Selective sweep with significant positive selection serves as the driving force for the differentiation of japonica and indica rice cultivars

BMC Genomics

Research Article

Qijun Zhang¹  Xiaohui Zhang²  Shuiyun Zeng²  Weina Si²  Sihai Yang²  Longjiang Gu²  Long Wang²  Dacheng Tian²  Yang Yuan³ 

[1] Jiangsu Academy of Agricultural Sciences, 210014, Nanjing, China;State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210023, Nanjing, China;The Applied Plant Genomics Laboratory, College of Agricultural Sciences, Nanjing Agricultural University, 210095, Nanjing, China;State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210023, Nanjing, China;

关键词: japonica;    indica;    Wild rice;    Domestication;    Resequencing;    Functional genes;   

DOI  :  10.1186/s12864-017-3702-x

 received in 2016-06-21, accepted in 2017-04-08,  发布年份 2017

来源: Springer

【 摘 要 】

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.ConclusionsThis research promoted a new possible model of the origin of the cultivated rice that DR-Is in japonica and indica maybe independently originated from the divergent wild rice in the Indo-China Peninsula to southern China, and then followed by frequent introgression. Genes with significant positive selection and biased functions were also detected which could play important roles in rice domestication and differentiation processes.

【 授权许可】

CC BY   
© The Author(s). 2017