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United States Department of Agriculture

Agricultural Research Service


Location: Corn Host Plant Resistance Research

Title: Molecular characterization of diverse CIMMYT maize inbred lines from eastern and southern Africa using single nucleotide polymorphic markers

item Semagn, Kassa
item Magorokosho, Cosmos
item Vivek, Bindiganaville
item Makumbi, Dan
item Beyene, Yoseph
item Mugo, Stepehen
item Prasanna, B
item Warburton, Marilyn

Submitted to: Biomed Central (BMC) Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/25/2012
Publication Date: 3/25/2012
Citation: Semagn, K., Magorokosho, C., Vivek, B.S., Makumbi, D., Beyene, Y., Mugo, S., Prasanna, B.M., Warburton, M.L. 2012. Molecular characterization of diverse CIMMYT maize inbred lines from eastern and southern Africa using single nucleotide polymorphic markers. BioMed Central (BMC) Genetics. 13:113. doi:10.1186/1471-2164-12-113.

Interpretive Summary: Plant breeding creates superior cultivars for farmers by selecting the best parents and crossing them, and then selecting the best offspring from among the many progeny lines that result from the cross. Knowing how all the potential parents are related to each other will allow breeders to select better possible crosses, thus saving time and money by ruling out many of the unsuitable crosses before they are even made. Molecular markers can be used to construct the patterns of relationships among lines in a breeding program, and this has been done in maize for most of the world’s important breeding programs. In Africa, however, this has only rarely been done, and this article presents the results of a molecular marker diversity analysis of 450 maize lines developed and/or widely used by CIMMYT breeding programs in Kenya and Zimbabwe. The molecular markers used are new SNP markers, and the performance of each marker and the most informative subset of markers are also presented here, thus allowing breeders to use only the best markers in future breeding work. The African maize lines studied contained a great deal of genetic diversity, which is essential for plant breeders to select new superior lines from.

Technical Abstract: Knowledge of germplasm diversity and relationships among elite breeding materials is fundamentally important in crop improvement. We genotyped 450 maize lines developed and/or widely used by CIMMYT breeding programs both in 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. 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. Population structure analysis, principal component analysis, cluster analysis and discriminant analysis revealed the presence of 3 major groups and generally agree with pedigree information. Several lines with similar pedigree clustered in the same group. 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 the presence of large differences among the SNP markers in terms of reproducibility, ease for scoring, polymorphism, minor allele frequency and polymorphic information. About 40% of the SNPs in the multiplexed chip-based GoldenGate assays were found uninformative in this study and we recommend 644 of the 1065 for low to medium density genotyping in tropical maize germplasm using uniplex assays. There were substantially high genetic distance and low kinship coefficients among most pairs of lines, clearly indicating the importance of the majority of the inbred lines in maize breeding programs. The results from this study are useful to breeders in selecting best parental combinations for new pedigree start, mapping population development, and marker assisted breeding.

Last Modified: 09/18/2017
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