Abstract
BackgroundMolecular genetic maps provide a means to link heritable traits with underlying genome sequence variation. Several genetic maps have been constructed for Brassica species, yet to date, there has been no simple means to compare this information or to associate mapped traits with the genome sequence of the related model plant, Arabidopsis.DescriptionWe 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 .ConclusionThis 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.
Highlights
Molecular genetic maps provide a means to link heritable traits with underlying genome sequence variation
Molecular genetic mapping has been applied for several Brassica species with identification of genomic regions and molecular genetic markers associated with heritable traits
Molecular marker information was processed within the BASC MarkerQTL database as described in Erwin et al [14], and genetic positions integrated within the comparative map database
Summary
Brassica species represent important crops providing a major source of cooking oil, vegetables and condiments across many countries [1,2]. In a more recent study by Parkin et al [11], syntenic blocks were identified covering almost 90% of the mapped length of the B. napus genome. CMap is one of the more powerful tools for viewing and comparing genetic maps and has been applied successfully for comparison of genetic maps within and between related grass species [12,13]. We have identified candidate loci within the sequenced genome of Arabidopsis corresponding to Brassica genetic markers enabling the linkage between mapped Brassica traits and candidate genes in Arabidopsis. The Brassica comparative mapping tool is publicly available and integrated with a custom marker and trait database as well as an EnsEMBL based Arabidopsis genome viewer [14]. A syntenic block requires a minimum correspondence between 4 mapped loci within 20 cM in Brassica to 4 regions within 4 Mb in Arabidopsis
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