Selection of trait-specific markers and multi-environment models improve genomic predictive ability in rice
Developing high yielding rice varieties that are tolerant to drought stress is crucial for the sustainable livelihood of rice farmers in rainfed rice cropping ecosystems. Genomic selection (GS) promises to be an effective breeding option for these complex traits. We evaluated the effectiveness of tw...
| Autores principales: | , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
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Public Library of Science
2019
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| Acceso en línea: | https://hdl.handle.net/10568/164688 |
| _version_ | 1855542501832654848 |
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| author | Bhandari, Aditi Bartholomé, Jérôme Cao-Hamadoun, Tuong-Vi Kumari, Nilima Frouin, Julien Kumar, Arvind Ahmadi, Nourollah |
| author_browse | Ahmadi, Nourollah Bartholomé, Jérôme Bhandari, Aditi Cao-Hamadoun, Tuong-Vi Frouin, Julien Kumar, Arvind Kumari, Nilima |
| author_facet | Bhandari, Aditi Bartholomé, Jérôme Cao-Hamadoun, Tuong-Vi Kumari, Nilima Frouin, Julien Kumar, Arvind Ahmadi, Nourollah |
| author_sort | Bhandari, Aditi |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Developing high yielding rice varieties that are tolerant to drought stress is crucial for the sustainable livelihood of rice farmers in rainfed rice cropping ecosystems. Genomic selection (GS) promises to be an effective breeding option for these complex traits. We evaluated the effectiveness of two rather new options in the implementation of GS: trait and environment-specific marker selection and the use of multi-environment prediction models. A reference population of 280 rainfed lowland accessions endowed with 215k SNP markers data was phenotyped under a favorable and two managed drought environments. Trait-specific SNP subsets (28k) were selected for each trait under each environment, using results of GWAS performed with the complete genotype dataset. Performances of single-environment and multi-environment genomic prediction models were compared using kernel regression based methods (GBLUP and RKHS) under two cross validation scenarios: availability (CV2) or not (CV1) of phenotypic data for the validation set, in one of the environments. Trait-specific marker selection strategy achieved predictive ability (PA) of genomic prediction up to 22% higher than markers selected on the bases of neutral linkage disequilibrium (LD). Tolerance to drought stress was up to 32% better predicted by multi-environment models (especially RKHS based models) under CV2 strategy. Under the less favorable CV1 strategy, the multi-environment models achieved similar PA than the single-environment predictions. We also showed that reasonable PA could be obtained with as few as 3,000 SNP markers, even in a population of low LD extent, provided marker selection is based on pairwise LD. The implications of these findings for breeding for drought tolerance are discussed. The most resource sparing option would be accurate phenotyping of the reference population in a favorable environment and under a managed drought, while the candidate population would be phenotyped only under one of those environments |
| format | Journal Article |
| id | CGSpace164688 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2019 |
| publishDateRange | 2019 |
| publishDateSort | 2019 |
| publisher | Public Library of Science |
| publisherStr | Public Library of Science |
| record_format | dspace |
| spelling | CGSpace1646882025-01-24T14:21:00Z Selection of trait-specific markers and multi-environment models improve genomic predictive ability in rice Bhandari, Aditi Bartholomé, Jérôme Cao-Hamadoun, Tuong-Vi Kumari, Nilima Frouin, Julien Kumar, Arvind Ahmadi, Nourollah general agricultural and biological sciences general biochemistry genetics and molecular biology general medicine Developing high yielding rice varieties that are tolerant to drought stress is crucial for the sustainable livelihood of rice farmers in rainfed rice cropping ecosystems. Genomic selection (GS) promises to be an effective breeding option for these complex traits. We evaluated the effectiveness of two rather new options in the implementation of GS: trait and environment-specific marker selection and the use of multi-environment prediction models. A reference population of 280 rainfed lowland accessions endowed with 215k SNP markers data was phenotyped under a favorable and two managed drought environments. Trait-specific SNP subsets (28k) were selected for each trait under each environment, using results of GWAS performed with the complete genotype dataset. Performances of single-environment and multi-environment genomic prediction models were compared using kernel regression based methods (GBLUP and RKHS) under two cross validation scenarios: availability (CV2) or not (CV1) of phenotypic data for the validation set, in one of the environments. Trait-specific marker selection strategy achieved predictive ability (PA) of genomic prediction up to 22% higher than markers selected on the bases of neutral linkage disequilibrium (LD). Tolerance to drought stress was up to 32% better predicted by multi-environment models (especially RKHS based models) under CV2 strategy. Under the less favorable CV1 strategy, the multi-environment models achieved similar PA than the single-environment predictions. We also showed that reasonable PA could be obtained with as few as 3,000 SNP markers, even in a population of low LD extent, provided marker selection is based on pairwise LD. The implications of these findings for breeding for drought tolerance are discussed. The most resource sparing option would be accurate phenotyping of the reference population in a favorable environment and under a managed drought, while the candidate population would be phenotyped only under one of those environments 2019-05-06 2024-12-19T12:54:12Z 2024-12-19T12:54:12Z Journal Article https://hdl.handle.net/10568/164688 en Open Access Public Library of Science Bhandari, Aditi; Bartholomé, Jérôme; Cao-Hamadoun, Tuong-Vi; Kumari, Nilima; Frouin, Julien; Kumar, Arvind and Ahmadi, Nourollah. 2019. Selection of trait-specific markers and multi-environment models improve genomic predictive ability in rice. PLoS ONE, Volume 14 no. 5 p. e0208871 |
| spellingShingle | general agricultural and biological sciences general biochemistry genetics and molecular biology general medicine Bhandari, Aditi Bartholomé, Jérôme Cao-Hamadoun, Tuong-Vi Kumari, Nilima Frouin, Julien Kumar, Arvind Ahmadi, Nourollah Selection of trait-specific markers and multi-environment models improve genomic predictive ability in rice |
| title | Selection of trait-specific markers and multi-environment models improve genomic predictive ability in rice |
| title_full | Selection of trait-specific markers and multi-environment models improve genomic predictive ability in rice |
| title_fullStr | Selection of trait-specific markers and multi-environment models improve genomic predictive ability in rice |
| title_full_unstemmed | Selection of trait-specific markers and multi-environment models improve genomic predictive ability in rice |
| title_short | Selection of trait-specific markers and multi-environment models improve genomic predictive ability in rice |
| title_sort | selection of trait specific markers and multi environment models improve genomic predictive ability in rice |
| topic | general agricultural and biological sciences general biochemistry genetics and molecular biology general medicine |
| url | https://hdl.handle.net/10568/164688 |
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