The presence (to varying degrees of intensity) or absence of anthocyanin pigmentation within plant tissues (awn, auricle, lemma nerve) is controlled by the genetic locus ANTHOCYANINLESS 2 (ANT2), thought to be encoded by HvbHLH1. A 16bp exonic deletion within HvbHLH1 results in a truncated predicted protein that is diagnostic for the recessive ant2 allele that results in the absence of anthocyanin in all tissues. This assay tests for a SNP found to be in perfect linkage disequilibrium with the 16bp deletion in all UK barley varieties assayed to date. SNP T = anthocyanin non-expresser (diagnostic for haplotype 1), SNP C = anthocyanin expresser. Note: see position 4289bp in reference sequence alignment.

Note: a marker designed to directly assay the 16bp HvbHLH1 InDel failed to convert to the KASPar platform. However, a PCR/agarose-gel based marker for the 16bp InDel is published (PMID: 21115826).

PMID:21115826