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Gan J, Qiu Y, Tao Y, Zhang L, Okita TW, Yan Y, Tian L. RNA-seq analysis reveals transcriptome reprogramming and alternative splicing during early response to salt stress in tomato root. FRONTIERS IN PLANT SCIENCE 2024; 15:1394223. [PMID: 38966147 PMCID: PMC11222332 DOI: 10.3389/fpls.2024.1394223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 05/30/2024] [Indexed: 07/06/2024]
Abstract
Salt stress is one of the dominant abiotic stress conditions that cause severe damage to plant growth and, in turn, limiting crop productivity. It is therefore crucial to understand the molecular mechanism underlying plant root responses to high salinity as such knowledge will aid in efforts to develop salt-tolerant crops. Alternative splicing (AS) of precursor RNA is one of the important RNA processing steps that regulate gene expression and proteome diversity, and, consequently, many physiological and biochemical processes in plants, including responses to abiotic stresses like salt stress. In the current study, we utilized high-throughput RNA-sequencing to analyze the changes in the transcriptome and characterize AS landscape during the early response of tomato root to salt stress. Under salt stress conditions, 10,588 genes were found to be differentially expressed, including those involved in hormone signaling transduction, amino acid metabolism, and cell cycle regulation. More than 700 transcription factors (TFs), including members of the MYB, bHLH, and WRKY families, potentially regulated tomato root response to salt stress. AS events were found to be greatly enhanced under salt stress, where exon skipping was the most prevalent event. There were 3709 genes identified as differentially alternatively spliced (DAS), the most prominent of which were serine/threonine protein kinase, pentatricopeptide repeat (PPR)-containing protein, E3 ubiquitin-protein ligase. More than 100 DEGs were implicated in splicing and spliceosome assembly, which may regulate salt-responsive AS events in tomato roots. This study uncovers the stimulation of AS during tomato root response to salt stress and provides a valuable resource of salt-responsive genes for future studies to improve tomato salt tolerance.
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Affiliation(s)
- Jianghuang Gan
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, Zhejiang, China
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Yongqi Qiu
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, Zhejiang, China
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Yilin Tao
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, Zhejiang, China
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Laining Zhang
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, Zhejiang, China
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Thomas W. Okita
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - Yanyan Yan
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, Zhejiang, China
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Li Tian
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, Zhejiang, China
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A&F University, Hangzhou, Zhejiang, China
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Han X, Yang R, Zhang L, Wei Q, Zhang Y, Wang Y, Shi Y. A Review of Potato Salt Tolerance. Int J Mol Sci 2023; 24:10726. [PMID: 37445900 DOI: 10.3390/ijms241310726] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 06/16/2023] [Accepted: 06/24/2023] [Indexed: 07/15/2023] Open
Abstract
Potato is the world's fourth largest food crop. Due to limited arable land and an ever-increasing demand for food from a growing population, it is critical to increase crop yields on existing acreage. Soil salinization is an increasing problem that dramatically impacts crop yields and restricts the growing area of potato. One possible solution to this problem is the development of salt-tolerant transgenic potato cultivars. In this work, we review the current potato planting distribution and the ways in which it overlaps with salinized land, in addition to covering the development and utilization of potato salt-tolerant cultivars. We also provide an overview of the current progress toward identifying potato salt tolerance genes and how they may be deployed to overcome the current challenges facing potato growers.
