Executive Summary NSF Plant Genome Project 9872664
The legume family is one of the most important groups of plants worldwide, as an important source of protein in the human diet, of fodder and forage crops for animals, of oil crops, and for available nitrogen in the biosphere. Moreover, several crop legumes are among the best characterized plant genetic systems, with numerous classical genetic markers, well developed DNA marker maps, and basic tools for genome analysis. Nevertheless, despite the investment of considerable resources from private and public sources, features such as large and complex genomes, and difficulties with introduction of foreign genes have severely limited the pace of scientific discovery in crop legumes. In response to the need for a simple genetic system in legumes, investigators selected Medicago truncatula as a model species for legume biology. Unlike the major crop legumes, Medicago truncatula is amenable to efficient molecular and genetic analyses and it is well suited for study of biological issues important to the related crop legume species.
This project involves the large scale analysis of Medicago truncatula's total DNA, called its "genome". In particular, a map of the organization of genes (comparative genomics), and of their functions in plant biology (functional genomics), are the emphases of this project. Recent results from this research team document the first indications of conserved genome structure between Medicago truncatula and crop legumes and between Medicago truncatula and the well-characterized model plant Arabidopsis thaliana. Conserved genome structure between model plants and related crop species is significant because it is expected to accelerate the pace of cloning and characterization of agronomically important genes and traits.
Research activities conducted under this program encompasses the following approaches: (1) comparative genomics, which involves comparing the organization of genes between Medicago truncatula, the crop legumes pea, alfalfa, and soybean, and the well-characterized model plant Arabidopsis thaliana; (2) functional genomics, which involves constructing and characterizing a library of expressed gene sequences, and conducting large scale gene expression analysis to study gene function, and (3) bioinformatics, which involves experts in computing to develop databases and database resources for analysis and dissemination of Medicago truncatula genome information.
Already researchers have sequenced over 53,000 expressed gene sequences (called ESTs) from Medicago truncatula, both in Europe and the USA. From these ESTs scientists are constructing DNA "chips" to enable massively parallel analysis of gene function. Another product of these research activities is the construction of sequence-based genetic maps, and these genetic maps are providing a glimpse into the conservation of genome structure between the grain legumes, as well as between legumes and Arabidopsis. The composite Medicago map now contains over 2,000 DNA markers, which should provide a powerful toolbox to accelerate the pace of new discovery. Finally, the genome project in Medicago truncatula is accompanied by the development of computer tools for organising and mining these large datasets. Importantly, information from these projects is publicly available on the World Wide Web, and such open communication is an important hallmark of the Medicago truncatula research community.
This NSF Medicago truncatula Plant Genome Project is having a significant impact on legume research, worldwide. Currently a database of M. truncatula researchers lists approximately 150 researchers, from 16 different countries, working on M. truncatula. Meetings in Knoxville, TN, USA (1996), Paris, France (1997 and 1999), and Amsterdam, The Netherlands (1999), have attracted the participation and interest of hundreds of legume researchers, worldwide. Recently, several large multi-institutional and multi-national research projects have been funded in this species. The two largest projects include this NSF Plant Genome Project (NSF 9872664) and a recently funded project through the European Union's Genome Program ($2.2 million Euros). Other genome projects have also recently been funded, in France through the Centre National de Sequencage, in Canada through Agriculture Canada, and a multinational project funded through the Human Frontier Science Program Organization. A privately funded effort through the Samuel Roberts Noble Foundation, in Ardmore, Oklahoma, has enabled a substantial project in M. truncatula functional genomics in Ardmore and a bioinformatics project through the National Center for Genome Resources in Santa Fe, New Mexico. The influx of resources and scientific interest in M. truncatula is due in large part to the activities of this NSF funded genomic research.
The long term impact of this research will be to integrate genetic and functional information across legumes, and thereby expand opportunities for basic and applied agronomic research in economically important legume species. This knowledge will enable more efficient cloning and characterization of valuable genes and traits, such as those involved in disease resistance and crop productivity, and it will ultimately facilitate the development of improved crop varieties. Thus, many of the genes identified in the course of this research will become the focus of crop improvement strategies and of continued scientific investigation by plant biologists throughout the world. The work described in this progress report benefits enormously from previous NSF-sponsored research on the model plant Arabidopsis thaliana. Likewise, completion of the project will benefit not only research on legumes, but the broader scientific and lay communities as well.
Read the full report
Read the "Medicago truncatula as the Nodal Species for Comparative and Functiona
l genomics", NSF Award Abstract