Originally published as Genetics Published Articles Ahead of Print on March 17, 2006.

Genetics, Vol. 173, 975-983, June 2006, Copyright © 2006
doi:10.1534/genetics.106.056473

Selection Under Domestication: Evidence for a Sweep in the Rice Waxy Genomic Region

Kenneth M. Olsen^*,1, Ana L. Caicedo^*, Nicholas Polato, Anna McClung, Susan McCouch and Michael D. Purugganan^*,2

^* Department of Genetics, North Carolina State University, Raleigh, North Carolina 27695, Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York 14853-1901 and USDA–Agriculture Research Service, Beaumont, Texas 77713

² Corresponding author: Department of Genetics, North Carolina State University, 3513 Gardner Hall, Raleigh, NC 27695.
E-mail: michaelp{at}unity.ncsu.edu

Rice (Oryza sativa) was cultivated by Asian Neolithic farmers >11,000 years ago, and different cultures have selected for divergent starch qualities in the rice grain during and after the domestication process. An intron 1 splice donor site mutation of the Waxy gene is responsible for the absence of amylose in glutinous rice varieties. This mutation appears to have also played an important role in the origin of low amylose, nonglutinous 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 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, with an inferred selection coefficient that is higher than similar estimates from maize domestication genes or wild species. These findings demonstrate that selection pressures associated with crop domestication regimes can exceed by one to two orders of magnitude those observed for genes under even strong selection in natural systems.

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