Phaseolus beans (navy and black beans; great northern, small red, and pinto beans; red kidney, yellow or azufrado, and cranberrry or borlotto beans; green or stringless beans) represent the most important legume species for direct human consumption. They fulfill an important role in human nutrition as a source of protein, fibers, minerals, and vitamins. They also include a much-needed complement in rotations and cropping systems as a source of nitrogen (Broughton et al. 2003).
Why a genetic and genome database for Phaseolus? Bean breeders were among the early adopters of marker technology to facilitate the mapping and transfer of genes of agronomic interest, particularly disease resistance (e.g., Haley et al. 1993, Miklas et al. 1993; Nodari et al. 1993).
Since then, bean breeders have added many additional markers to their toolbox (Kelly et al. 2003; Miklas et al. 2006), but the results and information have remained dispersed among journals, databases and, yes, laboratory notebooks and cabinets. Furthermore, the lack of DNA sequences has limited the development of additional markers.
In recent years, additional tools and sources of genomic information about the bean genome have become available, including molecular linkage maps, EST collections, BAC libraries, a physical map, and, soon, a whole-genome sequence for Phaseolus vulgaris (McClean et al. 2008, Gepts et al. 2008).
Concurrently, genomics efforts are well under way in other species, including legume species (soybean, lotus and Medicago). Using DNA as the lingua franca of genetics, results such as gene location and expression of individual and their phenotypes can be extrapolated for mutual gene discovery.
These additional genomic resources, especially the mapped sequences, provide an exciting opportunity to design additional markers that complement the existing markers and speed up the application of genomic information to bean breeding.
The main goals of this genome and genetic database are to facilitate the use of existing markers and the development of new markers by breeders (“bean breeder's marker toolbox”), to associate genetic and phenotypic information useful to breeders. to coordinate information with other legume databases (especially soybean), and, eventually, to assure its integration into the Legume Information System.
We are grateful to our funders, the Kirkhouse Trust in the U.K., who provided the impetus for this database, specifically in support of the African Bean Consortium project to introduce the capability for marker-assisted selection (MAS) among East African bean breeders. The MAS effort will focus specifically on five diseases: BCNV/BCMNV, anthracnose, angular leafspot, common bacterial blight, and Pythium root rot. A 1x sequencing of the methyl-filtrated bean genome DNA will provide much-needed additional sequence resources.
The BeanCAP project, funded by USDA/NIFA will strengthen the PhaseolusGenes database by integration of the Phaseolus whole-genome sequence developed by Purdue University and the Joint Genome Institute of the Department of Energy; SNP, CAPS, and dCAPS markers; and phenotypic information related to field performance and nutritional quality traits, from the main U.S. market classes.