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Blue aleurone is a useful and interesting trait in common wheat that was derived from related species. Here, transcriptomes of blue and white aleurone were compared for isolating  Blue aleurone 1  ( Ba1 ) transferred from  Thinopyrum ponticum . In the genes involved in anthocyanin biosynthesis, only a basic helix-loop-helix (bHLH) transcription factor,  ThMYC4E , had a higher transcript level in blue aleurone phenotype, and was homologous to the genes on chromosome 4 of  Triticum aestivum .  ThMYC4E  carried the characteristic domains (bHLH-MYC_N, HLH and ACT-like) of a bHLH transcription factor, and clustered with genes regulating anthocyanin biosynthesis upon phylogenetic analysis. The over-expression of  ThMYC4E  regulated anthocyanin biosynthesis with the coexpression of the MYB transcription factor  ZmC1  from maize.  ThMYC4E  existed in the genomes of the addition, substitution and near isogenic lines with the blue aleurone trait derived from  Th .  ponticum , and could not be detected in any germplasm of  T .  urartu ,  T .  monococcum ,  T .  turgidum ,  Aegilops tauschii  or  T .  aestivum , with white aleurone. These results suggested that  ThMYC4E  was candidate  Ba1  gene controlling the blue aleurone trait in  T .  aestivum  genotypes carrying  Th .  ponticum  introgression. The  ThMYC4E  isolation aids in better understanding the genetic mechanisms of the blue aleurone trait and in its more effective use during wheat breeding.

ThMYC4E, candidate Blue aleurone 1 gene controlling the associated trait in Triticum aestivum