Structural genes encoding F3’5’h in 4d chromosome control the blue grain trait in wheat

Blue grained wheat contained a higher quantity of natural anthocyanin compounds while normal commercial wheat does not have. Though the genes related to several colours of wheat have been identified, the major genes in blue wheat are still unrevealed. Hence, combining the SNP mapping, and transcriptome analysis, pivotal genes regulating blue grain trait was identified. SNP genotyping was carried out in an F2 blue and white wheat population. The blue trait was controlled by a gene/locus located between two SNP markers of IWB 18525 and IWB16381 on the 4D chromosome. Comparative transcriptome analysis revealed that 40 structural differentially expressed genes (DEGs) related to anthocyanin biosynthesis had significant expression differences between blue and non-blue samples. Among them, 12 DEGs expressed only in blue samples while 2 DEGs were specific to blue wheat. Only two F3’5’H genes located in 4D (Traes_4DL_27C195FDE, Traes_4DL_5A3D8F519) were consistent with the location results performed in SNP genotyping. Further, F3’5’H is considered as the main enzyme for Delphinidin compounds, cause for blue colouration. Hence, two genes encoding F3’5’H in the 4D chromosome preferentially account for the blue pigmentation in wheat.