National Plant Genome Initiative, Progress Report * January 2005


Dear Colleague Letter

Interagency Working Group on Plant Genomes
* Committee on Science
* National Science and Technology Council

Current Status of Plant Genomes Sequences


Plans for the Next Year

URLs for Major Resources

About the National Science and Technology Council

Image Credits





Domestication of corn had a big impact involving relatively few genes. The corn cultivated across the US as a major crop was domesticated from a wild grass relative, teosinte, about 6,000 years ago. Teosinte looks very different from corn. The major changes in plant architecture include a reduction in branching, a malepoplardecrease in the number of ears and an increase in ear size. A group led by investigators at the University of Wisconsin, Madison recently reported that while these phenotypic changes are dramatic, only about 1,200 of the estimated 50,000 – 60,000 genes of corn appear to be involved in domestication. Some of these genes have been identified and characterized in detail. One gene, teosinte branched 1 (tb1), is responsible for regulation of side branching while the ramosa genes regulate the branching of the tassels and ears.

Genome-Enabled Modification of Poplar Root Development for Increased Carbon Sequestration. Trees play a significant role in collecting carbon from the air and sequestering it in the soil. A group of investigators at Oak Ridge National Laboratory, Purdue University, and Michigan Technological University are using the poplar genome sequence to identify key genetic regulators that might enhance lateral root proliferation in poplar.

The project will contribute to our basic understanding of the genomic basis for root architecture and may lead to the development of strategies to increase carbon storage in soils through roots with enhanced capacity to sequester carbon.

Understanding Late Potato Blight - The Cause of the Irish Potato Famine. Late Potato Blight is once again becoming a problem in agriculture more than a century after the Irish Potato Famine. Outbreaks are still reported regularly around the world and throughout the US and new strains are emerging that no longer respond to traditional chemical controls. The causative agent is Phytophthora infestans, an oomycete or “water mold” that has features of fungi and algae. Researchers at Ohio State University potato flowerrecently made a breakthrough in understanding how this pathogen expresses certain avirulence genes that enable it to infect plants like potatoes.

Plants that have resistance to Late Potato Blight express genes that can ward off infection by detecting and counteracting these avirulence genes. These findings will be important for development of disease resistant potatoes as well as for dealing with related Phytophthora species causing Sudden Oak Death and Soybean Root Rot.

Novel Tocopherol (Vitamin E) Profiles in Sunflower. Sunflower (Helianthus annuus L.) produces naturally high concentrations of α-tocopherol (Vitamin E) in seeds and leaves. Researchers at the University of Georgia are studying the synthesis of α-tocopherol using induced mutations to greatly increase β-, γ-, or δ-tocopherol levels. Their findings suggest that intragenic and intergenic effects can broaden the spectrum of novel tocopherols produced in sunflower and reveal strategies underlying manipulation of seed oils of other genera.
arabHow do plants grow? Like animals, plants produce hormones. One class of plant hormone, called “auxins” plays a role in many aspects of plant growth and development, including cell enlargement, formation of buds, roots, flowers, and fruit, and autumnal loss of leaves. While the roles of auxins in plant development have been described in detail, it has been very difficult to determine how auxins actually work. Researchers at Indiana University, Bloomington, used genomics tools to find a molecular receptor of auxin called TIR 1 in the model plant Arabidopsis. They further showed that binding of auxin to TIR1 forms a complex that allows de-repression of genes required for growth. This finding is a first step towards understanding how auxin regulates so many different developmental processes in plants and can be translated into economically important crop plants. Other research conducted at the University of Wisconsin, Madison recently uncovered the three dimensional structure of the plant photoreceptor phytochrome, revealing an unusual knot structure that enables it to act as a molecular switch regulating many aspects of plant growth and development.
Coordinated Agricultural Projects (CAP). RiceCAP ( The University of Arkansas, Fayetteville is leading a project to coordinate a multi-institutional research, education and extension effort to study sheath blight resistance and milling quality traits. The project will develop new technology for rice production and educate the next generation of scientists in use of this technology for plant breeding. Extension efforts will inform farmers and consumers of the value of using genomic information to improve agricultural crops. RiceCAP is utilizing the recently completed rice genome sequence, and other tools and resources to solve problems in rice production and improvement that cannot easily be solved by traditional plant breeding. WheatCAP The goal of this new project is to transfer new developments in genomics to wheat improvement by combining the expertise of genomics researchers, wheat breeders, educators, extension specialists and end-users. Led by the University of California, Davis, WheatCAP will establish a multi-institutional network of public wheat breeding programs wheatand high throughput genotyping laboratories. This network will discover high value Quantitative Trait Loci (QTL) and genes and rapidly deploy them into adapted varieties. Gene mapping and QTL information will be incorporated into the GrainGenes, Gramene and Marker Assisted Selection (MAS) wheat databases. The wheat populations used for mapping will be deposited into the USDA Small Grain Collection, providing long-term public access of genetic resources for the wheat community.
foxtailPhytoremediation of Ionic and Methylmercury Pollution. Scientists at the University of Georgia, Athens are applying genomic techniques to develop new strategies for using plants to remediate mercury contamination in the environment. Multiple genes are being introduced in concert into plants, to enhance mercury resistance or accumulation from soil, as well as to accelerate conversion of mercury into less toxic volatile forms. Data are beginning to emerge from field-testing of transgenic poplars for their ability to detoxify and extract mercury from polluted soil and water.

