Single nucleotide polymorphism (SNP) genotyping is nowadays widely used in wheat genetics and breeding. Examples for uses are the analysis of population structure and genetic relationships, the identification and location of qualitative and quantitative (QTLs) traits in appropriate populations, marker-assisted selection and backcrossing, and the identification marker-trait associations. Currently in most cases, SNP genotyping arrays are used which permit the simultaneous analysis of many thousands of SNP markers in a cost-efficient way with unparalleled precision. These relatively low-priced SNP arrays have also become a major tool in Genomic Selection within routine wheat breeding.

We describe the continuous development and optimization of our wheat genotyping arrays designed for wheat genome analyses and Genomic Selection based on important criteria: One is marker quality including the detection of only one specific locus in one of the wheat genomes and clear calling of the three allelic states.

Another emphasis is furthermore placed on the detection of as many haplotype blocks as possible based on a genotyping database including several thousand wheat varieties from the entire world. With this data set, we have selected 1-3 markers per identified haplotype block so that a maximum of information can be obtained with these arrays. A detailed analysis revealed that on the wheat genome sequence these haplotype-specific markers are highly clustered towards the end of the chromosomes where also most of the recombination events occur. To further increase the use of these arrays, we have added a set of several hundred publicly available markers that have been reported to be linked to specific traits in the literature.

Currently, we use two different genotyping arrays that include approximately 25,000 and 8,000 markers, respectively. The 25K SNP marker array is optimized for the detection of many haplotype blocks while the reduced 8K marker array can further decrease the costs per genotyped sample and is widely used for wheat breeding including marker imputation based on previous genotyping of parental lines with the 25K marker array or other available wheat genotyping arrays based on defined sets of common markers. These two arrays have been used for the genotyping of several hundred-thousands of lines from all over the world mainly in hexaploid wheat but also in tetraploid Durum wheat.