Indeed, of the approximately 5,300 consensus sequences from the 5' set homologous to a barley sequence, 78% can be associated to a wheat 3' sequence in this way.
In the absence of a barley genome sequence, sequence information is restricted to EST databases.
For the cluster shown in Figure 7A, if the correlation between the profile for the barley sequence B and the wheat sequence W1 (C B, W1)) is similar to the correlation between B and W2(C B, W2)), one would conclude that there is little relation between functional and sequence divergence.
A Clo3 ortholog was not identified in the barley sequence databases.
The sequence identities at the amino acid level between BX2 to BX5 orthologs (e.g. from 76 to 79% identity between maize and wheat sequences, 76 to 81% between maize and wild barley sequences) and the BX enzyme substrate specificities are very high [ 8, 15- 17].
The Barley 1.0 Affymetrix microarray GeneChip array consists of 22,795 probe sets designed from an exemplar set of barley sequences derived from 350,000 high-quality expressed sequence tag (EST) contigs.
Second, despite established syntenic relationships between the Oryza, Hordeum and Brachypodium genomes, the inefficient mapping of barley sequenced RAD markers across species is likely a result of the majority of RAD loci emanating from areas of the barley genome which have significantly diverged at the nucleotide level since the speciation of the Poaceae [ 27, 28].
A similar success rate has also been achieved for the amplification of barley sequences harbouring published SNPs.
A barley IRI-like sequence contig (HvC3) with no IRI-domain still seems to play a functional role under etiolation.
When a complete barley genome sequence is available, the sequence identity and location of RAD loci will become clear.
