria is an important first step in transferring this process to non-legumes. If this could be achieved we could dramatically reduce the need for inorganic nitrogen fertilizers, in turn reducing environmental pollution and energy use. However, we still have a lot of work before we can generate nodulation in non-legumes."

Professor Julia Goodfellow, Chief Executive of BBSRC, commented: "BBSRC is the principal funder of fundamental plant research in the UK and commits millions of pounds a year to furthering our understanding of basic plant biology. Such fundamental research may seem disconnected from the every day world for many people but this project shows how potentially important such science is. The findings have the potential to lead to a practical application with substantial economic impact for the UK."

Victoria Just
Matt Goode
Tracey Jewitt

The JIC is grant-aided by the Biotechnology and Biological Sciences Research Council.

28 June 2006

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1.10  Gene controlling aphid resistance in soybean reported

The soybean aphid is a serious pest of the crop, and has caused millions of dollars in economic losses. Farmers controlled the pest by applying chemical insecticides, until scientists discovered that plants could be resistant to aphid infestation. Scientists are now busy mapping the gene or genes involved in aphid resistance, and Curtis B. Hilla and colleagues of the University of Illinois are no different. Their articles, "Soybean Aphid Resistance in Soybean Jackson Is Controlled by a Single Dominant Gene" and "A Single Dominant Gene for Resistance to the Soybean Aphid in the Soybean Cultivar Dowling" appear in the latest issue of Crop Science.

Researchers aimed to determine the inheritance of soybean aphid resistance in two cultivars, Jackson and Dowling. They crossed the cultivars with Loda and Williams, soybean cultivars susceptible to aphids. By testing parents and F2 plants for aphid susceptibility in the greenhouse, and then performing statistical tests to determine inheritance patterns, researchers traced the soybean aphid resistance trait to a single dominant gene.

The gene is Rag1 in Dowling, but as yet unknown in Jackson. Because there is no known genetic relationship between the two resistant cultivars, it is possible that the resistance gene found in Jackson is unique and distinct from the Rag1 found in Dowling. Since aphid resistance is controlled by only one gene in soybean, however, breeders will have an easier time converting existing susceptible cultivars to resistant cultivars using backcrossing procedures.

Read more at and

Source: CropBiotech Update 7 July 2006

Contributed by Margaret E. Smith
Dept. of Plant Breeding & Genetics
Cornell University

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1.11  Peru launches new kiwicha cultivar

The Agrarian Experimental Station Canaán Ayacucho of the Peruvian National Institute of Agrarian Research and Extension (INIEA) has released a new improved variety of kiwicha, or amaranth grain. The Kiwicha Variety 413, "INIA Morocho Ayacuchano," has an early germination phenotype, a yield of 3 to 4 tones/ha, and a high grain quality.

The project is in line with the policies of the Ministry of Agriculture and of the Institutional Strategic Program, and aims to introduce new technologies to the Peruvian agricultural sector. The objective is to increase the use of national genetic resources and promote the competitiveness and sustainability of the sector for the benefit of all.

Kiwicha, a natural plant from the Peruvian Andes, and a traditional Incan crop, has been under cultivation for over 8000 years. However, as kiwicha has continued to grow in the wild as a weed, this crop has a very large base of genetic diversity. Kiwicha seeds have a high caloric nutrient content, and provide, besides protein, dietary fiber and minerals such as iron, magnesium, phosphorus, copper, and manganese.

Read more at:

Source: CropBiotech Update 21 July 2006

Contributed by Margaret E. Smith
Dept. of Plant Breeding & Genetics
Cornell University

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1.12  IITA takes on banana virus with UV, juice help

Scientists from the International Institute of Tropical Agriculture (IITA) are using vegetable juice and near ultraviolet (UV) light to help them select the best banana plantlets in the laboratory. This is part of the IITA's rapid screening process for resistant banana plants; field evaluations for plant susceptibility to the Black Sigatoka fungus can be time consuming and expensive, so scientists use a combination of UV and juice to grow large amounts of fungal spores to transmit the disease and challenge culture plantlets in test tubes.

Once resistant plantlets are identified, they can be propagated in the laboratory, and subsequently distributed to banana farmers. IITA is now focusing on refining their screening methods and determining the relationship between early screening results and adult plant reaction.

Black Sigatoka is a common, widespread disease of bananas in sub-Saharan Africa. It can cause yield losses as high as 76%. Read the complete news article at

Source: CropBiotech Update 28 July 2006:

Contributed by Margaret E. Smith
Dept. of Plant Breeding & Genetics
Cornell University

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1.13  New barley has higher yields, available phosphorous

Scientists from the Agricultural Research Service, of the United States Department of Agriculture (AR-USDA), have developed a new high-yielding barley that provides more bio-available phosphorous. That is, the phosphorous is present in a form more readily absorbed and used by animals that feed on the crop; this also means that the phosphorous is less likely to end up in animal manure and be carried away by rain runoff from pastures and fields into freshwater supplies.

Named "Herald," the barley should save growers the cost of feeding phosphorus supplements to farm animals.

For more information, contact Marcia Wood of the ARS at Read the complete press release at

Source: CropBiotech Update 28 July 2006:

Contributed by Margaret E. Smith
Dept. of Plant Breeding & Genetics
Cornell University

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1.14  Pinto bean lines developed to resist mold

Two new white mold-resistant, high-yielding pinto bean lines have recently been developed by scientists of the United States Department of Agriculture's Agricultural Research Service (USDA-ARS). Designated as USPT-WM-1 and USPT-WM-2, these lines were developed by cross-breeding the pinto bean Aztec, a semi-upright breed of pinto, with ND88-106-4, an upright navy bean breeding line.

White mold is an endemic disease affecting pinto and other dry edible bean crops throughout the United States. Crop losses can be minimized with fungicides, careful irrigation, or widely spaced rows, but the fungus that causes white mold can elude these measures and spread quickly through the air. Severe outbreaks of the disease can reduce bean yield and quality.

Read the complete article at For more information, contact Jan Suszkiw of the ARS News Service at

Source: CropBiotech Update 28 July 2006:

Contributed by Margaret E. Smith
Dept. of Plant Breeding & Genetics
Cornell University

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1.15  Cloned oil palm making its way in Malaysia

Applied Agricultural Resources Sdn Bhd (AAR), an agricultural advisory firm based in Malaysia, has successfully developed cloned plantlets of oil palm through tissue culture clonal propagation, a technology the firm uses to clone high-yielding oil palms. These plantlets have 20 - 25% higher oil extraction rate, which translates to higher revenue for plantation companies. The clonal propagation technique, though developed in the 1970's, was commercialized only by two firms in Malaysia, including AAR. Currently, seven firms have invested in the research and development of tissue culture clonal propagation.

