High-throughput SNP profiling of genetic resources in crop plants using genotyping arrays

Abstract

Using high-throughput DNA sequencing technologies, it is now possible to quickly and reliably identify many thousands to millions of SNPs in a species. They can subsequently serve as markers for the development of large genotyping arrays. Large numbers of individuals derived from gene banks, landraces, breeding material and varieties can be genotyped with such arrays at an extremely high marker density in a fast, efficient and highly reproducible way. Based on our experience, we provide in this chapter an overview on various aspects that have to be considered within the process of developing such genotyping arrays, including the SNP discovery and/or collection, possible selection criteria for SNPs to be put on the array, SNP scoring and allele calling as well as data assembly for the analysis of millions of genotypes. To make the best use of these genotyping data, it will be very important to establish databases containing marker data from many genotyping experiments in order to simplify downstream data processing for scientific as for breeding purposes.