Domestication and geographic origin of Oryza sativa in China: insights from multilocus analysis of nucleotide variation of O. sativa and O. rufipogon XIN WEI,* † WEI-HUA QIAO, † YOU-TAO CHEN, † RONG-SHENG WANG, † LI-RONG CAO, † WAN-XIA ZHANG, † NAN-NAN YUAN, † ZI-CHAO LI, ‡ HAN-LAI ZENG* andQING-WEN YANG † *College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China, †Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China, ‡College of Agronomy and Biotechnology, Chinese Agricultural University, Beijing, 100193, China Abstract Previous studies have indicated that China is one of the domestication centres of Asian cultivated rice (Oryza sativa), and common wild rice (O. rufipogon) is the progenitor of O. sativa. However, the number of domestication times and the geographic origin of Asian cultivated rice in China are still under debate. In this study, 100 accessions of Asian cultivated rice and 111 accessions of common wild rice in China were selected to examine the relationship between O. sativa and O. rufipogon and thereby infer the domestication and evolution of O. sativa in China through sequence analyses of six gene regions, trnC-ycf6 in chloroplast genomes, cox3 in mitochondrial genomes and ITS, Ehd1, Waxy, Hd1 in nuclear genomes. The results indicated that the two subspe- cies of O. sativa (indica and japonica) were domesticated independently from different populations of O. rufipogon with gene flow occurring later from japonica to indica; Southern China was the genetic diversity centre of O. rufipogon, and the Pearl River basin near the Tropic of Cancer was the domestication centre of O. sativa in China. Keywords: domestication, geographic origin, nucleotide diversity, Oryza rufipogon, Oryza sativa, Pearl River basin Received 11 July 2011; revision received 2 July 2012; accepted 10 July 2012 Introduction The genus Oryza consists of twenty-one wild and two cultivated species (Khush 1997), O. glaberrima and O. sativa. Generally, O. glaberrima is grown in West Africa, whereas O. sativa is cultivated globally with a high concentration in Asia. The previous research has definitely identified that O. glaberrima was domesticated from O. bar- thii about 3500 years ago in Africa (Vaughan 1989). And O. sativa was identified to be domesticated from O. rufipo- gon approximately 10 000 years ago by East Asian people but with some disputes (Jiang & Liu 2006). The number of domestication times and the geo- graphic origin of a given crop are two of the most fundamental questions regarding the domestication of crop species (Diamond 2002). For several crops such as corn, wheat and barley, these questions have been answered through molecular, biochemical and genetic researches. For instance, corn was domesticated from Balsas teosinte in Mexico approximately 8000 years ago (Doebley 2004; Doebley et al. 2006), whereas wheat and barley were domesticated from Triticum dicoccoides and Hordeum spontaneum, respectively, in the Fertile Cres- cent approximately 10 000 years ago (Badr et al. 2000; Ozkan et al. 2002). In contrast, the number of times domestication has occurred and the geographic origin of O. sativa are still under debate (Kovach et al. 2007; Sang & Ge 2007a,b; Sweeney & McCouch 2007). The debated question about the number of domestica- tion times of O. sativa is focused on whether O. sativa ssp. indica and O. sativa ssp. japonica were domesticated from one or two progenitor populations Correspondence: Han-lai Zeng, Fax: 86 27 87283465; E-mail: zenghl@mail.hzau.edu.cn; Qing-wen Yang, Fax: +86 10 62189165; E-mail: qwyang@mail.caas.net.cn © 2012 Blackwell Publishing Ltd Molecular Ecology (2012) doi: 10.1111/j.1365-294X.2012.05748.x