For more information, contact Mahaletchumy Arujanan of the Malaysian Biotechnology Information Center (MABIC) at Find out more about MABIC at

Source: CropBiotech Update 28 July 2006

Contributed by Margaret E. Smith
Dept. of Plant Breeding & Genetics
Cornell University

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1.16  UCSD biologists solve plant growth hormone enigma

By Sherry Seethaler
Gardeners and farmers have used the plant hormone auxin for decades, but how plants produce and distribute auxin has been a long-standing mystery. Now researchers at the University of California, San Diego have found the solution, which has valuable applications in agriculture.

The study, published in the July 1 issue of the journal Genes and Development, describes the discovery of a whole family of auxin genes, and shows that each gene is switched on at a distinct location in the plant. Contrary to the current thinking in the field, the research shows that the patterns in which auxin is produced in the plant influence development, a finding that can be applied to improving crops.

“The auxin field dates back to Charles Darwin, who first reported that plants produced a substance that made them bend toward light,” said Yunde Zhao, an assistant professor of biology at UCSD. “But until now, the auxin genes have been elusive. Our discovery of these genes and the locations where auxin is produced in the plant can be applied to agricultural problems, such as how to make seedless fruit or plants with stronger stems.”

Applying auxin to plants can have many different effects. For example, it can promote root development in cuttings, stimulate fruit development in the absence of fertilization or, in excess, kill weeds. However, this study is the first to show what happens in a plant when auxin production is turned off.

The researchers identified a family of 11 genes (YUCCA 1-11) that are involved in the synthesis of auxin. In Arabidopsis­a small plant favored by biologists because it is easy to manipulate genetically­Zhao’s team inactivated combinations of the YUCCA genes and studied the effects of the inactivations on plant growth and development.

“Plant biologists have wanted to do this experiment for a long time, but only recently have new genetic tools such as ‘reverse genetics’ and ‘activation tagging’ made it possible,” explained Youfa Cheng, a postdoctoral fellow working with Zhao. “Even with the advances in technology, it took about three years to produce plants lacking at least four of the 11 YUCCA genes.

Disrupting one YUCCA gene did not have any obvious effects. Therefore, there is overlap in the functions of the genes in this family. However, when two or more YUCCA genes were inactivated, the plants had developmental defects. The defects, including flowers with missing or misshapen parts, or deformations in the tissues that transport water and nutrients throughout the plant, differed depending on which combinations of genes were deleted.

The researchers say that this finding was surprising because most people in the field thought that where auxin was made did not really matter. The widely held view was that auxin could just be transported wherever it was needed. Not so, because turning auxin off in specific tissues of the plant led to defects in those tissues, while the rest of the plant appeared normal.

“Knowing which auxin genes are activated when should make it possible to modify plant development,” said Zhao. “It wouldn’t require adding any new genes to the plant, just changing when the appropriate auxin genes were on or off could alter growth. For example, to make seedless tomatoes, one could activate auxin in the floral organs before fertilization has taken place.”

Applying auxin to the flowers by hand can also induce seedless tomatoes, or other seedless fruit, but this method is too tedious to be useful for commercial purposes. Seedless fruits would not just be novelty items. For example, Zhao points out that seeds significantly increase the effort and waste involved in producing tomato sauce.

“This study is a real tour de force,” commented Martin Yanofsky, a professor of biology at UCSD, who was not one of the authors of the study. “People have been trying to figure out auxin for decades. By carefully inactivating the genes for auxin synthesis one by one, the team was able to show how the localized production of auxin controls the architecture of a plant.”

Xinhua Dai, a research associate working with Zhao, also contributed to the study. This research was supported by the National Institutes of Health.
Media Contact: Sherry Seethaler

30 June 2006

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1.17  Grass roots research will help develop new energy crops

Norwich, United Kingdom
 The John Innes Centre (JIC) has recently entered into a partnership with the US Dept of Agriculture (USDA) and Department of Energy (DOE) to study the genome of the grass Brachypodium as part of the Joint Genome Institute’s Community Sequencing Programme. The genetic information from this project will be used as a template for analysing the much larger and more complex genomes of wheat and barley which will accelerate progress towards improving food production and help develop sustainable production of biofuel from grass crops.

Brachypodium distachyon, commonly known as Purple False Brome, is a close relative of wheat, barley and forage grasses. Its small size, rapid growth time and small genome size make it an ideal plant model for the in-depth study of temperate grasses such as wheat and barley. The JIC scientists, led by Prof Michael Bevan and Prof John Snape, aim to generate a “map” or rough outline of the Brachypodium genome. This will then be used by the DOE scientists to assemble and analyse the vast amount of DNA sequence data. It can then be used to identify important genes in food and fuel crops. This work will help scientists to develop grasses into superior energy crops and to improve grain crops and forage grasses that are the foundations of our food supply.

“Our collaboration with the DOE and USDA laboratories provides an important new foundation for understanding and utilising members of the grass family for food and fuel”, says Mike Bevan, Head of the Cell and Developmental Biology Dept at the John Innes Centre. “The Brachypodium genome sequence will accelerate progress in developing new generations of crop plants and lead to new approaches to increase biomass productivity for energy production and as a chemical feedstock. This work will be an important contribution to developing a sustainable energy economy”.

Work will start in late 2007 and the 300 mega-base genome should be completed towards the end of 2008. All of the data will be placed in the public domain so scientists worldwide can benefit from this useful resource.

The Joint Genome Institute (JGI), supported by the US Department of Energy Office of Science, unites the expertise of five national laboratories, Lawrence Berkeley, Lawrence Livermore, Los Alamos, Oak Ridge, and Pacific Northwest, along with the Stanford Human Genome Center to advance genomics with the mission to enable scientific approaches to challenges in energy and the environment. The Community Sequencing Program (CSP) provides the scientific community with access to high-throughput sequencing at the JGI.

JGI press release for this project: Energy-rich portfolio of new genome sequencing targets for U.S. Department of Energy Joint Genome Institute

The JIC, Norwich, UK is an independent, world-leading research centre in plant and microbial sciences with over 800 staff. JIC carries out high quality fundamental, strategic and applied research to understand how plants and microbes work at the molecular, cellular and genetic levels. The JIC also trains scientists and students, collaborates with many other research laboratories and communicates its science to end-users and the general public. The JIC is grant-aided by the Biotechnology and Biological Sciences Research Council.

