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Ren X, Fan J, Li X, Shan Y, Wang L, Ma L, Li Y, Li X. Application of RNA sequencing to understand the response of rice seedlings to salt-alkali stress. BMC Genomics 2023; 24:21. [PMID: 36641451 PMCID: PMC9840837 DOI: 10.1186/s12864-023-09121-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 01/06/2023] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Salt-alkali stress represents one of the most stressful events with deleterious consequences for plant growth and crop productivity. Despite studies focusing on the effects of salt-alkali stress on morphology and physiology, its molecular mechanisms remain unclear. Here, we employed RNA-sequencing (RNA-seq) to understand how Na2CO3 stress inhibits rice seedling growth. RESULTS Na2CO3 stress significantly inhibited the growth of rice seedlings. Through RNA-seq, many differentially expressed genes (DEGs) were shown to be potentially involved in the rice seedling response to salt-alkali stress. After 1-day and 5-day treatments, RNA-seq identified 1780 and 2315 DEGs in the Na2CO3-treated versus -untreated rice seedling shoots, respectively. According to the gene ontology enrichment and the Kyoto Encylopedia of Genes and Genomes annotation of DEGs, the growth-inhibition processes associated with salt-alkali stress involve a myriad of molecular events, including biosynthesis and metabolism, enzyme activity, and binding, etc. CONCLUSION: Collectively, the transcriptome analyses in the present work revealed several potential key regulators of plant response to salt-alkali stress, and might pave a way to improve salt-alkali stress tolerance in rice.
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Affiliation(s)
- Xiaoning Ren
- grid.263484.f0000 0004 1759 8467College of Life Science, Shenyang Normal University, 110034 Shenyang, China
| | - Jiahui Fan
- grid.263484.f0000 0004 1759 8467College of Life Science, Shenyang Normal University, 110034 Shenyang, China
| | - Xin Li
- grid.263484.f0000 0004 1759 8467College of Life Science, Shenyang Normal University, 110034 Shenyang, China
| | - Yu Shan
- grid.263484.f0000 0004 1759 8467College of Life Science, Shenyang Normal University, 110034 Shenyang, China
| | - Lanlan Wang
- grid.263484.f0000 0004 1759 8467College of Life Science, Shenyang Normal University, 110034 Shenyang, China
| | - Lianju Ma
- grid.263484.f0000 0004 1759 8467College of Life Science, Shenyang Normal University, 110034 Shenyang, China
| | - Yueying Li
- grid.263484.f0000 0004 1759 8467College of Life Science, Shenyang Normal University, 110034 Shenyang, China
| | - Xuemei Li
- grid.263484.f0000 0004 1759 8467College of Life Science, Shenyang Normal University, 110034 Shenyang, China
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Guo J, Zhang G, Song Y, Ma S, Niu N, Wang J. Comparative transcriptome profiling of multi-ovary wheat under heterogeneous cytoplasm suppression. Sci Rep 2019; 9:8301. [PMID: 31165748 PMCID: PMC6549160 DOI: 10.1038/s41598-019-43277-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 04/17/2019] [Indexed: 11/18/2022] Open
Abstract
DUOII is a multi-ovary wheat line with two or three pistils and three stamens in each floret. The multi-ovary trait of DUOII is controlled by a dominant gene, whose expression can be suppressed by the heterogeneous cytoplasm of TeZhiI (TZI), a line with the nucleus of common wheat and the cytoplasm of Aegilops. DUOII (♀) × TZI (♂) shows multi-ovary trait, while TZI (♀) × DUOII (♂) shows mono-ovary. Observing the developmental process, we found that the critical stage of additional pistil primordium development was when the young spikes were 2–6 mm long. To elucidate the molecular mechanisms that are responsible for the heterogeneous cytoplasmic suppression of the multi-ovary gene, we RNA-sequenced the entire transcriptome of 2–6 mm long young spikes obtained from the reciprocal crosses between DUOII and TZI. A total of 600 differentially expressed genes (DEGs) was identified. Functional annotation of these DEGs showed that the heterogeneous cytoplasmic suppression of additional pistil development mainly involved four pathways, i.e., chloroplast metabolism, DNA replication and repair, hormone signal transduction, and trehalose-6-phosphate in the primordium development stage, which cooperated to modulate the multi-ovary gene expression under heterogeneous cytoplasmic suppression.
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Affiliation(s)
- Jialin Guo
- College of Agronomy, Northwest A & F University, Yangling, Shaanxi, 712100, P.R. China.,National Yangling Agricultural Biotechnology & Breeding Center, Yangling, Shaanxi, 712100, P.R. China.,Yangling Branch of State Wheat Improvement Centre, Yangling, Shaanxi, 712100, P.R. China.,Wheat Breeding Engineering Research Center, Ministry of Education, Yangling, Shaanxi, 712100, P.R. China.,Key Laboratory of Crop Heterosis of Shaanxi Province, Yangling, Shaanxi, 712100, P.R. China
| | - Gaisheng Zhang
- College of Agronomy, Northwest A & F University, Yangling, Shaanxi, 712100, P.R. China. .,National Yangling Agricultural Biotechnology & Breeding Center, Yangling, Shaanxi, 712100, P.R. China. .,Yangling Branch of State Wheat Improvement Centre, Yangling, Shaanxi, 712100, P.R. China. .,Wheat Breeding Engineering Research Center, Ministry of Education, Yangling, Shaanxi, 712100, P.R. China. .,Key Laboratory of Crop Heterosis of Shaanxi Province, Yangling, Shaanxi, 712100, P.R. China.
