Breeding for nitrogen use efficiency: Lessons from genomic prediction experiments based on a broad-based population of upland rice
In the context of subsistence farming in Madagascar, upland rice producers have limited access to mineral fertilizers and yields remain very low. Genetic improvement of yield through the nitrogen use efficiency (NUE) component is an avenue to be explored in breeding programs. A recent GWAS study carried out on an upland rice diversity panel allowed to detect genomic regions involved in NUE variability, nevertheless these regions explained only a moderate part of the total genetic diversity observed in the panel. We investigated the potential of genomic prediction for NUE in order to optimize our upland rice breeding program for this trait. We evaluated the predictive ability of genomic prediction using two validation experiments. The first consisted of a standard cross-validation with 5-fold subdivision of the diversity panel (DP) and the second consisted of an independent experiment involving a breeding population (BP) derived from the DP. The DP was structured into five genetic clusters of different sizes and with some degree of admixture, while the BP was composed of two main clusters. The best prediction ability for NUE was obtained in crossvalidation within the DP. The predictive ability in the independent validation experiment was weak (r = 0.25), about three times less than those obtained in the cross-validation. The low kinship between DP and BP, different genetic structures and slightly different LD patterns probably explains the low predictive ability of across populations genomic prediction. Practical implications for our rice breeding program are discussed.
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dig-cirad-fr-6001842024-08-04T16:02:22Z http://agritrop.cirad.fr/600184/ http://agritrop.cirad.fr/600184/ Breeding for nitrogen use efficiency: Lessons from genomic prediction experiments based on a broad-based population of upland rice. Rakotomalala Joël, Vom Brocke Kirsten, Frouin Julien, Pot David, Rabekijana Ravonantenaina Rhodia, Ramanantsoanirina Alain, Ratsimiala Ramonta Isabelle, Cao Tuong-Vi. 2021. Rice Research: Open Access, 9 (9):1000264, 26 p.https://doi.org/10.4172/2375-4338.1000264 <https://doi.org/10.4172/2375-4338.1000264> Breeding for nitrogen use efficiency: Lessons from genomic prediction experiments based on a broad-based population of upland rice Rakotomalala, Joël Vom Brocke, Kirsten Frouin, Julien Pot, David Rabekijana, Ravonantenaina Rhodia Ramanantsoanirina, Alain Ratsimiala Ramonta, Isabelle Cao, Tuong-Vi eng 2021 Rice Research: Open Access Oryza sativa riz pluvial amélioration des plantes génétique des populations variation génétique génotype amélioration génétique adaptation aux changements climatiques phénotype rendement des cultures génome sélection récurrente ressource génétique végétale http://aims.fao.org/aos/agrovoc/c_5438 http://aims.fao.org/aos/agrovoc/c_8076 http://aims.fao.org/aos/agrovoc/c_5956 http://aims.fao.org/aos/agrovoc/c_34326 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_3225 http://aims.fao.org/aos/agrovoc/c_49902 http://aims.fao.org/aos/agrovoc/c_1374567058134 http://aims.fao.org/aos/agrovoc/c_5776 http://aims.fao.org/aos/agrovoc/c_10176 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_27595 http://aims.fao.org/aos/agrovoc/c_37419 Madagascar http://aims.fao.org/aos/agrovoc/c_4510 In the context of subsistence farming in Madagascar, upland rice producers have limited access to mineral fertilizers and yields remain very low. Genetic improvement of yield through the nitrogen use efficiency (NUE) component is an avenue to be explored in breeding programs. A recent GWAS study carried out on an upland rice diversity panel allowed to detect genomic regions involved in NUE variability, nevertheless these regions explained only a moderate part of the total genetic diversity observed in the panel. We investigated the potential of genomic prediction for NUE in order to optimize our upland rice breeding program for this trait. We evaluated the predictive ability of genomic prediction using two validation experiments. The first consisted of a standard cross-validation with 5-fold subdivision of the diversity panel (DP) and the second consisted of an independent experiment involving a breeding population (BP) derived from the DP. The DP was