12 July 2006

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1.18  Energy-rich portfolio of new genome sequencing targets for DOE JGI

WALNUT CREEK, CA--Bioenergy crop plants switchgrass and cassava, other important agricultural commodities such as cotton, and microbes geared to break down plant material to render biofuels, round out the roster of more than 40 projects to be tackled by the U.S. Department of Energy Joint Genome Institute (DOE JGI) over the next year. Drawing submissions from DOE JGI's more than 400-strong user community, the genomes of these organisms will be sequenced and characterized as part of the DOE JGI Community Sequencing Program (CSP). Over 15 billion letters of genetic code--or the equivalent of the human genome five times over--will be processed through the DNA sequencers at the DOE JGI Production Genomics Facility for this year's program and ultimately, the information will be made freely available to the greater scientific community.

"By coupling DNA sequencing technology with fundamental research, we seek to make cellulosic ethanol a major part of the nation's energy future," said DOE JGI Director Eddy Rubin. His remarks and the CSP selections echo recommendations outlined in the "Breaking the Biological Barriers to Cellulosic Ethanol" report issued by DOE on July 7 ( "The newest direction in biosciences research--systems biology--is built on a strong foundation of DOE's investment in genomics, with DNA sequence as the starting material of that endeavor and DOE JGI as the generator of that information through the CSP. Downstream characterization of the pathways inferred by the genetic code of the target CSP organisms is then supported through the DOE Genomics:GTL program."

In his 2006 State of the Union Address, President George W. Bush specifically cited the promise of switchgrass as a bioenergy crop. A tall perennial grass, a dominant species of the North American prairie, switchgrass (Panicum virgatum) is particularly compelling because of its relatively low production costs, minimal nutrient and pesticide requirements, perennial growth habit, as well as its ability to adapt to a broad range of growing conditions. The net energy gain for ethanol production from switchgrass is exceptionally favorable, coupled with low greenhouse gas emissions. The switchgrass project, which entails sequencing the gene transcripts, or Expressed Sequence Tags (ESTs) of the plant, is led by Christian Tobias and researchers at the U.S. Department of Agriculture Western Regional Research Center in Albany, Calif. and Gautam Sarath at the University of Nebraska, Lincoln.

"Switchgrass has enormous potential as an energy crop and environmental benefits that are associated with its cultivation," said Chris Somerville, professor of biological sciences at Stanford University and director of the Carnegie Institution's department of plant biology. "I envision that switchgrass will be an important feedstock for the emerging lignocellulose to ethanol industry. An enhanced understanding of gene structure and diversity at the molecular level may lead to new approaches to enhance both biomass productivity and feedstock quality for bioenergy production."

In complement to switchgrass, DOE JGI will be sequencing Brachypodium distachyon, a temperate grass model system with a simple genome more amenable to sequencing. This choice responds to the urgent need for developing grasses into superior energy crops and improving grain crops and forage grasses for food production. Brachypodium will be undertaken via a two-pronged strategy: the first, a whole-genome shotgun sequencing approach, a collaboration between John Vogel and David Garvin, both of the USDA, and Michael Bevan at the John Innes Centre in England; and the second, an expressed gene sequencing effort, led by Todd Mockler and Jeff Chang at Oregon State University, with Todd Michael of The Salk Institute for Biological Studies, and Samuel Hazen from The Scripps Research Institute.

Another major CSP project is the selection of cassava (Manihot esculenta), an excellent energy source and food for approximately one billion people around the planet. Its roots contain 20 to 40 percent starch, from which ethanol can be derived, making it an attractive and strategic source of renewable energy. Cassava grows in diverse environments, from extremely dry to humid climates, acidic to alkaline soils, from sea level to high altitudes, and in nutrient-poor soil.

"Sequencing the cassava genome will help bring this important crop to the forefront of modern science and generate new possibilities for agronomic and nutritional improvement," said Norman Borlaug, Nobel laureate, father of the "Green Revolution," and Distinguished Professor of International Agriculture, Texas A&M University. "It is a most welcome development."

The cassava project will extend broad benefits to its vast research community, including a better understanding of starch and protein biosynthesis, root storage, and stress controls, and enable crop improvements, while shedding light on such mechanisms shared by other important related plants, including the rubber tree and castor bean.

The cassava project, led by Claude M. Fauquet, Director of the International Laboratory for Tropical Agricultural Biotechnology and colleagues at the Danforth Plant Science Center in St. Louis, and includes contributions from the USDA laboratory in Fargo, ND; Washington University St Louis; University of Chicago; The Institute for Genomic Research (TIGR); Missouri Botanical Garden; the Broad Institute; Ohio State University; the International Center for Tropical Agriculture (CIAT) in Cali, Colombia; and the Smithsonian Institution.

Adding to the list of crops to be sequenced by DOE JGI is the oyster mushroom, Pleurotus ostreatus, for its prospective role in bioenergy and bioremediation. This white-rot fungus is an active lignin degrader in the forests. Lignin, a poly-aromatic hydrocarbon, is the second most abundant biopolymer on earth and its breakdown is a necessary step for making cellulose--the most abundant carbon biopolymer--available for conversion to biofuels. This organism will serve as a valuable comparison to the reference genome of white-rot fungus Phanerochaete chrysosporium, previously sequenced by DOE JGI, which belongs to a different phylogenetic branch and carries a different set of ligninolytic enzymes. Understanding the whole-genome regulation of the P. ostreatus will add further value in that its lignocellulolytic enzymes could facilitate bioremediation and other biotechnological processes. The poly-aromatic hydrocarbon oxidizing enzymes present in P. ostreatus can participate in the biodegradation of dyes, of contaminating wastes produced in agroindustries, and of forest, pulp and paper industrial by-products. This project is led by Antonio Pisabarro of the Public University of Navarre, Spain and includes more than a dozen other institutions including University of Wisconsin, Michigan State, Texas A&M, Duke, and Southeast Missouri State.

The CSP has tapped important projects from the most extreme locales, including the pristine cold environment described by a system of lakes in the Vestfold Hills region of Antarctica. This project, led by Rick Cavicchioli of the University of New South Wales in Sydney, Australia, seeks to define a microbial model for the biogeochemical process that take place in extreme cold conditions. This project entails the strategy of metagenomics, pioneered by DOE JGI, for isolating, sequencing, and characterizing DNA extracted directly from environmental samples. These data are then used to define a profile of the microbial community residing in a particular environment.

