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APA citation
Qu. J., Chassaigne, A. A., Fu, F., Yu, H., Dreher, K. A., Nair, S., Gowda, M., Beyene, Y., Makumbi, D., Dhliwayo, T., San Vicente, F. M., 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
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Abstract
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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.
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Journal
Plants
Journal volume
11
Journal issue
22
Article number
3092
Place of Publication
Basel (Switzerland)
Publisher
MDPI
Related Datasets
CGIAR Initiatives
Initiative
Genebanks
Accelerated Breeding
Accelerated Breeding
Impact Area
Environmental health & biodiversity
Nutrition, health & food security
Nutrition, health & food security
Action Area
Genetic Innovation
Donor or Funder
Bill & Melinda Gates Foundation (BMGF)
CGIAR Trust Fund
United States Agency for International Development (USAID)
Foundation for Food & Agriculture Research (FFAR)
CGIAR Trust Fund
United States Agency for International Development (USAID)
Foundation for Food & Agriculture Research (FFAR)