structured into five genetic clusters of different sizes and with some degree of admixture, while the BP was composed of two main clusters. The best prediction ability for NUE was obtained in crossvalidation within the DP. The predictive ability in the independent validation experiment was weak (r = 0.25), about three times less than those obtained in the cross-validation. The low kinship between DP and BP, different genetic structures and slightly different LD patterns probably explains the low predictive ability of across populations genomic prediction. Practical implications for our rice breeding program are discussed. article info:eu-repo/semantics/article Journal Article info:eu-repo/semantics/publishedVersion http://agritrop.cirad.fr/600184/1/Rakotomalala%20et%20al.%20-%202021%20-%20Breeding%20for%20Nitrogen%20use%20Efficiency%20Lessons%20from.pdf text cc_by info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/ https://doi.org/10.4172/2375-4338.1000264 10.4172/2375-4338.1000264 info:eu-repo/semantics/altIdentifier/doi/10.4172/2375-4338.1000264 info:eu-repo/semantics/altIdentifier/purl/https://doi.org/10.4172/2375-4338.1000264 info:eu-repo/semantics/reference/purl/https://www.omicsonline.org/open-access/breeding-for-nitrogen-use-efficiency-lessons-from-two-genomic-predictionexperiments-within-a-broadbased-population-of-upland-rice-117421.html |
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Oryza sativa riz pluvial amélioration des plantes génétique des populations variation génétique génotype amélioration génétique adaptation aux changements climatiques phénotype rendement des cultures génome sélection récurrente ressource génétique végétale http://aims.fao.org/aos/agrovoc/c_5438 http://aims.fao.org/aos/agrovoc/c_8076 http://aims.fao.org/aos/agrovoc/c_5956 http://aims.fao.org/aos/agrovoc/c_34326 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_3225 http://aims.fao.org/aos/agrovoc/c_49902 http://aims.fao.org/aos/agrovoc/c_1374567058134 http://aims.fao.org/aos/agrovoc/c_5776 http://aims.fao.org/aos/agrovoc/c_10176 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_27595 http://aims.fao.org/aos/agrovoc/c_37419 http://aims.fao.org/aos/agrovoc/c_4510 Oryza sativa riz pluvial amélioration des plantes génétique des populations variation génétique génotype amélioration génétique adaptation aux changements climatiques phénotype rendement des cultures génome sélection récurrente ressource génétique végétale http://aims.fao.org/aos/agrovoc/c_5438 http://aims.fao.org/aos/agrovoc/c_8076 http://aims.fao.org/aos/agrovoc/c_5956 http://aims.fao.org/aos/agrovoc/c_34326 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_3225 http://aims.fao.org/aos/agrovoc/c_49902 http://aims.fao.org/aos/agrovoc/c_1374567058134 http://aims.fao.org/aos/agrovoc/c_5776 http://aims.fao.org/aos/agrovoc/c_10176 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_27595 http://aims.fao.org/aos/agrovoc/c_37419 http://aims.fao.org/aos/agrovoc/c_4510 |
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Oryza sativa riz pluvial amélioration des plantes génétique des populations variation génétique génotype amélioration génétique adaptation aux changements climatiques phénotype rendement des cultures génome sélection récurrente ressource génétique végétale http://aims.fao.org/aos/agrovoc/c_5438 http://aims.fao.org/aos/agrovoc/c_8076 http://aims.fao.org/aos/agrovoc/c_5956 http://aims.fao.org/aos/agrovoc/c_34326 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_3225 http://aims.fao.org/aos/agrovoc/c_49902 http://aims.fao.org/aos/agrovoc/c_1374567058134 http://aims.fao.org/aos/agrovoc/c_5776 http://aims.fao.org/aos/agrovoc/c_10176 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_27595 http://aims.fao.org/aos/agrovoc/c_37419 http://aims.fao.org/aos/agrovoc/c_4510 Oryza sativa riz pluvial amélioration des plantes génétique des populations variation génétique génotype amélioration génétique adaptation aux changements climatiques phénotype rendement des cultures génome sélection récurrente ressource génétique végétale http://aims.fao.org/aos/agrovoc/c_5438 http://aims.fao.org/aos/agrovoc/c_8076 http://aims.fao.org/aos/agrovoc/c_5956 http://aims.fao.org/aos/agrovoc/c_34326 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_3225 http://aims.fao.org/aos/agrovoc/c_49902 http://aims.fao.org/aos/agrovoc/c_1374567058134 http://aims.fao.org/aos/agrovoc/c_5776 http://aims.fao.org/aos/agrovoc/c_10176 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_27595 http://aims.fao.org/aos/agrovoc/c_37419 http://aims.fao.org/aos/agrovoc/c_4510 Rakotomalala, Joël Vom Brocke, Kirsten Frouin, Julien Pot, David Rabekijana, Ravonantenaina Rhodia Ramanantsoanirina, Alain Ratsimiala Ramonta, Isabelle Cao, Tuong-Vi Breeding for nitrogen use efficiency: Lessons from genomic prediction experiments based on a broad-based population of upland rice |
