Why are the development and application of CAPS markers so different in bread wheat compared to barley?

Cleaved amplified polymorphic sequences (CAPS) are PCR-based markers utilising single nucleotide polymorphisms (SNPs) affecting recognition sites for restriction enzymes. The identification of a single or multiple SNPs plays a crucial role in CAPS marker development. Bread wheat and barley show large differences in SNP frequencies and, as a result, require different strategies for CAPS marker development. Differences between wheat and barley are based on the origin and evolutionary history of the species. Barley is a diploid species with highly polymorphic genetic regions containing multiple SNPs. Bread wheat contains only rare SNPs due to the double genetic 'bottle-neck' created by natural hybridisation and spontaneous polyploidisation. Author's own experiences and reports from the literature are described to support different strategies for CAPS marker development and application in these two crops. In barley, primers can be developed for genic regions flanking introns, where multiple SNPs can be easily identified and used for CAPS markers. By contrast, in bread wheat, several rounds of preliminary searches in silico for potential SNPs are necessary prior to identification of a suitable restriction site. However, following SNP and associated restriction enzyme identification, CAPS marker application in both crops is very similar. This chapter describes CAPS markers development in both wheat and barley.