SolRgene
Data source of accessions
The current database version contains information from 1062 accessions, obtained from different genebanks, i.e. the The Dutch-German Potato Collection at the Centre for Genetic Resources The Netherlands (CGN), The Commonwealth Potato Collection (CPC), The Groß Lüsewitz Potato Collecion (GLKS), The potato Collection of the Vavilov Institute (VIR), The Potato Collection of the International Potato Center (CIP), and The US Potato Genebank (NRS). Accessions were originally collected from 14 countries form South and Central America, i.e. Argentina, Bolivia, Brazil, Chile, Colombia, Costa Rica, Equador, Guatemala, Mexico, Paraguay, Peru, USA, Uruguay and Venezuela, and geographical collection data are all included. The accessions represent 197 Solanum species, belonging to Solanum section Petota and a few outgroup species. The prevalence of 15 R genes or QTL is analyzed in the plant collection, with links to published papers.
Resistance in genotypes
From each accession, on average five genotypes were accessed, and the data of 4867 wild Solanum genotypes were stored independently in the database. Resistance data were generated using three different inoculation methods, i.e. in vitro, detached leaf, or field trial, and with four P. infestans isolates, i.e. 90128, IPOC, 88069, and H30P04, the reference isolate of the P. infestans genome sequence. Pages explaining the disease assessment protocols supported with photographs are included. The graphical representation of the resistance data is facilitating a quick overview. The majority of the wild Solanum (3965 genotypes) were tested with isolate 90128 in the high throughput in vitro inoculation assay on vitro plants. Part of the genotypes were tested in a routine detached leaf assay in the laboratory with isolate 90128 (1345 genotypes) as well as isolate IPO-C (997 genotypes). Solanum genotypes were also tested in field trials in 2005 (812 genotypes) and 2007 (513 genotypes) with P. infestans isolate IPO-C. From the field trail, 694 photographic images displaying symptoms of 362 genotypes, are presented, including two time lapse overviews showing the progress of the disease in the field. Altogether, this results in generally 5 major sets of quantitative resistance data on the wild Solanum genotypes, and also averages are presented. In addition, 7602 offspring genotypes were assessed for P. infestans resistance and these data are also stored in the database, as well as the 1042 sexual crosses that were generated. The offspring genotypes were generally tested with the detached leaves, with P. infestans isolate 90128, IPO-C, 88069 and/or H30P04, and provide information for segregation of late blight R genes.
Phylogeny
Previously, we constructed a neighbor-joining (NJ) tree for 4929 genotypes. In this resource, we offer the interactive, searchable version of this NJ tree. The different groups, in the tree, can be highlighted using the three letter coded species codes. In addition, a NJ jackknife and a MP jackknife tree was calculated. Due to practical reasons, a condensed dataset was created consisting of one representative genotype from each available accession. Polytomy across large parts of both thees were shown. Some structure is still visible in both trees, supported by jackknife values above 69. We use these branches with > 69 jackknife support in the NJ jackknife tree as a basis for informal species groups. The informal species groups recognized are: Mexican diploids, Acaulia, Iopetala, Longipedicellata, polyploid Conicibaccata, diploid Conicibaccata, Circaeifolia, diploid Piurana and tetraploid Piurana. Information about these species groups and sub-groups are stored in the database.
R gene sequences
Allele-mining studies for the Rpi-vnt1 and R2 late blight resistance genes were performed on the SolRgene collection. Included are obtained sequences in FASTA format, and functional genes among the RGH link to Genbank at NCBI. Sequences can easily be selected and obtained in FASTA format.
Database and web application
SolRgene has been designed for simple and efficient data retrieval. It is composed of two major components: a relational database created using MySQL 5.1 and a web application which is implemented with PHP 5.2.6. The web interface runs on the Apache 2 Web server and is housed on a Debian lenny linux server. The PHP scripts dynamically execute complex SQL queries to retrieve data from the database according to user criteria. HTML output, formatted using CSS style sheets, is generated to display results to the end-users. The MySQL database schema is segmented into six main entities: Accession information, Genotype information, Population information, experiment information, disease observations and allele mining (Figure 1.) Supporting tables were implemented to store e.g. information about availability of one accession among multiple databases and availability of a genotype in vitro. Photos of many of the accessions are also stored. Hyperlinks to Google Scholar are provided for obtaining additional information about each accession/genotype, while the Google Earth API is used to show the original collection site of the accession/ group of selected accessions. All stored data is publicly accessible, so no authentication mechanism is build into the website.