Decoding developmental signaling pathways and the molecular details underlying cell structure and function.

• Dr. Klaus Apel
• Dr. Gary Blissard
• Dr. Carmen Catalá
• Dr. Jim Giovannoni
• Dr. Maria Harrison
• Dr. Eric Richards
• Dr. Frank Schroeder
• Dr. David Stern

BTI says goodbye to trustee emeritus and friend

Passing of Roy A. Young

Former board member and longtime supporter of the Boyce Thompson Institute Roy A. Young passed away on April 19th in Corvallis, Oregon. Young was chancellor of the University of Nebraska-Lincoln (UNL) from 1976-1980, overseeing and implementing a series of positive changes in departmental and administrative structure. From UNL, Young came to BTI and served as president from 1980-1986. For a full obituary, please visit http://newsroom.unl.edu/announce/todayatunl/2373/13283.

Cornell research helps meet world’s crop challenges

Read full article by Krishna Ramanujan

Article: Cornell research helps meet world’s crop challenges

Understanding the complex interactions between plants and other organisms.

• Maria Harrison
• Georg Jander
• Dan Klessig
• Gregory Martin
• Sorina Popescu

BTI hosts the AIPI meeting next week (May 6 – 8)

There will be an opportunity for the BTI community to attend the Tuesday morning session in the BTI Auditorium (9am to 12:30 pm), which will include a panel discussion of the National Plant Science Initiative (9-10:30am) and talks on inter-institution collaborations (11 am – 12:15 pm). If you are interested in attending these sessions, please send me (netid: ejr77) an RSVP by Monday morning.

There will be room for up to forty people in addition to the meeting registrants.

If you would like to learn more about AIPI, please visit http://www.plantinstitutes.org/

Understanding the complex interactions between plants and other organisms.

• Maria Harrison
• Georg Jander
• Dan Klessig
• Gregory Martin
• Sorina Popescu

Applying chemistry to the study of biological problems.

• Georg Jander
• Frank Schroeder

Building and refining tools for biological discovery.

• Gary Blissard
• Zhangjun Fei
• Lukas Mueller
• Sorina Popescu
• Frank Schroeder
• Joyce Van Eck

Six months after the launch of the $25.2M NEXTGEN Cassava project at Cornell University, scientists on the project have released Cassavabase, a database that promotes open access data sharing.

www.cassavabase.org features all phenotypic and genotypic data generated by cassava breeding programs involved in the NEXTGEN Cassava project, and makes the data immediately and openly accessible to all users prior to publication. It is being developed by Lukas Mueller, at the Boyce Thompson Institute in Ithaca, NY, adjunct professor of plant breeding and genetics at Cornell.

“In the plant breeding community, data-sharing can be delayed until publication, which can limit the opportunity to use the knowledge by the international plant breeding communities,” said Mueller.

Chiedozie Egesi, assistant director and head of cassava breeding at the National Root Crops Research Institute (NRCRI), Nigeria, and Katherine Kahn, senior program officer at the Bill and Melinda Gates Foundation, co-presented about Cassavabase and the advantages of open access data sharing during the G8 International Conference on Open Data for Agriculture, in Washington DC, April 29-30, 2013.

“Open access databases such as Cassavabase enable better decisions based on good quality data by the global cassava breeding community,” said Egesi. “Cassavabase will lead to increased efficiency in agricultural research and ultimately improve the livelihoods of African cassava farmers.”

At the 2012 Summit at Camp David, G8 leaders implemented the New Alliance for Food Security and Nutrition with the aim of boosting agriculture production in six countries and lifting 50M people out of poverty in 10 years. Critical to food security in developed and developing countries was the implementation of policies and projects to make data readily accessible to users in Africa and worldwide.

“It’s great to see the cassava research community lead the way in sharing their data rapidly and openly to maximize opportunities for developing improved cassava varieties for small farmers in sub-Saharan Africa and indeed, globally,” said Kahn. She noted that the Bill & Melinda Gates Foundation supports increasing open access to data in all its projects.

“Different versions of cassava genes can be found in all breeding programs. What one program learns about its genes can benefit everybody,” said Jean-Luc Jannink, lead scientist on the NEXTGEN Cassava project, research geneticist with the US Department of Agriculture and adjunct professor in the Cornell University department of plant breeding and genetics. “All our learning is leveraged by sharing,”

The benefits of open data sharing through Cassavabase is being lauded by cassava breeders across sub-Saharan Africa, who “currently share a significant amount of cassava germplasm,” according to Peter Kulakow, plant breeder at the International Institute for Tropical Agriculture (IITA-Nigeria), a major contributor of data to Cassavabase. “Sharing information will create the opportunity for all African farmers to benefit from the best technologies available to improve the yield and quality of cassava that is needed for food and income.”

