SNP and SSR marker analysis and mapping of a maize population

Although highly polymorphic SSRs are currently the marker of choice worldwide in maize breeding, single nucleotide polymorphisms (SNPs) as a newer marker system are recently used more extensively. The objective of this study was investigate the utility of SSR and SNP markers for mapping of a maize population adapted to conditions of Southeast Europe. Total of 294 F2:3 lines derived from a biparental mapping population were genotyped using 121 polymorphic SNP and SSR markers. The SNP markers were analyzed using the SNPlex technology. 56 of the 142 tested SNPs (39%) were polymorphic between the parents of the mapping population and were successfully mapped. The remaining markers were either not functional (5 = 3.5%) or not polymorphic (81 = 57%). No mapped SNP marker showed more than 10% missing data. On average, the level of missing data for SNPs (1.5%) was considerably lower than that for SSRs (3.4%). For the mapping procedure, the SNP data were combined SSR data. A comparison of the mapping data with the publicly available mapping data on SSR markers and the proprietary mapping data indicates that the map is of good quality and that the map position of almost all markers agrees with their published map position. Thus, information obtained from both marker systems is utilizable for further QTL analysis