Genome-wide association mapping of root traits in a japonica rice panel

Courtois Brigitte, Audebert Alain, Dardou Audrey, Roques Sandrine, Ghneim Thaura, Droc Gaëtan, Frouin Julien, Rouan Lauriane, Gozé Eric, Kilian Andrzej, Ahmadi Nourollah, Dingkuhn Michaël. 2013. Genome-wide association mapping of root traits in a japonica rice panel. PloS One, 8 (11):e78037, 18 p.

Journal article ; Article de revue à facteur d'impact Revue en libre accès total
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Thème(s) HCERES des revues (en SHS) : Psychologie-éthologie-ergonomie; Staps

Abstract : Rice is a crop prone to drought stress in upland and rainfed lowland ecosystems. A deep root system is recognized as the best drought avoidance mechanism. Genome-wide association mapping offers higher resolution for locating quantitative trait loci (QTLs) than QTL mapping in biparental populations. We performed an association mapping study for root traits using a panel of 167 japonica accessions, mostly of tropical origin. The panel was genotyped at an average density of one marker per 22.5 kb using genotyping by sequencing technology. The linkage disequilibrium in the panel was high (r2>0.6, on average, for 20 kb mean distances between markers). The plants were grown in transparent 50 cm × 20 cm × 2 cm Plexiglas nailboard sandwiches filled with 1.5 mm glass beads through which a nutrient solution was circulated. Root system architecture and biomass traits were measured in 30- day-old plants. The panel showed a moderate to high diversity in the various traits, particularly for deep (below 30 cm depth) root mass and the number of deep roots. Association analyses were conducted using a mixed model involving both population structure and kinship to control for false positives. Nineteen associations were significant at P<1e-05, and 78 were significant at P<1e-04. The greatest numbers of significant associations were detected for deep root mass and the number of deep roots, whereas no significant associations were found for total root biomass or deep root proportion. Because several QTLs for different traits were co-localized, 51 unique loci were detected; several colocalized with meta-QTLs for root traits, but none co-localized with rice genes known to be involved in root growth. Several likely candidate genes were found in close proximity to these loci. Additional work is necessary to assess whether these markers are relevant in other backgrounds and whether the genes identified are robust candidates. (Résumé d'auteur)

Mots-clés Agrovoc : Oryza sativa, Carte génétique, Génome, Phénotype, Locus des caractères quantitatifs, Système racinaire, Profondeur, Stress dû à la sécheresse, Résistance à la sécheresse

Mots-clés complémentaires : QTL

Classification Agris : F30 - Plant genetics and breeding
F50 - Plant structure
H50 - Miscellaneous plant disorders

Champ stratégique Cirad : Axe 1 (2005-2013) - Intensification écologique

Auteurs et affiliations

  • Courtois Brigitte, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0003-2118-7102
  • Audebert Alain, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0002-5822-7166
  • Dardou Audrey, CIRAD-BIOS-UMR AGAP (FRA)
  • Roques Sandrine, CIRAD-BIOS-UMR AGAP (FRA)
  • Ghneim Thaura, Universidad Icesi (COL)
  • Droc Gaëtan, CIRAD-BIOS-UMR AGAP (FRA)
  • Frouin Julien, CIRAD-BIOS-UMR AGAP (FRA)
  • Rouan Lauriane, CIRAD-BIOS-UMR AGAP (FRA)
  • Gozé Eric, CIRAD-PERSYST-UPR SCA (FRA) ORCID: 0000-0001-9121-7835
  • Kilian Andrzej, Diversity Arrays Technology (AUS)
  • Ahmadi Nourollah, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0003-0072-6285
  • Dingkuhn Michaël, CIRAD-BIOS-UMR AGAP (PHL)

Source : Cirad - Agritrop (

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