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 decrease 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 recently 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.

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 (http://www.gramene.org/), 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.

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.

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.