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Open Access Highly Accessed Database

AlliumMap-A comparative genomics resource for cultivated Allium vegetables

John McCallum1*, Samantha Baldwin1, Masayoshi Shigyo2, Yanbo Deng3, Sjaak van Heusden4, Meeghan Pither-Joyce1 and Fernand Kenel1

Author Affiliations

1 The New Zealand Institute for Plant & Food Research Ltd, Christchurch, Private Bag 4704, New Zealand

2 Department of Biological and Environmental Sciences, Faculty of Agriculture, Yamaguchi University, 1677-1 Yoshida, Yamaguchi-shi, Yamaguchi 753-8515, Japan

3 Applied Computing Group, Faculty of Environment, Society and Design, PO Box 84, Lincoln University, Lincoln, 7647, New Zealand

4 Wageningen University and Research Centre, Postbus 16, 6700 AA, Wageningen, Netherlands

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BMC Genomics 2012, 13:168  doi:10.1186/1471-2164-13-168

Published: 4 May 2012

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 webcite. 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.