Low-density reference fingerprinting SNP dataset of CIMMYT maize lines for quality control and genetic diversity analyses
CIMMYT maize lines (CMLs), which represent the tropical maize germplasm, are freely available worldwide. All currently released 615 CMLs and fourteen temperate maize inbred lines were genotyped with 180 kompetitive allele-specific PCR single nucleotide polymorphisms to develop a reference fingerprin...
| Autores principales: | , , , , , , , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
MDPI
2022
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/127059 |
| _version_ | 1855521623077027840 |
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| author | Jingtao Qu Chassaigne-Ricciulli, Alberto A Fengling Fu Haoqiang Yu Dreher, Kate A. Nair, Sudha Krishnan Gowda, Manje Beyene, Yoseph Makumbi, Dan Dhliwayo, Thanda San Vicente, Felix M. Olsen, Michael Boddupalli, P.M. Wanchen Li Xuecai Zhang |
| author_browse | Beyene, Yoseph Boddupalli, P.M. Chassaigne-Ricciulli, Alberto A Dhliwayo, Thanda Dreher, Kate A. Fengling Fu Gowda, Manje Haoqiang Yu Jingtao Qu Makumbi, Dan Nair, Sudha Krishnan Olsen, Michael San Vicente, Felix M. Wanchen Li Xuecai Zhang |
| author_facet | Jingtao Qu Chassaigne-Ricciulli, Alberto A Fengling Fu Haoqiang Yu Dreher, Kate A. Nair, Sudha Krishnan Gowda, Manje Beyene, Yoseph Makumbi, Dan Dhliwayo, Thanda San Vicente, Felix M. Olsen, Michael Boddupalli, P.M. Wanchen Li Xuecai Zhang |
| author_sort | Jingtao Qu |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | CIMMYT maize lines (CMLs), which represent the tropical maize germplasm, are freely available worldwide. All currently released 615 CMLs and fourteen temperate maize inbred lines were genotyped with 180 kompetitive allele-specific PCR single nucleotide polymorphisms to develop a reference fingerprinting SNP dataset that can be used to perform quality control (QC) and genetic diversity analyses. The QC analysis identified 25 CMLs with purity, identity, or mislabeling issues. Further field observation, purification, and re-genotyping of these CMLs are required. The reference fingerprinting SNP dataset was developed for all of the currently released CMLs with 152 high-quality SNPs. The results of principal component analysis and average genetic distances between subgroups showed a clear genetic divergence between temperate and tropical maize, whereas the three tropical subgroups partially overlapped with one another. More than 99% of the pairs of CMLs had genetic distances greater than 0.30, showing their high genetic diversity, and most CMLs are distantly related. The heterotic patterns, estimated with the molecular markers, are consistent with those estimated using pedigree information in two major maize breeding programs at CIMMYT. These research findings are helpful for ensuring the regeneration and distribution of the true CMLs, via QC analysis, and for facilitating the effective utilization of the CMLs, globally. |
| format | Journal Article |
| id | CGSpace127059 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2022 |
| publishDateRange | 2022 |
| publishDateSort | 2022 |
| publisher | MDPI |
| publisherStr | MDPI |
| record_format | dspace |
| spelling | CGSpace1270592025-12-08T10:29:22Z Low-density reference fingerprinting SNP dataset of CIMMYT maize lines for quality control and genetic diversity analyses Jingtao Qu Chassaigne-Ricciulli, Alberto A Fengling Fu Haoqiang Yu Dreher, Kate A. Nair, Sudha Krishnan Gowda, Manje Beyene, Yoseph Makumbi, Dan Dhliwayo, Thanda San Vicente, Felix M. Olsen, Michael Boddupalli, P.M. Wanchen Li Xuecai Zhang heterotic groups quality control single nucleotide polymorphism maize data CIMMYT maize lines (CMLs), which represent the tropical maize germplasm, are freely available worldwide. All currently released 615 CMLs and fourteen temperate maize inbred lines were genotyped with 180 kompetitive allele-specific PCR single nucleotide polymorphisms to develop a reference fingerprinting SNP dataset that can be used to perform quality control (QC) and genetic diversity analyses. The QC analysis identified 25 CMLs with purity, identity, or mislabeling issues. Further field observation, purification, and re-genotyping of these CMLs are required. The reference fingerprinting SNP dataset was developed for all of the currently released CMLs with 152 high-quality SNPs. The results of principal component analysis and average genetic distances between subgroups showed a clear genetic divergence between temperate and tropical maize, whereas the three tropical subgroups partially overlapped with one another. More than 99% of the pairs of CMLs had genetic distances greater than 0.30, showing their high genetic diversity, and most CMLs are distantly related. The heterotic patterns, estimated with the molecular markers, are consistent with those estimated using pedigree information in two major maize breeding programs at CIMMYT. These research findings are helpful for ensuring the regeneration and distribution of the true CMLs, via QC analysis, and for facilitating the effective utilization of the CMLs, globally. 2022-11-14 2023-01-13T14:03:42Z 2023-01-13T14:03:42Z Journal Article https://hdl.handle.net/10568/127059 en Open Access application/pdf MDPI Qu, J., Chassaigne-Ricciulli, A. A., Fu, F., Yu, H., Dreher, K., Nair, S. K., Gowda, M., Beyene, Y., Makumbi, D., Dhliwayo, T., Vicente, F. S., Olsen, M., Prasanna, B. M., Li, W., & Zhang, X. (2022). Low-Density Reference Fingerprinting SNP Dataset of CIMMYT Maize Lines for Quality Control and Genetic Diversity Analyses. Plants, 11(22), 3092. https://doi.org/10.3390/plants11223092 |
| spellingShingle | heterotic groups quality control single nucleotide polymorphism maize data Jingtao Qu Chassaigne-Ricciulli, Alberto A Fengling Fu Haoqiang Yu Dreher, Kate A. Nair, Sudha Krishnan Gowda, Manje Beyene, Yoseph Makumbi, Dan Dhliwayo, Thanda San Vicente, Felix M. Olsen, Michael Boddupalli, P.M. Wanchen Li Xuecai Zhang Low-density reference fingerprinting SNP dataset of CIMMYT maize lines for quality control and genetic diversity analyses |
| title | Low-density reference fingerprinting SNP dataset of CIMMYT maize lines for quality control and genetic diversity analyses |
| title_full | Low-density reference fingerprinting SNP dataset of CIMMYT maize lines for quality control and genetic diversity analyses |
| title_fullStr | Low-density reference fingerprinting SNP dataset of CIMMYT maize lines for quality control and genetic diversity analyses |
| title_full_unstemmed | Low-density reference fingerprinting SNP dataset of CIMMYT maize lines for quality control and genetic diversity analyses |
| title_short | Low-density reference fingerprinting SNP dataset of CIMMYT maize lines for quality control and genetic diversity analyses |
| title_sort | low density reference fingerprinting snp dataset of cimmyt maize lines for quality control and genetic diversity analyses |
| topic | heterotic groups quality control single nucleotide polymorphism maize data |
| url | https://hdl.handle.net/10568/127059 |
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