Rice is considered as a crop sensitive to salinity; however, it is grown mainly in deltaic areas with salt problems all over Europe. European rice breeding programs (France, Greece, Italy, Portugal and Spain) have established an European Rice Genetic Resources Collection (ERGRC) of some 450 accessions, mainly temperate japonica, extensively characterised for agronomic traits and maintained by CIRAD. The main goal of the present study is to identify within this collection, a set of best performing genes and alleles for salinity tolerance, as well as the associated donors and molecular markers for use in breeding programs. In order to obtain the general organisation structure of the ERGRC we assessed its genetic diversity through a Bayesian analysis of genotypic data over 26 SSR loci. A sub-sample of 200 accessions maximizing simultaneously allele number and allelic associations was then extracted for association analysis. The sub-sample was phenotyped for salinity tolerance at an early vegetative stage under controlled conditions, being leaf Na+/K+ ratio the most discriminating trait. Based on literature review, we assembled a list with more than 100 rice candidate genes for salt tolerance, which are involved in signaling, ion homeostasis, stress tolerance, transcription regulation, general metabolism and unknown functions. With this information, we developed a database of rice QTLs and candidate genes for salinity tolerance (http://tropgenedb.cirad.fr/html/rice_QTL.html). We selected 16 of these candidate genes for association analysis. SSR markers were used for the association analysis. A first set of 58 common SSR (www.gramene.org) covering these particular genes was used. In addition, we designed 320 SSR markers covering 100 kb up and downstream each candidate gene. In the end, we selected four of the designed SSR markers, the two closest to the gene and one in each end of the linkage disequilibrium region (100 kb each gene side). Results of association analysis