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Uncovering the genetic secrets of purple rice

Uncovering the genetic secrets of purple rice


The mysterious ways of genes influencing the character of crop plants through long periods of domestication, selection and modern breeding continues to perplex genomics specialists, as found out by the genome researchers working on coloured rice, Purpleputtu recently. Even the whole Genome Sequencing (WGS) of the Purpleputtu rice variety has not fully opened the windows to the genetic secrets to the researchers.

Researchers at the SciGenom Research Foundation, Chennai, said the genome sequencing of Purpleputtu revealed around 65,000 unique genetic mutations compared with the reference sequence, of which about 50 are in the genes of the colour pathway. The question of how specific genes and gene networks control the expression of its uniqueness, the purple colour, still remains an unanswered mystery, say researchers.

In most cultivated white grain rice varieties, a regulatory gene, Rc is missing 14 base pairs, which is believed to have changed the phenotype of seeds from coloured to white. The presence of the 14 base pairs is believed to help regulate the anthocyanin pathway enzymes to produce coloured seeds, and its absence is accounted for the grains remaining more or less white. The sequencing revealed that the 14 base pairs of Rc gene were absent in Purpleputtu variety. Yet, its seeds remained true to the nomenclature and were found retaining the colour, explained George Thomas, Director, SGRF, and Arjula R. Reddy, advisor to the Foundation. This leads to the conclusion that there are alternative regulatory pathways operating in Purpleputtu, they explained.

The Foundation decided to focus on the purple rice variety as many traditional lines or their wild cousins have not yet been fully sequenced. This traditional variety, while being grown as a bio-barrier and as a marker line between test plots in rice fields to prevent cross-pollination, remained genetically uncorrupted and retained its unique characters over the years. The seed shattering gene and a few other domestication-related genes were found intact in a highly conserved area of about 4.5 million base pairs of Purpleputtu rice genome.

The whole genome sequence has been released in the public domain to serve as a reference point for indica rices, particularly coloured ones, they said.

The focus has now shifted to “understanding the molecular regulation of colour development, domestication and responses to stresses like drought, salt, extreme temperatures and photoperiodic insensitivity of this rice in order to improve it for better performance and its possible utility in breeding for these traits” they explained.



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