Epigenetic modification of ESP, encoding a putative long noncoding RNA, affects panicle architecture in rice
Abstract Epigenetic variants broaden phenotypic diversity in eukaryotes. Epialleles may also provide a new genetic source for crop breeding, but very few epialleles related to agricultural traits have been identified in rice. Here, we identified Epi-sp, a gain-of-function epiallele of the rice ESP (...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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SpringerOpen
2019-04-01
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| Series: | Rice |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12284-019-0282-1 |
| _version_ | 1818137887679447040 |
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| author | Xin Luan Shuchun Liu Shanwen Ke Hang Dai Xin-Ming Xie Tzung-Fu Hsieh Xiang-Qian Zhang |
| author_facet | Xin Luan Shuchun Liu Shanwen Ke Hang Dai Xin-Ming Xie Tzung-Fu Hsieh Xiang-Qian Zhang |
| author_sort | Xin Luan |
| collection | DOAJ |
| description | Abstract Epigenetic variants broaden phenotypic diversity in eukaryotes. Epialleles may also provide a new genetic source for crop breeding, but very few epialleles related to agricultural traits have been identified in rice. Here, we identified Epi-sp, a gain-of-function epiallele of the rice ESP (Epigenetic Short Panicle, Os01g0356951), which encodes a putative long noncoding RNA. The Epi-sp plants show a dense and short panicle phenotype, an agronomically important phenotypes that is inherited in a semidominant manner. We did not find any nucleotide sequence variation in ESP. Instead, we found hypomethylation in the transcriptional termination region (TTR) of ESP gene, which caused ectopic expression of ESP in Epi-sp plants. Bisulfite analysis revealed that the methylation status of 26 CGs and 13 CHGs within a continuous 313-bp region is essential for the regulation of ESP expression. Thus, our work identified a unique rice epiallele and demonstrated that epigenetic modification of ESP is associated with the regulation of panicle architecture in rice. |
| first_indexed | 2024-12-11T10:03:27Z |
| format | Article |
| id | doaj.art-72af1dc7a835474ea0fb22e89136e947 |
| institution | Directory Open Access Journal |
| issn | 1939-8425 1939-8433 |
| language | English |
| last_indexed | 2024-12-11T10:03:27Z |
| publishDate | 2019-04-01 |
| publisher | SpringerOpen |
| record_format | Article |
| series | Rice |
| spelling | doaj.art-72af1dc7a835474ea0fb22e89136e9472022-12-22T01:12:02ZengSpringerOpenRice1939-84251939-84332019-04-011211810.1186/s12284-019-0282-1Epigenetic modification of ESP, encoding a putative long noncoding RNA, affects panicle architecture in riceXin Luan0Shuchun Liu1Shanwen Ke2Hang Dai3Xin-Ming Xie4Tzung-Fu Hsieh5Xiang-Qian Zhang6Guangdong Engineering Research Center of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural UniversityGuangdong Engineering Research Center of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural UniversityGuangdong Engineering Research Center of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural UniversityGuangdong Engineering Research Center of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural UniversityGuangdong Engineering Research Center of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural UniversityPlants for Human Health Institute, North Carolina State UniversityGuangdong Engineering Research Center of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural UniversityAbstract Epigenetic variants broaden phenotypic diversity in eukaryotes. Epialleles may also provide a new genetic source for crop breeding, but very few epialleles related to agricultural traits have been identified in rice. Here, we identified Epi-sp, a gain-of-function epiallele of the rice ESP (Epigenetic Short Panicle, Os01g0356951), which encodes a putative long noncoding RNA. The Epi-sp plants show a dense and short panicle phenotype, an agronomically important phenotypes that is inherited in a semidominant manner. We did not find any nucleotide sequence variation in ESP. Instead, we found hypomethylation in the transcriptional termination region (TTR) of ESP gene, which caused ectopic expression of ESP in Epi-sp plants. Bisulfite analysis revealed that the methylation status of 26 CGs and 13 CHGs within a continuous 313-bp region is essential for the regulation of ESP expression. Thus, our work identified a unique rice epiallele and demonstrated that epigenetic modification of ESP is associated with the regulation of panicle architecture in rice.http://link.springer.com/article/10.1186/s12284-019-0282-1RicelncRNAEpigeneticPaniclePseudogene |
| spellingShingle | Xin Luan Shuchun Liu Shanwen Ke Hang Dai Xin-Ming Xie Tzung-Fu Hsieh Xiang-Qian Zhang Epigenetic modification of ESP, encoding a putative long noncoding RNA, affects panicle architecture in rice Rice Rice lncRNA Epigenetic Panicle Pseudogene |
| title | Epigenetic modification of ESP, encoding a putative long noncoding RNA, affects panicle architecture in rice |
| title_full | Epigenetic modification of ESP, encoding a putative long noncoding RNA, affects panicle architecture in rice |
| title_fullStr | Epigenetic modification of ESP, encoding a putative long noncoding RNA, affects panicle architecture in rice |
| title_full_unstemmed | Epigenetic modification of ESP, encoding a putative long noncoding RNA, affects panicle architecture in rice |
| title_short | Epigenetic modification of ESP, encoding a putative long noncoding RNA, affects panicle architecture in rice |
| title_sort | epigenetic modification of esp encoding a putative long noncoding rna affects panicle architecture in rice |
| topic | Rice lncRNA Epigenetic Panicle Pseudogene |
| url | http://link.springer.com/article/10.1186/s12284-019-0282-1 |
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