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Xu X, Hu Q, Wang J, Wang X, Lou L, Xu J, Yang X, Chen X. A 2-bp deletion in the protein kinase domain region of the ERECTA-like receptor kinase gene in cucumber results in short internode phenotype. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 327:111536. [PMID: 36402238 DOI: 10.1016/j.plantsci.2022.111536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 10/31/2022] [Accepted: 11/10/2022] [Indexed: 06/16/2023]
Abstract
Cucumber varieties with shortend internodes require less space than regular vining varieties, thus have great significance for germplasm improvement. Here, we found a novel spontaneous cucumber mutant si107 that exhibited short intenodes (si), smaller leaves, fruits, and seeds. The decrease in longitudinal cell length led to the shortened internodes of si107. The genetic analysis revealed a single recessive gene si-2 that was responsible for the mutation. Through multiple lines of evidence, we demonstrated that CsSI is the possible candidate gene for si-2, which encodes an ERECTA leucine-rich repeat receptor-like kinase. The shortened internode in si107 is attributed to a 2-bp deletion in the protein kinase domain region of this gene. The expression of CsSI was higher in the internodes, petioles, and fruit peels of si107 than in the wild type (WT). The transcriptome analysis between the si107 mutant and WT indicated that differentially expressed genes were significantly enriched in the plant hormone signal transduction pathway, in which auxin signal genes comprised the largest group, and all were downregulated in si107. Phytohormone quantitation confirmed that endogenous auxin levels in the stems of si107 were decreased. Our results provide new insights into the molecular mechanisms underlying the internode length control in cucumber.
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Affiliation(s)
- Xuewen Xu
- School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, Jiangsu 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Qiming Hu
- School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Jiaxi Wang
- School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Xueting Wang
- School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Lina Lou
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, China
| | - Jun Xu
- School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Xiaodong Yang
- School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Xuehao Chen
- School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, Jiangsu 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu 225009, China.
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Du Y, Luo S, Zhao J, Feng Z, Chen X, Ren W, Liu X, Wang Z, Yu L, Li W, Qu Y, Liu J, Zhou L. Genome and transcriptome-based characterization of high energy carbon-ion beam irradiation induced delayed flower senescence mutant in Lotus japonicus. BMC PLANT BIOLOGY 2021; 21:510. [PMID: 34732128 PMCID: PMC8564971 DOI: 10.1186/s12870-021-03283-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 10/20/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Flower longevity is closely related to pollen dispersal and reproductive success in all plants, as well as the commercial value of ornamental plants. Mutants that display variation in flower longevity are useful tools for understanding the mechanisms underlying this trait. Heavy-ion beam irradiation has great potential to improve flower shapes and colors; however, few studies are available on the mutation of flower senescence in leguminous plants. RESULTS A mutant (C416) exhibiting blossom duration eight times longer than that of the wild type (WT) was isolated in Lotus japonicus derived from carbon ion beam irradiation. Genetic assays supported that the delayed flower senescence of C416 was a dominant trait controlled by a single gene, which was located between 4,616,611 Mb and 5,331,876 Mb on chromosome III. By using a sorting strategy of multi-sample parallel genome sequencing, candidate genes were narrowed to the gene CUFF.40834, which exhibited high identity to ethylene receptor 1 in other model plants. A physiological assay demonstrated that C416 was insensitive to ethylene precursor. Furthermore, the dynamic changes of phytohormone regulatory network in petals at different developmental stages was compared by using RNA-seq. In brief, the ethylene, jasmonic acid (JA), and salicylic acid (SA) signaling pathways were negatively regulated in C416, whereas the brassinosteroid (BR) and cytokinin signaling pathways were positively regulated, and auxin exhibited dual effects on flower senescence in Lotus japonicus. The abscisic acid (ABA) signaling pathway is positively regulated in C416. CONCLUSION So far, C416 might be the first reported mutant carrying a mutation in an endogenous ethylene-related gene in Lotus japonicus, rather than through the introduction of exogenous genes by transgenic techniques. A schematic of the flower senescence of Lotus japonicus from the perspective of the phytohormone regulatory network was provided based on transcriptome profiling of petals at different developmental stages. This study is informative for elucidating the molecular mechanism of delayed flower senescence in C416, and lays a foundation for candidate flower senescence gene identification in Lotus japonicus. It also provides another perspective for the improvement of flower longevity in legume plants by heavy-ion beam.
