Genetics. Published Articles Ahead of Print: May 27, 2008, Copyright © 2008
doi:10.1534/genetics.106.068072


A more recent version of this article appeared on June 1, 2008.

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Non-independent Domestication of the Two Rice Subspecies, Oryza sativa subsp. indica and subsp. japonica, Demonstrated by Multilocus Microsatellites

Li-zhi Gao 1* and Hideki Innan 2

1 Kunming Institute of Botany, Chinese Academy of Sciences
2 Graduate University for Advanced Studies

* To whom correspondence should be addressed. E-mail: lgao{at}mail.kib.ac.cn.

Submitted on October 27, 2007
Revised on December 4, 2007
Accepted on 1 April 2008


Abstract

The origins of the Asian cultivated rice Oryza sativa from its wild ancestor O. rufipogon have been debated for decades. The question mainly concerns whether it originated monophyletically or polyphyletically. To shed light on the origins and demographic history of rice domestication, we genotyped a total of 92 individual plants from the two O. sativa subspecies and O. rufipogon for 60 microsatellites. An approximate Bayesian method was applied to estimate demographic parameters for O. rufipogon vs. O. sativa subsp. indica and O. rufipogon vs. O. sativa subsp. japonica. We showed that the japonica subspecies suffered a more severe bottleneck than the indica subspecies and thus a greater loss of genetic variation during its domestication. Across microsatellite loci there is a significant positive correlation in the reduction of genetic diversity between the two subspecies. The results suggest that completely independent domestication of indica and japonica subspecies may not explain our data, and that the two subspecies have at least partial sharing of their ancestral populations.

Key Words: Asian cultivated rice, bottleneck, domestication, microsatellite, selection