Evidence for selection events during domestication by extensive mitochondrial genome analysis between japonica and indica in cultivated rice
Evidence for selection events during domestication by extensive mitochondrial genome analysis between japonica and indica in cultivated rice
复制标题
DOI：
10.1038/s41598-019-47318-x
复制
发表时间：
2019-07-26
影响因子：
4.6
通讯作者：
Park, Yong-Jin
中科院分区：
文献类型：
--
作者：
Cheng, Lin;Kim, Kyu-Won;Park, Yong-Jin
水稻驯化的历史是有争议的，因为它仍然不知道驯化过程是否发生一次或多次。迄今为止，基于水稻核基因组的遗传结构和系统发育研究已得到广泛的研究，但结果却大相径庭。在这里，我们发现了有趣的结果，不同的选择在水稻线粒体（mt）基因组的综合研究的基础上。具体而言，从世界各地收集了412份水稻种质用于变异结构研究。在mt基因组中共检测到10632个变异，包括7277个SNPs和3355个InDel。选择信号（pi（w）/pi（c））表明水稻中的选择位点是多位点的。SSP. japonica与Oryza sativa L.籼稻籼粳间的固着指数（F-ST）高于籼野间。此外，单倍型和系统发育分析还显示，籼稻和粳稻聚类，以及从野生稻分离。如上所述，我们的研究表明，籼稻类型的选择位点不同于粳稻类型。这意味着籼稻和粳稻经历了不同的驯化过程。我们还发现，粳稻在驯化过程中可能经历了一个瓶颈事件。
The history of the domestication of rice is controversial, as it remains unknown whether domestication processes occurred once or multiple times. To date, genetic architecture and phylogenetic studies based on the rice nuclear genome have been extensively studied, but the results are quite different. Here, we found interesting results for different selections in Oryza sativa based on comprehensive studies of the rice mitochondrial (mt) genome. In detail, 412 rice germplasms were collected from around the world for variant architecture studies. A total of 10632 variants were detected in the mt genome, including 7277 SNPs and 3355 InDels. Selection signal (pi(w)/pi(c)) indicated that the selection sites in Oryza sativa L. ssp. japonica were different from those of Oryza sativa L. indica rice. The fixation index (F-ST) was higher between indica and japonica than between indica and wild rice. Moreover, haplotype and phylogenetic analyses also revealed indica clusters and japonica clusters that were well separated from wild rice. As mentioned above, our studies indicate that the selection sites of the indica type were different from those of the japonica type. This means that indica and japonica have experienced different domestication processes. We also found that japonica may have experienced a bottleneck event during domestication.