The Rd Gene: Its Effects on the Pigmentation of Red Rice

Erica Cole and Ken Olsen

Biology Department, Washington University in St. Louis

 

Within most Oryza sativa varieties, Asian domesticated rice, the seeds are light-colored or “white”, while in the weedy and wild strains of Oryza, the seeds contain a dark red or brown pigmentation.  Light coloration is present when mutations knock out the function of pigment-creating genes.

Two essential genes that contribute to this pigment production are Rc and Rd.  When both function, the rice pericarp is dark red or brown.  When neither work or Rd functions while Rc does not, the pericarp is light-colored.  When Rc is functioning without Rd, the pericarp is a lighter brown.  We focused on Rd, investigating its role in the cause of lighter brown pigmentation in several red rice when it lacked function.

In doing this, 33 different weedy red rice samples were examined through pericarp pigmentation, hull color and lack/presence of awns (hull extension of seed to help disperse the weedy seed). The DNA from ten samples showing pigmentation extremes (the lightest and darkest pericarps) was then extracted.  Each sample went through PCR to amplify a portion of Rd, followed by PCR-product purification.  Gels were run to observe DNA bands of the red rice samples, which were around 689 bps.  From there PCR direct sequencing was performed to align sequences and identify nucleotide variation that could contribute to a loss of function within Rd.

However, our results indicated that the DNA sequence variation in Rd within red rice strains does not influence the nucleotide variation responsible for pigmentation dissimilarity (15 more samples were sequenced to prove this).  The sequencing of the ten samples of red rice DNA matched the standard sequence lettering of the genomic code except for one nucleotide (A, at nucleotide position 505).  This substitution results in a change from the standard (GTC) to ATC, resulting in the following amino acid change: valine to isoleucine.  This amino acid change is unlikely to change the function of the protein.  Our data indicate that the observed phenotypic variation in weedy rice pericarp color is apparently not due to any genetic variation in the portion of Rd that we have examined.