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BackgroundAfrican 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.ResultsUsing 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 demonstrated that we could successfully retrieve known genes from the rice flowering pathway, and identified new genomic regions that would deserve more study. Then we applied our pipeline to panicle- and resistance-related traits, highlighting some interesting QTLs and candidate genes (including Rymv1 for resistance and SP1, Ghd7.1, APO1 and OsMADS1 for panicle architecture). 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.ConclusionOur 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.

Rice is one of the staple crops in Burkina Faso. However, the local production covers only 47% of the population demands. One of the main reasons of the poor productivity in Burkina Faso is iron toxicity which is related mainly to the activity of Iron Reducing Bacteria in the rice field’s ecosystems. In order to control the harmful effects of Iron Reducing Bacterial populations and to improve rice productivity, a pots experiment was conducted at the experimental site of the University Ouaga I Pr. Joseph KI-ZERBO. An iron toxic soil from Kou Valley (West of Burkina Faso) and two rice varieties, BOUAKE-189 and ROK-5, sensitive and tolerant to iron toxicity, respectively, were used for the experiment. The pots were drained for 14 days (D2) and amended with chemical fertilizers (NPK + Urea and NPK + Urea + Ca + Mg + Zn complexes). Control pots without drainage and fertilization (D0/NF) were prepared similarly. The kinetics of Iron Reducing Bacterial populations and ferrous iron content in soil near rice roots were monitored throughout the cultural cycle using MPN and colorimetric methods, respectively. The total iron content was evaluated in rice plant using a spectrometric method. Data obtained were analyzed in relation to drainage and fertilization mode, rice growth stage and rice yield using the Student’s t-test and XLSTAT 2014 statistical software. The experiment showed that the combined application of subsurface drainage and NPK + Urea + Ca + Mg + Zn fertilization, reduced significantly the number of IRB in the soil near rice roots for both rice varieties (p = 0.050 and p = 0.020) increased the leaf tissue tolerance to excess amounts of Fe, and rice yield.

Rice yellow mottle virus (RYMV), which is only found in Africa, threatens rice farming on the continent. A local Oryza sativa cultivar collected from Burkina Faso (named BM24), was evaluated with that of well known highly resistant and tolerant cultivars. Firstly, three RYMV isolates were used to characterise the differential interaction within the cultivars. Secondly, disease kinetics of symptom expression and virus titer on leaves at 21 days after inoculation were assessed using the BF1 isolate. Thirdly, the allelic profile of O. sativa varieties using SSR marker RM101 located on chromosome 12 was also assessed. IR64 showed susceptibility to all isolates; while Tog5681 was resistant to all isolates. Ng122 overcame the resistance of Gigante, with mild leaf symptoms at 42 dpi. Azucena and BM24 had, therefore, different resistance level regarding the three isolates (Ng117b, Ng122 and Ng144). When infected with the isolate, BF1, BM24 and Azucena exhibited same resistance patterns in early growth stages with delayed of symptoms appearance, but BM24 outperformed Azucena at later stages. The virus content in the two accessions, at 14 days post inoculation, was statistically different with BM24, showing less virus compared to Azucena. However, the two accessions depicted an identical allelic profile at RM101 locus. Key words: Azucena, Burkina Faso, local variety, Oryza sativa