Signatures of differential selection in chloroplast genome between japonica and indica
Abstract Background The domestication process of Asian rice (Oryza sativa L.) is complicated. It’s well established that Oryza rufipogon is the ancestor of Asian rice, although the number of domestication events still controversial. Recently, numerous types of studies based on rice nuclear genome ha...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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SpringerOpen
2019-08-01
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| Series: | Rice |
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| Online Access: | http://link.springer.com/article/10.1186/s12284-019-0322-x |
| _version_ | 1811294911329206272 |
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| author | Lin Cheng Jungrye Nam Sang-Ho Chu Phitaktansakul Rungnapa Myeong-hyeon Min Yuan Cao Ji-min Yoo Jee-Su Kang Kyu-Won Kim Yong-Jin Park |
| author_facet | Lin Cheng Jungrye Nam Sang-Ho Chu Phitaktansakul Rungnapa Myeong-hyeon Min Yuan Cao Ji-min Yoo Jee-Su Kang Kyu-Won Kim Yong-Jin Park |
| author_sort | Lin Cheng |
| collection | DOAJ |
| description | Abstract Background The domestication process of Asian rice (Oryza sativa L.) is complicated. It’s well established that Oryza rufipogon is the ancestor of Asian rice, although the number of domestication events still controversial. Recently, numerous types of studies based on rice nuclear genome have been conducted, but the results are quite different. Chloroplasts (cp) are also part of the rice genome and have a conserved cyclic structure that is valuable for plant genetics and evolutionary studies. Therefore, we conducted chloroplast-based studies, aiming to provide more evidence for the domestication of Asian rice. Results A total of 1389 variants were detected from the chloroplast genomes of 412 accessions obtained through the world. Oryza sativa L. ssp. japonica exhibited slightly less diversity (π) than Oryza sativa L. indica and wild rice. The fixation index values (F ST) revealed that indica and japonica exhibited farther genetic distances compared with wild rice. Across cp genome, Tajima’s D test demonstrated that different selection sites occurred in Asian rice. Principal component analyses (PCA) and multidimensional scaling (MDS) clearly classify the Asian rice into different groups. Furthermore, introgression patterns identified that indica and japonica shared no introgression events in cp level, and phylogenetic studies showed cultivated rice were well separated from different type of wild rice. Conclusions Here, we focus on the domestication of Asian rice (indica and japonica). Diversity and phylogenetic analyses revealed some selection characteristics in the chloroplast genome that potentially occurred in different Asian rice during the domestication. The results shown that Asian rice had been domesticated at least twice. In additional, japonica may experience a strong positive selection or bottleneck event during the domestication. |
| first_indexed | 2024-04-13T05:24:33Z |
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| institution | Directory Open Access Journal |
| issn | 1939-8425 1939-8433 |
| language | English |
| last_indexed | 2024-04-13T05:24:33Z |
| publishDate | 2019-08-01 |
| publisher | SpringerOpen |
| record_format | Article |
| series | Rice |
| spelling | doaj.art-3d4a51abd39b429f85adef89bfbb859d2022-12-22T03:00:37ZengSpringerOpenRice1939-84251939-84332019-08-0112111310.1186/s12284-019-0322-xSignatures of differential selection in chloroplast genome between japonica and indicaLin Cheng0Jungrye Nam1Sang-Ho Chu2Phitaktansakul Rungnapa3Myeong-hyeon Min4Yuan Cao5Ji-min Yoo6Jee-Su Kang7Kyu-Won Kim8Yong-Jin Park9Department of Plant Resources, College of Industrial Science, Kongju National UniversityCenter for Crop Breeding on Omics and Artifical Intelligence, Kongju National UniversityCenter for Crop Breeding on Omics and Artifical Intelligence, Kongju National UniversityDepartment of Plant Resources, College of Industrial Science, Kongju National UniversityDepartment of Plant Resources, College of Industrial Science, Kongju National UniversityDepartment of Plant Resources, College of Industrial Science, Kongju National UniversityDepartment of Plant Resources, College of Industrial Science, Kongju National UniversityDepartment of Plant Resources, College of Industrial Science, Kongju National UniversityCenter for Crop Breeding on Omics and Artifical Intelligence, Kongju National UniversityDepartment of Plant Resources, College of Industrial Science, Kongju National UniversityAbstract Background The domestication process of Asian rice (Oryza sativa L.) is complicated. It’s well established that Oryza rufipogon is the ancestor of Asian rice, although the number of domestication events still controversial. Recently, numerous types of studies based on rice nuclear genome have been conducted, but the results are quite different. Chloroplasts (cp) are also part of the rice genome and have a conserved cyclic structure that is valuable for plant genetics and evolutionary studies. Therefore, we conducted chloroplast-based studies, aiming to provide more evidence for the domestication of Asian rice. Results A total of 1389 variants were detected from the chloroplast genomes of 412 accessions obtained through the world. Oryza sativa L. ssp. japonica exhibited slightly less diversity (π) than Oryza sativa L. indica and wild rice. The fixation index values (F ST) revealed that indica and japonica exhibited farther genetic distances compared with wild rice. Across cp genome, Tajima’s D test demonstrated that different selection sites occurred in Asian rice. Principal component analyses (PCA) and multidimensional scaling (MDS) clearly classify the Asian rice into different groups. Furthermore, introgression patterns identified that indica and japonica shared no introgression events in cp level, and phylogenetic studies showed cultivated rice were well separated from different type of wild rice. Conclusions Here, we focus on the domestication of Asian rice (indica and japonica). Diversity and phylogenetic analyses revealed some selection characteristics in the chloroplast genome that potentially occurred in different Asian rice during the domestication. The results shown that Asian rice had been domesticated at least twice. In additional, japonica may experience a strong positive selection or bottleneck event during the domestication.http://link.springer.com/article/10.1186/s12284-019-0322-xChloroplast genomeIndicaJaponicaDomesticationDiversityRice |
| spellingShingle | Lin Cheng Jungrye Nam Sang-Ho Chu Phitaktansakul Rungnapa Myeong-hyeon Min Yuan Cao Ji-min Yoo Jee-Su Kang Kyu-Won Kim Yong-Jin Park Signatures of differential selection in chloroplast genome between japonica and indica Rice Chloroplast genome Indica Japonica Domestication Diversity Rice |
| title | Signatures of differential selection in chloroplast genome between japonica and indica |
| title_full | Signatures of differential selection in chloroplast genome between japonica and indica |
| title_fullStr | Signatures of differential selection in chloroplast genome between japonica and indica |
| title_full_unstemmed | Signatures of differential selection in chloroplast genome between japonica and indica |
| title_short | Signatures of differential selection in chloroplast genome between japonica and indica |
| title_sort | signatures of differential selection in chloroplast genome between japonica and indica |
| topic | Chloroplast genome Indica Japonica Domestication Diversity Rice |
| url | http://link.springer.com/article/10.1186/s12284-019-0322-x |
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