Faith Steffen
Domestication of African vs. Asian Rice:  Parallel Evolution in Response to Selection by Humans
Mentor:  Dr. Ken Olsen, Biology Department, Washington University in St. Louis

Oryza sativa (Asian rice) and Oryza glaberrima (African rice) represent two independent domestications from two different wild Oryza species. Since the wild ancestors of the two crop species are phylogenetically closely related, they have similar genes, and the evolution of those genes can be easily compared. This allows us to look at whether selection by humans leads to genetic changes at the same loci (evolutionary parallelism) in the two separate domestication events.

White pericarp (seed coat) is strongly selected for in domesticated rice, but natural selection favors red pericarp in wild Oryza species, as the red pigment (proanthocyanidin) is protective against pathogens and predators.  Rc (located on chromosome 7) is one gene responsible for pigmentation in rice. Previous research on Asian rice showed that in some crop varieties, white pericarp results from a 14-bp deletion in Rc exon 6 that results in two premature stop codons and knocks out a basic helix-loop-helix protein domain of the gene product. A second, single base-pair mutation was shown to cause a premature stop codon, resulting in a light red pericarp in a different Asian rice variety.

We examined exon 6 of Rc in both Asian and African rice to determine whether the same mutations are responsible for pigment loss in both species and to look for other possible differences between them. This was done through DNA extraction, PCR of Rc exon 6, and direct sequencing, using plants from both species. Our results verified a loss of pigmentation associated with a 14-bp deletion in Oryza sativa. We also found the previously reported single base-pair mutation that resulted in the premature stop codon; however, our data suggested that this mutation caused a complete loss of pigmentation instead of a partial loss. Some of the Oryza sativa plants in our sample had a white pericarp with no obvious loss-of-function mutations in exon 6, suggesting that other gene regions are likely to be involved in pericarp color. In one African rice sample, we found white pericarp to be associated with a single base-pair mutation resulting in a premature stop codon. Both species were found to have a synonymous substitution that had no effect on phenotype. Taken together, these results indicate that: 1) the Rc exon 6 region is important for white pericarp in both domesticated species; 2) there are separate mutations involved in the loss of pigmentation in Asian and African rice; and 3) other genes are likely to be involved in pigment loss in both domesticated species.