In the area of genome analysis -- which includes physical and genetic mapping, DNA sequencing, and functional analysis of mutated and cloned genes -- progress has been excellent. The physical map now covers a high proportion of the genome, with large chromosomal regions, such as almost all of chromosome IV, covered in fine detail. New yeast artificial chromosome (YAC) libraries containing very large genomic DNA inserts have been produced in the past year, adding to the several other YAC libraries that have been made available in previous years. P1 libraries have been made and are now being prepared for general distribution by the stock centers. Although still incomplete, the linkage of the Arabidopsis genome using YACs, cosmids, and now, P1 clones, has been sufficient to increase the numbers of genes cloned by map-based methods.
An important goal for 1995 is to complete the physical linkage of YACs so an ordered set of YACs spanning the entire genome can be generated. This set of YACs will allow immediate mapping of any DNA probe and greatly ease chromosome walking. Constructing a library of Arabidopsis DNA in a bacterial artificial chromosome vector -- which, like P1 and YAC libraries, contains large genomic DNA fragments but which also easily facilitates the use of Escherichia coli colonies for screening and amplification -- is another goal for the program's next year.
In complementary DNA (cDNA) sequencing, one goal for the coming year is to add another 10,000 expressed sequence tags (ESTs) to the more than 8,000 cDNA Arabidopsis ESTs already in the database. Another goal is to map 500 of these ESTs to YACs or to chromosome locations using restriction fragment length polymorphism, simple sequence length polymorphism, or cleaved amplified polymorphic sequence technology. Meeting this goal will provide a set of mapped markers located at high density throughout the genome.
The major new initiative for the coming year is to begin the systematic sequencing of the nuclear genome. In both the European Community and the United States, this will involve preparing stretches of overlapping clones ready for sequencing as well as starting large-scale sequencing projects at several sites. This genomic sequencing is a major initiative and is in accord with the original goal of completing the entire sequence of the Arabidopsis genome. The effort has just begun in Europe: Starting a complementary effort in the United States is a high priority.
Progress has been remarkable in the areas of cloning genes known through their mutant phenotypes, isolating new and revealing mutations, and understanding the functions and interactions of genes. As described elsewhere in this report, the basic processes of all higher plants -- such as flower and root development, hormone action, and disease resistance -- are becoming better understood as a result of Arabidopsis research. This work should continue in 1995, with new emphasis on collections of interacting genes, so that a complete description of the development and physiology of higher plants can be achieved.
A new area of concentration should be subcellular function, so that the cellular basis of plant processes can be understood at the level of gene and gene products. The problem of cloning genes, once mutant forms are available, has been solved, though faster methods are still needed. However, the problem of learning the function of a gene when only its sequence is available remains to be solved. One of the major scientific aims of the program therefore must be to develop a gene knockout system, which allows the identification of gene function from gene sequence. Together, sequencing and functional data will allow modification of plant function in new and useful ways.
The seed and clone stock centers need expanded capability and space. They now provide a critical service to the Arabidopsis community in distributing biological materials. However, they need to grow in order to cope with the ever-increasing demands from both Arabidopsis and other plant scientists for the many new ESTs, mutants, specific cloned genes and DNA libraries now available. Any expansion will need a concomitant increase in staffing support. Renewed effort must be placed on finding sources for long-term support for the stock centers and their critical mission. One new initiative, an electronic Arabidopsis newsletter called Weeds World, has been started by Mary Anderson of the Nottingham Arabidopsis Stock Centre at the University of Nottingham, United Kingdom. Efforts to make the excellent stock centers more accessible, and to make them sources of new information and research materials, should be supported.
With ever-increasing amounts of data being produced by the sequencing, mapping, and positional cloning projects, the database network needs to be upgraded. This need is a measure of the success of the Arabidopsis project itself. The goal for the coming year is to move the existing database system to a new generation of databases, with appropriate curatorial support. The Multinational Science Steering Committee has endorsed this assessment, and a proposal for the next generation Arabidopsis database has been submitted to the National Science Foundation for review. One of the objectives of the new database is to collect all available information on YAC positions, mutant locations, and EST mapping. Sharing of these data will benefit all Arabidopsis researchers by making new information available before publication, presenting data organized in a way that avoids duplication of effort, and accommodating completion of the physical linkage map.
A key goal in the human resources area is to find support for multinational postdoctoral fellowships, short-term exchanges, and short courses. While the Cold Spring Harbor Arabidopsis course is now well-established, and other courses have been given, there is little support for multinational postdoctoral fellowships. Training young researchers and coordinating international efforts are the very future of Arabidopsis genome work. Both improved training and coordination result from researchers being able to study and work in different Arabidopsis laboratories at early stages of their careers. At present, there is inadequate support for this key area. A goal for 1995 is thus to establish new programs for international postdoctoral fellowships.
The Arabidopsis community has grown to a size and achieved a rate of scientific progress that require an Arabidopsis meeting each year. Thus, at the June 1994 meeting of the Multinational Science Steering Committee, plans for future Arabidopsis research conferences were announced. Specifically, conferences will be held June 7-11, 1995, at the University of Wisconsin in Madison (the contact is Rick Amasino, Department of Biochemistry, University of Wisconsin); June 24-28, 1996, in Norwich, United Kingdom; and the second week of June 1 997 at the University of Wisconsin. These international meetings, devoted solely to Arabidopsis research, should continue to be supported so that they can be attended by all Arabidopsis researchers, and thereby serve a coordinating function for the Arabidopsis genome project.
Arabidopsis is now such a focus for plant science researchers in such diverse fields as developmental biology, signal transduction, and plant-pathogen interactions, that many genes are being first identified in Arabidopsis. The Multinational Coordinated Arabidopsis thaliana Genome Research Project has supported many of these advances. Because the project is international and collaborative, it has provided an essential framework for hundreds of researchers. The development of an electronic mail network; various databases; and specialized symposia, meetings, and biological resource centers have fostered an international spirit of cooperation and the free exchange of ideas. As a result, studies of Arabidopsis have accelerated, greatly enhancing our understanding of the molecular basis of all plant processes.
Our overall goal for the coming year should be to press ahead with the specific objectives of the project, with the ultimate aim of fully understanding the genetic, molecular, and cellular basis of all plant life.