Multi-environment Genomic Selection in Rice Elite Breeding Lines
Abstract Background Assessing the performance of elite lines in target environments is essential for breeding programs to select the most relevant genotypes. One of the main complexities in this task resides in accounting for the genotype by environment interactions. Genomic prediction models that i...
| Main Authors: | , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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SpringerOpen
2023-02-01
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| Series: | Rice |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12284-023-00623-6 |
| _version_ | 1811165690669826048 |
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| author | Van Hieu Nguyen Rose Imee Zhella Morantte Vitaliano Lopena Holden Verdeprado Rosemary Murori Alexis Ndayiragije Sanjay Kumar Katiyar Md Rafiqul Islam Roselyne Uside Juma Hayde Flandez-Galvez Jean-Christophe Glaszmann Joshua N. Cobb Jérôme Bartholomé |
| author_facet | Van Hieu Nguyen Rose Imee Zhella Morantte Vitaliano Lopena Holden Verdeprado Rosemary Murori Alexis Ndayiragije Sanjay Kumar Katiyar Md Rafiqul Islam Roselyne Uside Juma Hayde Flandez-Galvez Jean-Christophe Glaszmann Joshua N. Cobb Jérôme Bartholomé |
| author_sort | Van Hieu Nguyen |
| collection | DOAJ |
| description | Abstract Background Assessing the performance of elite lines in target environments is essential for breeding programs to select the most relevant genotypes. One of the main complexities in this task resides in accounting for the genotype by environment interactions. Genomic prediction models that integrate information from multi-environment trials and environmental covariates can be efficient tools in this context. The objective of this study was to assess the predictive ability of different genomic prediction models to optimize the use of multi-environment information. We used 111 elite breeding lines representing the diversity of the international rice research institute breeding program for irrigated ecosystems. The lines were evaluated for three traits (days to flowering, plant height, and grain yield) in 15 environments in Asia and Africa and genotyped with 882 SNP markers. We evaluated the efficiency of genomic prediction to predict untested environments using seven multi-environment models and three cross-validation scenarios. Results The elite lines were found to belong to the indica group and more specifically the indica-1B subgroup which gathered improved material originating from the Green Revolution. Phenotypic correlations between environments were high for days to flowering and plant height (33% and 54% of pairwise correlation greater than 0.5) but low for grain yield (lower than 0.2 in most cases). Clustering analyses based on environmental covariates separated Asia’s and Africa's environments into different clusters or subclusters. The predictive abilities ranged from 0.06 to 0.79 for days to flowering, 0.25–0.88 for plant height, and − 0.29–0.62 for grain yield. We found that models integrating genotype-by-environment interaction effects did not perform significantly better than models integrating only main effects (genotypes and environment or environmental covariates). The different cross-validation scenarios showed that, in most cases, the use of all available environments gave better results than a subset. Conclusion Multi-environment genomic prediction models with main effects were sufficient for accurate phenotypic prediction of elite lines in targeted environments. These results will help refine the testing strategy to update the genomic prediction models to improve predictive ability. |
| first_indexed | 2024-04-10T15:40:43Z |
| format | Article |
| id | doaj.art-2eae306c1bda47dbabd2ad3fd6dbb91c |
| institution | Directory Open Access Journal |
| issn | 1939-8425 1939-8433 |
| language | English |
| last_indexed | 2024-04-10T15:40:43Z |
| publishDate | 2023-02-01 |
| publisher | SpringerOpen |
| record_format | Article |
| series | Rice |
