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Chen X, Meng L, He B, Qi W, Jia L, Xu N, Hu F, Lv Y, Song W. Comprehensive Transcriptome Analysis Uncovers Hub Long Non-coding RNAs Regulating Potassium Use Efficiency in Nicotiana tabacum. FRONTIERS IN PLANT SCIENCE 2022; 13:777308. [PMID: 35432399 PMCID: PMC9008783 DOI: 10.3389/fpls.2022.777308] [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: 09/15/2021] [Accepted: 03/01/2022] [Indexed: 06/01/2023]
Abstract
Potassium (K) is the essential element for plant growth. It is one of the critical factors that determine crop yield, quality, and especially leaf development in tobacco. However, the molecular mechanism of potassium use efficiency (KUE), especially non-coding RNA, is still unknown. In this study, tobacco seedlings were employed, and their hydro-cultivation with K treatments of low and sufficient concentrations was engaged. Physiological analysis showed that low potassium treatment could promote malondialdehyde (MDA) accumulation and antioxidant enzyme activities such as peroxidase (POD), ascorbate-peroxidase (APX). After transcriptomic analysis, a total of 10,585 LncRNA transcripts were identified, and 242 of them were significantly differently expressed under potassium starvation. Furthermore, co-expression networks were constructed and generated 78 potential regulation modules in which coding gene and LncRNAs are involved and functional jointly. By further module-trait analysis and module membership (MM) ranking, nine modules, including 616 coding RNAs and 146 LncRNAs, showed a high correlation with K treatments, and 20 hub K-responsive LncRNAs were finally predicted. Following gene ontology (GO) analysis, the results showed potassium starvation inducing the pathway of antioxidative stress which is consistent with the physiology result mentioned above. Simultaneously, a part of detected LncRNAs, such as MSTRG.6626.1, MSTRG.11330.1, and MSTRG.16041.1, were co-relating with a bench of MYB, C3H, and NFYC transcript factors in response to the stress. Overall, this research provided a set of LncRNAs that respond to K concentration from starvation and sufficient supply. Simultaneously, the regulation network and potential co-functioning genes were listed as well. This massive dataset would serve as an outstanding clue for further study in tobacco and other plant species for nutrient physiology and molecular regulation mechanism.
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Affiliation(s)
- Xi Chen
- Key Laboratory of Tobacco Biology and Processing, Ministry of Agriculture, Tobacco Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Qingdao, China
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Lin Meng
- Key Laboratory of Tobacco Biology and Processing, Ministry of Agriculture, Tobacco Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Qingdao, China
| | - Bing He
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Weicong Qi
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Letian Jia
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Na Xu
- Key Laboratory of Tobacco Biology and Processing, Ministry of Agriculture, Tobacco Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Qingdao, China
| | - Fengqin Hu
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Yuanda Lv
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Wenjing Song
- Key Laboratory of Tobacco Biology and Processing, Ministry of Agriculture, Tobacco Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Qingdao, China
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Yang D, Li F, Yi F, Eneji AE, Tian X, Li Z. Transcriptome Analysis Unravels Key Factors Involved in Response to Potassium Deficiency and Feedback Regulation of K + Uptake in Cotton Roots. Int J Mol Sci 2021; 22:3133. [PMID: 33808570 PMCID: PMC8003395 DOI: 10.3390/ijms22063133] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/16/2021] [Accepted: 03/16/2021] [Indexed: 01/19/2023] Open
Abstract
