Abstract Anthocyanin biosynthesis in plants is complex, especially in a polyploid monocot wheat plant. Using whole-genome sequencing, transcriptomics, and LC-MS/MS, we investigated anthocyanin production in pigmented (black, blue, and purple) wheat seeds. According to differential gene expression profiling, 2AS-MYC, 7DL-MYB, WD40 regulatory genes controls purple pericarp coloration, 4DL-MYC, 2AS-MYC, 7DL-MYB, WD40 controls blue aleurone coloration, and 4DL-MYC, 7DL-MYB, WD40 controls black aleurone colour. We believe that at least one MYC and MYB isoform is sufficient to regulate the anthocyanin synthesis in pericarp or aleurone. Based upon the reduced expressions of the genes belonging to the 4D, SSR molecular marker mapping, variant calling using genome sequencing and IGV browser gene structure visualization, it was inferred that the advanced black and blue wheat lines were substitution lines (4E{4D}), with very small recombinations. Pericarp anthocyanin profiling is controlled by a mutation in chromosome 2AS of purple wheat, and environmental variations more influence pigmented pericarp trait. The expression patterns of anthocyanin structural and other genes varied in different colored wheat, corroborating differences in agronomical metrics.

Transcriptional signature pattern in black, blue and purple wheat and impact on seed pigmentation and other associated features: Comparative transcriptomics, genomics and metabolite profiling