HvGST plays a key role in anthocyanin accumulation in colored barley

SUMMARY Blue aleurone of barley is caused by the accumulation of delphinidin‐based derivatives. Although these compounds are ideal nutrients for human health, they are undesirable contaminants in malt brewing. Therefore, the ability to add and remove this trait easily would facilitate breeding barley for different purposes. Here we identified a glutathione S‐transferase gene (HvGST) that was responsible for the blue aleurone trait in Tibetan qingke barley by performing a genome‐wide association study and RNA‐sequencing analysis. Gene variation and expression analysis indicated that HvGST also participates in the transport and accumulation of anthocyanin in purple barley. Haplotype and the geographic distribution analyses of HvGST alleles revealed two independent natural variants responsible for the emergence of white aleurone: a 203‐bp deletion causing premature termination of translation in qingke barley and two key single nucleotide polymorphisms in the promoter resulting in low transcription in Western barley. This study contributes to a better understanding of mechanisms of colored barley formation, and provides a comprehensive reference for marker‐assisted barley breeding. Significance Statement The aleurone color of barley is one of the important traits for different purposes. However, the genetic mechanism of the formation of colored barley has not been well clarified so far. Here we discovered a blue aleurone candidate gene HvGST, which encodes a glutathione S‐transferase responsible for anthocyanin transport for the first time in barley. In addition, HvGST is one of the key genes that participated in the accumulation of anthocyanin in purple barley. Further analysis revealed two independent natural variants responsible for the emergence of white aleurone. The two variants also exhibited regional differences between the Eastern and the Western white barley.