Submitted to: Genetics
Publication Type: Proceedings
Publication Acceptance Date: 12/30/2004
Publication Date: 2/1/2005
Citation: Olsen, Kenneth M., Caicedo, Ana L., Polato, Nick, McClung, A.M., McCouch, S., Purugganan, M.D. 2005. Selection under domestication: Evidence for a sweep in the rice 'waxy' genomic region. Genetics. 17(2):965-974. Interpretive Summary: Rice is an important cereal grain that feeds over one third of the world. Cultivated subspecies of rice have been derived from the wide weed progenitor, O. rfipogon. The cooking quality of rice varies in different regions whereas firm cooking rice is desired in tropical areas. Cooked rice texture is largely controlled by the Waxy gene, located on chromosome six. This research demonstrates that domestication of rice in temeprate regions has resulted in intense selection for a large 250 kb region around the Waxy gene. When compared to over 100 other regions across the genome, this region was found to be largely lacking in genetic diversity. Because of the high density of genes in the relatively small rice genome, selection at this region has impacted some 39 genes around the Waxy gene. This demonstrates that directed selecitn and genetic hitch-hiking result in much greater impact than natural selection.
Technical Abstract: Rice (Oryza sativa) was cultivated by Asian Neolithic farmers more than 11,000 years ago, making it one of the earliest domesticated crops. During and after the domestication process, different cultures have selected for divergent starch qualities in the rice grain. Previous studies have shown that a mutation in an intron 1 splice donor site of the Waxy gene is responsible for the characteristic absence of amylose in glutinous rice varieties. Here we demonstrate that this same mutation has also played an important role in the origin of low amylose, non-glutinous temperate japonica rice varieties, which form a primary component of Northeast Asian cuisines. Waxy DNA sequence analyses indicate that the splice donor mutation is prevalent in temperate japonica rice varieties, but that it is rare or absent in tropical japonica, indica, aus, and aromatic varieties. Sequence analysis across a 500-kb genomic region centered on Waxy reveals patterns consistent with a selective sweep in the temperate japonicas associated with the mutation. The size of the selective sweep (>250 kb) indicates very strong selection in this region; the inferred selection coefficient is comparable to values for domestication and crop diversification genes in maize. Starch assays confirm that temperate japonicas have low amylose content, consistent with the observed selection on the Waxy splice donor mutation. These findings indicate a fundamental role for the Waxy splice donor mutation in intraspecific diversification in the O. sativa, and they demonstrate that selection pressures under domestication can far exceed those observed for genes under even strong selection in natural systems.