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Genome-wide association mapping for root cone angle in rice

Bettembourg Mathilde, Dardou Audrey, Audebert Alain, Thomas Emilie, Frouin Julien, Guiderdoni Emmanuel, Ahmadi Nourollah, Perin Christophe, Dievart Anne, Courtois Brigitte. 2017. Genome-wide association mapping for root cone angle in rice. Rice, 10:45, 17 p.

Journal article ; Article de recherche ; Article de revue à facteur d'impact
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Url - jeu de données : https://figshare.com/collections/Genome-wide_association_mapping_for_root_cone_angle_in_rice/3894799

Quartile : Q1, Sujet : AGRONOMY

Abstract : Background: Plant root systems play a major role in anchoring and in water and nutrient uptake from the soil. The root cone angle is an important parameter of the root system architecture because, combined with root depth, it helps to determine the volume of soil explored by the plant. Two genes, DRO1 and SOR1, and several QTLs for root cone angle have been discovered in the last 5 years. Results: To find other QTLs linked to root cone angle, a genome-wide association mapping study was conducted on two panels of 162 indica and 169 japonica rice accessions genotyped with two sets of SNP markers (genotyping-by-sequencing set with approximately 16,000 markers and high-density-rice-array set with approximately 300,000 markers). The root cone angle of all accessions was measured using a screen protractor on images taken after 1 month of plant growth in the Rhizoscope phenotyping system. The distribution of the root cone angle in the indica panel was Gaussian, but several accessions of the japonica panel (all the bulus from Indonesia and three temperate japonicas from Nepal or India) appeared as outliers with a very wide root cone angle. The data were submitted to association mapping using a mixed model with control of structure and kinship. A total of 15 QTLs for the indica panel and 40 QTLs for the japonica panel were detected. Genes underlying these QTLs (+/−50 kb from the significant markers) were analyzed. We focused our analysis on auxin-related genes, kinases, and genes involved in root developmental processes and identified 8 particularly interesting genes. Conclusions: The present study identifies new sources of wide root cone angle in rice, proposes ways to bypass some drawbacks of association mapping to further understand the genetics of the trait and identifies candidate genes deserving further investigation. (Résumé d'auteur)

Mots-clés Agrovoc : Oryza sativa, Génome, Carte génétique, Système racinaire, Anatomie végétale, Racine, Locus des caractères quantitatifs, Marqueur génétique, Phénotype, Génétique des populations

Mots-clés complémentaires : QTL, Oryza sativa indica, Oryza sativa japonica

Classification Agris : F30 - Plant genetics and breeding
F50 - Plant structure
F61 - Plant physiology - Nutrition
U40 - Surveying methods

Champ stratégique Cirad : Axe 1 (2014-2018) - Agriculture écologiquement intensive

Agence(s) de financement européenne(s) : European Commission

Programme de financement européen : FP7

Projet(s) de financement européen(s) : Enhancing resource Uptake from Roots under stress in cereal crops

Auteurs et affiliations

Source : Cirad-Agritrop (https://agritrop.cirad.fr/586753/)

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