| spelling | doaj.art-2eae306c1bda47dbabd2ad3fd6dbb91c2023-02-12T12:22:45ZengSpringerOpenRice1939-84251939-84332023-02-0116111710.1186/s12284-023-00623-6Multi-environment Genomic Selection in Rice Elite Breeding LinesVan Hieu Nguyen0Rose Imee Zhella Morantte1Vitaliano Lopena2Holden Verdeprado3Rosemary Murori4Alexis Ndayiragije5Sanjay Kumar Katiyar6Md Rafiqul Islam7Roselyne Uside Juma8Hayde Flandez-Galvez9Jean-Christophe Glaszmann10Joshua N. Cobb11Jérôme Bartholomé12CIRAD, UMR AGAP InstitutRice Breeding Innovation Platform, International Rice Research InstituteRice Breeding Innovation Platform, International Rice Research InstituteRice Breeding Innovation Platform, International Rice Research InstituteRice Breeding Innovation Platform, International Rice Research InstituteRice Breeding Innovation Platform, International Rice Research InstituteRice Breeding Innovation Platform, International Rice Research InstituteRice Breeding Innovation Platform, International Rice Research InstituteRice Breeding Innovation Platform, International Rice Research InstituteInstitute of Crop Science, College of Agriculture and Food Science, University of the PhilippinesCIRAD, UMR AGAP InstitutRice Breeding Innovation Platform, International Rice Research InstituteUMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut AgroAbstract Background Assessing the performance of elite lines in target environments is essential for breeding programs to select the most relevant genotypes. One of the main complexities in this task resides in accounting for the genotype by environment interactions. Genomic prediction models that integrate information from multi-environment trials and environmental covariates can be efficient tools in this context. The objective of this study was to assess the predictive ability of different genomic prediction models to optimize the use of multi-environment information. We used 111 elite breeding lines representing the diversity of the international rice research institute breeding program for irrigated ecosystems. The lines were evaluated for three traits (days to flowering, plant height, and grain yield) in 15 environments in Asia and Africa and genotyped with 882 SNP markers. We evaluated the efficiency of genomic prediction to predict untested environments using seven multi-environment models and three cross-validation scenarios. Results The elite lines were found to belong to the indica group and more specifically the indica-1B subgroup which gathered improved material originating from the Green Revolution. Phenotypic correlations between environments were high for days to flowering and plant height (33% and 54% of pairwise correlation greater than 0.5) but low for grain yield (lower than 0.2 in most cases). Clustering analyses based on environmental covariates separated Asia’s and Africa's environments into different clusters or subclusters. The predictive abilities ranged from 0.06 to 0.79 for days to flowering, 0.25–0.88 for plant height, and − 0.29–0.62 for grain yield. We found that models integrating genotype-by-environment interaction effects did not perform significantly better than models integrating only main effects (genotypes and environment or environmental covariates). The different cross-validation scenarios showed that, in most cases, the use of all available environments gave better results than a subset. Conclusion Multi-environment genomic prediction models with main effects were sufficient for accurate phenotypic prediction of elite lines in targeted environments. These results will help refine the testing strategy to update the genomic prediction models to improve predictive ability.https://doi.org/10.1186/s12284-023-00623-6RiceOryza sativaElite linesGenomic predictionGenotype by environment interactionsEnvironmental covariates |
| spellingShingle | Van Hieu Nguyen Rose Imee Zhella Morantte Vitaliano Lopena Holden Verdeprado Rosemary Murori Alexis Ndayiragije Sanjay Kumar Katiyar Md Rafiqul Islam Roselyne Uside Juma Hayde Flandez-Galvez Jean-Christophe Glaszmann Joshua N. Cobb Jérôme Bartholomé Multi-environment Genomic Selection in Rice Elite Breeding Lines Rice Rice Oryza sativa Elite lines Genomic prediction Genotype by environment interactions Environmental covariates |
| title | Multi-environment Genomic Selection in Rice Elite Breeding Lines |
| title_full | Multi-environment Genomic Selection in Rice Elite Breeding Lines |
| title_fullStr | Multi-environment Genomic Selection in Rice Elite Breeding Lines |
| title_full_unstemmed | Multi-environment Genomic Selection in Rice Elite Breeding Lines |
| title_short | Multi-environment Genomic Selection in Rice Elite Breeding Lines |
| title_sort | multi environment genomic selection in rice elite breeding lines |
| topic | Rice Oryza sativa Elite lines Genomic prediction Genotype by environment interactions Environmental covariates |
| url | https://doi.org/10.1186/s12284-023-00623-6 |
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