"Microbes are too small to be seen with the naked eye," said Carl Woese, professor of microbiology at the University of Illinois at Urbana-Champaign, whose pioneering contribution of phylogenetic taxonomy of 16S ribosomal RNA led to the definition of the domain of life known as Archaea. "That is why the average person and most scientists pay little or no attention to them--except, of course, when they cause us problems or make us money.  Nature does not look at the living world this way," Woese said. His remarks on the significance of the Antarctic project ring true for other CSP microbial investigations.

"Microbes constitute as much or more of the living mass on this planet than do the 'higher forms,'" Woese said. "Microbes are absolutely basal to the great flows of organic matter and energy that underlie the biosphere; without them macroscopic life on this planet is impossible. In other words, the existence of macroscopic life is totally conditioned upon the prior and continued existence of microbial life. You can see why the proposed work delights an old evolutionist like myself. Here you see the microbial world in its full glory--its true significance to the biosphere, and so to mankind. Here is the microbiology of the 21st century."

The genomic and functional data gleaned from the Antarctic environmental samples, linked to meteorological, geological, chemical and physical data, will provide a better understanding about how these microorganisms have evolved, transformed, and presently interact with their frigid environment. These studies, while basic to understanding how microbes cope with environmental challenges, also seek to unlock the potential of cold-adapted microbes as sources of fuel, for example, transforming carbon dioxide effluent into methane. The work has even more astronomical ramifications--modeling extraterrestrial environments and processes.

Plant pests are the target of another international collaboration, linking researchers in Sweden, France, Norway, Germany, Canada and at the University of California, Berkeley. Heterobasidion annosum is the most economically devastating forest pathogen in the northern hemisphere, causing root rot in conifers, a major renewable biological energy resource. These forests support biodiversity and serve as an important CO2 sink buffering global climate change. Improved knowledge of this tree pathogen will help build strategies to protect these wooden resources and enable a better understanding of important enzymatic systems involved in oxidation and degradation of polyphenolic substances--pollutants that are targets for bioremediation.

Actinobacteria, which can be found in soil, can be harnessed for environmental clean-up as well. Strains, the subject of another CSP project, proposed by researchers at the Swedish University of Agricultural Sciences and Hebrew University, have promise for the development of environmentally sound, cost effective biological strategies to reduce environmental pollution.

For a full list of the CSP 2007 sequencing projects, see:
The DOE Joint Genome Institute, supported by the DOE Office of Science, unites the expertise of five national laboratories, Lawrence Berkeley, Lawrence Livermore, Los Alamos, Oak Ridge, and Pacific Northwest, along with the Stanford Human Genome Center to advance genomics in support of the DOE mission related to clean energy generation and environmental characterization and clean-up. DOE JGI's Walnut Creek, Calif. Production Genomics Facility provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges.

For more information, contact
David Gilbert
DOE JGI Public Affairs Manager

11 July 2006

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1.19  Full-length switchgrass genes sequenced and genetic variation characterized

Thousand Oaks, California
Ceres, Inc. announced today that they have achieved a major milestone in their switchgrass (Panicum virgatum) genomics program for enhancing biomass yield, completing analysis of over 12,000 switchgrass genes and characterizing the genetic variation associated with them. Switchgrass is a perennial grass native to the prairies of North America. It has been identified by the U.S. Department of Energy as the primary perennial plant species for development as a dedicated cellulosic energy crop. It is estimated that switchgrass and other plant species grown in the U.S. have the potential to produce over 100 billion gallons of biofuels per year while still allowing food, animal feed and export demands for other crops, including corn, to be met. Moreover, switchgrass has the potential to produce cellulose for biofuels such as ethanol and butanol on lands incapable of supporting traditional food crops.

The large-scale Ceres switchgrass sequencing effort has utilized libraries of full-length cDNAs rather than ESTs (partial genes), in order to capture information not only on complete gene sequences and encoded proteins but also on genetic variation associated with these genes that enables targeted, marker-assisted breeding programs for switchgrass improvement. The generation of large numbers of full-length cDNA sequences, which are notably absent from most high-throughput gene sequencing programs because of technical difficulties, represents an important component of Ceres' intellectual property strategy. To date, Ceres has filed patent applications covering over 70,000 full-length plant genes from Arabidopsis, corn, soybean, wheat and cotton, amongst others.

"These switchgrass sequences are being utilized in our integrated genomics platforms and high-throughput product development pipeline," said Dr. Richard Hamilton, Chief Executive Officer of Ceres. "Using the sequences of these genes as well as the physical clones of our proprietary collection of full- length plant genes enhances our leading position in dedicated energy crop genomics and will accelerate breeding and commercialization of elite switchgrass varieties. These genes may also be useful in improvement programs of other crops such as corn."

The switchgrass sequencing project is part of an agreement with the USDA Western Regional Research Center and of the recently announced collaboration with The Samuel Roberts Noble Foundation, Inc. for the development and commercialization of new, advanced biomass crops for biofuels production.

Ceres, Inc. (, headquartered in Thousand Oaks, CA, is a privately-held plant biotechnology company utilizing cutting-edge genomics technologies to deliver sustainable solutions in energy production, agriculture, human health and nutrition.

10 July 2006

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1.20  Plan to boost rice photosynthesis with inserted genes

Mike Shanahan, SciDev.Net
Scientists have announced plans to radically boost rice yields, warning that unless production increases millions of people could fall back into poverty.

Delegates who met at the International Rice Research Institute in the Philippines this month (17-21 July) said they hope to manipulate the crop's genetics to enable it to grow faster and bigger.

Traditional methods of increasing rice production ­ such as crossing different varieties ­ have been pushed to the limits of what is scientifically possible. But now that researchers have sequenced rice's entire genetic code, more advanced approaches could become available.

Key to the strategy discussed at the workshop is a difference in the way that rice and other plants convert sunlight and carbon dioxide into sugar for growth ­ a process called photosynthesis.

Rice photosynthesis is less efficient than that of some other plants such as maize that use an extra chemical process for capturing carbon dioxide.

The researchers say it should be possible to transfer this process to rice by inserting genes from maize or from wild relatives of rice that also use it.

The project is ambitious. The specialists who met this month say it would take about four years to determine whether the technique is feasible and another 10-15 years until the first improved varieties are available.

Related article: Chinese scientists complete rice gene map

Source: via
27 July 2006

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1.21  Potato blight pathogenicity explained by genome plasticity

Wageningen, The Netherlands
'Adjustable' genes are essential for inducing infection in potato plants

A team of researchers from Wageningen University report in this month's issue of Genome Research that they have identified a unique genetic fingerprint in the pathogen responsible for potato blight. Some strains of the pathogen possess multiple copies of a specific gene, while other strains possess only a single copy. Certain potato plants do not recognize strains of the pathogen with only the single gene copy, making them susceptible to infection. This is the first report of gene amplification in a non-bacterial organism that is associated with pathogenicity, and it provides insight into how plant pathogens tailor their genomes to adapt to their environments.

