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

Molecular characterization of open-pollinated maize varieties (OPVs) is fundamentally important in maize germplasm improvement. 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 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. 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 2–4 possible groups, primarily by maturity groups but also with overlapping variation between breeding programs, mega-environments, and specific agronomic traits. Nearly all OPVs in group 1 and group 2 belong to the intermediate-late and early maturity groups, respectively. Group 3 consisted of mainly intermediate maturing OPVs, while group 4 contained OPVs of different maturity groups. 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 might 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.