18Background 19 African rice, Oryza glaberrima, is an invaluable resource for rice cultivation and for the improvement of biotic and 20 abiotic resistance properties. Since its domestication in the inner Niger delta ca. 2500 years BP, African rice has 21 colonized a variety of ecologically and climatically diverse regions. However, little is known about the genetic basis of 22 quantitative traits and adaptive variation of agricultural interest for this species. 23
Results 24Using a reference set of 163 fully re-sequenced accessions, we report the results of a Genome Wide Association Study 25 carried out for African rice. We investigated a diverse panel of traits, including flowering date, panicle architecture and 26 resistance to Rice yellow mottle virus. For this, we devised a pipeline using complementary statistical association 27 methods. First, using flowering time as a target trait, we demonstrated that we could successfully retrieve known genes 28 from the rice flowering pathway, and identified new genomic regions that would deserve more study. Then we applied 29 our pipeline to panicle-and resistance-related traits, highlighting some interesting QTLs and candidate genes (including 30Rymv1 for resistance and SP1, Ghd7.1, APO1 and OsMADS1 for panicle architecture). Lastly, using a high-resolution 31 climate database, we performed an association analysis based on climatic variables, searching for genomic regions that 32 might be involved in adaptation to climatic variations. 33
Conclusion 34Our results collectively provide insights into the extent to which adaptive variation is governed by sequence diversity 35 within the O. glaberrima genome, paving the way for in-depth studies of the genetic basis of traits of interest that might 36 be useful to the rice breeding community. 37 38