Sparse phenotyping and haplotype-based models for genomic prediction in rice
The multi-environment genomic selection enables plant breeders to select varieties resilient to diverse environments or particularly adapted to specific environments, which holds a great potential to be used in rice breeding. To realize the multi-environment genomic selection, a robust training set...
| Autores principales: | , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Springer
2023
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/163941 |
| _version_ | 1855530238566465536 |
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| author | He, Sang Liang, Shanshan Meng, Lijun Cao, Liyong Ye, Guoyou |
| author_browse | Cao, Liyong He, Sang Liang, Shanshan Meng, Lijun Ye, Guoyou |
| author_facet | He, Sang Liang, Shanshan Meng, Lijun Cao, Liyong Ye, Guoyou |
| author_sort | He, Sang |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | The multi-environment genomic selection enables plant breeders to select varieties resilient to diverse environments or particularly adapted to specific environments, which holds a great potential to be used in rice breeding. To realize the multi-environment genomic selection, a robust training set with multi-environment phenotypic data is of necessity. Considering the huge potential of genomic prediction enhanced sparse phenotyping on the cost saving of multi-environment trials (MET), the establishment of a multi-environment training set could also benefit from it. Optimizing the genomic prediction methods is also crucial to enhance the multi-environment genomic selection. Using haplotype-based genomic prediction models is able to capture local epistatic effects which could be conserved and accumulated across generations much like additive effects thereby benefitting breeding. However, previous studies often used fixed length haplotypes composed by a few adjacent molecular markers disregarding the linkage disequilibrium (LD) which is of essential role in determining the haplotype length. In our study, based on three rice populations with different sizes and compositions, we investigated the usefulness and effectiveness of multi-environment training sets with varying phenotyping intensities and different haplotype-based genomic prediction models based on LD-derived haplotype blocks for two agronomic traits, i.e., days to heading (DTH) and plant height (PH). Results showed that phenotyping merely 30% records in multi-environment training set is able to provide a comparable prediction accuracy to high phenotyping intensities; the local epistatic effects are much likely existent in DTH; dividing the LD-derived haplotype blocks into small segments with two or three single nucleotide polymorphisms (SNPs) helps to maintain the predictive ability of haplotype-based models in large populations; modelling the covariances between environments improves genomic prediction accuracy. Our study provides means to improve the efficiency of multi-environment genomic selection in rice. |
| format | Journal Article |
| id | CGSpace163941 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2023 |
| publishDateRange | 2023 |
| publishDateSort | 2023 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace1639412024-12-19T14:12:58Z Sparse phenotyping and haplotype-based models for genomic prediction in rice He, Sang Liang, Shanshan Meng, Lijun Cao, Liyong Ye, Guoyou additive effect agronomic characters genomes linkage disequilibrium marker-assisted selection plant breeders plant height single nucleotide polymorphism The multi-environment genomic selection enables plant breeders to select varieties resilient to diverse environments or particularly adapted to specific environments, which holds a great potential to be used in rice breeding. To realize the multi-environment genomic selection, a robust training set with multi-environment phenotypic data is of necessity. Considering the huge potential of genomic prediction enhanced sparse phenotyping on the cost saving of multi-environment trials (MET), the establishment of a multi-environment training set could also benefit from it. Optimizing the genomic prediction methods is also crucial to enhance the multi-environment genomic selection. Using haplotype-based genomic prediction models is able to capture local epistatic effects which could be conserved and accumulated across generations much like additive effects thereby benefitting breeding. However, previous studies often used fixed length haplotypes composed by a few adjacent molecular markers disregarding the linkage disequilibrium (LD) which is of essential role in determining the haplotype length. In our study, based on three rice populations with different sizes and compositions, we investigated the usefulness and effectiveness of multi-environment training sets with varying phenotyping intensities and different haplotype-based genomic prediction models based on LD-derived haplotype blocks for two agronomic traits, i.e., days to heading (DTH) and plant height (PH). Results showed that phenotyping merely 30% records in multi-environment training set is able to provide a comparable prediction accuracy to high phenotyping intensities; the local epistatic effects are much likely existent in DTH; dividing the LD-derived haplotype blocks into small segments with two or three single nucleotide polymorphisms (SNPs) helps to maintain the predictive ability of haplotype-based models in large populations; modelling the covariances between environments improves genomic prediction accuracy. Our study provides means to improve the efficiency of multi-environment genomic selection in rice. 2023-12 2024-12-19T12:53:13Z 2024-12-19T12:53:13Z Journal Article https://hdl.handle.net/10568/163941 en Open Access Springer He, Sang; Liang, Shanshan; Meng, Lijun; Cao, Liyong and Ye, Guoyou. 2023. Sparse phenotyping and haplotype-based models for genomic prediction in rice. Rice, Volume 16, no. 1 |
| spellingShingle | additive effect agronomic characters genomes linkage disequilibrium marker-assisted selection plant breeders plant height single nucleotide polymorphism He, Sang Liang, Shanshan Meng, Lijun Cao, Liyong Ye, Guoyou Sparse phenotyping and haplotype-based models for genomic prediction in rice |
| title | Sparse phenotyping and haplotype-based models for genomic prediction in rice |
| title_full | Sparse phenotyping and haplotype-based models for genomic prediction in rice |
| title_fullStr | Sparse phenotyping and haplotype-based models for genomic prediction in rice |
| title_full_unstemmed | Sparse phenotyping and haplotype-based models for genomic prediction in rice |
| title_short | Sparse phenotyping and haplotype-based models for genomic prediction in rice |
| title_sort | sparse phenotyping and haplotype based models for genomic prediction in rice |
| topic | additive effect agronomic characters genomes linkage disequilibrium marker-assisted selection plant breeders plant height single nucleotide polymorphism |
| url | https://hdl.handle.net/10568/163941 |
| work_keys_str_mv | AT hesang sparsephenotypingandhaplotypebasedmodelsforgenomicpredictioninrice AT liangshanshan sparsephenotypingandhaplotypebasedmodelsforgenomicpredictioninrice AT menglijun sparsephenotypingandhaplotypebasedmodelsforgenomicpredictioninrice AT caoliyong sparsephenotypingandhaplotypebasedmodelsforgenomicpredictioninrice AT yeguoyou sparsephenotypingandhaplotypebasedmodelsforgenomicpredictioninrice |