Genetic characterization of CIMMYT inbred maize lines and open pollinated populations using large scale fingerprinting methods

The International Maize and Wheat Improvement Center (CIM-MYT) currently holds about 17 000 samples of maize (Zea mays L.) and teosinte (Z. mays, several subspecies), a wild relative of maize. Seven CIMMYT populations and 57 inbreds were characterized by simple sequence repeat (SSR) markers. SSRs chosen from almost every bin in the maize genetic map were tested for repeatability, ease of automation in allele calling, and discrimination (information content). Eighty-five SSRs were found to be repeatable and easily automated, and were run on all material in the study. Fifty-three of these SSRs were found to be the most discriminatory and will be used in future routine fingerprinting studies. The seven breeding populations clustered as would be predicted on the basis of pedigree and heterotic grouping. Genetic diversity within each population was significantly higher than diversity between populations, indicating that the populations are heterogeneous at the molecular level. The inbreds also showed a high level of genetic diversity, indicating that CIMMYT breeders have successfully incorporated considerable genetic diversity into CIMMYT maize germplasm. Only lines closely related by pedigree clustered together. Population of origin and heterotic grouping were not associated with the clusters formed on the basis of SSR markers, a result consistent with the high level of diversity within source populations of the inbreds. Although this will make it more difficult to assign CIMMYT inbred lines to currently existing heterotic groups by means of markers, the markers may be useful in refining the CIMMYT heterotic groups into additional and more uniform groups.