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Affiliation(s)
- Xue Han
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Ruijie Yang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Lili Zhang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Qiaorong Wei
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Yu Zhang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Yazhi Wang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Ying Shi
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
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Li L, Zheng Q, Jiang W, Xiao N, Zeng F, Chen G, Mak M, Chen ZH, Deng F. Molecular Regulation and Evolution of Cytokinin Signaling in Plant Abiotic Stresses. PLANT & CELL PHYSIOLOGY 2023; 63:1787-1805. [PMID: 35639886 DOI: 10.1093/pcp/pcac071] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 05/04/2022] [Accepted: 05/26/2022] [Indexed: 06/15/2023]
Abstract
The sustainable production of crops faces increasing challenges from global climate change and human activities, which leads to increasing instances of many abiotic stressors to plants. Among the abiotic stressors, drought, salinity and excessive levels of toxic metals cause reductions in global agricultural productivity and serious health risks for humans. Cytokinins (CKs) are key phytohormones functioning in both normal development and stress responses in plants. Here, we summarize the molecular mechanisms on the biosynthesis, metabolism, transport and signaling transduction pathways of CKs. CKs act as negative regulators of both root system architecture plasticity and root sodium exclusion in response to salt stress. The functions of CKs in mineral-toxicity tolerance and their detoxification in plants are reviewed. Comparative genomic analyses were performed to trace the origin, evolution and diversification of the critical regulatory networks linking CK signaling and abiotic stress. We found that the production of CKs and their derivatives, pathways of signal transduction and drought-response root growth regulation are evolutionarily conserved in land plants. In addition, the mechanisms of CK-mediated sodium exclusion under salt stress are suggested for further investigations. In summary, we propose that the manipulation of CK levels and their signaling pathways is important for plant abiotic stress and is, therefore, a potential strategy for meeting the increasing demand for global food production under changing climatic conditions.
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Affiliation(s)
- Lijun Li
- Hubei Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Qingfeng Zheng
- Hubei Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Wei Jiang
- Hubei Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Nayun Xiao
- Hubei Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Fanrong Zeng
- Hubei Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Guang Chen
- Central Laboratory, Zhejiang Academy of Agricultural Science, Hangzhou 310021, China
| | - Michelle Mak
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia
| | - Zhong-Hua Chen
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW 2751, Australia
| | - Fenglin Deng
- Hubei Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou 434025, China
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Zhang M, Wang F, Wang X, Feng J, Yi Q, Zhu S, Zhao X. Mining key genes related to root morphogenesis through genome-wide identification and expression analysis of RR gene family in citrus. FRONTIERS IN PLANT SCIENCE 2022; 13:1068961. [PMID: 36483961 PMCID: PMC9725114 DOI: 10.3389/fpls.2022.1068961] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 11/07/2022] [Indexed: 05/21/2023]
Abstract
Morphogenesis of root is a vital factor to determine the root system architecture. Cytokinin response regulators (RRs) are the key transcription factors in cytokinin signaling, which play important roles in regulating the root morphogenesis. In this study, 29 RR proteins, including 21 RRs and 8 pseudo RRs, were identified from the genome of citrus, and termed as CcRR1-21 and CcPRR1-8, respectively. Phylogenetic analysis revealed that the 29 CcRRs could be classified into four types according to their representative domains. Analysis of cis-elements of CcRRs indicated that they were possibly involved in the regulation of growth and abiotic stress resistance in citrus. Within the type A and type B CcRRs, CcRR4, CcRR5, CcRR6 and CcRR16 highly expressed in roots and leaves, and dramatically responded to the treatments of hormones and abiotic stresses. CcRR2, CcRR10, CcRR14 and CcRR19 also highly expressed in roots under different treatments. Characteristic analysis revealed that the above 8 CcRRs significantly and differentially expressed in the three zones of root, suggesting their functional differences in regulating root growth and development. Further investigation of the 3 highly and differentially expressed CcRRs, CcRR5, CcRR10 and CcRR14, in 9 citrus rootstocks showed that the expression of CcRR5, CcRR10 and CcRR14 was significantly correlated to the length of primary root, the number of lateral roots, and both primary root and the number of lateral roots, respectively. Results of this study indicated that CcRRs were involved in regulating the growth and development of the root in citrus with different functions among the members.
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Affiliation(s)
- Manman Zhang
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing, China
- National Citrus Engineering Research Center, Chongqing, China
| | - Fusheng Wang
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing, China
- National Citrus Engineering Research Center, Chongqing, China
| | - Xiaoli Wang
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing, China
- National Citrus Engineering Research Center, Chongqing, China
| | - Jipeng Feng
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing, China
- National Citrus Engineering Research Center, Chongqing, China
| | - Qian Yi
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing, China
- National Citrus Engineering Research Center, Chongqing, China
| | - Shiping Zhu
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing, China
- National Citrus Engineering Research Center, Chongqing, China
- *Correspondence: Shiping Zhu, ; Xiaochun Zhao,
| | - Xiaochun Zhao
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing, China
- National Citrus Engineering Research Center, Chongqing, China
- *Correspondence: Shiping Zhu, ; Xiaochun Zhao,
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