Background African rice, Oryza glaberrima, is an invaluable resource for rice cultivation and for the improvement of biotic and abiotic resistance properties. Since its domestication in the inner Niger delta ca. 2500 years BP, African rice has colonized a variety of ecologically and climatically diverse regions. However, little is known about the genetic basis of quantitative traits and adaptive variation of agricultural interest for this species. Results Using a reference set of 163 fully re-sequenced accessions, we report the results of a Genome Wide Association Study carried out for African rice. We investigated a diverse panel of traits, including flowering date, panicle architecture and resistance to Rice yellow mottle virus. For this, we devised a pipeline using complementary statistical association methods. First, using flowering time as a target trait, we found several association peaks, one of which co-localised with a well described gene in the Asian rice flowering pathway, OsGi, and identified new genomic regions that would deserve more study. Then we applied our pipeline to panicle- and resistance-related traits, highlighting some interesting genomic regions and candidate genes. Lastly, using a high-resolution climate database, we performed an association analysis based on climatic variables, searching for genomic regions that might be involved in adaptation to climatic variations. Conclusion Our results collectively provide insights into the extent to which adaptive variation is governed by sequence diversity within the O. glaberrima genome, paving the way for in-depth studies of the genetic basis of traits of interest that might be useful to the rice breeding community.

In order to evaluate genetic variability of agro-morphological traits and also determine the correlation between grain yield with its components in rice lines, 17 recombinants inbred lines, their parents and a check variety were grown in research station of Africa rice center in Benin republic during two consecutive years 2013 and 2014. The experiments were laid out in a randomized complete block design with four replications. Phenotypic coefficients of variance were higher than genotypic coefficients of variance in all the characters across the two years. High heritability in broad sense (H 2 ) estimates were obtained for biomass (68.77%), date of 50% flowering (98.11%), plant height (81.94%), leaf area (82.90%), number of panicles (64.40%), leaf dry weight (72.91%), root weight (67.43%) and yield/plant (62.23%) suggesting that the traits were primarily under genetic control. A joint consideration of broad sense heritability (H 2 ) and genetic advance as per cent mean expected (GAM) revealed that leaves dries weight and roots weight combined high heritability and high GAM. Furthermore, high (H 2 ) and high GAM recorded in these characters could be explained by additive gene action. However, high estimates (H 2 ) combined with moderate GAM recorded for biomass, day to 50% flowering, leaf area, number of panicle and yield/plant could be due to non-additive gene effect. Grain yield/plant recorded positive and significant correlation with stem weight (r=0.5262) and biomass (r=0.9291). This result indicates that selection based on these two characters will be highly effective for yield improvement in rice.

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

The genetic diversity of cultivated rice in farmers’ fields remains understudied in West Africa despite the importance of rice for food security in this region. In this study, we genotyped rice samples from Burkina Faso using the C6AIR SNP (Single Nucleotide Polymorphism) array (IRRI), including 27 registered cultivars and 50 rice samples collected in rice fields from three geographical zones in western Burkina Faso. Most of the registered cultivars clustered with the indica genetic group, except seven assigned to japonica and one admix. All but one of the rice samples from farmers’ fields belonged to the indica group. The other field sample, which unexpectedly clustered with the Aus genetic group, originated from a rainfed lowland site known to differ in terms of agronomic practices, and which revealed to be highly differentiated from the five other sites. Apart from this peculiar site, the rice grown in irrigated areas did not differ from rice sampled in rainfed lowlands. Finally, obtained genetic data confirmed the high frequency of one cultivar, in congruence with farmers’ interviews. We argue on the importance to document and preserve the high agro-biodiversity observed in rice from Burkina Faso as a prerequisite to face the current challenges of growing rice demand and global change.

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