Optimized Marker Sets for Array-Based Plant Genotyping – a Continuous Improvement Process

Using genotyping arrays, large sets of varieties and SNP markers can be analyzed in 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 many thousands of markers. Such information is crucial for the development of optimized array-based marker sets for plant breeding and genome research that provide a low amount of ascertainment bias and can be analyzed in a cost-effective way. For wheat as an example, we show that through a continuous analysis of new data generated from different genotyping arrays, it was possible to incrementally generate more comprehensive genotyping arrays which deliver a maximum of information. These optimized marker sets are ideal for marker-assisted selection and backcrossing, variety identification, the analysis genes associated with specific traits and genomic selection. With such arrays, TraitGenetics analyzes now many ten-thousands of samples each year for breeding companies and academic researchers.