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Background  Among natural populations, there are different colours of barley ( Hordeum vulgare  L.). The colour of barley grains is directly related to the accumulation of different pigments in the aleurone layer, pericarp and lemma. Blue grain colour is due to the accumulation of anthocyanins in the aleurone layer, which is dependent on the presence of five  Blx  genes that are not sequenced yet ( Blx1 ,  Blx3  and  Blx4  genes clustering on chromosome 4HL and  Blx2  and  Blx5  on 7HL). Due to the health benefits of anthocyanins, blue-grained barley can be considered as a source of dietary food. The goal of the current study was to identify and characterize components of the anthocyanin synthesis regulatory network for the aleurone layer in barley.    Results  The candidate genes for components of the regulatory complex MBW (consisting of transcription factors  M YB,  b HLH/MYC and  W D40) for anthocyanin synthesis in barley aleurone were identified. These genes were designated  HvMyc2  (4HL),  HvMpc2  (4HL), and  HvWD40  (6HL).  HvMyc2  was expressed in aleurone cells only. A loss-of-function (frame shift) mutation in  HvMyc2  of non-coloured compared to blue-grained barley was revealed. Unlike aleurone-specific  HvMyc2 , the  HvMpc2  gene was expressed in different tissues; however, its activity was not detected in non-coloured aleurone in contrast to a coloured aleurone, and allele-specific mutations in its promoter region were found. The single-copy gene  HvWD40 , which encodes the required component of the regulatory MBW complex, was expressed constantly in coloured and non-coloured tissues and had no allelic differences.  HvMyc2  and  HvMpc2  were genetically mapped using allele-specific developed CAPS markers developed.  HvMyc2  was mapped in position between SSR loci  XGBS0875-4H  (3.4 cM distal) and  XGBM1048-4H  (3.4 cM proximal) matching the region chromosome 4HL where the  Blx- cluster was found. In this position, one of the anthocyanin biosynthesis structural genes ( HvF3’5’H ) was also mapped using an allele-specific CAPS-marker developed in the current study.    Conclusions  The genes involved in anthocyanin synthesis in the barley aleurone layer were identified and characterized, including components of the regulatory complex MBW, from which the MYC-encoding gene ( HvMyc2 ) appeared to be the main factor underlying variation of barley by aleurone colour.    Electronic supplementary material  The online version of this article (10.1186/s12870-017-1122-3) contains supplementary material, which is available to authorized users.

Identification and characterization of regulatory network components for anthocyanin synthesis in barley aleurone