Rice
Background
Rice is the major staple food for more than half of the world population. Rice belongs to the Poaceae family. Because of the small size of its genome (390 Mb) and simple genetics (diploid crop with n=12) and the availability of vast genetic and molecular resources, it has long been the model crop for the Monocot species. The genome of the cultivated species Oryza sativa has been sequenced twice in 2005 using a mapi-based method (cultivari Nipponbare) or a whole genome shot gun method (cultivar 93-11), followed by the sequencing of the genome of the other cultivated species O. glaberrima and some wild species of the same genus. In parallel, the genome of hundred of rice accessions have been sequenced and realigned on the Nipponbare sequence giving access to millions of SNPs. Comparative genomics, notably in cereals, offers additional clues to the function of candidate sequences by allowing the reciprocal transfer of information accumulated in other related species to and from rice.
Link between South Green and Rice
The platform hosts two dedicated databases OryGenesDB for flanking sequence tag and OryzaTagLine, for phenotypic and reporter gene expression data.
South Green hosts OryGenesDB, which is a database developed for rice reverse genetics where a genome browser enables to look at the two sequenced genome of Nipponbare and 93-11. It offers several tools (blast, primer designer, primer verification, sequence or gene extraction, etc.). OryGenesDB contains the FSTs (flanking sequence tags) of mutants from international collections that can be used for functional genomics, notably the rice insertion lines developed by CIRAD in the framework of a Génoplante project.
South Green hosts OryzaTagLine, a searchable database integrating phenotypic data resulting from the evaluation of the Génoplante rice insertion line library. The phenotypic characterization involves description of morpho-physiological modifications observed on the mutants and results of GUS/GFP expression assays. Oryza Tag Line is linked to OryGenesDB by a GGB-derived interface and can display the sequence information of the FSTs .
South Green hosts GreenPhylDB, a web resource designed for comparative and functional genomics in plants that contains a catalogue of gene families based on complete genomes. The database was initially constructed to enable comparisons between rice and /Arabidopsis/ genomes and assess orthology relationships but has since be extended to other sequenced genomes.
South Green hosts the rice module of TropGeneDB in which are stored the information on genetic analyses conducted in the framework of various international projects such as EURIGEN, EURoot, Orytage or Haploryza. It gives access to passport data on rice accessions, genetic markers, genetic maps, list of QTLs and metaQTLs, large scale genotyping and phenotypic data or genes. The information can be downloaded or browsed (for the smallest datasets).
