Optimized Marker Sets for Plant Breeding Based on Array Data

Using genotyping arrays, large sets of varieties and SNP markers have been analyzed for many crop plants. Based on such data, it is now possible to generate marker databases that include mapping data, allele frequency data and haplotype information for thousands of markers in the respective species. Such information is crucial for the development of optimized marker sets for plant breeding that can be analyzed in a cost-effective way. TraitGenetics has started to exploit proprietary marker databases that have been generated with current varieties. In one example, we demonstrate the use of such a database for the generation of optimized marker sets for marker-assisted backcrossing and variety identification based on technical quality, distribution along chromosomes, allele frequency and haploytpe data. Another example is an array containing a selected marker set that provides non-redundant data at very low costs for genomic selection, association analysis and material characterization.