Bioinformatics. The massive amount of data emerging from NPGI-supported projects has led to new challenges in data management and analysis. The full potential of the current resources has yet to be realized, in part, because of a need for new analysis tools as well as uniform data standards and ontologies to allow comparisons across multiple plants and multiple data types.

At the request of the Interagency Working Group on Plant Genomes, the curators of the major plant databases recently undertook a needs assessment for plant databases. The resulting white paper (, describes, as a most pressing need, the research community’s need for a system of curated data repositories where information is actively acquired, organized, maintained and distributed. The group further points out that in order to meet this need, a trained cadre of skilled knowledge workers who are able to curate complex biological data, as well as a system of stable funding that enables such repositories to be established and maintained for extended periods of time. The white paper detailed a number of recommendations for the NPGI to consider, including the establishment of standardized data formats and user interfaces, and the development and deployment of new technologies explicitly aimed at integrating across species-specific databases and clade-oriented databases.

Stakeholders Workshop. A USDA Cooperative State Research, Education and Extension Service (CSREES) Stakeholders Workshop on Research Priorities was held on November 16, 2005 in Alexandria, Virginia, with a goal of obtaining the perspectives of the agricultural community for future CSREES program development in plant and pest biology. Stakeholders from various scientific organizations were invited to review their organizations’ research priorities as they relate to the major issue areas CSREES is considering for multi-year competitive funding. National Program Leaders from both CSREES and the National Research Initiative Competitive Grants Program, as well as from USDA-Agricultural Research Service (ARS), DOE and NSF, participated in a panel presentation and a question and answer session on funding opportunities across the federal government.
Marker Assisted Selection Workshop for Plant Breeders. A Marker Assisted Selection (MAS) workshop for plant breeders was held at the University of Arkansas Research and Extension Station and the USDA National Rice Research Center in Stuttgart, Arkansas. The goals were to better understand the reliability and versatility of molecular markers, as well as to increase precision and selection for the best trait combinations. Breeders were shown how the use of genomics tools such as molecular markers could provide improvements over existing breeding techniques, offering savings in time and labor.
The University of California, Davis Partnership for Plant Genomics Education (PPGE). PPGE is a consortium of investigators dedicated to integrating plant genomics and biotechnology into secondary school curriculum. In addition to creating and providing educational software and on-line materials, associated hands-on activities, and equipment loan programs to local schools (, PPGE hosted two workshops in genomics and biotechnology last summer on the University of California, Davis campus. “Genomics: from Mendel to Microchips” included teacher participants from eight states, many of whom serve underrepresented minority students. “Biotechnology: Techniques, Applications, and Implications” was conducted in collaboration with the Southern AgBiotech Consortium for Underserved Communities, a group of 11 Historically Black Colleges and Universities (HBCUs) dedicated to promoting agricultural biotechnology outreach and strengthening pre-college science education. In this effort, PPGE provided the instructors, training facilities, materials and on-going support for the teacher participants from schools serving students of low-income or rural isolation. In FY 2005, PPGE trained and/or distributed information to over 800 teachers, impacting approximately 8,000 students across the US.