description |
In the context of subsistence farming in Madagascar, upland rice producers have limited access to mineral fertilizers and yields remain very low. Genetic improvement of yield through the nitrogen use efficiency (NUE) component is an avenue to be explored in breeding programs. A recent GWAS study carried out on an upland rice diversity panel allowed to detect genomic regions involved in NUE variability, nevertheless these regions explained only a moderate part of the total genetic diversity observed in the panel. We investigated the potential of genomic prediction for NUE in order to optimize our upland rice breeding program for this trait. We evaluated the predictive ability of genomic prediction using two validation experiments. The first consisted of a standard cross-validation with 5-fold subdivision of the diversity panel (DP) and the second consisted of an independent experiment involving a breeding population (BP) derived from the DP. The DP was structured into five genetic clusters of different sizes and with some degree of admixture, while the BP was composed of two main clusters. The best prediction ability for NUE was obtained in crossvalidation within the DP. The predictive ability in the independent validation experiment was weak (r = 0.25), about three times less than those obtained in the cross-validation. The low kinship between DP and BP, different genetic structures and slightly different LD patterns probably explains the low predictive ability of across populations genomic prediction. Practical implications for our rice breeding program are discussed. |
format |
article |
topic_facet |
Oryza sativa riz pluvial amélioration des plantes génétique des populations variation génétique génotype amélioration génétique adaptation aux changements climatiques phénotype rendement des cultures génome sélection récurrente ressource génétique végétale http://aims.fao.org/aos/agrovoc/c_5438 http://aims.fao.org/aos/agrovoc/c_8076 http://aims.fao.org/aos/agrovoc/c_5956 http://aims.fao.org/aos/agrovoc/c_34326 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_3225 http://aims.fao.org/aos/agrovoc/c_49902 http://aims.fao.org/aos/agrovoc/c_1374567058134 http://aims.fao.org/aos/agrovoc/c_5776 http://aims.fao.org/aos/agrovoc/c_10176 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_27595 http://aims.fao.org/aos/agrovoc/c_37419 http://aims.fao.org/aos/agrovoc/c_4510 |
author |
Rakotomalala, Joël Vom Brocke, Kirsten Frouin, Julien Pot, David Rabekijana, Ravonantenaina Rhodia Ramanantsoanirina, Alain Ratsimiala Ramonta, Isabelle Cao, Tuong-Vi |
author_facet |
Rakotomalala, Joël Vom Brocke, Kirsten Frouin, Julien Pot, David Rabekijana, Ravonantenaina Rhodia Ramanantsoanirina, Alain Ratsimiala Ramonta, Isabelle Cao, Tuong-Vi |
author_sort |
Rakotomalala, Joël |
title |
Breeding for nitrogen use efficiency: Lessons from genomic prediction experiments based on a broad-based population of upland rice |
title_short |
Breeding for nitrogen use efficiency: Lessons from genomic prediction experiments based on a broad-based population of upland rice |
title_full |
Breeding for nitrogen use efficiency: Lessons from genomic prediction experiments based on a broad-based population of upland rice |
title_fullStr |
Breeding for nitrogen use efficiency: Lessons from genomic prediction experiments based on a broad-based population of upland rice |
title_full_unstemmed |
Breeding for nitrogen use efficiency: Lessons from genomic prediction experiments based on a broad-based population of upland rice |
title_sort |
breeding for nitrogen use efficiency: lessons from genomic prediction experiments based on a broad-based population of upland rice |
url |
http://agritrop.cirad.fr/600184/ http://agritrop.cirad.fr/600184/1/Rakotomalala%20et%20al.%20-%202021%20-%20Breeding%20for%20Nitrogen%20use%20Efficiency%20Lessons%20from.pdf |
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