Multi-omics analyses reveal the crosstalk between the circadian clock and the response to herbicide application in Oryza sativa
Plants have evolved circadian clock systems that enable biological processes to occur in tandem with periodic changes in the environment. However, it is largely unknown whether crosstalk occurs between the circadian clock and the response to herbicide in rice. We identified 19 conserved rhythmic met...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-03-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2023.1155258/full |
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| author | Ke Chen Ke Chen Ke Chen Xiao Su Haona Yang Haona Yang Yajun Peng Yajun Peng Lamei Wu Lamei Wu Zhenghong Zhao Zhenghong Zhao Zhenghong Zhao Tao Lin Lianyang Bai Lianyang Bai Lianyang Bai Lifeng Wang Lifeng Wang Lifeng Wang |
| author_facet | Ke Chen Ke Chen Ke Chen Xiao Su Haona Yang Haona Yang Yajun Peng Yajun Peng Lamei Wu Lamei Wu Zhenghong Zhao Zhenghong Zhao Zhenghong Zhao Tao Lin Lianyang Bai Lianyang Bai Lianyang Bai Lifeng Wang Lifeng Wang Lifeng Wang |
| author_sort | Ke Chen |
| collection | DOAJ |
| description | Plants have evolved circadian clock systems that enable biological processes to occur in tandem with periodic changes in the environment. However, it is largely unknown whether crosstalk occurs between the circadian clock and the response to herbicide in rice. We identified 19 conserved rhythmic metabolites which were response to pesticide application and their metabolic abundance peaked mainly at ZT2 or ZT14-ZT18. We found a series of glyphosate, s-Metolachlor, fenclorim, metcamifen and GA3 response genes were expressed following stable circadian rhythms. In order to determine the patterns of their temporal expression, co-expression network analysis was done on 10,467 genes that were periodically expressed throughout a 24-hour period. Next, we identified 4,031 potential direct target genes of OsCCA1 in using DAP-seq data for OsCCA1. Of these, 339, 22, 53, 53 and 63 genes showed a response to glyphosate, s-Metolachlor, fenclorim, metcamifen and GA3 application, respectively. And they were mainly phased from dusk to midnight. Interestingly, we identified significant OsCCA1 binding peaks in the promoter regions of four herbicide resistance genes, including OsCYP81A12, OsCYP81E22, OsCYP76C2, and OsCYP76C4. Finally, we found that herbicide application could affects the expression of some of the central oscillator genes of the rice circadian clock. Here, we used multi-omics data to reveal the crosstalk between the circadian clock and herbicide response processes at the epigenomics, transcriptome, and metabolome levels in rice. This work will serve as a theoretical guide for identifying rhythmic herbicide targets, leading to the creation of new herbicides or the breeding of crops resistant to herbicides. |
| first_indexed | 2024-04-09T21:56:48Z |
| format | Article |
| id | doaj.art-cd06ead34dff40e5b870e24615c7535c |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-09T21:56:48Z |
| publishDate | 2023-03-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Plant Science |
| spelling | doaj.art-cd06ead34dff40e5b870e24615c7535c2023-03-24T05:07:56ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2023-03-011410.3389/fpls.2023.11552581155258Multi-omics analyses reveal the crosstalk between the circadian clock and the response to herbicide application in Oryza sativaKe Chen0Ke Chen1Ke Chen2Xiao Su3Haona Yang4Haona Yang5Yajun Peng6Yajun Peng7Lamei Wu8Lamei Wu9Zhenghong Zhao10Zhenghong Zhao11Zhenghong Zhao12Tao Lin13Lianyang Bai14Lianyang Bai15Lianyang Bai16Lifeng Wang17Lifeng Wang18Lifeng Wang19Longping Branch, College of Biology, Hunan University, Changsha, ChinaKey Laboratory of Indica Rice Genetics and Breeding in the Middle and Lower Reaches of Yangtze River Valley, Ministry of Agriculture and Rural Affairs, Hunan Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha, ChinaHuangpu Research Institute of Longping Agricultural Science and Technology, Guangzhou, ChinaState Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, ChinaLongping Branch, College of Biology, Hunan University, Changsha, ChinaHuangpu Research Institute of Longping Agricultural Science and Technology, Guangzhou, ChinaLongping Branch, College of Biology, Hunan University, Changsha, ChinaHuangpu Research Institute of Longping Agricultural Science and Technology, Guangzhou, ChinaLongping Branch, College of Biology, Hunan University, Changsha, ChinaHuangpu Research Institute of Longping Agricultural Science and Technology, Guangzhou, ChinaLongping