Genome Wide Association Study Pinpoints Key Agronomic QTLs in African Rice Oryza glaberrima - Archive ouverte HAL Access content directly
Journal Articles Rice Year : 2020

Genome Wide Association Study Pinpoints Key Agronomic QTLs in African Rice Oryza glaberrima

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Philippe Cubry
Hélène Pidon
  • Function : Author
Kim Nhung Ta
  • Function : Author
Christine Tranchant-Dubreuil
  • Function : Author
Anne-Céline Thuillet
  • Function : Author
Maria Holzinger
  • Function : Author
Hélène Adam
  • Function : Author
Honoré Kam
  • Function : Author
Harold Chrestin
  • Function : Author
Alain Ghesquière
  • Function : Author
Olivier François
François Sabot
  • Function : Author
Yves Vigouroux
Laurence Albar
Stefan Jouannic


Abstract 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.

Dates and versions

hal-03289676 , version 1 (18-07-2021)



Philippe Cubry, Hélène Pidon, Kim Nhung Ta, Christine Tranchant-Dubreuil, Anne-Céline Thuillet, et al.. Genome Wide Association Study Pinpoints Key Agronomic QTLs in African Rice Oryza glaberrima. Rice, 2020, 13 (1), ⟨10.1186/s12284-020-00424-1⟩. ⟨hal-03289676⟩
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