To properly understand cotton responses to potassium (K+) deficiency and how its shoot feedback regulates K+ uptake and root growth, we analyzed the changes in root transcriptome induced by low K+ (0.03 mM K+, lasting three days) in self-grafts of a K+ inefficient cotton variety (CCRI41/CCRI41, scion/rootstock) and its reciprocal grafts with a K+ efficient variety (SCRC22/CCRI41). Compared with CCRI41/CCRI41, the SCRC22 scion enhanced the K+ uptake and root growth of CCRI41 rootstock. A total of 1968 and 2539 differently expressed genes (DEGs) were identified in the roots of CCRI41/CCRI41 and SCRC22/CCRI41 in response to K+ deficiency, respectively. The overlapped and similarly (both up- or both down-) regulated DEGs in the two grafts were considered the basic response to K+ deficiency in cotton roots, whereas the DEGs only found in SCRC22/CCRI41 (1954) and those oppositely (one up- and the other down-) regulated in the two grafts might be the key factors involved in the feedback regulation of K+ uptake and root growth. The expression level of four putative K+ transporter genes (three GhHAK5s and one GhKUP3) increased in both grafts under low K+, which could enable plants to cope with K+ deficiency. In addition, two ethylene response factors (ERFs), GhERF15 and GhESE3, both down-regulated in the roots of CCRI41/CCRI41 and SCRC22/CCRI41, may negatively regulate K+ uptake in cotton roots due to higher net K+ uptake rate in their virus-induced gene silencing (VIGS) plants. In terms of feedback regulation of K+ uptake and root growth, several up-regulated DEGs related to Ca2+ binding and CIPK (CBL-interacting protein kinases), one up-regulated GhKUP3 and several up-regulated GhNRT2.1s probably play important roles. In conclusion, these results provide a deeper insight into the molecular mechanisms involved in basic response to low K+ stress in cotton roots and feedback regulation of K+ uptake, and present several low K+ tolerance-associated genes that need to be further identified and characterized.
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Affiliation(s)
- Doudou Yang
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing 100193, China
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Fangjun Li
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Fei Yi
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - A Egrinya Eneji
- Department of Soil Science, Faculty of Agriculture, Forestry and Wildlife Resources Management, University of Calabar, Calabar 540271, Nigeria
| | - Xiaoli Tian
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing 100193, China
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Zhaohu Li
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing 100193, China
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
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He Y, Li R, Lin F, Xiong Y, Wang L, Wang B, Guo J, Hu C. Transcriptome Changes Induced by Different Potassium Levels in Banana Roots. PLANTS (BASEL, SWITZERLAND) 2019; 9:E11. [PMID: 31861661 PMCID: PMC7020221 DOI: 10.3390/plants9010011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 12/14/2019] [Accepted: 12/16/2019] [Indexed: 12/14/2022]
Abstract
Potassium plays an important role in enhancing plant resistance to biological and abiotic stresses and improving fruit quality. To study the effect of potassium nutrient levels on banana root growth and its regulation mechanism, four potassium concentrations were designed to treat banana roots from no potassium to high potassium. The results indicated that K2 (3 mmol/L K2SO4) treatment was a relatively normal potassium concentration for the growth of banana root, and too high or too low potassium concentration was not conducive to the growth of banana root. By comparing the transcriptome data in each treatment in pairs, 4454 differentially expressed genes were obtained. There were obvious differences in gene function enrichment in root systems treated with different concentrations of potassium. Six significant expression profiles (profile 0, 1, 2, 7, 9 and 13) were identified by STEM analysis. The hub genes were FKF1, HsP70-1, NRT1/PTR5, CRY1, and ZIP11 in the profile 0; CYP51 in profile 1; SOS1 in profile 7; THA, LKR/SDH, MCC, C4H, CHI, F3'H, 2 PR1s, BSP, TLP, ICS, RO, chitinase and peroxidase in profile 9. Our results provide a comprehensive and systematic analysis of the gene regulation network in banana roots under different potassium stress.
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Affiliation(s)
- Yingdui He
- College of Resource and Environment, Huazhong Agricultural University, Wuhan 430070, China;
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (F.L.); (Y.X.); (L.W.); (B.W.)
- College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Ruimei Li
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China;
| | - Fei Lin
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (F.L.); (Y.X.); (L.W.); (B.W.)
| | - Ying Xiong
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (F.L.); (Y.X.); (L.W.); (B.W.)
