Vol. 9, Special Issue 12, Part D (2025)

The Chakhao poreitin, a variety of black rice exclusively found in the northeastern state of Manipur in India and its black colour is imparted by anthocyanin, a primary pigment that is responsible for the presence of black, red and blue colouration in various grains, flowers, fruits and vegetables. To identify the genes responsible for anthocyanin enrichment in Chakhao poreitin, an in-silico transcriptome study between white rice and black rice was performed to identify the differentially expressed genes in black rice. The genes were then subjected to COG and GO analysis, which resulted in a total of 135 genes related to anthocyanin production in some way or the other. Pathway enrichment and mapping to the existing flavonoid pathway to identify the underlying genes resulted in 24 biosynthetic genes being present in the pathway. These genes were mapped to the chromosomes of the rice genome to identify their genetic map positions. Phylogenetic reconstruction of these genes together with their homologous genes in A. thaliana was carried out using the maximum-likelihood method. A protein-protein interaction network between the expected regulatory genes (belonging to either MYB, WD40 or bHLH domains) and the biosynthetic genes was constructed and also mapped to a repository for regulatory element information for plants to identify the genes that regulate the biosynthetic genes. From the results, it can be predicted that the early biosynthetic genes (EBGs) are mainly regulated by R2R3-MYB genes, namely, MYB55 and MYBS3 whereas the late biosynthetic genes (LBGs) are regulated by the WD40 gene, TTG1 and the helix-loop-helix gene, Rc. Thus, we have highlighted the possible interaction of differentially expressed regulators and structural genes encoding potential biomarkers for the pigmentation trait in Black rice.