Single-feature polymorphism discovery in the barley transcriptome

Whole-genome sequences of Arabidopsis and rice have provided a fundamental platform for the discovery of gene content and function in dicot and monocot plants. Research on the model species has provided a wealth of knowledge on universal biochemical and genetic processes, as well as the development of analytical tools that are applicable to other plant species [1-3].The availability of abundant, high-throughput sequence-based markers is the key for detailed genome-wide trait analysis. Single-nucleotide polymorphisms (SNP) are the most common sequence variation and a significant amount of effort has been invested in resequencing alleles to discovery SNPs. In fully sequenced small-genome model organisms SNP discovery is relatively straightforward, although high-throughput SNP discovery in natural populations remains both expensive and time-consuming [4].A number of recent studies have reported the use of oligonucleotide arrays, including expression arrays, for SNP detection in a highly parallel manner [5]. In these studies, whole genomic DNA was demonstrated to work very well for simple organisms such as yeast [6,7], and even complex, albeit relatively small genomes, such as Arabidopsis [8]. However, the application of oligonucleotide arrays for SNP detection in large genomes, such as human, has relied on prior complexity reduction using PCR-based enrichment [9,10]. The use of oligonucleotide arrays for simultaneous genotyping and gene-expression analysis using RNA target has also been reported in yeast [11]. While there is arguably little need for enhanced SNP discovery in yeast, the real power of the approach came from coupling genotyping and gene expression analysis.For large-genome species, including crops such as wheat and barley, full-genome sequences may not be available in the near future. This has been compensated to some extent by model species that have allowed conserved biological processes to be studied. However, while Arabidopsis and rice provide insight