Multiple domestications of Asian rice: evidence from domestication genes across the genome
ID: 613 / 325
Proposed Symposium Title: Multiple domestications of Asian rice: evidence from domestication genes across the genome
Chun-Yan Jing1, 2, Fu-Min Zhang1,2, Xiu-Hua Wang1, Mei-Xia Wang1, Song Ge1, 2
Affiliations: 1. State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China. 2. University of Chinese Academy of Sciences, Beijing 100049, China.
Asian rice (Oryza sativa L.) is not only one of the world’s most important crops but also serves as a model for studying crop evolution and understanding the progression of human civilization. However, the origin of Asian rice remains controversial for more than half a century. The controversy arises from four main factors: (i) the ambiguous population structure and genetic relationship of rice progenitors; (ii) poorly annotated samples that do not represent the gene pools of cultivated rice and especially wild rice; (iii) substantial gene flow and introgression among cultivar groups; and (iv) the lack of an effective approach to test for alternative hypotheses about domestication history. Of various speculations and opinions, two leading hypotheses stand out with empirical evidence: a single domestication event in China or multiple domestication events in geographically separate areas. These two hypotheses differ in their predicted history of genes/alleles selected during domestication. Here we amassed a dataset of 459 newly resequenced and 1119 publicly available genomes of wild and cultivated accessions that cover entire geographic range of wild rice and all known cultivar groups. With this large dataset, we developed a strategy to test for single vs. multiple domestication events; this strategy differs from previous studies by analyzing the selective sweep regions/selected genes that have single-origins across domesticated germplasm. We identified 993 selected genes that generated phylogenetic trees on which japonica and indica formed a monophyletic group, suggesting that the domestication alleles of these genes originated only once in either japonica or indica. Importantly, the domestication alleles of most selected genes (~80%) stemmed from wild rice in China, but the domestication alleles of a substantial minority of selected genes (~20%) originated from wild rice in South and Southeast Asia, demonstrating separate domestication events of Asian rice.