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AlliumMap-A comparative genomics resource for cultivated Allium vegetables.

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

SUBMITTER: McCallum J

PROVIDER: S-EPMC3423043 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

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AlliumMap-A comparative genomics resource for cultivated Allium vegetables.

McCallum John J Baldwin Samantha S Shigyo Masayoshi M Deng Yanbo Y van Heusden Sjaak S Pither-Joyce Meeghan M Kenel Fernand F

BMC genomics 20120504

<h4>Background</h4>Vegetables of the genus Allium are widely consumed but remain poorly understood genetically. Genetic mapping has been conducted in intraspecific crosses of onion (Allium cepa L.), A. fistulosum and interspecific crosses between A. roylei and these two species, but it has not been possible to access genetic maps and underlying data from these studies easily.<h4>Description</h4>An online comparative genomics database, AlliumMap, has been developed based on the GMOD CMap tool at ...[more]

PMID: 22559261

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Dataset Information

AlliumMap-A comparative genomics resource for cultivated Allium vegetables.

Publications

AlliumMap-A comparative genomics resource for cultivated Allium vegetables.

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