The fast and the cheap: SNP and DArT-based whole genome profiling for crop improvement

Abstract

In this paper we focus on two technologies that appear to be best suited for whole-genome profiling: SNP and DArT. Sequencing accomplishments in several model species have shown that the value of sequencing is limited without comprehensive infor-mation about genome diversity. In the sequenced genomes, large studies are fuelling the development of SNP typing techniques. These techniques will eventually replace DNA typing methods with lower throughput such as SSRs, AFLP, CAPs and RFLPs. The most popular SNP typing assays and the most promising SNP technology platforms are briefly reviewed here. The slow uptake of SNP markers in plants, especially those plants for which limited resources are invested, is caused partly by the small or nonexistent market demand and partly by the lack of sequence information. DArT is an upcoming techno-logy that avoids most of the problems of lower-throughput typing technologies and does not require sequence information. Here we describe the principles of DArT and the cur-rent status of development of this technology. We also discuss the requirements for an effective application of whole-genome profiling to plant breeding.