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Affiliation(s)
- Yan Du
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, 730000, Lanzhou, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100000, People's Republic of China
| | - Shanwei Luo
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, 730000, Lanzhou, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100000, People's Republic of China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, China
| | - Jian Zhao
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, 730000, Lanzhou, People's Republic of China
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, 730000, People's Republic of China
| | - Zhuo Feng
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, 730000, Lanzhou, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100000, People's Republic of China
| | - Xia Chen
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, 730000, Lanzhou, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100000, People's Republic of China
| | - Weibin Ren
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, 730000, Lanzhou, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100000, People's Republic of China
| | - Xiao Liu
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, 730000, Lanzhou, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100000, People's Republic of China
| | - Zhuanzi Wang
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, 730000, Lanzhou, People's Republic of China
| | - Lixia Yu
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, 730000, Lanzhou, People's Republic of China
| | - Wenjian Li
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, 730000, Lanzhou, People's Republic of China
| | - Ying Qu
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, 730000, Lanzhou, People's Republic of China
- Kejin Innovation Institute of Heavy Ion Beam Biological Industry, Baiyin, 730900, People's Republic of China
| | - Jie Liu
- Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100000, People's Republic of China
| | - Libin Zhou
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, 730000, Lanzhou, People's Republic of China.
- University of Chinese Academy of Sciences, Beijing, 100000, People's Republic of China.
- Kejin Innovation Institute of Heavy Ion Beam Biological Industry, Baiyin, 730900, People's Republic of China.
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Li J, Yu CP, Li Q, Chang S, Xie LL, Wang S. Large-scale omics data reveal the cooperation of mutation-circRNA-miRNA-target gene network in liver cancer oncogenesis. Future Oncol 2021; 18:163-178. [PMID: 34677082 DOI: 10.2217/fon-2021-0940] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Aims: Clarifying the initial trigger of the differentially expressed genes in cancers helps researchers understand the cellular system as a whole network. Materials & methods: We retrieve the transcriptome and translatome of tumor and normal tissues from ten liver cancer patients and define differentially expressed genes and tumor-specific mutations. We associate the oncogenesis with the mutations by target prediction and experimental verification. Results: Upregulated genes have tumor-specific mutations in 3'UTRs that abolish the binding of miRNAs. For downregulated genes, their corresponding miRNAs are mutually targeted by two circRNAs, with mutations in base-pairing regions. Transfection experiments support the oncogenic role of these mutations. Conclusions: The tumor-specific mutations serve as the initial trigger of liver cancer. The mutation-circRNA-miRNA-target gene chain is completed.
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Affiliation(s)
- Jian Li
- Department of Interventional Radiology, The Affiliated Hospital of Qingdao University, Qingdao, 266011, China
| | - Chun-Peng Yu
- Department of Interventional Radiology, The Affiliated Hospital of Qingdao University, Qingdao, 266011, China
| | - Qun Li
- Department of Interventional Radiology, The Affiliated Hospital of Qingdao University, Qingdao, 266011, China
| | - Shuai Chang
- Department of Interventional Radiology, The Affiliated Hospital of Qingdao University, Qingdao, 266011, China
| | - Ling-Ling Xie
- Department of Interventional Radiology, The Affiliated Hospital of Qingdao University, Qingdao, 266011, China
| | - Song Wang
- Department of Interventional Radiology, The Affiliated Hospital of Qingdao University, Qingdao, 266011, China
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