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United States Department of Agriculture

Agricultural Research Service

Research Project: Genetic Improvement of Maize with Enhanced Resistance to Aflatoxin and Insects

Location: Corn Host Plant Resistance Research

Title: Genetic relationships and structure among open pollinated maize varieties adapted to eastern and southern Africa using microsatellite markers

Authors
item Semagn, Kassa -
item Magorokosho, Cosmos -
item Ogugo, Veronica -
item Makumbi, Dan -
item Warburton, Marilyn

Submitted to: Molecular Breeding
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: May 27, 2014
Publication Date: June 10, 2014
Citation: Semagn, K., Magorokosho, C., Ogugo, V., Makumbi, D., Warburton, M.L. 2014. Genetic relationships and structure among open-pollinated maize varieties adapted to eastern and southern Africa using microsatellite markers. Molecular Breeding. DOI 10.1007/s11032-014-0126-z

Interpretive Summary: The International Maize and Wheat Improvement Center (CIMMYT), in collaboration with the national agricultural systems in sub-Saharan Africa (SSA), have developed various stress-tolerant and more nutritious open-pollinated varieties (OPVs) of maize that are suitable for smallholder farmers’ growing conditions in the region. In this study, we investigated how the OPVs bred in different countries of SSA are related to each other, and if they show differentiation at the genetic level due to growing conditions, breeding program, or the physical attributes that each OPV contains. In total, 218 diverse OPVs widely used in southern and eastern Africa were analyzed with 51 microsatellite (SSR) genetic markers. Our data showed the presence large amounts of genetic variability in the sample, but there were no patterns of relationships easily discernible based on but breeding programs, maturity groups, mega-environments, and specific agronomic traits. This indicates that OPVs from different regions, bred by different groups, and for different end uses, are all somewhat related to each other. This may be due to recycling of the best parental lines in developing the OPVs in all regions, or it may be that the parents used in developing the OPVs are genetically related. Either way, this study indicates that improvement may be made by selecting OPVs that are specifically adapted to each growing region rather than growing the same germplasm (or related germplasm) across large geographical areas.

Technical Abstract: The International Maize and Wheat Improvement Center (CIMMYT), in collaboration with the national agricultural systems (NARS) in sub-Saharan Africa (SSA), have developed various stress-tolerant and more nutritious open-pollinated varieties (OPVs) of maize that are suitable for smallholder farmers’ growing conditions in the region. We investigated the extent of genetic differences, patterns of relationships and population structure among 218 diverse OPVs widely used in southern and eastern Africa using the model-based population structure, analysis of molecular variance, cluster analysis, principal component analysis, and discriminant analysis. The OPVs were genotyped in bulk with 51 microsatellite markers and the fluorescent detection system of the Applied Biosystems 3730 Capillary Sequencer.The number of alleles detected in each OPV varied from 72 to 155, with an overall mean of 127.6, suggesting the presence of large genetic variability among the OPVs. Genetic distance among the OPVs varied from 0.051 to 0.434, with a mean of 0.227. The different multivariate methods suggest the presence of 2 or 3 possible groups among the OPVs with overlapping variation between breeding programs, maturity groups, mega-environments, and specific agronomic traits. The OPVs widely used in eastern Africa either originated from the southern African maize breeding programs or the majority of inbred lines used as parents by the two breeding programs in developing the OPVs may be genetically related. Some of the OPVs are much older than others but they still did not show a clear pattern of genetic differentiation as compared with the recently developed ones, which is most likely due to recycling of the best parental lines in forming new OPVs. Only 5.8% and 10.8 of the pairwise kinship estimates were < 0.1 and < 0.25, respectively, clearly suggesting the presence of large proportion of common genes among the OPVs. Our data showed the presence of larger genetic variability but lower genetic distance and no clear population structure between breeding programs, maturity groups, mega-environments, and specific agronomic traits. Such results may be due to recycling of the best parental lines in developing the OPVs or the parents used in developing the OPVs may be genetically related.

Last Modified: 7/22/2014
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