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Rani V, Rana S, Muthamilarasan M, Joshi DC, Yadav D. Expression profiling of Nuclear Factor-Y (NF-Y) transcription factors during dehydration and salt stress in finger millet reveals potential candidate genes for multiple stress tolerance. Planta 2024; 259:136. [PMID: 38679693 DOI: 10.1007/s00425-024-04417-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 04/15/2024] [Indexed: 05/01/2024]
Abstract
MAIN CONCLUSION Expression profiling of NF-Y transcription factors during dehydration and salt stress in finger millet genotypes contrastingly differing in tolerance levels identifies candidate genes for further characterization and functional studies. The Nuclear Factor-Y (NF-Y) transcription factors are known for imparting abiotic stress tolerance in different plant species. However, there is no information on the role of this transcription factor family in naturally drought-tolerant crop finger millet (Eleusine coracana L.). Therefore, interpretation of expression profiles against drought and salinity stress may provide valuable insights into specific and/or overlapping expression patterns of Eleusine coracana Nuclear Factor-Y (EcNF-Y) genes. Given this, we identified 59 NF-Y (18 NF-YA, 23 NF-YB, and 18 NF-YC) encoding genes and designated them EcNF-Y genes. Expression profiling of these genes was performed in two finger millet genotypes, PES400 (dehydration and salt stress tolerant) and VR708 (dehydration and salt stress sensitive), subjected to PEG-induced dehydration and salt (NaCl) stresses at different time intervals (0, 6, and 12 h). The qRT-PCR expression analysis reveals that the six EcNF-Y genes namely EcNF-YA1, EcNF-YA5, EcNF-YA16, EcNF-YB6, EcNF-YB10, and EcNF-YC2 might be associated with tolerance to both dehydration and salinity stress in early stress condition (6 h), suggesting the involvement of these genes in multiple stress responses in tolerant genotype. In contrast, the transcript abundance of finger millet EcNF-YA5 genes was also observed in the sensitive genotype VR708 under late stress conditions (12 h) of both dehydration and salinity stress. Therefore, the EcNF-YA5 gene might be important for adaptation to salinity and dehydration stress in sensitive finger millet genotypes. Therefore, this gene could be considered as a susceptibility determinant, which can be edited to impart tolerance. The phylogenetic analyses revealed that finger millet NF-Y genes share strong evolutionary and functional relationship to NF-Ys governing response to abiotic stresses in rice, sorghum, maize, and wheat. This is the first report of expression profiling of EcNF-Ys genes identified from the finger millet genome and reveals potential candidate for enhancing dehydration and salt tolerance.
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Affiliation(s)
- Varsha Rani
- Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, Uttar Pradesh, 273009, India
| | - Sumi Rana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, 500046, India
| | - Mehanathan Muthamilarasan
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, 500046, India
| | - D C Joshi
- ICAR-Vivekananda Institute of Hill Agriculture, Almora, Uttarakhand, 263601, India
| | - Dinesh Yadav
- Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, Uttar Pradesh, 273009, India.
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Chen Y, Shi H, Yang G, Liang X, Lin X, Tan S, Guo T, Wang H. OsCRLK2, a Receptor-Like Kinase Identified by QTL Analysis, is Involved in the Regulation of Rice Quality. Rice (N Y) 2024; 17:24. [PMID: 38587574 PMCID: PMC11001810 DOI: 10.1186/s12284-024-00702-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 03/18/2024] [Indexed: 04/09/2024]
Abstract
The quality of rice (Oryza sativa L) is determined by a combination of appearance, flavor, aroma, texture, storage characteristics, and nutritional composition. Rice quality directly influences acceptance by consumers and commercial value. The genetic mechanism underlying rice quality is highly complex, and is influenced by genotype, environment, and chemical factors such as starch type, protein content, and amino acid composition. Minor variations in these chemical components may lead to substantial differences in rice quality. Among these components, starch is the most crucial and influential factor in determining rice quality. In this study, quantitative trait loci (QTLs) associated with eight physicochemical properties related to the rapid viscosity analysis (RVA) profile were identified using a high-density sequence map constructed using recombinant inbred lines (RILs). Fifty-nine QTLs were identified across three environments, among which qGT6.4 was a novel locus co-located across all three environments. By integrating RNA-seq data, we identified the differentially expressed candidate gene OsCRLK2 within the qGT6.4 interval. osclrk2 mutants exhibited decreased gelatinization temperature (GT), apparent amylose content (AAC) and viscosity, and increased chalkiness. Furthermore, osclrk2 mutants exhibited downregulated expression of the majority of starch biosynthesis-related genes compared to wild type (WT) plants. In summary, OsCRLK2, which encodes a receptor-like protein kinase, appears to consistently influence rice quality across different environments. This discovery provides a new genetic resource for use in the molecular breeding of rice cultivars with improved quality.
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Affiliation(s)
- Ying Chen
- National Engineering Research Center of Plant Aerospace-mutation Breeding, South China Agricultural University, 510642, Guangzhou, China
| | - Hanfeng Shi
- National Engineering Research Center of Plant Aerospace-mutation Breeding, South China Agricultural University, 510642, Guangzhou, China
| | - Guili Yang
- National Engineering Research Center of Plant Aerospace-mutation Breeding, South China Agricultural University, 510642, Guangzhou, China
| | - Xueyu Liang
- National Engineering Research Center of Plant Aerospace-mutation Breeding, South China Agricultural University, 510642, Guangzhou, China
| | - Xiaolian Lin
- National Engineering Research Center of Plant Aerospace-mutation Breeding, South China Agricultural University, 510642, Guangzhou, China
| | - Siping Tan
- National Engineering Research Center of Plant Aerospace-mutation Breeding, South China Agricultural University, 510642, Guangzhou, China
| | - Tao Guo
- National Engineering Research Center of Plant Aerospace-mutation Breeding, South China Agricultural University, 510642, Guangzhou, China.
| | - Hui Wang
- National Engineering Research Center of Plant Aerospace-mutation Breeding, South China Agricultural University, 510642, Guangzhou, China.
