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Plant breeding and genomics are focus of new national web resource

January 14, 2011

As global food needs increase, so does the need for crops that can be efficiently and safely produced.  Traditional plant breeding methods have served well in the past and breakthrough technologies are now available to aid this process.  These breakthroughs include key information on the genetics, or “genomes” of crops. A group of researchers and educators from America’s land-grant universities, government agencies and industry, have banded together to create the first-ever internet resource aimed at quickly putting basic research on crop genomes into practice through plant breeding programs across the U.S. to more efficiently improve crops. The resource is a new online community housed at eXtension (pronounced E-extension), www.extension.org, at the www.extension.org/plant_breeding_genomics.

eXtension resource areas
The researchers and educators working on this project are what the new national U.S. Cooperative Extension System project calls an eXtension Web Community. This group, the Plant Breeding and Genomics (PB&G) community of practice, is one of many within eXtension.  Other communities in eXtension include geospatial technology; corn and soybean production; cotton production; horticulture; pest management; science, engineering and technology for youth; organic agriculture; bee health and more.  There are currently 37 published resource areas. Each community continues adding new information on a regular basis. New communities are also being added every month.
Putting Research into Practice
Development of crop varieties through plant breeding has traditionally focused on selection of the best plant lines based on traits (phenotypes).  In the past decade, research has yielded extensive databases of gene sequences and of the complete genetic makeup (genomes) of entire plants.  As sequencing technology improves, available information to aide in crop improvement is expanding rapidly.  This basic research information is utilized when linking important agricultural traits to genetic sequence variations and incorporating this knowledge into crop improvement strategies. 
David Francis, associate professor at The Ohio State University noted, “The eXtension portal provides an entry point into the research knowledge of the Land-Grant University System. We’ve developed a resource to help train the next generation of plant breeders, help current professionals keep abreast of new developments, as well as inform growers and processors about the technological advances that bring them new varieties.”
In 2009 the international community was still working to complete the first draft of the tomato genome sequence, in 2010 two draft sequences became public.  The research community expects as many as 100 Solanaceae genomes to be available within the next year or two. This complements whole genome sequences already known in key crops such as potato, rice, poplar, soybean, maize, cotton and cucumber to mention a few. David Francis explained, “This information explosion means that practitioners need resources for continuing education to keep up with new developments.”
Dave Douches, a Michigan State University potato breeder, and leader of the Solanaceae Coordinated Agricultural Project (SolCAP) highlighted the need for this eXtension outreach effort, “SolCAP developed over 5.7 GB of sequence data for three potato varieties, we mined this data for genetic differences and developed a tool that allows breeders and their support crews to quickly survey breeding populations for 8,300 genetic differences.  The outreach material will help the breeding community make better use of genetic information and will increase the likelihood that plant breeding will benefit from genotype-based selection processes”.
Allen Van Deynze, director of research for the Seed Biotechnology Center at the University of California, Davis emphasized the importance of accessibility to information “The goal of the Plant Breeding and Genomics resource on eXtension is to act as a portal to the vast number of public databases in crops and genetic and genomic resources.”
Resource for Agricultural Producers 
Another important function of the eXtension site will be to provide up to date production information on new varieties available to agricultural producers.  Members of the barley Coordinated Agricultural Project (Barley CAP) provided a template for this goal by including information on barley production practices and other basic barley information needed by barley producers and growers. 
Gary Muehlbauer, professor at the University of Minnesota and lead PI of the Barley Coordinated Agricultural Project (CAP), emphasizes that “providing helpful information on barley improvement efforts is a central goal of eXtension and CAPs”. He states that the barley grower site on eXtension “highlights information available for growers regarding planting and production of existing varieties, as well as those improved through the genomics and breeding efforts of Barley CAP research”.
An example of information provided for producers and plant breeders alike is the Barley CAP-produced podcast on the threat of a new rust virus.  Barley, like all crops, is attacked by disease-causing organisms. One potential threat, which can dramatically reduce yield and quality, is the fungus, Ug99, first detected in Uganda in 1999. “Although Ug99 is not yet confirmed in the U.S., this highly virulent strain is spreading in Africa and to the Middle East and will ultimately come to the U.S.” Brian Steffenson, plant pathologist at the University of Minnesota, points out.  He states “what concerns barley researchers and growers is that most U.S. varieties are susceptible to the fungus”.
Barley CAP researchers, partnering with the USDA-ARS Ug99 Cereal Rust Initiative, screened over 2000 U.S. breeding lines in Africa, identified Ug99 resistance in several advanced barley lines and were able to find molecular markers associated with the resistance. Leading this study, Steffenson shares that, “the genomics efforts of Barley CAP made it possible to identify the genes responsible for resistance and develop the tools that will dramatically accelerate breeders’ efforts to develop stem rust-resistant barley varieties for growers”.
Experienced researchers and extension personnel in the United States contributed to the new site. The effort is led by SolCAP, a USDA National Institute of Food and Agriculture (NIFA)-funded program focused on potato and tomato.  SolCAP recruited a community of experts from a wider range of Coordinated Agricultural Projects (CAP). The Barley CAP, another ongoing CAP project, played a pivotal role in organizing a template for other groups to develop information pages geared toward growers' needs. Other educational information in the CAP eXtension materials included those developed by Wheat CAP and Rosaceae CAP (RosBREED). The PBG community currently has 195 members who represent 30 universities and federal agencies, 11 educational institutions outside of the USA, and 5 industry groups.  Over forty individuals representing 15 Universities and agencies have directly written, edited, and reviewed the content, which includes articles, videos, and tutorials.  Content continues to be written and updated, with new information to be published monthly.
 Terry Meisenbach, a Communications and Marketing expert with eXtension explained, "eXtension is a direct response to concerns about information quality on the Internet. Users can access eXtension with the same confidence they access their own state extension networks.”
 eXtension is an educational partnership of more than 70 land grant universities helping Americans improve their lives with access to timely, objective, research-based information and educational opportunities. eXtension's interactive Web site is customized with links to local Cooperative Extension sites. Land-grant universities were founded on the ideals that higher education should be accessible to all, that universities should teach liberal and practical subjects and share knowledge with people throughout their states. eXtension is an educational resource designed to help people acquire skills and knowledge to help them grow and empower them to improve their quality of life. eXtension takes the best university-based research and turns it into practical information people can use to solve today’s problems and develop skills to build a better future.

Published: January 14, 2011

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