| | - Yulong Song
- College of Agronomy, Northwest A & F University, Yangling, Shaanxi, 712100, P.R. China.,National Yangling Agricultural Biotechnology & Breeding Center, Yangling, Shaanxi, 712100, P.R. China.,Yangling Branch of State Wheat Improvement Centre, Yangling, Shaanxi, 712100, P.R. China.,Wheat Breeding Engineering Research Center, Ministry of Education, Yangling, Shaanxi, 712100, P.R. China.,Key Laboratory of Crop Heterosis of Shaanxi Province, Yangling, Shaanxi, 712100, P.R. China
| | - Shoucai Ma
- College of Agronomy, Northwest A & F University, Yangling, Shaanxi, 712100, P.R. China.,National Yangling Agricultural Biotechnology & Breeding Center, Yangling, Shaanxi, 712100, P.R. China.,Yangling Branch of State Wheat Improvement Centre, Yangling, Shaanxi, 712100, P.R. China.,Wheat Breeding Engineering Research Center, Ministry of Education, Yangling, Shaanxi, 712100, P.R. China.,Key Laboratory of Crop Heterosis of Shaanxi Province, Yangling, Shaanxi, 712100, P.R. China
| | - Na Niu
- College of Agronomy, Northwest A & F University, Yangling, Shaanxi, 712100, P.R. China.,National Yangling Agricultural Biotechnology & Breeding Center, Yangling, Shaanxi, 712100, P.R. China.,Yangling Branch of State Wheat Improvement Centre, Yangling, Shaanxi, 712100, P.R. China.,Wheat Breeding Engineering Research Center, Ministry of Education, Yangling, Shaanxi, 712100, P.R. China.,Key Laboratory of Crop Heterosis of Shaanxi Province, Yangling, Shaanxi, 712100, P.R. China
| | - Junwei Wang
- College of Agronomy, Northwest A & F University, Yangling, Shaanxi, 712100, P.R. China.,National Yangling Agricultural Biotechnology & Breeding Center, Yangling, Shaanxi, 712100, P.R. China.,Yangling Branch of State Wheat Improvement Centre, Yangling, Shaanxi, 712100, P.R. China.,Wheat Breeding Engineering Research Center, Ministry of Education, Yangling, Shaanxi, 712100, P.R. China.,Key Laboratory of Crop Heterosis of Shaanxi Province, Yangling, Shaanxi, 712100, P.R. China
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Zhang Z, Ke M, Qu Q, Peijnenburg WJGM, Lu T, Zhang Q, Ye Y, Xu P, Du B, Sun L, Qian H. Impact of copper nanoparticles and ionic copper exposure on wheat (Triticum aestivum L.) root morphology and antioxidant response. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 239:689-697. [PMID: 29715688 DOI: 10.1016/j.envpol.2018.04.066] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Revised: 04/12/2018] [Accepted: 04/15/2018] [Indexed: 06/08/2023]
Abstract
Copper nanoparticles (nCu) are widely used in industry and in daily life, due to their unique physical, chemical, and biological properties. Few studies have focused on nCu phytotoxicity, especially with regard to toxicity mechanisms in crop plants. The present study examined the effect of 15.6 μM nCu exposure on the root morphology, physiology, and gene transcription levels of wheat (Triticum aestivum L.), a major crop cultivated worldwide. The results obtained were compared with the effects of exposing wheat to an equivalent molar concentration of ionic Cu (Cu2+ released from CuSO4) and to control plants. The relative growth rate of roots decreased to approximately 60% and the formation of lateral roots was stimulated under nCu exposure, possibly due to the enhancement of nitrogen uptake and accumulation of auxin in lateral roots. The expression of four of the genes involved in the positive regulation of cell proliferation and negative regulation of programmed cell death decreased to 50% in the Cu2+ treatment compared to that of the control, while only one gene was down-regulated to about half of the control in nCu treatment. This explained the decreased root cell proliferation and higher extent of induced cell death in Cu2+- than in nCu-exposed plants. The increased methane dicarboxylic aldehyde accumulation (2.17-fold increase compared with the control) and decreased antioxidant enzyme activities (more than 50% decrease compared with the control) observed in the Cu2+ treatment in relation to the nCu treatment indicated higher oxidative stress in Cu2+- than in nCu-exposed plants. Antioxidant (e.g., proline) synthesis was pronouncedly induced by nCu to scavenge excess reactive oxygen species, alleviating phytotoxicity to wheat exposed to this form of Cu. Overall, oxidative stress and root growth inhibition were the main causes of nCu toxicity.
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Affiliation(s)
- Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Mingjing Ke
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Qian Qu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - W J G M Peijnenburg
- Institute of Environmental Sciences (CML), Leiden University, 2300 RA, Leiden, The Netherlands; National Institute of Public Health and the Environment (RIVM), Center for Safety of Substances and Products, P.O. Box 1, Bilthoven, The Netherlands
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Qi Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Yizhi Ye
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Pengfei Xu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Benben Du
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Liwei Sun
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China; Xinjiang Key Laboratory of Environmental Pollution and Bioremediation, Chinese Academy of Sciences, Urumqi 830011, PR China.
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