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. 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.
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Subjects: | F30 - Génétique et amélioration des plantes, F50 - Anatomie et morphologie des plantes, H50 - Troubles divers des plantes, Oryza sativa, carte génétique, génome, phénotype, locus des caractères quantitatifs, système racinaire, profondeur, stress dû à la sécheresse, résistance à la sécheresse, http://aims.fao.org/aos/agrovoc/c_5438, http://aims.fao.org/aos/agrovoc/c_24002, http://aims.fao.org/aos/agrovoc/c_3224, http://aims.fao.org/aos/agrovoc/c_5776, http://aims.fao.org/aos/agrovoc/c_37974, http://aims.fao.org/aos/agrovoc/c_16034, http://aims.fao.org/aos/agrovoc/c_2190, http://aims.fao.org/aos/agrovoc/c_24993, http://aims.fao.org/aos/agrovoc/c_2392, |
Online Access: | http://agritrop.cirad.fr/571207/ http://agritrop.cirad.fr/571207/1/document_571207.pdf |
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dig-cirad-fr-5712072024-01-28T21:43:12Z http://agritrop.cirad.fr/571207/ http://agritrop.cirad.fr/571207/ 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. PloS One, 8 (11):e78037, 18 p.https://doi.org/10.1371/journal.pone.0078037 <https://doi.org/10.1371/journal.pone.0078037> 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 eng 2013 PloS One F30 - Génétique et amélioration des plantes F50 - Anatomie et morphologie des plantes H50 - Troubles divers des plantes Oryza sativa carte génétique génome phénotype locus des caractères quantitatifs système racinaire profondeur stress dû à la sécheresse résistance à la sécheresse http://aims.fao.org/aos/agrovoc/c_5438 http://aims.fao.org/aos/agrovoc/c_24002 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_5776 http://aims.fao.org/aos/agrovoc/c_37974 http://aims.fao.org/aos/agrovoc/c_16034 http://aims.fao.org/aos/agrovoc/c_2190 http://aims.fao.org/aos/agrovoc/c_24993 http://aims.fao.org/aos/agrovoc/c_2392 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. article info:eu-repo/semantics/article Journal Article info:eu-repo/semantics/publishedVersion http://agritrop.cirad.fr/571207/1/document_571207.pdf application/pdf Cirad license info:eu-repo/semantics/openAccess https://agritrop.cirad.fr/mention_legale.html https://doi.org/10.1371/journal.pone.0078037 10.1371/journal.pone.0078037 info:eu-repo/semantics/altIdentifier/doi/10.1371/journal.pone.0078037 info:eu-repo/semantics/altIdentifier/purl/https://doi.org/10.1371/journal.pone.0078037 |
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F30 - Génétique et amélioration des plantes F50 - Anatomie et morphologie des plantes H50 - Troubles divers des plantes Oryza sativa carte génétique génome phénotype locus des caractères quantitatifs système racinaire profondeur stress dû à la sécheresse résistance à la sécheresse http://aims.fao.org/aos/agrovoc/c_5438 http://aims.fao.org/aos/agrovoc/c_24002 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_5776 http://aims.fao.org/aos/agrovoc/c_37974 http://aims.fao.org/aos/agrovoc/c_16034 http://aims.fao.org/aos/agrovoc/c_2190 http://aims.fao.org/aos/agrovoc/c_24993 http://aims.fao.org/aos/agrovoc/c_2392 F30 - Génétique et amélioration des plantes F50 - Anatomie et morphologie des plantes H50 - Troubles divers des plantes Oryza sativa carte génétique génome phénotype locus des caractères quantitatifs système racinaire profondeur stress dû à la sécheresse résistance à la sécheresse http://aims.fao.org/aos/agrovoc/c_5438 http://aims.fao.org/aos/agrovoc/c_24002 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_5776 http://aims.fao.org/aos/agrovoc/c_37974 http://aims.fao.org/aos/agrovoc/c_16034 http://aims.fao.org/aos/agrovoc/c_2190 http://aims.fao.org/aos/agrovoc/c_24993 http://aims.fao.org/aos/agrovoc/c_2392 |
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F30 - Génétique et amélioration des plantes F50 - Anatomie et morphologie des plantes H50 - Troubles divers des plantes Oryza sativa carte génétique génome phénotype locus des caractères quantitatifs système racinaire profondeur stress dû à la sécheresse résistance à la sécheresse http://aims.fao.org/aos/agrovoc/c_5438 http://aims.fao.org/aos/agrovoc/c_24002 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_5776 http://aims.fao.org/aos/agrovoc/c_37974 http://aims.fao.org/aos/agrovoc/c_16034 http://aims.fao.org/aos/agrovoc/c_2190 http://aims.fao.org/aos/agrovoc/c_24993 http://aims.fao.org/aos/agrovoc/c_2392 F30 - Génétique et amélioration des plantes F50 - Anatomie et morphologie des plantes H50 - Troubles divers des plantes Oryza sativa carte génétique génome phénotype locus des caractères quantitatifs système racinaire profondeur stress dû à la sécheresse résistance à la sécheresse http://aims.fao.org/aos/agrovoc/c_5438 http://aims.fao.org/aos/agrovoc/c_24002 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_5776 http://aims.fao.org/aos/agrovoc/c_37974 http://aims.fao.org/aos/agrovoc/c_16034 http://aims.fao.org/aos/agrovoc/c_2190 http://aims.fao.org/aos/agrovoc/c_24993 http://aims.fao.org/aos/agrovoc/c_2392 Courtois, Brigitte Audebert, Alain Dardou, Audrey Roques, Sandrine Ghneim, Thaura Droc, Gaëtan Frouin, Julien Rouan, Lauriane Gozé, Eric Kilian, Andrzej Ahmadi, Nourollah Dingkuhn, Michaël 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 (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. |
format |
article |
topic_facet |
F30 - Génétique et amélioration des plantes F50 - Anatomie et morphologie des plantes H50 - Troubles divers des plantes Oryza sativa carte génétique génome phénotype locus des caractères quantitatifs système racinaire profondeur stress dû à la sécheresse résistance à la sécheresse http://aims.fao.org/aos/agrovoc/c_5438 http://aims.fao.org/aos/agrovoc/c_24002 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_5776 http://aims.fao.org/aos/agrovoc/c_37974 http://aims.fao.org/aos/agrovoc/c_16034 http://aims.fao.org/aos/agrovoc/c_2190 http://aims.fao.org/aos/agrovoc/c_24993 http://aims.fao.org/aos/agrovoc/c_2392 |
author |
Courtois, Brigitte Audebert, Alain Dardou, Audrey Roques, Sandrine Ghneim, Thaura Droc, Gaëtan Frouin, Julien Rouan, Lauriane Gozé, Eric Kilian, Andrzej Ahmadi, Nourollah Dingkuhn, Michaël |
author_facet |
Courtois, Brigitte Audebert, Alain Dardou, Audrey Roques, Sandrine Ghneim, Thaura Droc, Gaëtan Frouin, Julien Rouan, Lauriane Gozé, Eric Kilian, Andrzej Ahmadi, Nourollah Dingkuhn, Michaël |
author_sort |
Courtois, Brigitte |
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 |
url |
http://agritrop.cirad.fr/571207/ http://agritrop.cirad.fr/571207/1/document_571207.pdf |
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_version_ |
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