Global Expression Studies of the Arabidopsis Genome

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The elucidation of the DNA sequence of the 130 Mb Arabidopsis genome by the end of the year 2000 is estimated to reveal the presence of approximately 25,000 genes using various computational approaches. In order for this vast structural information to be most useful to plant biologists, another large-scale project is needed to characterize the expression patterns of the entire genome. This project will provide a framework for the identification of all the transcriptional units and the construction of full-length cDNAs for all the genes in the Arabidopsis genome. Such an endeavor will allow the precise determination of the molecular mass of each protein encoded by each transcriptional unit. In addition, this approach is much more cost effective than having different laboratories isolate and sequence individual cDNAs of interest. The central focus of this project is the development of molecular resources (infrastructure) for the entire plant biology community by utilizing emerging genomic technologies for understanding various aspects of plant growth and development. The project takes advantage of the rapid growth in Arabidopsis genomic sequence and the advent of new technologies to achieve this long term goal.This award will support the following objectives: (1) Construction and development of a high density Affymetrix oligonucleotide chip that contains all the predicted genes from the Arabidopsis Genome Initiative. The chip will be updated annually until the entire genome sequence is available. (2) Global expression studies for determining the expression pattern of all the Arabidopsis genes utilizing the Affymetrix chip and mRNAs isolated from ~100 different treatment conditions of various tissues from dark and light grown plants. The chips will be available to the entire scientific community (3) Isolation and sequencing of 8,000 full-length cDNAs. The completion of this goal will provide experimental annotation of 1/3 of all Arabidopsis genes and determine the accuracy of computational approaches currently utilized for gene prediction. The cDNAs will be useful tools for a variety of experimental purposes.An important feature of this proposal is that all of the above-described materials will be made freely available to the plant biology community as soon as they are produced. These new resources will allow the advancement of plant biology and by extension, world agriculture and plant biotechnology.