AlliumMap-A comparative genomics resource for cultivated <it>Allium</it> vegetables

• Main Authors: McCallum John, Baldwin Samantha, Shigyo Masayoshi, Deng Yanbo, van Heusden Sjaak, Pither-Joyce Meeghan, Kenel Fernand
• Format: Article
• Language: English
• Published: BMC 2012-05-01
• Series: BMC Genomics
• Online Access: http://www.biomedcentral.com/1471-2164/13/168

<p>Abstract</p> <p>Background</p> <p>Vegetables of the genus <it>Allium</it> are widely consumed but remain poorly understood genetically. Genetic mapping has been conducted in intraspecific crosses of onion (<it>Allium cepa</it> L.), <it>A. fistulosum</it> and interspecific crosses between <it>A. roylei</it> and these two species, but it has not been possible to access genetic maps and underlying data from these studies easily.</p> <p>Description</p> <p>An online comparative genomics database, AlliumMap, has been developed based on the GMOD CMap tool at <url>http://alliumgenetics.org</url>. It has been populated with curated data linking genetic maps with underlying markers and sequence data from multiple studies. It includes data from multiple onion mapping populations as well as the most closely related species <it>A. roylei</it> and <it>A. fistulosum</it>. Further onion EST-derived markers were evaluated in the <it>A. cepa</it> x <it>A. roylei</it> interspecific population, enabling merging of the AFLP-based maps. In addition, data concerning markers assigned in multiple studies to the <it>Allium</it> physical map using <it>A. cepa</it>-<it>A. fistulosum</it> alien monosomic addition lines have been compiled. The compiled data reveal extensive synteny between onion and <it>A. fistulosum</it>.</p> <p>Conclusions</p> <p>The database provides the first online resource providing genetic map and marker data from multiple <it>Allium</it> species and populations. The additional markers placed on the interspecific <it>Allium</it> map confirm the value of <it>A. roylei</it> as a valuable bridge between the genetics of onion and <it>A. fistulosum</it> and as a means to conduct efficient mapping of expressed sequence markers in <it>Allium</it>. The data presented suggest that comparative approaches will be valuable for genetic and genomic studies of onion and <it>A. fistulosum</it>. This online resource will provide a valuable means to integrate genetic and sequence-based explorations of <it>Allium</it> genomes.</p>