Plant & Animal Genomes XI Conference

January 11-15, 2003
Town & Country Convention Center
San Diego, CA

Workshop: Brassicas
            

GENE TO GENE ALIGNMENT BETWEEN THE ARABIDOPSIS AND Brassica oleracea GENOMES

¹ Dept. of Biochemistry, U. of Saskatchewan, Saskatoon, SK S7N 5E5, Canada

² Dept. of Vegetable Crops, U. of California, Davis, CA 95616

A global gene for gene alignment of the Brassica oleracea and Arabidopsis thaliana genomes was assembled by construction of a transcriptome map based on B. oleracea cDNAs from leaf tissue. cDNAs were synthesized from total RNA extracted from single plants of an F2 mapping population generated from doubled haploids broccoli and cauliflower. The map consisted of 247 cDNA markers obtained by the SRAP technique. After sequencing 190 of the polymorphic cDNA bands, FASTA detected 169 sequences having similarity to genes reported in Arabidopsis allowing gene for gene alignment of the two genomes. There was extensive collinearity between the two genomes but for chromosomal segments rather than for whole chromosomes, often displaying inversions and deletions/insertions. Broad duplication was observed in the B. oleracea genome, but unevenly distributed, arguing against ancient triplication of the entire genome. The most duplicated segments corresponded to those found on Arabidopsis chromosome 1 and 5, whereas the least represented were chromosomes 2 and 4. Clear differences in the similarity score value of related sequences allowed the identification of orthologs, eliminating the ambiguity often observed by EST mapping. Furthermore, transcriptome mapping excludes repetitive DNA, introns and gene spacers thus effectively reducing genome size making it easier to find a marker closely linked to a gene. Finally, this technique has the capability to dissect the whole genome into different pools, by isolating RNA for map construction from different tissues.