Plant & Animal Genomes XI Conference

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

Workshop: Brassicas
            

A QUANTITATIVE APPROACH TOWARD BRASSICA AND ARABIDOPSIS GENOME ALIGNMENT

¹ Department of Plant Agriculture, University of Guelph, Guelph, Ontario, N1G 2W1, Canada

² Department of Biostatistics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599

³ Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, S7N 0X2, Canada

⁴ Department of Agronomy, University of Wisconsin, Madison, WI 53706 USA

Comparative maps have great potential to identify genes that are associated with specific traits, but in practice their development and use is challenging. There are both biological and methodological reasons for this. Many complex eukaryotic genomes have diverged greatly from each other and are thus inherently difficult to align. In addition, false assignments of orthology in comparative mapping are common. To address these problems, we have developed a novel computational approach to automate the detection of shared genomic regions so as to minimize the noise of both local chromosomal change and data errors. Using this algorithm, we compared the positions of sequenced Brassica loci with a known position on Brassica genetic maps to the positions of their putative orthologs within the Arabidopsis thaliana genome. In our analysis of B. oleracea, we identified 34 significant, putatively orthologous A. thaliana regions that cover over 28% of the B. oleracea genetic map with a mean of 3.3 shared markers spanning 2.1 Mbp of the A. thaliana genome and 2.5 cM of the B. oleracea genetic map. Several regions of the A. thaliana genome are present in more than one copy in B. oleracea, and several translocations and at least one duplication differentiate the two genomes. Our findings are consistent with the hypothesis that the base Brassica genomes have been highly rearranged since divergence from A. thaliana, likely as a result of polyploidization.