The potato late blight pathogen, known to scientists as Phytophthora infestans, is a fungus-like organism that was responsible for the Irish Potato Famine of the 1840s and continues to cause devastating agricultural losses worldwide today. Infected plants are characterized by dark lesions on the stems, leaves, and tubers; damage to the tuber surface allows other fungi and bacteria to enter and destroy the core, often resulting in a foul odor. P. infestans is related to approximately 65 other pathogens that cause similar damage to commercial crops as well as natural vegetation.

In the potato-Phytophthora system, the host-pathogen response has evolved in a highly specific way: resistance (R) genes from wild species, which are introduced into cultivated potato by breeding, are matched by avirulence (Avr) genes in Phytophthora. While many such gene matches are predicted, only a few have been confirmed by molecular and functional studies. Avr genes are thought to undergo rapid changes to evade detection by plants that possess R genes, which means that many strains of Phytophthora and potato are likely to be evolving at the present time.

"P. infestans is notorious for its ability to change in response to R genes," says Dr. Francine Govers, the principal investigator on the project. "These changes are probably facilitated by its underlying genomic plasticity. Field isolates of P. infestans are known to be genetically highly variable."

Govers, along with colleagues Rays Jiang, Rob Weide, and Peter van de Vondervoort, set out to identify the genetic basis for the virulence of specific Dutch P. infestans strains. The outcome of their efforts was the identification of single gene, called pi3.4, that was present as a single, full-length copy in both the virulent and avirulent strains. They also identified multiple copies of pi3.4 only in the avirulent strain – but, interestingly, these copies represented only part of the pi3.4 gene.

The authors speculate that the partial gene copies could function as a source of modules for generating new genes. These new genes could be produced by unequal crossing-over, or exchange of genetic material, during development. The partial copies may also serve as alternative protein-coding units, which allow the pathogen to produce a diverse array of proteins and, consequently, to adapt to its environment.

"Surprisingly, the pi3.4 gene does not code for an effector – a small protein that elicits a defense response in plants," adds Govers. "Effectors are quite common in fungal and bacterial plant pathogens, including Phytophthora. But in our case, the gene appears to produce a large regulatory protein that exerts its effect by regulating the expression of other genes, possibly effector genes."

While the exact mechanism by which these partial gene copies function as a source of modular diversity remains to be resolved, this study highlights the importance of genome plasticity in evolution. Understanding genome plasticity as a mechanism for environmental response and ecological adaptation in pathogenic organisms has important implications. "The efforts of plant breeders to obtain resistant varieties by introducing R genes, either by classical breeding or by genetic modification, may be a waste of time and resources when the genome dynamics of the pathogen population is not understood," says Govers. "Monitoring field populations of plant pathogens at the genome level will be instrumental for predicting the durability of R genes in crop plants."

Contact: Maria Smit
Cold Spring Harbor Laboratory

3 July 2006

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1.22  South Africa halts 'super sorghum' study

The project aims to boost nutrient levels in sorghum, a major crop in Africa

[NAIROBI] South Africa has blocked trials of genetically modified sorghum that leaders of a multi-million-dollar project hope can boost nutrition in Africa.

Kenyan scientist Florence Wambugu, who heads the Africa Harvest Biotech Foundation International, has secured US$18.6 millionover five years from the Bill and Melinda Gates Foundation to develop new sorghum varieties with elevated levels of iron, zinc and vitamins.

She says her organisation wished to run their greenhouse trials in South Africa because of its legal guidelines and policy framework on genetically modified (GM) crops, which are so far absent in Kenya.

But last week (12 July) South Africa rejected the application to set up a laboratory and greenhouse on its soil.

According to Kenya's Sunday Nation, the South African government expressed concern that the GM sorghum could contaminate wild varieties.

Wambugu is hopeful that South African authorities will approve a second application.

She says the project was asked to increase 'biosecurity' measures aimed at containing the GM sorghum. "Once we comply, we will certainly go back and reapply to be allowed to start the project."

On the same day the sorghum project was put on hold, the Kenyan parliament overwhelmingly defeated a motion by Davies Nakitare, the member of parliament for Saboti, that sought a blanket ban on all production, consumption and sale of genetically modified foods.

The government said the country had capacity to deal with GM biosafety issues.

Ochieng’ Ogodo

Source: SciDev.Net
20 July 2006

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1.23  Biotechnology opens new opportunities for flavor and fragrance industry

Auckland, New Zealand, 10 July 2006 – New research designed to build scientific understanding of fruit genes could revolutionise the way foods, cosmetics and perfumes are created.

Researchers at New Zealand-based life sciences company HortResearch say they have fine-tuned the science of gene discovery to such a degree that they can now accurately determine which genes create the individual flavours and fragrances found in fruits and flowers.

Combined with traditional biofermentation techniques – the same process that helps bread rise or grape juice to become wine - this means that it should be possible for the natural tastes and aromas of fruit to be recreated.

According to HortResearch Industrial Biotechnology scientist Dr Richard Newcomb, that's exciting news for the world's food, perfume and cosmetic producers, who have for years sought synthetic solutions to mimic nature's flavours and fragrances in products ranging from ice cream to shampoo.

"While manufacturers have largely been successful in copying natural tastes and scents, they generally do so either through a chemical synthesis process or extraction from harvested raw ingredients.

"Neither approach is ideal. Chemical synthesis requires heat and pressure, so is reliant on increasingly expensive and polluting fossil fuels for energy. What's more, chemical synthesis can never truly recreate nature; the flavour or fragrance will typically be slightly different to that found naturally in fruits and flowers.

"Extraction is expensive and produces only limited quantities of product, reducing the number of commercially viable options for the extract," says Dr Newcomb.

Biofermentation however can produce large amounts of a desired compound at a low cost and with little environmental impact. And because biofermentation uses the actual genes that plants use in the wild, the resulting flavour or fragrance compound has exactly the same molecular make-up. It is, as the scientists say; "Nature Identical".

While the possibility of 'fermenting' genes to produce compounds has been well understood for many years, science has generally lagged behind in identifying which genes are needed to produce the desired outcome. HortResearch has now overcome this issue by using research initially intended to speed up the process of fruit breeding, says Dr Newcomb.

"Through decades of fruit breeding research HortResearch has developed extensive fruit gene and compound databases. Now we have developed techniques that help determine which genes create each compound, and how those compounds combine to create a flavour or fragrance. It's a complicated and time-consuming process – some fruit flavours for example may be comprised of over thirty different compounds, each in a precise volume.

