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SNP marker analysis and mapping of a maize population

Three multiplexes of 48/47/47 SNP (single nucleotide polymorphism) markers were analyzed on the 294 S4 lines of a biparental maize population as part of a quantitative trait loci (QTL) analysis. The three SNP multiplexes of maize were derived from a proprietary SNP marker set that has been generated at TraitGenetics GmbH. Following the extraction of the DNA, whole genome amplification (WGA) was performed in order to obtain DNA of equal quality for all samples. The SNP markers were analyzed using the SNPlex technology performed on an ABI 3730xl DNA sequencer. 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 SNP markers showed only 1.5% of missing data. One marker was of dominant inheritance. For the mapping procedure, the SNP data were combined with previously obtained microsatellite data. A comparison of the mapping data with the publicly available mapping data on microsatellite 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, the marker information can be used for QTL analysis.

SNP markers; maize; mapping

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