Genomic prediction of kernel zinc concentration in multiple maize populations using genotyping-by-sequencing and repeat amplification sequencing markers
Enriching of kernel zinc (Zn) concentration in maize is one of the most effective ways to solve the problem of Zn deficiency in low and middle income countries where maize is the major staple food, and 17% of the global population is affected with Zn deficiency. Genomic selection (GS) has shown to b...
| Main Authors: | , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
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Frontiers Media
2020
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| Online Access: | https://hdl.handle.net/10568/171383 |
| _version_ | 1855534643299745792 |
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| author | Guo, Rui Dhliwayo, Thanda Mageto, Edna K. Palacios-Rojas, Natalia Lee, Michael |
| author_browse | Dhliwayo, Thanda Guo, Rui Lee, Michael Mageto, Edna K. Palacios-Rojas, Natalia |
| author_facet | Guo, Rui Dhliwayo, Thanda Mageto, Edna K. Palacios-Rojas, Natalia Lee, Michael |
| author_sort | Guo, Rui |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Enriching of kernel zinc (Zn) concentration in maize is one of the most effective ways to solve the problem of Zn deficiency in low and middle income countries where maize is the major staple food, and 17% of the global population is affected with Zn deficiency. Genomic selection (GS) has shown to be an effective approach to accelerate genetic gains in plant breeding. In the present study, an association-mapping panel and two maize double-haploid (DH) populations, both genotyped with genotyping-by-sequencing (GBS) and repeat amplification sequencing (rAmpSeq) markers, were used to estimate the genomic prediction accuracy of kernel Zn concentration in maize. Results showed that the prediction accuracy of two DH populations was higher than that of the association mapping population using the same set of markers. The prediction accuracy estimated with the GBS markers was significantly higher than that estimated with the rAmpSeq markers in the same population. The maximum prediction accuracy with minimum standard error was observed when half of the genotypes were included in the training set and 3,000 and 500 markers were used for prediction in the association mapping panel and the DH populations, respectively. Appropriate levels of minor allele frequency and missing rate should be considered and selected to achieve good prediction accuracy and reduce the computation burden by balancing the number of markers and marker quality. Training set development with broad phenotypic variation is possible to improve prediction accuracy. The transferability of the GS models across populations was assessed, the prediction accuracies in a few pairwise populations were above or close to 0.20, which indicates the prediction accuracies across years and populations have to be assessed in a larger breeding dataset with closer relationship between the training and prediction sets in further studies. GS outperformed MAS (marker-assisted-selection) on predicting the kernel Zn concentration in maize, the decision of a breeding strategy to implement GS individually or to implement MAS and GS stepwise for improving kernel Zn concentration in maize requires further research. Results of this study provide valuable information for understanding how to implement GS for improving kernel Zn concentration in maize. |
| format | Journal Article |
| id | CGSpace171383 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2020 |
| publishDateRange | 2020 |
| publishDateSort | 2020 |
| publisher | Frontiers Media |
| publisherStr | Frontiers Media |
| record_format | dspace |
| spelling | CGSpace1713832025-01-29T12:58:06Z Genomic prediction of kernel zinc concentration in multiple maize populations using genotyping-by-sequencing and repeat amplification sequencing markers Guo, Rui Dhliwayo, Thanda Mageto, Edna K. Palacios-Rojas, Natalia Lee, Michael maize trace elements crops biofortification zinc iron retinol Enriching of kernel zinc (Zn) concentration in maize is one of the most effective ways to solve the problem of Zn deficiency in low and middle income countries where maize is the major staple food, and 17% of the global population is affected with Zn deficiency. Genomic selection (GS) has shown to be an effective approach to accelerate genetic gains in plant breeding. In the present study, an association-mapping panel and two maize double-haploid (DH) populations, both genotyped with genotyping-by-sequencing (GBS) and repeat amplification sequencing (rAmpSeq) markers, were used to estimate the genomic prediction accuracy of kernel Zn concentration in maize. Results showed that the prediction accuracy of two DH populations was higher than that of the association mapping population using the same set of markers. The prediction accuracy estimated with the GBS markers was significantly higher than that estimated with the rAmpSeq markers in the same population. The maximum prediction accuracy with minimum standard error was observed when half of the genotypes were included in the training set and 3,000 and 500 markers were used for prediction in the association mapping panel and the DH populations, respectively. Appropriate levels of minor allele frequency and missing rate should be considered and selected to achieve good prediction accuracy and reduce the computation burden by balancing the number of markers and marker quality. Training set development with broad phenotypic variation is possible to improve prediction accuracy. The transferability of the GS models across populations was assessed, the prediction accuracies in a few pairwise populations were above or close to 0.20, which indicates the prediction accuracies across years and populations have to be assessed in a larger breeding dataset with closer relationship between the training and prediction sets in further studies. GS outperformed MAS (marker-assisted-selection) on predicting the kernel Zn concentration in maize, the decision of a breeding strategy to implement GS individually or to implement MAS and GS stepwise for improving kernel Zn concentration in maize requires further research. Results of this study provide valuable information for understanding how to implement GS for improving kernel Zn concentration in maize. 2020 2025-01-29T12:58:06Z 2025-01-29T12:58:06Z Journal Article https://hdl.handle.net/10568/171383 en Open Access Frontiers Media Guo, Rui; Dhliwayo, Thanda; Mageto, Edna K.; Palacios-Rojas, Natalia; Lee, Michael; et al. 2020. Genomic prediction of kernel zinc concentration in multiple maize populations using genotyping-by-sequencing and repeat amplification sequencing markers. Frontiers in Plant Science 11: 534. https://doi.org/10.3389/fpls.2020.00534 |
| spellingShingle | maize trace elements crops biofortification zinc iron retinol Guo, Rui Dhliwayo, Thanda Mageto, Edna K. Palacios-Rojas, Natalia Lee, Michael Genomic prediction of kernel zinc concentration in multiple maize populations using genotyping-by-sequencing and repeat amplification sequencing markers |
| title | Genomic prediction of kernel zinc concentration in multiple maize populations using genotyping-by-sequencing and repeat amplification sequencing markers |
| title_full | Genomic prediction of kernel zinc concentration in multiple maize populations using genotyping-by-sequencing and repeat amplification sequencing markers |
| title_fullStr | Genomic prediction of kernel zinc concentration in multiple maize populations using genotyping-by-sequencing and repeat amplification sequencing markers |
| title_full_unstemmed | Genomic prediction of kernel zinc concentration in multiple maize populations using genotyping-by-sequencing and repeat amplification sequencing markers |
| title_short | Genomic prediction of kernel zinc concentration in multiple maize populations using genotyping-by-sequencing and repeat amplification sequencing markers |
| title_sort | genomic prediction of kernel zinc concentration in multiple maize populations using genotyping by sequencing and repeat amplification sequencing markers |
| topic | maize trace elements crops biofortification zinc iron retinol |
| url | https://hdl.handle.net/10568/171383 |
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