Chapter 1 - High-Throughput Genotyping for Cereal Research and Breeding

Abstract

Genotyping with single-nucleotide polymorphism (SNP) markers is now widely applied in genetic research and breeding of small grain cereals. Through various technologies including the sequencing of specific fractions of the genome such as transcribed sequences or the resequencing of varieties and lines, an essentially unlimited source of SNP markers has become available. Routine genotyping of many samples, especially within the framework of genomic selection (GS), is now being applied using two specific approaches which are genotyping-by-sequencing (GBS) and array-based genotyping with fixed marker sets. In small grain breeding, array-based genotyping is undergoing a development from expensive large arrays to smaller, newly developed second-generation arrays. Such arrays include markers for specific traits as well as high-quality polymorphic markers, which are evenly distributed along the chromosomes and which have little ascertainment bias. In this chapter, we provide an overview on the available high-throughput genotyping systems mainly for the small grain cereals such as barley, wheat, rye, and oats.