Branch, College of Biology, Hunan University, Changsha, ChinaKey Laboratory of Indica Rice Genetics and Breeding in the Middle and Lower Reaches of Yangtze River Valley, Ministry of Agriculture and Rural Affairs, Hunan Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha, ChinaHuangpu Research Institute of Longping Agricultural Science and Technology, Guangzhou, ChinaState Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, ChinaLongping Branch, College of Biology, Hunan University, Changsha, ChinaKey Laboratory of Indica Rice Genetics and Breeding in the Middle and Lower Reaches of Yangtze River Valley, Ministry of Agriculture and Rural Affairs, Hunan Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha, ChinaHuangpu Research Institute of Longping Agricultural Science and Technology, Guangzhou, ChinaLongping Branch, College of Biology, Hunan University, Changsha, ChinaKey Laboratory of Indica Rice Genetics and Breeding in the Middle and Lower Reaches of Yangtze River Valley, Ministry of Agriculture and Rural Affairs, Hunan Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha, ChinaHuangpu Research Institute of Longping Agricultural Science and Technology, Guangzhou, ChinaPlants have evolved circadian clock systems that enable biological processes to occur in tandem with periodic changes in the environment. However, it is largely unknown whether crosstalk occurs between the circadian clock and the response to herbicide in rice. We identified 19 conserved rhythmic metabolites which were response to pesticide application and their metabolic abundance peaked mainly at ZT2 or ZT14-ZT18. We found a series of glyphosate, s-Metolachlor, fenclorim, metcamifen and GA3 response genes were expressed following stable circadian rhythms. In order to determine the patterns of their temporal expression, co-expression network analysis was done on 10,467 genes that were periodically expressed throughout a 24-hour period. Next, we identified 4,031 potential direct target genes of OsCCA1 in using DAP-seq data for OsCCA1. Of these, 339, 22, 53, 53 and 63 genes showed a response to glyphosate, s-Metolachlor, fenclorim, metcamifen and GA3 application, respectively. And they were mainly phased from dusk to midnight. Interestingly, we identified significant OsCCA1 binding peaks in the promoter regions of four herbicide resistance genes, including OsCYP81A12, OsCYP81E22, OsCYP76C2, and OsCYP76C4. Finally, we found that herbicide application could affects the expression of some of the central oscillator genes of the rice circadian clock. Here, we used multi-omics data to reveal the crosstalk between the circadian clock and herbicide response processes at the epigenomics, transcriptome, and metabolome levels in rice. This work will serve as a theoretical guide for identifying rhythmic herbicide targets, leading to the creation of new herbicides or the breeding of crops resistant to herbicides.https://www.frontiersin.org/articles/10.3389/fpls.2023.1155258/fullOryza sativa L.circadian clockherbicidesRNA-seqmetabolome |
| spellingShingle | Ke Chen Ke Chen Ke Chen Xiao Su Haona Yang Haona Yang Yajun Peng Yajun Peng Lamei Wu Lamei Wu Zhenghong Zhao Zhenghong Zhao Zhenghong Zhao Tao Lin Lianyang Bai Lianyang Bai Lianyang Bai Lifeng Wang Lifeng Wang Lifeng Wang Multi-omics analyses reveal the crosstalk between the circadian clock and the response to herbicide application in Oryza sativa Frontiers in Plant Science Oryza sativa L. circadian clock herbicides RNA-seq metabolome |
| title | Multi-omics analyses reveal the crosstalk between the circadian clock and the response to herbicide application in Oryza sativa |
| title_full | Multi-omics analyses reveal the crosstalk between the circadian clock and the response to herbicide application in Oryza sativa |
| title_fullStr | Multi-omics analyses reveal the crosstalk between the circadian clock and the response to herbicide application in Oryza sativa |
| title_full_unstemmed | Multi-omics analyses reveal the crosstalk between the circadian clock and the response to herbicide application in Oryza sativa |
| title_short | Multi-omics analyses reveal the crosstalk between the circadian clock and the response to herbicide application in Oryza sativa |
| title_sort | multi omics analyses reveal the crosstalk between the circadian clock and the response to herbicide application in oryza sativa |
| topic | Oryza sativa L. circadian clock herbicides RNA-seq metabolome |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2023.1155258/full |
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