New Integrative Graduate Education and Research Traineeship Program (IGERT) Projects in FY 2005. The NSF IGERT program supports graduate education programs that integrate training and research expertise from across a wide range of disciplines not typically aligned in more traditional graduate training programs. In FY 2005, two new IGERTs were initiated in the area of plant genomics.medicagoblooms

An IGERT award to the University of California, Riverside will establish ChemGen, a doctoral training program in advanced chemical genomics. The goal of the program is to prepare a cohort of scientists with depth and breadth of understanding across the disciplines of cell biology, chemistry, computational sciences and engineering, with competence in collaborative research aimed at solving complex problems in biology. An IGERT award to the University of California, San Diego will train students in plant systems biology at the interface of computational genomics, systems modeling and plant sciences. This program should provide a unique training environment for graduate students and will position them at the frontier of systems biology to address major challenges facing plant scientists and agricultural biotechnology.

A Microarray Workshop for Faculty at Historically Black Colleges and Universities (HBCUs) The Genome Consortium for Active Teaching (GCAT) was established in 1999 to bring functional genomic methods into undergraduate curriculum primarily through student research, particularly at predominantly undergraduate institutions and minority-serving institutions ( GCAT held two best practices workshops for faculty members who conduct research with undergraduate students and/or teach undergraduate courses at minority serving institutions on the use of microarrays. The workshops were held in Summer 2005 at Morehouse College, an HBCU. Each workshop trained about 50 faculty in analysis of gene expression via microarrays, thereby enabling them to incorporate their experiences into teaching and research activities at their own institutions.
Developing Country Collaborations in Plant Genome Research (DCC-PGR). The DCC-PGR program was started in FY 2004 by NSF to accelerate the application of new tools and resources to agriculture in developing countries. In FY 2005, DCC-PGR awards were made to 13 different projects involving collaborators in eight different countries. Some of the first projects are already bearing fruit. For example, a collaboration between the University of Missouri, Columbia and the Research Laboratory for Agricultural Biotechnology and Biochemistry (RLABB) in Katmandu, Nepal, is focused on extending the project’s study of the proteomics of oil seed filling (deposition of stores of proteins and oils) in Brassica species to varieties local to Nepal. The goal is to develop new plants with improved oil and reduced erucic acid content amenable to processing for food and feed. A research visit of RLABB personnel to the University of Missouri led to the development and publication of a simple, cost-effective procedure for detecting phosphoprotein profiles in developing seeds. To the surprise and delight of the project participants, many of the phosphoproteins identified are involved in intermediary metabolism and fatty acid synthesis and are thus likely to serve as potential targets for developing improved Nepalese Brassica varieties.
Rice SNPs and the IRFGC ( Researchers at Colorado State University Ft. Collins, The Institute for Genomic Research, North Carolina State University Raleigh, Perlegen Sciences, and the International Rice Research Institute are participating in an effort led by the International Rice Functional Genomics Consortium (IRFGC) to identify a large fraction of the Single Nucleotide Polymorphisms (SNPs) in cultivated rice. This will provide rice researchers access to most of the genetic variation that exists within and between diverse rice germplasm. The SNPs discovered will be anchored to the sequenced Nipponbare “reference” genome and a public database will be developed to house the SNP and related data. The phenotypes of all rice varieties used in this project will be evaluated and catalogued to facilitate association of traits with the mapped SNP variation. These experiments represent an unprecedented collaborative effort to apply sequence information to discover gene function in a model crop plant, an approach that has been successfully demonstrated in understanding human diseases.
Genomics for Biofuels. A December 2005 DOE workshop entitled “Biomass to Biofuels” was jointly sponsored by the Office of Energy Efficiency and Renewable Energy/ Office of Biomass Program and the Office of Science/ Office of Biological and Environmental Research. Researchers from academic, federal, and industrial sectors identified science and technology challenges ranging from feedstock genomics to bioconversion of cellulose that must be met in order to realize the potential for biological conversion of biomass to biofuels.

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