Exploring japonica rice epigenetic diversity in the main production regions of Heilongjiang Province
Abstract As a major epigenetic modification, DNA methylation plays an important role in coordinating plant responses to environmental changes. Methylation-sensitive amplified polymorphism (MSAP) technology was used in this study to investigate the epigenetic diversity of fifty japonica rice samples...
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| Format: | Article |
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Nature Portfolio
2022-03-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-022-08683-2 |
| _version_ | 1818673453954236416 |
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| author | Guifang Zhang Nuo Li Dongjie Zhang Zhijiang Li Aiwu Zhang Xijuan Guo |
| author_facet | Guifang Zhang Nuo Li Dongjie Zhang Zhijiang Li Aiwu Zhang Xijuan Guo |
| author_sort | Guifang Zhang |
| collection | DOAJ |
| description | Abstract As a major epigenetic modification, DNA methylation plays an important role in coordinating plant responses to environmental changes. Methylation-sensitive amplified polymorphism (MSAP) technology was used in this study to investigate the epigenetic diversity of fifty japonica rice samples from five regions in Heilongjiang Province, China. In addition, the phenotypic indicators of japonica rice samples and the environmental conditions of the sampling sites were investigated and analysed. Based on the MSAP analysis technique, using eight pairs of selective primers, we identified a total of 551 amplified loci, of which 267 (48.5%) were classified as methylation loci. The methylation status and levels of the japonica rice genome in different regions differed significantly (p < 0.05). The results of the analysis of molecular variance (AMOVA) revealed that most of the molecular variation (91%) came from within the groups (regions) and was caused by individual variation within the region. Furthermore, the results of principal coordinates analysis (PCoA), cluster analysis, and population structure analysis indicated that there was no obvious correlation between the epigenetic differences and geographical locations, which may have been due to the limited range of sampling sites. When environmental factors, phenotypic indicators, and epigenetic data analysis are combined, it is easy to conclude that japonica rice grown in the same latitudinal region has increased epigenetic and phenotypic similarities due to similar climatic conditions and production practices. |
| first_indexed | 2024-12-17T07:56:02Z |
| format | Article |
| id | doaj.art-78585792345b46e9a5dbbb91a3611aee |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-12-17T07:56:02Z |
| publishDate | 2022-03-01 |
| publisher | Nature Portfolio |
| record_format | Article |
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| spelling | doaj.art-78585792345b46e9a5dbbb91a3611aee2022-12-21T21:57:42ZengNature PortfolioScientific Reports2045-23222022-03-0112111310.1038/s41598-022-08683-2Exploring japonica rice epigenetic diversity in the main production regions of Heilongjiang ProvinceGuifang Zhang0Nuo Li1Dongjie Zhang2Zhijiang Li3Aiwu Zhang4Xijuan Guo5National Coarse Cereal Engineering Technology Research Center, Heilongjiang Bayi Agricultural UniversityCollege of Food Science, Heilongjiang Bayi Agricultural UniversityNational Coarse Cereal Engineering Technology Research Center, Heilongjiang Bayi Agricultural UniversityCollege of Food Science, Heilongjiang Bayi Agricultural UniversityCollege of Food Science, Heilongjiang Bayi Agricultural UniversityCollege of Food Science, Heilongjiang Bayi Agricultural UniversityAbstract As a major epigenetic modification, DNA methylation plays an important role in coordinating plant responses to environmental changes. Methylation-sensitive amplified polymorphism (MSAP) technology was used in this study to investigate the epigenetic diversity of fifty japonica rice samples from five regions in Heilongjiang Province, China. In addition, the phenotypic indicators of japonica rice samples and the environmental conditions of the sampling sites were investigated and analysed. Based on the MSAP analysis technique, using eight pairs of selective primers, we identified a total of 551 amplified loci, of which 267 (48.5%) were classified as methylation loci. The methylation status and levels of the japonica rice genome in different regions differed significantly (p < 0.05). The results of the analysis of molecular variance (AMOVA) revealed that most of the molecular variation (91%) came from within the groups (regions) and was caused by individual variation within the region. Furthermore, the results of principal coordinates analysis (PCoA), cluster analysis, and population structure analysis indicated that there was no obvious correlation between the epigenetic differences and geographical locations, which may have been due to the limited range of sampling sites. When environmental factors, phenotypic indicators, and epigenetic data analysis are combined, it is easy to conclude that japonica rice grown in the same latitudinal region has increased epigenetic and phenotypic similarities due to similar climatic conditions and production practices.https://doi.org/10.1038/s41598-022-08683-2 |
| spellingShingle | Guifang Zhang Nuo Li Dongjie Zhang Zhijiang Li Aiwu Zhang Xijuan Guo Exploring japonica rice epigenetic diversity in the main production regions of Heilongjiang Province Scientific Reports |
| title | Exploring japonica rice epigenetic diversity in the main production regions of Heilongjiang Province |
| title_full | Exploring japonica rice epigenetic diversity in the main production regions of Heilongjiang Province |
| title_fullStr | Exploring japonica rice epigenetic diversity in the main production regions of Heilongjiang Province |
| title_full_unstemmed | Exploring japonica rice epigenetic diversity in the main production regions of Heilongjiang Province |
| title_short | Exploring japonica rice epigenetic diversity in the main production regions of Heilongjiang Province |
| title_sort | exploring japonica rice epigenetic diversity in the main production regions of heilongjiang province |
| url | https://doi.org/10.1038/s41598-022-08683-2 |
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