Selective sweep with significant positive selection serves as the driving force for the differentiation of japonica and indica rice cultivars.
Selective sweep with significant positive selection serves as the driving force for the differentiation of japonica and indica rice cultivars.
复制标题
具有显着正选择的选择性扫除是粳稻和籼稻品种分化的驱动力
DOI：
10.1186/s12864-017-3702-x
复制
发表时间：
2017-04-19
期刊：
影响因子：
4.4
通讯作者：
Wang L
中科院分区：
文献类型：
--
作者：
Yuan Y;Zhang Q;Zeng S;Gu L;Si W;Zhang X;Tian D;Yang S;Wang L
背景亚洲栽培稻（Oryza sativa L.），包括粳稻和籼稻，毫无疑问是亚洲乃至全世界最重要的作物。然而，其起源和驯化过程仍然缺乏决定性的结论。如今，大量水稻样本的高通量测序数据不断增加，为我们接近这些问题的答案提供了新的机会。 结果通过对296个全基因组测序的水稻品种和39个不同野生稻进行测序，检测到了两类在不同群体之间具有强选择性扫描信号的驯化区域（DR-I和DR-II）。 DR-I 区域包括 28 个在粳稻和籼稻亚种之间显着区分的块，而 DR-II 区域则由另外 28 个在野生稻和栽培稻之间显着区分的块组成，每个块分别覆盖 890 kb 和 640 kb。深入分析表明，DR-Is和DR-IIs都可能起源于中南半岛至中国南方，DR-IIs可能是从籼稻渐渗到粳稻的。 DR-I基因中也检测到了具有显着正选择功能的基因，表明选择性清除在粳稻和籼稻分化过程中发挥着重要作用。结论还检测到了具有显着正选择和偏功能的基因，这些基因可能在水稻驯化和分化过程中发挥重要作用。
BackgroundAsian cultivated rice (Oryza sativa L.), including japonica and indica, is unarguable the most important crop in Asia as well as worldwide. However, a decisive conclusion of its origination and domestication processes are still lacking. Nowadays, the ever-increasing high-throughput sequencing data of numerous rice samples have provided us new opportunities to get close to the answer of these questions.ResultsBy compiling 296 whole-genome sequenced rice cultivars and 39 diverse wild rice, two types of domesticated regions (DR-I and DR-II) with strong selective sweep signals between different groups were detected. DR-I regions included 28 blocks which significantly differentiated between japonica and indica subspecies, while DR-II regions were consisted of another 28 blocks which significantly differentiated between wild and cultivated rice, each covered 890 kb and 640 kb, respectively. In-depth analysis suggested that both DR-Is and DR-IIs could have originated from Indo-China Peninsula to southern China, and DR-IIs might be introgressed from indica to japonica. Functional bias with significant positive selection has also been detected in the genes of DR-I, suggesting important role of the selective sweep in differentiation of japonica and indica.Conclusions Genes with significant positive selection and biased functions were also detected which could play important roles in rice domestication and differentiation processes.