Selective sweep with significant positive selection serves as the driving force for the differentiation of japonica and indica rice cultivars
Abstract Background Asian 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-throughp...
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doaj-ff1370e3ba144c1da484ea0440960a582020-11-24T21:51:47ZengBMCBMC Genomics1471-21642017-04-0118111310.1186/s12864-017-3702-xSelective sweep with significant positive selection serves as the driving force for the differentiation of japonica and indica rice cultivarsYang Yuan0Qijun Zhang1Shuiyun Zeng2Longjiang Gu3Weina Si4Xiaohui Zhang5Dacheng Tian6Sihai Yang7Long Wang8The Applied Plant Genomics Laboratory, College of Agricultural Sciences, Nanjing Agricultural UniversityJiangsu Academy of Agricultural SciencesState Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing UniversityState Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing UniversityState Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing UniversityState Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing UniversityState Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing UniversityState Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing UniversityState Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing UniversityAbstract Background Asian 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. Results By 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 This 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.http://link.springer.com/article/10.1186/s12864-017-3702-xjaponicaindicaWild riceDomesticationResequencingFunctional genes |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Yang Yuan Qijun Zhang Shuiyun Zeng Longjiang Gu Weina Si Xiaohui Zhang Dacheng Tian Sihai Yang Long Wang |
spellingShingle |
Yang Yuan Qijun Zhang Shuiyun Zeng Longjiang Gu Weina Si Xiaohui Zhang Dacheng Tian Sihai Yang Long Wang Selective sweep with significant positive selection serves as the driving force for the differentiation of japonica and indica rice cultivars BMC Genomics japonica indica Wild rice Domestication Resequencing Functional genes |
author_facet |
Yang Yuan Qijun Zhang Shuiyun Zeng Longjiang Gu Weina Si Xiaohui Zhang Dacheng Tian Sihai Yang Long Wang |
author_sort |
Yang Yuan |
title |
Selective sweep with significant positive selection serves as the driving force for the differentiation of japonica and indica rice cultivars |
title_short |
Selective sweep with significant positive selection serves as the driving force for the differentiation of japonica and indica rice cultivars |
title_full |
Selective sweep with significant positive selection serves as the driving force for the differentiation of japonica and indica rice cultivars |
title_fullStr |
Selective sweep with significant positive selection serves as the driving force for the differentiation of japonica and indica rice cultivars |
title_full_unstemmed |
Selective sweep with significant positive selection serves as the driving force for the differentiation of japonica and indica rice cultivars |
title_sort |
selective sweep with significant positive selection serves as the driving force for the differentiation of japonica and indica rice cultivars |
publisher |
BMC |
series |
BMC Genomics |
issn |
1471-2164 |
publishDate |
2017-04-01 |
description |
Abstract Background Asian 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. Results By 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 This 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. |
topic |
japonica indica Wild rice Domestication Resequencing Functional genes |
url |
http://link.springer.com/article/10.1186/s12864-017-3702-x |
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