Oryza glaberrima is one of the two cultivated species of rice, and harbors various interesting agronomic traits, especially in biotic and abiotic resistance, compared with its Asian cousin O. sativa. A previous reference genome was published but newer studies highlighted some missing parts. Moreover, global species diversity is known nowadays to be represented by more than one single individual. For that purpose, we sequenced, assembled and annotated de novo three different cultivars from O. glaberrima. After validating our assemblies, we were able to better solve complex regions than the previous assembly and to provide a first insight in pan-genomic divergence between individuals. The three assemblies shown large common regions, but almost 25% of the genome present collinearity breakpoints or are even individual specific.

to be limited in comparison with the number of publications that report genetic linkage between markers and genes of interest. This may be explained by the delay observed in the theoretical development of a methodology and its practical outputs or absence of information on the methodology used (Collard and Mackill, 2008). Van Damme et al. (2011) hypothesize that it may result from a lack of access to the information in some developing countries and these authors therefore developed a database that synthesizes all the markers available for MAS in 19 species. Rice, the staple food of half of the world's population, has two cultivated species, Oryza sativa that originated from Asia and is cultivated worldwide, and Oryza glaberrima, which is endemic to Africa. Oryza sativa is high yielding, but lacks sources of resistance to some strains of rice diseases and insect pests specific to African rice-cropping agro-ecosystems. Conversely, O. glaberrima is low yielding, shatters spontaneously and has few panicle branches, but often constitutes a source of resistance to African pests and diseases. Some of its 'rustic' characteristics were successfully transferred into

The Africa Rice Center Gene Bank hold about 2,500 accessions of Oryza glaberrima. To understand well the genetic diversity in O. glaberrima and its wild species, the use of molecular tools is prominent. The sample consisted of 217 accessions of O. glaberrima, 46 of O. barthii and 7 of O. sativa (checks) was genotyped with 21 polymorphic microsatellites markers. A total of 245 alleles were detected with average 11.67 alleles per locus. Number of alleles was ranged from 2 (RM124) to 20 (RM536). The polymorphic information content value was 0.49 while the heterozygosity was 0.091. The result showed that the sample can be clustered into four genotypic groups. Two groups among them were homogeneous. The first one consisted of O. barthii accessions with 82 alleles in total with average 3.90 alleles per locus. However, the second one consisted of only O. glaberrima accessions with 122 alleles with average 5.80 alleles per locus. O. glaberrima accessions were analyzed using model-based population structure. Results revealed two groups among O. glaberrima accessions. At the end, the identified core collection has 26 accessions consisted of 16 O. glaberrima and 10 O. barthii based on 21 microsatellites markers.