Data is publicly shared on Cassavabase through adherence to the Toronto Agreement on pre-publication data sharing (Nature 461, 168-170, 2009), by informing users on the data quality and standards, as well as plans for publication. Users are expected to respect etiquette and allow data generators to publish analyses from their data sets first.

Cassavabase will be hosted at IITA-Nigeria by the NEXTGEN Cassava project, providing a “one-stop shop” for cassava researchers and breeders worldwide. In addition to phenotypic and genotypic data, Cassavabase offers access to all Genomic Selection analysis tools and phenotyping tools developed by the NEXTGEN Cassava project, as well as links to auxiliary genome browsers, ontology tools and social networking tools for the cassava community.

Project partners and donors envisage Cassavabase as a tool that will serve the whole cassava community, and that it will last beyond the lifetime of the NEXTGEN Cassava project.

No other continent depends on cassava to feed as many people as does Africa, where 500 million people consume it daily. Africa’s small farmers produce more than half of the world’s cassava, or about 86 million tons from over 10 million hectares. The tough plant requires few inputs and can withstand drought, marginal soils and long-term underground storage. A cash crop as well as a subsistence crop, the storage roots of the perennial woody shrub are processed, consumed freshly boiled or raw, and eaten by people as well as animals as a low-cost source of carbohydrates.

Despite diverse growing conditions and multiple uses of cassava across sub-Saharan Africa, farmers face similar challenges fighting cassava viruses and drought conditions that adversely affect yield.

The NEXTGEN Cassava project aims to use the latest advances in breeding methodology to improve productivity and yield in cassava production, incorporate cassava germplasm diversity from South America into African breeding programs, train the next generation of plant breeders, and improve infrastructure at African institutions. NEXTGEN Cassava is supported by a $25.2M grant from the Bill & Melinda Gates Foundation and the Department for International Development of the United Kingdom.

For more information, visit www.nextgencassava.org

Image Captions:

Image 1. Cassavabase developer Lukas Mueller (center), of the Boyce Thompson Institute and Cornell, in Ithaca, NY, works with researchers from the National Root Crops Research Institute in Nigeria, to develop protocols for the barcoding tools used to submit data to the open-access Cassavabase. CREDIT: C. Egesi

Image 2. Small-holder producers of cassava in Africa, like Chukwuma (left) and Akuoma (right) Obisike of Ahaba Imenyi, Nigeria, produce more than half of the world’s cassava. CREDIT: H.Tufan

By Linda McCandless

An international team, led by Dr. Zhangjun Fei at the Boyce Thompson Institute for Plant Research, Dr. Yongsheng Liu at Hefei University of Technology and Dr. Hongwen Huang at South China Botanical Garden, has sequenced and assembled a draft genome of kiwifruit (Actinidia chinensis). A heterozygous diploid Chinese kiwifruit variety, called Hongyang, was used to generate the draft genome sequence, which is accessible at the online Kiwifruit Genome Database (http://bioinfo.bti.cornell.edu/kiwi).

Kiwifruit belongs to Actinidiaceae, the basal family within Ericales. It has long been considered “the king of fruits” due to its remarkably high vitamin C content and balanced nutritional density of minerals, dietary fiber, and other health-beneficial metabolites. Kiwifruit originated in the mountains and ranges of southwestern China, and has experienced a relatively short history of domestication beginning only in the early 20th century when its seeds were introduced to New Zealand, and since then numerous varieties have been developed and cultivated. Today, kiwifruit is an important fresh fruit worldwide with annual production of 1.44 million tons in 2011 (http://faostat.fao.org).

The draft kiwifruit genome represents the first genome sequence of a member in the order Ericales, and the third in the entire asterid lineage, after potato and tomato. The sequence of the kiwifruit genome provides a valuable resource for comparative genomics and evolutionary studies especially in the asterid lineage, which has much less genomic resources available when compared to the rosid lineage. This information also provides a great opportunity to develop a deeper understanding of agronomical and/or biological important traits such as vitamin C metabolism and provide information for the fruit breeders to further enhance the fruit’s nutritional value.

Image: The kiwifruit know as Hongyang, which was used to generate the draft genome sequence.