Genomic prediction of rice mesocotyl length indicative of directing seeding suitability using a half-sib hybrid population
Direct seeding has been widely adopted as an economical and labor-saving technique in rice production, though problems such as low seedling emergence rate, emergence irregularity and poor lodging resistance are existing. These problems are currently partially overcome by increasing seeding rate, how...
| Autores principales: | , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
2023
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/163964 |
| _version_ | 1855516417537867776 |
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| author | Chen, Liang Liu, Jindong He, Sang Cao, Liyong Ye, Guoyou |
| author_browse | Cao, Liyong Chen, Liang He, Sang Liu, Jindong Ye, Guoyou |
| author_facet | Chen, Liang Liu, Jindong He, Sang Cao, Liyong Ye, Guoyou |
| author_sort | Chen, Liang |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Direct seeding has been widely adopted as an economical and labor-saving technique in rice production, though problems such as low seedling emergence rate, emergence irregularity and poor lodging resistance are existing. These problems are currently partially overcome by increasing seeding rate, however it is not acceptable for hybrid rice due to the high seed cost. Improving direct seeding by breeding is seen as the ultimate solution to these problems. For hybrid breeding, identifying superior hybrids among a massive number of hybrids from crossings between male and female parental populations by phenotypic evaluation is tedious and costly. Contrastingly, genomic selection/prediction (GS/GP) could efficiently detect the superior hybrids capitalizing on genomic data, which holds a great potential in plant hybrids breeding. In this study, we utilized 402 rice inbred varieties and 401 hybrids to investigate the effectiveness of GS on rice mesocotyl length, a representative indicative trait of direct seeding suitability. Several GP methods and training set designs were studied to seek the optimal scenario of hybrid prediction. It was shown that using half-sib hybrids as training set with the phenotypes of all parental lines being fitted as a covariate could optimally predict mesocotyl length. Partitioning the molecular markers into trait-associated and -unassociated groups based on genome-wide association study using all parental lines and hybrids could further improve the prediction accuracy. This study indicates that GS could be an effective and efficient method for hybrid breeding for rice direct seeding. |
| format | Journal Article |
| id | CGSpace163964 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2023 |
| publishDateRange | 2023 |
| publishDateSort | 2023 |
| record_format | dspace |
| spelling | CGSpace1639642025-10-26T12:52:25Z Genomic prediction of rice mesocotyl length indicative of directing seeding suitability using a half-sib hybrid population Chen, Liang Liu, Jindong He, Sang Cao, Liyong Ye, Guoyou direct seeding lodging resistance seeding rate breeding molecular markers efficiency Direct seeding has been widely adopted as an economical and labor-saving technique in rice production, though problems such as low seedling emergence rate, emergence irregularity and poor lodging resistance are existing. These problems are currently partially overcome by increasing seeding rate, however it is not acceptable for hybrid rice due to the high seed cost. Improving direct seeding by breeding is seen as the ultimate solution to these problems. For hybrid breeding, identifying superior hybrids among a massive number of hybrids from crossings between male and female parental populations by phenotypic evaluation is tedious and costly. Contrastingly, genomic selection/prediction (GS/GP) could efficiently detect the superior hybrids capitalizing on genomic data, which holds a great potential in plant hybrids breeding. In this study, we utilized 402 rice inbred varieties and 401 hybrids to investigate the effectiveness of GS on rice mesocotyl length, a representative indicative trait of direct seeding suitability. Several GP methods and training set designs were studied to seek the optimal scenario of hybrid prediction. It was shown that using half-sib hybrids as training set with the phenotypes of all parental lines being fitted as a covariate could optimally predict mesocotyl length. Partitioning the molecular markers into trait-associated and -unassociated groups based on genome-wide association study using all parental lines and hybrids could further improve the prediction accuracy. This study indicates that GS could be an effective and efficient method for hybrid breeding for rice direct seeding. 2023-04-05 2024-12-19T12:53:14Z 2024-12-19T12:53:14Z Journal Article https://hdl.handle.net/10568/163964 en Open Access Chen, Liang; Liu, Jindong; He, Sang; Cao, Liyong and Ye, Guoyou. 2023. Genomic prediction of rice mesocotyl length indicative of directing seeding suitability using a half-sib hybrid population. PLoS ONE, Volume 18 no. 4 p. e0283989 |
| spellingShingle | direct seeding lodging resistance seeding rate breeding molecular markers efficiency Chen, Liang Liu, Jindong He, Sang Cao, Liyong Ye, Guoyou Genomic prediction of rice mesocotyl length indicative of directing seeding suitability using a half-sib hybrid population |
| title | Genomic prediction of rice mesocotyl length indicative of directing seeding suitability using a half-sib hybrid population |
| title_full | Genomic prediction of rice mesocotyl length indicative of directing seeding suitability using a half-sib hybrid population |
| title_fullStr | Genomic prediction of rice mesocotyl length indicative of directing seeding suitability using a half-sib hybrid population |
| title_full_unstemmed | Genomic prediction of rice mesocotyl length indicative of directing seeding suitability using a half-sib hybrid population |
| title_short | Genomic prediction of rice mesocotyl length indicative of directing seeding suitability using a half-sib hybrid population |
| title_sort | genomic prediction of rice mesocotyl length indicative of directing seeding suitability using a half sib hybrid population |
| topic | direct seeding lodging resistance seeding rate breeding molecular markers efficiency |
| url | https://hdl.handle.net/10568/163964 |
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