Tong Wei, Kim Tae-Sung, Park Yong-Jin
Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan, 32439, Republic of Korea.
Department of Agricultural Sciences, College of Natural Sciences, Korea National Open University, Seoul, 03087, Republic of Korea.
Rice (N Y). 2016 Dec;9(1):57. doi: 10.1186/s12284-016-0129-y. Epub 2016 Oct 18.
Chloroplast genome variations have been detected, despite its overall conserved structure, which has been valuable for plant population genetics and evolutionary studies. Here, we described chloroplast variation architecture of 383 rice accessions from diverse regions and different ecotypes, in order to mine the rice chloroplast genome variation architecture and phylogenetic.
A total of 3677 variations across the chloroplast genome were identified with an average density of 27.33 per kb, in which wild rice showing a higher variation density than cultivated groups. Chloroplast genome nucleotide diversity investigation indicated a high degree of diversity in wild rice than in cultivated rice. Genetic distance estimation revealed that African rice showed a low level of breeding and connectivity with the Asian rice, suggesting the big distinction of them. Population structure and principal component analysis revealed the existence of clear clustering of African and Asian rice, as well as the indica and japonica in Asian cultivated rice. Phylogenetic analysis based on maximum likelihood and Bayesian inference methods and the population splits test suggested and supported the independent origins of indica and japonica within Asian cultivated rice. In addition, the African cultivated rice was thought to be domesticated differently from Asian cultivated rice.
The chloroplast genome variation architecture in Asian and African rice are different, as well as within Asian or African rice. Wild rice and cultivated rice also have distinct nucleotide diversity or genetic distance. In chloroplast level, the independent origins of indica and japonica within Asian cultivated rice were suggested and the African cultivated rice was thought to be domesticated differently from Asian cultivated rice. These results will provide more candidate evidence for the further rice chloroplast genomic and evolution studies.
尽管叶绿体基因组结构总体保守，但已检测到其变异，这对植物群体遗传学和进化研究具有重要价值。在此，我们描述了来自不同地区和不同生态型的383份水稻种质的叶绿体变异结构，以挖掘水稻叶绿体基因组变异结构和系统发育关系。
在叶绿体基因组中总共鉴定出3677个变异，平均密度为每千碱基27.33个，其中野生稻的变异密度高于栽培群体。叶绿体基因组核苷酸多样性调查表明，野生稻的多样性程度高于栽培稻。遗传距离估计显示，非洲稻与亚洲稻的育种和关联性较低，表明它们之间存在很大差异。群体结构和主成分分析揭示了非洲稻和亚洲稻以及亚洲栽培稻中的籼稻和粳稻存在明显的聚类。基于最大似然法和贝叶斯推断法的系统发育分析以及群体分裂测试表明并支持了亚洲栽培稻中籼稻和粳稻的独立起源。此外，非洲栽培稻被认为与亚洲栽培稻的驯化方式不同。
亚洲稻和非洲稻的叶绿体基因组变异结构不同，亚洲稻或非洲稻内部也是如此。野生稻和栽培稻也有不同的核苷酸多样性或遗传距离。在叶绿体水平上，表明了亚洲栽培稻中籼稻和粳稻的独立起源，并且认为非洲栽培稻与亚洲栽培稻的驯化方式不同。这些结果将为进一步的水稻叶绿体基因组和进化研究提供更多候选证据。
