Molecular characterization of diverse CIMMYT maize inbred lines from eastern and southern Africa using single nucleotide polymorphic markers
Background: Knowledge of germplasm diversity and relationships among elite breeding materials is fundamentally important in crop improvement. We genotyped 450 maize inbred lines developed and/or widely used by CIMMYT breeding programs in both Kenya and Zimbabwe using 1065 SNP markers to (i) investigate population structure and patterns of relationship of the germplasm for better exploitation in breeding programs; (ii) assess the usefulness of SNPs for identifying heterotic groups commonly used by CIMMYT breeding programs; and (iii) identify a subset of highly informative SNP markers for routine and low cost genotyping of CIMMYT germplasm in the region using uniplex assays. Results. Genetic distance for about 94% of the pairs of lines fell between 0.300 and 0.400. Eighty four percent of the pairs of lines also showed relative kinship values ≤ 0.500. Model-based population structure analysis, principal component analysis, neighbor-joining cluster analysis and discriminant analysis revealed the presence of 3 major groups and generally agree with pedigree information. The SNP markers did not show clear separation of heterotic groups A and B that were established based on combining ability tests through diallel and line x tester analyses. Our results demonstrated large differences among the SNP markers in terms of reproducibility, ease of scoring, polymorphism, minor allele frequency and polymorphic information content. About 40% of the SNPs in the multiplexed chip-based GoldenGate assays were found to be uninformative in this study and we recommend 644 of the 1065 for low to medium density genotyping in tropical maize germplasm using uniplex assays. Conclusions. There were high genetic distance and low kinship coefficients among most pairs of lines, clearly indicating the uniqueness of the majority of the inbred lines in these maize breeding programs. The results from this study will be useful to breeders in selecting best parental combinations for new breeding crosses, mapping population development and marker assisted breeding.
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BioMed Central
2012
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Subjects: | AGRICULTURAL SCIENCES AND BIOTECHNOLOGY, MAIZE, INBRED LINES, SINGLE NUCLEOTIDE POLYMORPHISM, GENETIC MARKERS, |
Online Access: | http://hdl.handle.net/10883/1881 |
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dig-cimmyt-10883-18812024-03-12T20:56:16Z Molecular characterization of diverse CIMMYT maize inbred lines from eastern and southern Africa using single nucleotide polymorphic markers Fentaye Kassa Semagn Magorokosho, C. Vivek, B. Makumbi, D. Beyene, Y. Mugo, S.N. Prasanna, B.M. Warburton, M.L. AGRICULTURAL SCIENCES AND BIOTECHNOLOGY MAIZE INBRED LINES SINGLE NUCLEOTIDE POLYMORPHISM GENETIC MARKERS Background: Knowledge of germplasm diversity and relationships among elite breeding materials is fundamentally important in crop improvement. We genotyped 450 maize inbred lines developed and/or widely used by CIMMYT breeding programs in both Kenya and Zimbabwe using 1065 SNP markers to (i) investigate population structure and patterns of relationship of the germplasm for better exploitation in breeding programs; (ii) assess the usefulness of SNPs for identifying heterotic groups commonly used by CIMMYT breeding programs; and (iii) identify a subset of highly informative SNP markers for routine and low cost genotyping of CIMMYT germplasm in the region using uniplex assays. Results. Genetic distance for about 94% of the pairs of lines fell between 0.300 and 0.400. Eighty four percent of the pairs of lines also showed relative kinship values ≤ 0.500. Model-based population structure analysis, principal component analysis, neighbor-joining cluster analysis and discriminant analysis revealed the presence of 3 major groups and generally agree with pedigree information. The SNP markers did not show clear separation of heterotic groups A and B that were established based on combining ability tests through diallel and line x tester analyses. Our results demonstrated large differences among the SNP markers in terms of reproducibility, ease of scoring, polymorphism, minor allele frequency and polymorphic information content. About 40% of the SNPs in the multiplexed chip-based GoldenGate assays were found to be uninformative in this study and we recommend 644 of the 1065 for low to medium density genotyping in tropical maize germplasm using uniplex assays. Conclusions. There were high genetic distance and low kinship coefficients among most pairs of lines, clearly indicating the uniqueness of the majority of the inbred lines in these maize breeding programs. The results from this study will be useful to breeders in selecting best parental combinations for new breeding crosses, mapping population development and marker assisted breeding. 2013-06-07T21:02:52Z 2013-06-07T21:02:52Z 2012 Article http://hdl.handle.net/10883/1881 10.1186/1471-2164-13-113 English CIMMYT manages Intellectual Assets as International Public Goods. The user is free to download, print, store and share this work. In case you want to translate or create any other derivative work and share or distribute such translation/derivative work, please contact CIMMYT-Knowledge-Center@cgiar.org indicating the work you want to use and the kind of use you intend; CIMMYT will contact you with the suitable license for that purpose. Open Access PDF KENYA ZIMBABWE BioMed Central 13 BMC Genomics 113 |
