Contrasting genome organisation: two regions of the Brassica oleracea genome compared with collinear regions of the Arabidopsis thaliana genome

Brassica crop species are of worldwide importance and are closely related t o the model plant Arabidopsis thaliana for which the complete genome sequen ce has recently been established. We investigated collinearity of marker or der by comparing two contrasting regions of the Brassica oleracea genome wi th homologous regions of A. thaliana. Although there is widespread replicat ion of marker loci in both A. thaliana and B. oleracea, we found that a com bination of genetic markers mapped in B. oleracea, including RFLPs, CAPS, a nd SSRs allowed comparison and interpretation of medium-scale chromosomal o rganisation and rearrangements. The interpretation of data was facilitated by hybridising probes onto the whole A. thaliana genome, as represented by BAC contigs. Twenty marker loci were sampled from the whole length of the s hortest B. oleracea linkage group, O6, and 21 from a 30.4-cM section of the longest linkage group, O3. There is evidence of locus duplication on linka ge group O6. Locus order is well conserved between a putative duplicated re gion of 10.5 cM and a discrete region comprising 25 cM of A. thaliana chrom osome I. This was supported by evidence from seven paralogous loci, three o f which were duplicated in a 30.6-cM region of linkage group O6. The patter n of locus order for the remainder of linkage group O6 and the sampled sect ion of linkage group O3 was more complex when compared with the A. thaliana genome. Although there was some conservation of locus order between marker s on linkage group O3 and approximately 9 cM of A. thaliana chromosome I, t his was superimposed upon a complex pattern of additional loci that were re plicated in both A. thaliana and B. oleracea. The results are discussed in the context of the ability to use collinear information to assist map-based cloning.