Colored wheat has always been a popular
research area because of
its high performance in the field and significant medical uses. Progress
has been made mapping the genes of purple or blue grains; however,
the reason why different grain colors form in wheat is not well understood.
We created wheat lines with different grain colors (purple and blue)
using the white grain cultivar Xiaoyan22 and located the candidate
region related to the purple and blue grains in chromosome 2A, 2B,
and 4D, 2A, respectively, by the bulked segregant RNA-seq. The transcriptomic
and metabolomic analyses of the three grains at different developmental
stages indicated that the upregulation of flavonoid 3′-hydroxylase/flavonoid 3′,5′hydroxylase 2 and TaMYC1/TaMYC4 was important for the formation
of purple/blue grains. The blue TaMYC4 had 16 nonsynonymous
single nucleotide variants verified by Sanger sequencing and possessed
a different splicing mode in the bHLH_MYC_N domain compared with the
reference database. Targeted high-performance liquid chromatography-mass
spectrometry/mass spectrometry analysis of anthocyanins found that
the purple and blue grains contained more pelargonidin, cyanidin,
and delphinidin, respectively. This study provides a comprehensive
understanding of the different color formations of wheat grains and
useful information about genetic improvements in wheat and other crops.