"Much of this information is fed back into the breeding programme, allowing naturally-bred new fruit varieties with desired traits to be quickly recognised amongst young breeding populations that frequently number in the tens of thousands.

"However, it is also possible for us to isolate genes that produce desirable flavour and fragrance compounds for use in industrial biotechnology applications."

HortResearch has proven the bioproduction concept can be used to produce fruit flavours and fragrances by perfectly recreating a fruit compound called alpha-farnesene, responsible for the distinctive aroma of green apples.

The company has filed international patent applications on the use of the applicable gene in creating the fragrance, and for another plant gene responsible for making a compound that smells like the heady scent of red roses.

Dr Newcomb says HortResearch scientists are continuing to seek new gene/compound combinations which they believe will find ready demand in the marketplace.

"Alongside colour, flavour and fragrance rank as some of the most important guides to the natural world. The ability for manufacturers to recreate them exactly as they occur in nature will open new opportunities for high-quality, novel products and foods."

While many biofermented compounds will undoubtedly end up in non-food consumer products such as make-up or household cleaners, Dr Newcomb is confident they will also play a role in the expanding health food market.

"Researchers are finding ever greater numbers of foods and food compounds that can enhance human heath and wellbeing. The trouble is, they don't always taste very good – and until they do it will be difficult to encourage consumers to make them part of their regular diet," he says.

"Adding synthetic flavours destroys the credibility of any health food, so natural flavours produced through bioproduction would be a huge advantage to the health industry."

Dr Newcomb has been invited to present details of HortResearch's flavour and fragrance science programme to delegates at the World Congress on Industrial Biotechnology which is being held in Toronto, Canada from July 11-14.

Contact: Joan Kureczka

10 July 2006

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1.24  How purple corn and RNA break genetic laws

A newly cloned gene in corn will help explain how unusual interactions between a parent's genes can have lasting effects in future generations. The finding has implications for breeding better crop plants and unraveling complex genetic diseases.

The new research indicates that an additional molecule, DNA's little cousin RNA, is needed for the intriguing gene interactions known as paramutation. Paramutation doesn't follow the laws of classical Mendelian genetics.

"Paramutation is this incredibly interesting, tantalizing violation of Mendel's laws," said senior author Vicki L. Chandler, director of BIO5 Institute at The University of Arizona in Tucson. "It's been known to exist for 50 years, but nobody understood the underlying mechanism."

Classical genetics states that when offspring inherit genes from their parents, the genes function in the children the same way the genes functioned in the parent.

When paramutation occurs, one version of the parent's gene orders the other to act differently in the next generation. The gene functions differently in the offspring, even though its DNA is identical to the parent's version.

It happens even when the kids don't inherit the bossy version of the gene. The phenomenon was originally found in corn and has since been found in other organisms, including mammals.

"In previous work we identified a gene that is absolutely required for paramutation to happen," said Chandler, a UA Regents' Professor of plant sciences and of molecular and cellular biology. "Now we've figured out what that gene does, and it's exciting because it suggests a mechanism for how this process works."

Chandler's work is the first to point out that an enzyme known as an RNA-dependent RNA polymerase is needed for paramutation.

Corn, also known as maize, is the most economically important crop plant in the United States. Better understanding of plant genetics will help breeders develop improved strains of crops.

Understanding paramutation and similar non-Mendelian genetic phenomena also has implications for human health. For some human diseases, a genetic component is known to exist but has been hard to decipher. Non-Mendelian effects may be at work in those diseases.

"Gene interactions in parents that change the way a gene functions in the progeny are going to contribute to very unexpected inheritance patterns that complicate identifying genes involved in human disease," said Chandler, who holds the Carl E. and Patricia Weiler Endowed Chair for Excellence in Agriculture and Life Sciences at UA.

Chandler and her colleagues will publish their new findings in the July 20 issue of the journal Nature. The article's title and a complete list of authors and their affiliations is at the end of the release. The National Science Foundation, the National Institutes of Health and the Howard Hughes Medical Institute funded the research.

The Chandler lab investigated a gene called b1 that controls whether a corn plant has a purple or green stalk. A plant has two copies of each gene, one from each parent.

One version, or allele, of the gene codes for a purple pigment. Generally, plants need just one copy of that allele, known as B-Intense or B-I, to be the color purple.

But whether a B-I-carrying plant is actually purple depends on the company B-I keeps. If the plant's other b1 allele is the "paramutagenic" B' variety, the B-I allele is silenced. The resulting plant is mostly green.

And although B-I's DNA doesn't change, in subsequent generations the silenced B-I allele behaves as if it had mutated -- the B-I-carrying progeny are mostly green, rather than being deep purple.

"It cannot revert -- it's a one-way street," said co-author Lyudmila Sidorenko, an assistant research scientist in Chandler's lab.

Chandler and her colleagues wanted to know how the B' allele changed B-I's behavior without actually changing B-I's DNA. They already knew that paramutation required normal versions of the mediator of paramutation 1 (mop1) gene.

Plants with normal mop1 genes and one B-I allele and one B' allele turned out as expected -- mostly green.

However, B-I/B' plants with two mutant mop1 genes were deep purple -- they looked as if the purple-suppressing B' allele wasn't present. This demonstrated that normal mop1 was necessary for the B' allele to silence B-I.

The scientists mapped mop1's location on one of the corn's chromosomes and cloned the gene. The mop1 gene makes an enzyme called RNA-dependent RNA polymerase (RDRP). Mutant mop1 genes can't produce the enzyme.

The team had previously suspected a role for RNA, best known for mediating the transfer of information from DNA to a cell's protein-making machinery. This new result provides strong evidence that RNA is indeed involved.

The researchers hypothesize that mop1 amplifies the RNA signals coming from a key region of the B-I and B' allele. That key region is a particular DNA sequence that is repeated seven times.

The researchers hypothesize that those many RNA molecules silence the B-I and B' alleles.

Chandler said, "It's exciting because it's a new role for RNA."

The researchers' next step is figuring out exactly how RNA suppresses the function of the b1 gene and how those cease-and-desist orders are faithfully transmitted to progeny in the absence of changes in the DNA.

