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Originally published as Genetics Published Articles Ahead of Print on May 27, 2008.
Genetics, Vol. 179, 965-976, June 2008, Copyright © 2008
doi:10.1534/genetics.106.068072
Nonindependent Domestication of the Two Rice Subspecies, Oryza sativa ssp. indica and ssp. japonica, Demonstrated by Multilocus Microsatellites
Li-zhi Gao*,1,2 and
Hideki Innan
,
,1
* Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, People's Republic of China, Human Genetics Center, School of Public Health, University of Texas Health Science Center, Houston, Texas 77030 and School of Advanced Sciences, Graduate University for Advanced Studies, Hayama, Kanagawa 240-0193, Japan
2 Corresponding author: Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Rd., Kunming 650204, People's Republic of China.
E-mail: lgao{at}mail.kib.ac.cn
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 ssp. indica and O. rufipogon vs. O. sativa ssp. 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 there is at least partial sharing of their ancestral populations and/or recent gene flow between them.
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Genetics 2008 179: NP.