A comparative map viewer integrating genetic maps for Brassica and Arabidopsis

We have developed a comparative genetic map database for the viewing, comparison and analysis of Brassica and Arabidopsis genetic, physical and trait map information. This web-based tool allows users to view and compare genetic and physical maps, search for traits and markers, and compare genetic linkage groups within and between the amphidiploid and diploid Brassica genomes. The inclusion of Arabidopsis data enables comparison between Brassica maps that share no common markers. Analysis of conserved syntenic blocks between Arabidopsis and collated Brassica genetic maps validates the application of this system. This tool is freely available over the internet on http://bioinformatics.pbcbasc.latrobe.edu.au/cmap webcite.This database enables users to interrogate the relationship between Brassica genetic maps and the sequenced genome of A. thaliana, permitting the comparison of genetic linkage groups and mapped traits and the rapid identification of candidate genes.Brassica species represent important crops providing a major source of cooking oil, vegetables and condiments across many countries [1,2]. The species relationship of cultivated Brassicas was described by the "triangle of U"[3] with the three amphidiploid Brassica species B. juncea (AABB, 2n = 36), B. napus (AACC, 2n = 38) and B. carinata (BBCC, 2n = 34) formed through interspecific hybridization between the diploid Brassica species, B. rapa (AA, 2n = 20), B. nigra (BB, 2n = 16) and B. oleracea (CC, 2n = 18) [4,3]. Brassicas are closely related to the model species, Arabidopsis thaliana, for which the genome sequence was determined in 2000 [5]. Molecular genetic mapping has been applied for several Brassica species with identification of genomic regions and molecular genetic markers associated with heritable traits.Genetic mapping in Brassicas has been predominantly based on Restriction Fragment Length Polymorphism (RFLP) and Simple Sequence Repeat (SSR) molecular markers [2,6-8]. In total, more than 900 dif