Chandler's co-authors on the article, "An RNA-dependent RNA polymerase is required for paramutation in maize," are Mary Alleman of Duquesne University in Pittsburgh; Lyudmila Sidorenko, Karen McGinnis and Kristin Sikkink of UA; Vishwas Seshadri, now of Biologics Development Center Developing Businesses in Andhra Pradesh, India; Jane E. Dorweiler, now of Marquette University in Milwaukee; and Joshua White, now of the University of Texas at Austin.
Contact: Mari N. Jensen
Vicki L. Chandler


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1.25  Selections from Update 5-2006 of FAO-BiotechNews

4) Electronic Journal of Biotechnology - REDBIO Argentina 2005 The Electronic Journal of Biotechnology is a free international scientific journal that publishes papers on all areas of biotechnology, including agricultural biotechnology. It is supported, among others, by the United Nations Educational Scientific and Cultural Organization (UNESCO) MIRCEN (Microbial Resources Centres) network and has been operational since April 1998. All papers are freely available on the web and UNESCO also disseminates the journal by CD-ROM to a number of partners in developing countries. A special issue (June 2006) of the journal has just been published, including the complete versions of a significant number of papers presented during the VI Symposium of REDBIO Argentina 2005, held on 7-11 June 2005 in Buenos Aires, Argentina. REDBIO is the Technical Co-operation Network on Plant Biotechnology in Latin America and the Caribbean, based at the FAO Regional Office for Latin America and the Caribbean in Santiago, Chile. See or contact for more information.

5) UN-Biotech meeting report The report of the 3rd meeting of UN-Biotech, the inter-agency cooperation network in biotechnology, that took place on 16 May 2006 in Geneva, Switzerland, is now available. At the meeting, the focus was on the establishment of a web portal on biotechnology and it was also agreed that FAO would hold chairmanship of UN-Biotech for the 2006-2007 biennium, with the United Nations Conference on Trade and Development (UNCTAD) continuing to act as secretariat. See or contact for more information

13) The impacts of AMBIONET The International Maize and Wheat Improvement Center (CIMMYT) has just published "The Asian Maize Biotechnology Network (AMBIONET): A model for strengthening national agricultural research systems" by C. Pray. The 43-page report reviews the impacts of this network, which ended in 2005 and was organized by CIMMYT with funding from the Asian Development Bank to strengthen the capacity of public maize research institutions in China, India, Indonesia, the Philippines, Thailand and Vietnam to produce high-yielding, disease resistant, stress tolerant maize cultivars. The report is organised into the following sections: history and structure of AMBIONET; framework for impact assessment; impact on Asian maize research capacity; impact on research output and productivity; impact on farmers; and conclusions: impacts and the future. See (482 KB) or contact for more information

14) New WARDA website launched The Africa Rice Center (WARDA), one of the 15 research centres supported by the Consultative Group on International Agricultural Research, has recently launched its new website. It provides updated information about the centre (its history, structure etc.), its partnerships, publications and newsroom services as well as its research, including extensive information, inter alia, on the New Rice for Africa (NERICA) varieties developed using embryo rescue and anther culture techniques. See (in English and French) or contact for more information.

From: The Coordinator of FAO-BiotechNews, 21-7-2006
The Food and Agriculture Organization of the United Nations (FAO)

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3.01  New search portal for IPK’s genebank (Gatersleben, Germany) is online

The Genebank of the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) in Gatersleben, Germany, comprises ca. 150,000 accessions of a large number or crop plant species. Recently the new Internet search portal of the Genebank, GBIS/I, was activated under It is accessible via the IPK homepage ( and supersedes the previous three independent online databases of the genebank collection in Gatersleben (active since 1996) and those of the two branch stations in Malchow (oil and fodder crops) and in Groß Lüsewitz (potatoes).

The new Genebank Information System of IPK, GBIS, was developed in connection with the transfer of the former Braunschweig genebank collection to IPK.

GBIS/I is freely accessible. It allows searching for genebank material among more than 140,000 accessions, using passport data. The results of a query can be stored in a “wish list”. Registered users can order genebank material (seed or vegetative). Passport data of selected accessions can also be downloaded for further processing by the user.

Three possible search strategies are supported.

The step-wise search allows refining the search by combining several search criteria. Thus, if the number of hits for Genus = Hordeum is too large (21,473 accessions), the resulting set can be reduced, e.g., by adding Country of Origin = Afghanistan (355 accessions).

The free-text search option allows finding accessions containing one or several pieces of text in a number of text fields without specifying the descriptors to be searched. For example, by entering “Paris” into the search field, among the 32 results there are the pea (Pisum sativum) cultivar ‘Serpette de Paris’, a wheat accession (Triticum aestivum) collected in Mega Paristeri, Northern Greece, and two accessions of the caper-plant, Capparis spinosa.

The advanced search allows to formulate complex queries by combining multiple search criteria with the logical operators “and” and “or”, using parentheses if necessary.

After submitting a search request, an overview table showing some basic information for the accessions matching the criteria is shown. By clicking on an accession number, one will see the details of passport data for that accession. Both in the overview table and in the detailed view, the user can mark all or individual accessions for subsequent actions, such as inclusion in the wish list or in the shopping cart (if the user is registered and logged in), or downloading passport data.

The search portal is available in German and English; the user can switch between the two languages.

Researchers and breeders who want to order seeds from the IPK Genebank are encouraged to use the new search portal. We are looking forward to receiving users’ feedback via

The previous online databases for the collections in Gatersleben, Malchow and Groß Lüsewitz remain active and accessible till end of 2006.

Submitted by Helmut Knüpffer
Genebank Department
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)
D-06466 Gatersleben, Germany

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4.01  International Foundation for Science (IFS): Calls for applications

eNews No. 17, July 2006

A new application period is now open and IFS calls for applications for Research Grants from young scientists in developing countries. Details of eligibility criteria, areas of scientific research covered and application forms are available on the IFS website:

Application deadline: December 31, 2006

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* 2006-2008.  Plant Breeding Academy, University of California, Davis.

The University of California Seed Biotechnology Center would like to inform you of an exciting new course we are offering to teach the principles of plant breeding to seed industry personnel.

This two-year course addresses the reduced numbers of plant breeders being trained in academic programs. It is an opportunity for companies to invest in dedicated personnel who are currently involved in their own breeding programs, but lack the genetics and plant breeding background to direct a breeding program. Participants will meet at UC Davis for one week per quarter over two years (eight sessions) to allow participants to maintain their current positions while being involved in the course. 

