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...
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| Format: | Article |
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MDPI AG
2022-11-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/11/22/3092 |
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| author | Jingtao Qu Alberto A. Chassaigne-Ricciulli Fengling Fu Haoqiang Yu Kate Dreher Sudha K. Nair Manje Gowda Yoseph Beyene Dan Makumbi Thanda Dhliwayo Felix San Vicente Michael Olsen Boddupalli M. Prasanna Wanchen Li Xuecai Zhang |
| author_facet | Jingtao Qu Alberto A. Chassaigne-Ricciulli Fengling Fu Haoqiang Yu Kate Dreher Sudha K. Nair Manje Gowda Yoseph Beyene Dan Makumbi Thanda Dhliwayo Felix San Vicente Michael Olsen Boddupalli M. Prasanna Wanchen Li Xuecai Zhang |
| author_sort | Jingtao Qu |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-03-09T18:04:19Z |
| format | Article |
| id | doaj.art-c8ac1a8370ea40dbb69ad69b27d312f1 |
| institution | Directory Open Access Journal |
| issn | 2223-7747 |
| language | English |
| last_indexed | 2024-03-09T18:04:19Z |
| publishDate | 2022-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Plants |
| spelling | doaj.art-c8ac1a8370ea40dbb69ad69b27d312f12023-11-24T09:39:28ZengMDPI AGPlants2223-77472022-11-011122309210.3390/plants11223092Low-Density Reference Fingerprinting SNP Dataset of CIMMYT Maize Lines for Quality Control and Genetic Diversity AnalysesJingtao Qu0Alberto A. Chassaigne-Ricciulli1Fengling Fu2Haoqiang Yu3Kate Dreher4Sudha K. Nair5Manje Gowda6Yoseph Beyene7Dan Makumbi8Thanda Dhliwayo9Felix San Vicente10Michael Olsen11Boddupalli M. Prasanna12Wanchen Li13Xuecai Zhang14Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, ChinaInternational Maize and Wheat Improvement Center (CIMMYT), El Batan, Texcoco 56237, MexicoMaize Research Institute, Sichuan Agricultural University, Chengdu 611130, ChinaMaize Research Institute, Sichuan Agricultural University, Chengdu 611130, ChinaInternational Maize and Wheat Improvement Center (CIMMYT), El Batan, Texcoco 56237, MexicoAsia Regional Maize Program, International Maize and Wheat Improvement Center (CIMMYT), ICRISAT Campus, Patancheru, Hyderabad 502324, Telangana, IndiaInternational Maize and Wheat Improvement Center (CIMMYT), Village Market, P.O. Box 1041, Nairobi 00621, KenyaInternational Maize and Wheat Improvement Center (CIMMYT), Village Market, P.O. Box 1041, Nairobi 00621, KenyaInternational Maize and Wheat Improvement Center (CIMMYT), Village Market, P.O. Box 1041, Nairobi 00621, KenyaInternational Maize and Wheat Improvement Center (CIMMYT), El Batan, Texcoco 56237, MexicoInternational Maize and Wheat Improvement Center (CIMMYT), El Batan, Texcoco 56237, MexicoInternational Maize and Wheat Improvement Center (CIMMYT), Village Market, P.O. Box 1041, Nairobi 00621, KenyaInternational Maize and Wheat Improvement Center (CIMMYT), Village Market, P.O. Box 1041, Nairobi 00621, KenyaMaize Research Institute, Sichuan Agricultural University, Chengdu 611130, ChinaInternational Maize and Wheat Improvement Center (CIMMYT), El Batan, Texcoco 56237, MexicoCIMMYT 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.https://www.mdpi.com/2223-7747/11/22/3092tropical maizeCIMMYT maize line (CML)reference SNP datasetfingerprintingquality controlheterotic group |
| spellingShingle | Jingtao Qu Alberto A. Chassaigne-Ricciulli Fengling Fu Haoqiang Yu Kate Dreher Sudha K. Nair Manje Gowda Yoseph Beyene Dan Makumbi Thanda Dhliwayo Felix San Vicente Michael Olsen Boddupalli M. Prasanna Wanchen Li Xuecai Zhang Low-Density Reference Fingerprinting SNP Dataset of CIMMYT Maize Lines for Quality Control and Genetic Diversity Analyses Plants tropical maize CIMMYT maize line (CML) reference SNP dataset fingerprinting quality control heterotic group |
| 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 | tropical maize CIMMYT maize line (CML) reference SNP dataset fingerprinting quality control heterotic group |
| url | https://www.mdpi.com/2223-7747/11/22/3092 |
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