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AGRICULTURAL SCIENCES AND BIOTECHNOLOGY MAIZE INBRED LINES SINGLE NUCLEOTIDE POLYMORPHISM GENETIC MARKERS AGRICULTURAL SCIENCES AND BIOTECHNOLOGY MAIZE INBRED LINES SINGLE NUCLEOTIDE POLYMORPHISM GENETIC MARKERS |
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AGRICULTURAL SCIENCES AND BIOTECHNOLOGY MAIZE INBRED LINES SINGLE NUCLEOTIDE POLYMORPHISM GENETIC MARKERS AGRICULTURAL SCIENCES AND BIOTECHNOLOGY MAIZE INBRED LINES SINGLE NUCLEOTIDE POLYMORPHISM GENETIC MARKERS Fentaye Kassa Semagn Magorokosho, C. Vivek, B. Makumbi, D. Beyene, Y. Mugo, S.N. Prasanna, B.M. Warburton, M.L. Molecular characterization of diverse CIMMYT maize inbred lines from eastern and southern Africa using single nucleotide polymorphic markers |
description |
Background: Knowledge of germplasm diversity and relationships among elite breeding materials is fundamentally important in crop improvement. We genotyped 450 maize inbred lines developed and/or widely used by CIMMYT breeding programs in both Kenya and Zimbabwe using 1065 SNP markers to (i) investigate population structure and patterns of relationship of the germplasm for better exploitation in breeding programs; (ii) assess the usefulness of SNPs for identifying heterotic groups commonly used by CIMMYT breeding programs; and (iii) identify a subset of highly informative SNP markers for routine and low cost genotyping of CIMMYT germplasm in the region using uniplex assays. Results. Genetic distance for about 94% of the pairs of lines fell between 0.300 and 0.400. Eighty four percent of the pairs of lines also showed relative kinship values ≤ 0.500. Model-based population structure analysis, principal component analysis, neighbor-joining cluster analysis and discriminant analysis revealed the presence of 3 major groups and generally agree with pedigree information. The SNP markers did not show clear separation of heterotic groups A and B that were established based on combining ability tests through diallel and line x tester analyses. Our results demonstrated large differences among the SNP markers in terms of reproducibility, ease of scoring, polymorphism, minor allele frequency and polymorphic information content. About 40% of the SNPs in the multiplexed chip-based GoldenGate assays were found to be uninformative in this study and we recommend 644 of the 1065 for low to medium density genotyping in tropical maize germplasm using uniplex assays. Conclusions. There were high genetic distance and low kinship coefficients among most pairs of lines, clearly indicating the uniqueness of the majority of the inbred lines in these maize breeding programs. The results from this study will be useful to breeders in selecting best parental combinations for new breeding crosses, mapping population development and marker assisted breeding. |
format |
Article |
topic_facet |
AGRICULTURAL SCIENCES AND BIOTECHNOLOGY MAIZE INBRED LINES SINGLE NUCLEOTIDE POLYMORPHISM GENETIC MARKERS |
author |
Fentaye Kassa Semagn Magorokosho, C. Vivek, B. Makumbi, D. Beyene, Y. Mugo, S.N. Prasanna, B.M. Warburton, M.L. |
author_facet |
Fentaye Kassa Semagn Magorokosho, C. Vivek, B. Makumbi, D. Beyene, Y. Mugo, S.N. Prasanna, B.M. Warburton, M.L. |
author_sort |
Fentaye Kassa Semagn |
title |
Molecular characterization of diverse CIMMYT maize inbred lines from eastern and southern Africa using single nucleotide polymorphic markers |
title_short |
Molecular characterization of diverse CIMMYT maize inbred lines from eastern and southern Africa using single nucleotide polymorphic markers |
title_full |
Molecular characterization of diverse CIMMYT maize inbred lines from eastern and southern Africa using single nucleotide polymorphic markers |
title_fullStr |
Molecular characterization of diverse CIMMYT maize inbred lines from eastern and southern Africa using single nucleotide polymorphic markers |
title_full_unstemmed |
Molecular characterization of diverse CIMMYT maize inbred lines from eastern and southern Africa using single nucleotide polymorphic markers |
title_sort |
molecular characterization of diverse cimmyt maize inbred lines from eastern and southern africa using single nucleotide polymorphic markers |
publisher |
BioMed Central |
publishDate |
2012 |
url |
http://hdl.handle.net/10883/1881 |
work_keys_str_mv |
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