Background

The domestication process of Asian rice (Oryza sativa L.) is complicated. It’s well established that Oryza rufipogon is the ancestor of Asian rice, although the number of domestication events still controversial. Recently, numerous types of studies based on rice nuclear genome have been conducted, but the results are quite different. Chloroplasts (cp) are also part of the rice genome and have a conserved cyclic structure that is valuable for plant genetics and evolutionary studies. Therefore, we conducted chloroplast-based studies, aiming to provide more evidence for the domestication of Asian rice.

Results

A total of 1389 variants were detected from the chloroplast genomes of 412 accessions obtained through the world. Oryza sativa L. ssp. japonica exhibited slightly less diversity (π) than Oryza sativa L. indica and wild rice. The fixation index values (F_ST) revealed that indica and japonica exhibited farther genetic distances compared with wild rice. Across cp genome, Tajima’s D test demonstrated that different selection sites occurred in Asian rice. Principal component analyses (PCA) and multidimensional scaling (MDS) clearly classify the Asian rice into different groups. Furthermore, introgression patterns identified that indica and japonica shared no introgression events in cp level, and phylogenetic studies showed cultivated rice were well separated from different type of wild rice.

Conclusions

Here, we focus on the domestication of Asian rice (indica and japonica). Diversity and phylogenetic analyses revealed some selection characteristics in the chloroplast genome that potentially occurred in different Asian rice during the domestication. The results shown that Asian rice had been domesticated at least twice. In additional, japonica may experience a strong positive selection or bottleneck event during the domestication.

中文翻译：

---

粳稻和in稻的叶绿体基因组差异选择的特征。

背景

亚洲大米（Oryza sativa L.）的驯化过程很复杂。尽管驯化事件的数量仍存在争议，但Oryza rufipogon是亚洲大米的始祖已广为人知。最近，已经进行了许多基于水稻核基因组的研究，但是结果却大不相同。叶绿体（cp）也是水稻基因组的一部分，具有保守的环状结构，对植物遗传学和进化研究具有重要意义。因此，我们进行了基于叶绿体的研究，旨在为亚洲水稻的驯化提供更多证据。

结果

从全世界获得的412个种质的叶绿体基因组中检测到总共1389个变体。水稻（Oryza sativa L.ssp。）粳稻的多样性（π）比水稻和野生稻略低。固定索引值（˚F _ST）揭示籼稻和粳稻与野生稻相比表现出更远的遗传距离。在cp基因组中，田岛的D试验证明亚洲大米中有不同的选择位点。主成分分析（PCA）和多维尺度分析（MDS）清楚地将亚洲大米分为不同的组。此外，渐渗图案确定了籼稻和粳稻共享在CP水平没有渐渗的事件，和系统发育研究表明栽培稻中以及从不同类型的野生稻的分离。

结论

在这里，我们重点介绍亚洲大米（印度in和粳稻）的驯化。多样性和系统发育分析显示，在驯化过程中，不同亚洲水稻中可能发生的叶绿体基因组选择特征。结果表明，亚洲大米至少已驯化两次。此外，在驯化期间，粳稻可能会经历强烈的积极选择或瓶颈事件。