Instruction begins Fall 2006 and runs through Summer 2008 (actual dates to be determined)

For more information: (530) 754-7333, email,

* 2-6 July 2006. IX International Conference on Grape Genetics and Breeding, Udine (Italy), under the auspices of the ISHS Section Viticulture and the OIV. Info: Prof. Enrico Peterlunger, University of Udine, Dip. di Scienze Agrarie e Ambientale, Via delle Scienze 208, 33100 Udine, Italy. Phone: (39)0432558629, Fax: (39)0432558603, email:

* 31 July -1 August 2006, Grass Breeders’ Conference, Ames, IA.
Information available at, or by contacting Charlie Brummer, or Shui-zhang Fei (

* 31 July – 4 August 2006. African Rice Congress, WARDA , Dar es Salaam, Tanzania
Contact: Lawrence Narteh.

*8-10 August 2006. 7th Plant Genomics Conference, Heilongjiang University , Harbin, China. Contact: Rongtian Li, Zhenqiang Lu, Chunquan Ma.

* 13-19 August 2006: XXVII International Horticultural Congress, Seoul (Korea) web:

*16 - 19 August 2006.Tropical Crop Biotechnology Conference 2006, Cairns, Queensland, Australia.  Organized by: CSIRO Plant Industry. For more information: Contact: CSIRO Plant Industry .Website:

* 20-25 August 2006. The International Plant Breeding Symposium, Sheraton “Centro Historico” Hotel, Mexico City. Presentations by invited speakers will be published in a proceedings by Crop Science. More information is available at If you are unable to register online please send an e-mail to:

* 30 August – 1 September 2006. XIII EUCARPIA Biometrics in Plant Breeding Section Meeting, EUCARPIA , Zagreb, Croatia
Contact EUCARPIA Secretariat
Event Website

Meeting Announcement (PDF)
Pre-registration Form (Word Document)

* 10-14 September 2006. First Symposium on Sunflower Industrial Uses. Udine University, Udine Province, Friuli Venezia Giulia Region, Italy.
Sponsored by the International Sunflower Association (ISA)
* 11-15 September 2006. XXII International EUCARPIA Symposium - Section Ornamentals: Breeding for Beauty, San Remo (Italy). Info: Dr. Tito Shiva or Dr. Antonio Mercuri, CRA Istituto Sperimentale per la Floricoltura, Corso degli Inglesi 508, 18038 San Remo (IM), Italy. Phone: (39)0184694846, Fax: (39)0184694856, email: web:

* 17-21 September 2006. Cucurbitaceae 2006, Grove Park Inn Resort and Spa in Asheville, North Carolina, USA (in the scenic Blue Ridge Mountains).
Contact: Dr. Gerald Holmes, Department of Plant Pathology, North Carolina State University, Raleigh, NC 27695-7616, 919-515-9779 (
Conference website:

* 18-20 September 2006.The International Cotton Genome Initiative (ICGI) 2006 Research Conference, Blue Tree Park Hotel ( Brasília, D.F., Brazil. Details of the ICGI 2006 Research Conference will be posted on the ICGI website ( ) as they become available.

* 9-13 October 2006. Second International Rice Congress 2006 (IRC2006). New Delhi, India. Organized jointly by the International Rice Research Institute (IRRI) and Indian Council of Agricultural Research (ICAR), the theme of this congress is "Science, technology, and trade for peace and prosperity". It comprises four major events: the 26th International Rice Research Conference (including e.g. a session on 'genetics and genomics' and workshops on hybrid rice and on genetically modified rice and biosafety issues); the 2nd International Rice Commerce Conference; the 2nd International Rice Technology and Cultural Exhibition; and the 2nd International Ministers' Round Table Meeting. See or contact for more information.

* 11-14 October 2006 Plant Genomics European Meetings, Venice, Italy.
Contact person:

* 14 - 18 October 2006. The 6th New Crops Symposium: Creating Markets for Economic Development of New Crops and New Uses, University Center for New Crops and Plant Products,The Hilton Gaslamp Quarter Hotel, San Diego, CA
Sponsored by: Association for the Advancement of Industrial Crops and Purdue or

* 9-12 November 2006. 7th Australasian Plant Virology Workshop. Rottnest Island, Perth, Western Australia.
For further information contact: Prof Mike Jones, Murdoch University, Perth

* 4-22 November 2006. International training program on plant genetic resources and seeds: Policies, conservation and use, Karaj, Iran. For further information on the program please visit the websites of ICARDA: (see: Seed Systems Support), Wageningen International: (see: international education at Wageningen UR, courses), or the Generation Challenge Program: (see: capacity building corner, training courses

* 1-5 December 2006: The First International Meeting on Cassava Plant Breeding and Biotechnology, to be held in Brasilia, Brazil. For more details, email Dr. Nagib Nassar of the University of Brasilia at or visit the meeting website at

* 8-9 February 2007. A national workshop on “Sustaining plant breeding as a vital national capacity for the future of U.S. agriculture,” Raleigh, NC.
Co-hosted by the Departments of Crop Science and Horticultural Science North Carolina State University

* 24-28 June 2007. The 9th International Pollination Symposium on Plant-Pollinator Relationships­Diversity in Action. Scheman Center, Iowa State University, Ames, Iowa. The Conference webpage can be viewed at:

* 24-28 July 2007. The 9th International Pollination Symposium, Iowa State University (Note new dates, and see additional details in New Announcements, above). The official theme is: "Host-Pollinator Biology Relationships - Diversity in Action." For more information please visit

* 9-14 September 2007. The World Cotton Research Conference-4, Lubbock, Texas, USA ( There is no cost of pre-registration and if you pre-register you will receive all the up-coming information on WCRC-4.171 researchers from over 20 countries have pre-registered as of today.

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Plant Breeding News is an electronic forum for the exchange of information and ideas about applied plant breeding and related fields. It is published every four to six weeks throughout the year.

The newsletter is managed by the editor and an advisory group consisting of Elcio Guimaraes (, Margaret Smith (, and Anne Marie Thro ( The editor will advise subscribers one to two weeks ahead of each edition, in order to set deadlines for contributions.

REVIEW PAST NEWSLETTERS ON THE WEB: Past issues of the Plant Breeding Newsletter are now available on the web. The address is:   Please note that you may have to copy and paste this address to your web browser, since the link can be corrupted in some e-mail applications. We will continue to improve the organization of archival issues of the newsletter. Readers who have suggestions about features they wish to see should contact the editor at

Subscribers are encouraged to take an active part in making the newsletter a useful communications tool. Contributions may be in such areas as: technical communications on key plant breeding issues; announcements of meetings, courses and electronic conferences; book announcements and reviews; web sites of special relevance to plant breeding; announcements of funding opportunities; requests to other readers for information and collaboration; and feature articles or discussion issues brought by subscribers. Suggestions on format and content are always welcome by the editor, at We would especially like to see a broad participation from developing country programs and from those working on species outside the major food crops.

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