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

Rice

Anne-Céline Thuillet¹  Laurence Albar¹  Philippe Cubry¹  Harold Chrestin¹  Maria Holzinger¹  François Sabot¹  Hélène Adam¹  Yves Vigouroux¹  Christine Tranchant-Dubreuil¹  Alain Ghesquière¹  Stefan Jouannic²  Hélène Pidon³  Honoré Kam⁴  Kim Nhung Ta⁵  Olivier François⁶ 

[1]DIADE, Univ Montpellier, IRD, Montpellier, France

[2]DIADE, Univ Montpellier, IRD, Montpellier, France

[3]LMI RICE, AGI, IRD, Univ Montpellier, CIRAD, USTH, Hanoi, Vietnam

[4]DIADE, Univ Montpellier, IRD, Montpellier, France

[5]Present address: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany

[6]INERA, Bobo Dioulasso, Burkina Faso

[7]LMI RICE, AGI, IRD, Univ Montpellier, CIRAD, USTH, Hanoi, Vietnam

[8]Present address: National Institute of Genetics, Mishima, Shizuoka, Japan

[9]Université Grenoble-Alpes, Centre National de la Recherche Scientifique, Grenoble, France

关键词: African rice;    Genome wide association study;    Flowering time;    Panicle architecture;    RYMV;    Climate variation;   

DOI  :  10.1186/s12284-020-00424-1

来源: Springer

【 摘 要 】

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 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.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.

【 授权许可】

CC BY