The Rice Paradox: Multiple Origins but Single Domestication in Asian Rice.
The Rice Paradox: Multiple Origins but Single Domestication in Asian Rice.
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DOI：
10.1093/molbev/msx049
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发表时间：
2017-04-01
影响因子：
10.7
通讯作者：
Purugganan MD
中科院分区：
文献类型：
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作者：
Choi JY;Platts AE;Fuller DQ;Hsing YI;Wing RA;Purugganan MD
驯化亚洲水稻（Oryza sativa）的起源一直是一个有争议的话题，对于这一关键作物物种的单一或多重驯化有相互矛盾的证据。我们通过分析从驯化水稻及其野生祖先的从头组装的基因组来研究驯化水稻的进化历史。我们的研究结果表明，多个起源，其中每个驯化水稻亚群（粳稻，籼稻，和aus）分别从祖先O。rufipogon和/或O.尼瓦拉基于群体参数的聚结模型估计，第一个从O。rufipogon为O.莴苣japonica，出现于距今13.1- 24.1ka，比考古学上最早的驯化年代早一个数量级。然而，这一日期与O.末次盛冰期后的普通稻种群及中国早期野生稻管理的考古学证据我们还发现，从粳稻到籼稻（约17%）和原粳稻（约15%）都存在明显的基因流，这导致了驯化等位基因从早驯化的粳稻向原籼稻和原粳稻群体的转移。我们的研究结果支持了一个模型，在该模型中，不同的水稻亚种有不同的起源，但从头驯化只发生一次，在O。莴苣早粳与原籼、原粳稻的渐渗杂交，形成了籼、粳稻的驯化品种。
The origin of domesticated Asian rice (Oryza sativa) has been a contentious topic, with conflicting evidence for either single or multiple domestication of this key crop species. We examined the evolutionary history of domesticated rice by analyzing de novo assembled genomes from domesticated rice and its wild progenitors. Our results indicate multiple origins, where each domesticated rice subpopulation (japonica, indica, and aus) arose separately from progenitor O. rufipogon and/or O. nivara. Coalescence-based modeling of demographic parameters estimate that the first domesticated rice population to split off from O. rufipogon was O. sativa ssp. japonica, occurring at ∼13.1–24.1 ka, which is an order of magnitude older then the earliest archeological date of domestication. This date is consistent, however, with the expansion of O. rufipogon populations after the Last Glacial Maximum ∼18 ka and archeological evidence for early wild rice management in China. We also show that there is significant gene flow from japonica to both indica (∼17%) and aus (∼15%), which led to the transfer of domestication alleles from early-domesticated japonica to proto-indica and proto-aus populations. Our results provide support for a model in which different rice subspecies had separate origins, but that de novo domestication occurred only once, in O. sativa ssp. japonica, and introgressive hybridization from early japonica to proto-indica and proto-aus led to domesticated indica and aus rice.