Plant & Animal Genome V Conference
Town & Country Hotel, San Diego, CA, January 12-16, 1997.
PAG-V: W14 - GENOMIC ANALYSIS OF <i>Arabidopsis thaliana</i>
W14
GENOMIC ANALYSIS OF Arabidopsis thaliana
DAVIS, RONALD W.(1), Nancy A. Federspiel(1), Raymond J. Cho(1), Peter Oefner(1), Bertrand Lemieux(1), Ken Feldmann(2), Gene Buehler(3), Ken Dewar(3), Ji-Dong Feng(3), Chris Kim(3), Yaping Li(3), Paul Shinn(3), Hui Sun(3), Joseph Ecker(3), Brian Osborne(4), Valentina Vysotskaia(4), Athanasios Theologis(4)
1. Stanford Center for DNA Sequencing & Technology, 855 California Avenue, Palo Alto, CA 94304
2. Department of Plant Sciences, University of Arizona, Tucson, AZ 85721
3. University of Pennsylvania, Plant Sciences Institute, Department of Biology, Philadelphia, PA 19104
4. Plant Gene Expression Center, 800 Buchanan Street, Albany CA 94710
We have recently formed the SPP Consortium, composed of the Stanford DNA Sequencing and Technology Center, the Plant Gene Expression Center, and the University of Pennsylvania, to initiate sequencing on chromosome 1 of Arabidopsis thaliana. Our strategy involves mapping BAC clones from the TAMU and IGF libraries to chromosome 1, followed by the construction of sequencing libraries in M13 and plasmid vectors. Current progress in sequencing will be discussed. In addition, we are developing a set of markers for Arabidopsis thaliana that can be analyzed in an automated, non-gel based manner. We have used denaturing high performance liquid chromatography (DHPLC), a novel mismatch detection technology, to identify over 200 single-nucleotide changes between the Columbia and Landsberg erecta strains of A. thaliana. Sequencing of these polymorphisms from both strains reveals a variety of substitutions and small deletions. These markers will be the basis for the construction of an Affymetrix chip which can be used to integrate the physical and genetic map. We are also initiating the arraying of Arabidopsis cDNAs on glass slides using a robotic arrayer developed at Stanford. These arrays will be hybridized with two-color fluorescent probes for expression analysis and for identification of insertion mutant alleles in T-DNA tagged Arabidopsis strains.