Cubry Philippe, Pidon Hélène, Ta Kim Nhung, Tranchant-Dubreuil Christine, Thuillet Anne-Céline, Holzinger Maria, Adam Hélène, Kam Honoré, Chrestin Harold, Ghesquière Alain, François Olivier, Sabot François, Vigouroux Yves, Albar Laurence, Jouannic Stefan
DIADE, Univ Montpellier, IRD, Montpellier, France.
Present address: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.
Rice (N Y). 2020 Sep 16;13(1):66. doi: 10.1186/s12284-020-00424-1.
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.
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.
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.
非洲栽培稻（Oryza glaberrima）是水稻种植以及改善生物和非生物抗性特性的宝贵资源。自约2500年前在尼日尔河内陆三角洲驯化以来，非洲栽培稻已在各种生态和气候多样的地区繁衍。然而，对于该物种数量性状的遗传基础以及具有农业价值的适应性变异知之甚少。
我们使用一组由163份经过全基因组重测序的材料组成的参考集，报告了针对非洲栽培稻开展的全基因组关联研究结果。我们研究了一系列不同的性状，包括开花期、穗部形态以及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流程。首先，以开花时间作为目标性状，我们发现了几个关联峰，其中一个与亚洲栽培稻开花途径中一个已充分描述的基因OsGi共定位，并鉴定出了一些值得进一步研究的新基因组区域。然后，我们将我们的流程应用于穗部和抗性相关性状，突出了一些有趣的基因组区域和候选基因。最后，我们使用一个高分辨率气候数据库，基于气候变量进行了关联分析，寻找可能参与适应气候变化的基因组区域。
我们的结果共同揭示了非洲栽培稻基因组内序列多样性对适应性变异的影响程度，为深入研究可能对水稻育种群体有用的目标性状的遗传基础铺平了道路。
