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.

中文翻译：

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全基因组关联研究查明了非洲水稻 Oryza glaberrima 的关键农艺 QTL。

背景

非洲水稻（Oryza glaberrima）是水稻种植和提高生物和非生物抗性特性的宝贵资源。自从它在尼日尔三角洲内陆驯化以来，大约。距今 2500 年前，非洲稻米已经在多个生态和气候多样化的地区定居。然而，人们对该物种数量性状的遗传基础和农业利益的适应性变异知之甚少。

结果

我们使用 163 个完全重新测序的种质的参考集，报告了针对非洲水稻进行的全基因组关联研究的结果。我们研究了一系列不同的性状，包括开花日期、穗结构和对水稻黄斑驳病毒的抗性。为此，我们设计了一个使用互补统计关联方法的管道。首先，使用开花时间作为目标性状，我们发现了几个关联峰，其中一个与亚洲水稻开花途径中一个已被充分描述的基因OsGi共定位，并确定了值得更多研究的新基因组区域。然后，我们将我们的流程应用于穗和抗性相关性状，突出显示一些有趣的基因组区域和候选基因。最后，利用高分辨率气候数据库，我们进行了基于气候变量的关联分析，寻找可能参与适应气候变化的基因组区域。

结论

我们的结果共同提供了关于适应性变异在多大程度上受O. glaberrima基因组内序列多样性控制的见解，为深入研究可能对水稻育种界有用的感兴趣性状的遗传基础铺平了道路。