Progress towards a complete physical map

Caroline Dean* and Howard Goodman# 

*Cambridge Lab		#Department of Molecular Biology
JICPSR			Massachusetts General Hospital
Colney Lane		Boston, MA  02114
Norwich			USA	
NR4 7UH
UK
Written as a summary of the state of the physical map for the Multinational Coordinated Arabidopsis thaliana Genome Project Year Book.
The number of markers mapped using the Landsberg erecta x Columbia recombinant inbred lines continued to increase throughout the year (currently 379). As the new markers became available, they were hybridized to the YAC libraries to increase the YAC coverage of each chromosome. Use of new RFLP markers was generally more successful in linking YAC contigs than chromosome walking experiments. The biggest advances in the linking of YAC contigs was achieved once the CIC YAC library was distributed in May 94. This library, generated through a collaboration between CEPH/INRA/CNRS, France, consists of 1152 clones with an average insert size of 450kb. The library contains very few, if any chimaeric YAC clones. This library is being used by the Ecker and Goodman labs to add to the physical map of chromosomes 1, 2 and 3, and the Dean lab for chromosomes 4 and 5.

The combination of the CIC library, the increased marker coverage and a few successful walking experiments have resulted in chromosome 4 being covered by just 15 YAC contigs (Schmidt, West, Dean). Chromosome 5 is currently covered by 35-40 contigs (Schmidt, Love, Z. Lenehan, Dean) after having used over 100 markers on 4 YAC libraries. Chromosome 2 (Goodman lab) is covered by about 40 contigs for a total distance of about 17Mb. The largest contig on chromosome 2, constructed in part using YAC end probes, is ~ 3.2Mb covering ~ 5.7cM. A similar level of coverage has been achieved for chromosomes 1 (Ecker lab). Cosmid contigs from the Goodman laboratory and EST clones are also being integrated into the chromosome 2, 4, and 5 YAC contigs. Efforts are continuing to generate a 1.5Mb cosmid contig (Bancroft, Love, Cobbett, Goodman and Dean) covering the region of chromosome 4 being sequenced as part of the EC ESSA programme (co- ordinated by Mike Bevan, Norwich). Currently 9 cosmid contigs covering 730kb have been restriction mapped and distributed to participating laboratories. Joining of these contigs will require alternative strategies due to sequences within the gaps being repetitive or underrepresented in the cosmid libraries being screened. Strategies based on YAC subclones, rather than cosmids, providing the sequencing templates for the next phase of the genomic sequencing project are being investigated (Bancroft). On a smaller scale a ~800kb contig on chromosome 2 is being sequenced using the multiplex method (Goodman lab).