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

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....

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Autores principales: Brigitte Courtois, Alain Audebert, Audrey Dardou, Sandrine Roques, Thaura Ghneim-Herrera, Gaëtan Droc, Julien Frouin, Lauriane Rouan, Eric Gozé, Andrzej Kilian, Nourollah Ahmadi, Michael Dingkuhn
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Publicado: Public Library of Science (PLoS) 2013
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spelling oai:doaj.org-article:07840b21a10743599beb7fa742db77462021-11-18T08:48:22ZGenome-wide association mapping of root traits in a japonica rice panel.1932-620310.1371/journal.pone.0078037https://doaj.org/article/07840b21a10743599beb7fa742db77462013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24223758/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Rice 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 (r(2)>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 co-localized 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.Brigitte CourtoisAlain AudebertAudrey DardouSandrine RoquesThaura Ghneim-HerreraGaëtan DrocJulien FrouinLauriane RouanEric GozéAndrzej KilianNourollah AhmadiMichael DingkuhnPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 11, p e78037 (2013)
institution DOAJ
collection DOAJ
language EN
topic Medicine
R
Science
Q
spellingShingle Medicine
R
Science
Q
Brigitte Courtois
Alain Audebert
Audrey Dardou
Sandrine Roques
Thaura Ghneim-Herrera
Gaëtan Droc
Julien Frouin
Lauriane Rouan
Eric Gozé
Andrzej Kilian
Nourollah Ahmadi
Michael Dingkuhn
Genome-wide association mapping of root traits in a japonica rice panel.
description 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 (r(2)>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 co-localized 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.
format article
author Brigitte Courtois
Alain Audebert
Audrey Dardou
Sandrine Roques
Thaura Ghneim-Herrera
Gaëtan Droc
Julien Frouin
Lauriane Rouan
Eric Gozé
Andrzej Kilian
Nourollah Ahmadi
Michael Dingkuhn
author_facet Brigitte Courtois
Alain Audebert
Audrey Dardou
Sandrine Roques
Thaura Ghneim-Herrera
Gaëtan Droc
Julien Frouin
Lauriane Rouan
Eric Gozé
Andrzej Kilian
Nourollah Ahmadi
Michael Dingkuhn
author_sort Brigitte Courtois
title Genome-wide association mapping of root traits in a japonica rice panel.
title_short Genome-wide association mapping of root traits in a japonica rice panel.
title_full Genome-wide association mapping of root traits in a japonica rice panel.
title_fullStr Genome-wide association mapping of root traits in a japonica rice panel.
title_full_unstemmed Genome-wide association mapping of root traits in a japonica rice panel.
title_sort genome-wide association mapping of root traits in a japonica rice panel.
publisher Public Library of Science (PLoS)
publishDate 2013
url https://doaj.org/article/07840b21a10743599beb7fa742db7746
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