Distributed simple sequence repeat markers for efficient mapping from maize public mutagenesis populations

The genome sequence of the B73 maize inbred enables map-based cloning of genetic variants underlying phenotypes. In parallel to sequencing efforts, multiple public mutagenesis resources are being developed predominantly in the W22 and B73 inbreds. Efficient platforms to map mutants in these genetic backgrounds would aid molecular genetic analysis of the public resources. We screened 505 simple sequence repeat markers for polymorphisms between the B73, Mo17, and W22 inbreds. Using common thermocycling conditions, 47.1% of the markers showed co-dominant polymorphisms in at least one pair of inbreds. Based on these results, we identified 85 distributed markers for mapping in all three inbred pairs. For each inbred pair, the distributed set has 64–71 polymorphic markers with a mean distance of 27–29 cM between markers. The distributed markers give nearly complete coverage of the genetic map for each inbred pair. We demonstrate the utility of the marker set for efficient placement of mutants on the maize genetic map with an example mapping experiment of a seed mutant from the UniformMu mutagenesis resource. We conclude that these distributed molecular markers enable rapid mapping of phenotypic variants from public mutagenesis populations.