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China;
- College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Lixia Wang
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (F.L.); (Y.X.); (L.W.); (B.W.)
| | - Bizun Wang
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (F.L.); (Y.X.); (L.W.); (B.W.)
| | - Jianchun Guo
- College of Resource and Environment, Huazhong Agricultural University, Wuhan 430070, China;
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China;
- College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Chengxiao Hu
- College of Resource and Environment, Huazhong Agricultural University, Wuhan 430070, China;
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Song Z, Wu X, Gao Y, Cui X, Jiao F, Chen X, Li Y. Genome-wide analysis of the HAK potassium transporter gene family reveals asymmetrical evolution in tobacco ( Nicotiana tabacum). Genome 2019; 62:267-278. [PMID: 30865850 DOI: 10.1139/gen-2018-0187] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Being an essential mineral nutrient, potassium (K+) plays numerous important roles in plant growth and development and determines the yield and quality of crop products. The cellular level of K+ is controlled to a large extent by the K+ transporter, which belongs to the KT/HAK/KUP (HAK) family. However, little is known about these genes in tobacco. In this study, we surveyed the tobacco genome and identified 41 putative NtHAK genes (NtHAKS1-NtHAKS21 and NtHAKT1-NtHAKT20). Investigation of the cis-elements in upstream regions of these NtHAK genes suggests that members of this family respond to environmental cues and phytohormones. Expression data mining reveals that NtHAK genes showed clear sub-genome dominance. In all, these results will provide molecular insights into K+ transporter research in tobacco.
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Affiliation(s)
- Zhongbang Song
- a Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan 650021, China
- b National Center for Tobacco Gene Engineering, Kunming, Yunnan 650021, China
| | - Xingfu Wu
- a Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan 650021, China
- b National Center for Tobacco Gene Engineering, Kunming, Yunnan 650021, China
| | - Yulong Gao
- a Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan 650021, China
- b National Center for Tobacco Gene Engineering, Kunming, Yunnan 650021, China
| | - Xiang Cui
- c College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Fangchan Jiao
- a Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan 650021, China
- b National Center for Tobacco Gene Engineering, Kunming, Yunnan 650021, China
| | - Xuejun Chen
- a Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan 650021, China
- b National Center for Tobacco Gene Engineering, Kunming, Yunnan 650021, China
| | - Yongping Li
- a Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan 650021, China
- b National Center for Tobacco Gene Engineering, Kunming, Yunnan 650021, China
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Wang X, Hao L, Zhu B, Jiang Z. Plant Calcium Signaling in Response to Potassium Deficiency. Int J Mol Sci 2018; 19:E3456. [PMID: 30400321 PMCID: PMC6275041 DOI: 10.3390/ijms19113456] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 10/19/2018] [Accepted: 11/01/2018] [Indexed: 01/23/2023] Open
Abstract
Potassium (K⁺) is an essential macronutrient of living cells and is the most abundant cation in the cytosol. K⁺ plays a role in several physiological processes that support plant growth and development. However, soil K⁺ availability is very low and variable, which leads to severe reductions in plant growth and yield. Various K⁺ shortage-activated signaling cascades exist. Among these, calcium signaling is the most important signaling system within plant cells. This review is focused on the possible roles of calcium signaling in plant responses to low-K⁺ stress. In plants, intracellular calcium levels are first altered in response to K⁺ deficiency, resulting in calcium signatures that exhibit temporal and spatial features. In addition, calcium channels located within the root epidermis and root hair zone can then be activated by hyperpolarization of plasma membrane (PM) in response to low-K⁺ stress. Afterward, calcium sensors, including calmodulin (CaM), CaM-like protein (CML), calcium-dependent protein kinase (CDPK), and calcineurin B-like protein (CBL), can act in the sensing of K⁺ deprivation. In particular, the important components regarding CBL/CBL-interacting protein kinase (CBL/CIPK) complexes-involved in plant responses to K⁺ deficiency are also discussed.
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Affiliation(s)
- Xiaoping Wang
- Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Science, Guangdong Engineering Research Center for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China.
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China.
| | - Ling Hao
- Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Science, Guangdong Engineering Research Center for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China.
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China.
| | - Biping Zhu
- Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Science, Guangdong Engineering Research Center for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China.
| | - Zhonghao Jiang
- Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Science, Guangdong Engineering Research Center for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China.
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China.
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