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Wang J, Mao L, Li Y, Lu K, Qu C, Tang Z, Li J, Liu L. Natural variation in BnaA9.NF-YA7 contributes to drought tolerance in Brassica napus L. Nat Commun 2024; 15:2082. [PMID: 38453909 PMCID: PMC10920887 DOI: 10.1038/s41467-024-46271-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 02/21/2024] [Indexed: 03/09/2024] Open
Abstract
Rapeseed (Brassica napus) is one of the important oil crops worldwide. Its production is often threatened by drought stress. Here, we identify a transcription factor (BnaA9.NF-YA7) that negatively regulates drought tolerance through genome-wide association study in B. napus. The presence of two SNPs within a CCAAT cis element leads to downregulation of BnaA9.NF-YA7 expression. In addition, the M63I (G-to-C) substitution in the transactivation domain can activate low level expression of BnaA4.DOR, which is an inhibitory factor of ABA-induced stomatal closure. Furthermore, we determine that Bna.ABF3/4s directly regulate the expression of BnaA9.NF-YA7, and BnaA9.NF-YA7 indirectly suppresses the expression of Bna.ABF3/4s by regulation of Bna.ASHH4s. Our findings uncover that BnaA9.NF-YA7 serves as a supplementary role for ABA signal balance under drought stress conditions, and provide a potential molecular target to breed drought-tolerant B. napus cultivars.
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Affiliation(s)
- Jia Wang
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China
- Academy of Agricultural Science, Southwest University, Beibei, Chongqing, 400715, China
| | - Lin Mao
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China
- Academy of Agricultural Science, Southwest University, Beibei, Chongqing, 400715, China
| | - Yangyang Li
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China
- Academy of Agricultural Science, Southwest University, Beibei, Chongqing, 400715, China
| | - Kun Lu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China
- Academy of Agricultural Science, Southwest University, Beibei, Chongqing, 400715, China
| | - Cunmin Qu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China
- Academy of Agricultural Science, Southwest University, Beibei, Chongqing, 400715, China
| | - Zhanglin Tang
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China
- Academy of Agricultural Science, Southwest University, Beibei, Chongqing, 400715, China
| | - Jiana Li
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China
- Academy of Agricultural Science, Southwest University, Beibei, Chongqing, 400715, China
| | - Liezhao Liu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China.
- Academy of Agricultural Science, Southwest University, Beibei, Chongqing, 400715, China.
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Tian Y, Song K, Li B, Song Y, Zhang X, Li H, Yang L. Genome-wide identification and expression analysis of NF-Y gene family in tobacco (Nicotiana tabacum L.). Sci Rep 2024; 14:5257. [PMID: 38438470 PMCID: PMC10912202 DOI: 10.1038/s41598-024-55799-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 02/27/2024] [Indexed: 03/06/2024] Open
Abstract
Nuclear factor Y (NF-Y) gene family is an important transcription factor composed of three subfamilies of NF-YA, NF-YB and NF-YC, which is involved in plant growth, development and stress response. In this study, 63 tobacco NF-Y genes (NtNF-Ys) were identified in Nicotiana tabacum L., including 17 NtNF-YAs, 30 NtNF-YBs and 16 NtNF-YCs. Phylogenetic analysis revealed ten pairs of orthologues from tomato and tobacco and 25 pairs of paralogues from tobacco. The gene structure of NtNF-YAs exhibited similarities, whereas the gene structure of NtNF-YBs and NtNF-YCs displayed significant differences. The NtNF-Ys of the same subfamily exhibited a consistent distribution of motifs and protein 3D structure. The protein interaction network revealed that NtNF-YC12 and NtNF-YC5 exhibited the highest connectivity. Many cis-acting elements related to light, stress and hormone response were found in the promoter of NtNF-Ys. Transcriptome analysis showed that more than half of the NtNF-Y genes were expressed in all tissues, and NtNF-YB9/B14/B15/B16/B17/B29 were specifically expressed in roots. A total of 15, 12, 5, and 6 NtNF-Y genes were found to respond to cold, drought, salt, and alkali stresses, respectively. The results of this study will lay a foundation for further study of NF-Y genes in tobacco and other Solanaceae plants.
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Affiliation(s)
- Yue Tian
- College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Tai'an, 271018, China
| | - Kangkang Song
- College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Tai'an, 271018, China
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, College of Forestry, Shandong Agricultural University, Tai'an, China
- Mountain Tai Forest Ecosystem Research Station of State Forestry and Grassland Administration, College of Forestry, Shandong Agricultural University, Tai'an, China
| | - Bin Li
- College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Tai'an, 271018, China
| | - Yanru Song
- College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Tai'an, 271018, China
| | - Xiaohua Zhang
- College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Tai'an, 271018, China
| | - Haozhen Li
- College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Tai'an, 271018, China
| | - Long Yang
- College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Tai'an, 271018, China.
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Geng A, Lian W, Wang Y, Liu M, Zhang Y, Wang X, Chen G. Molecular Mechanisms and Regulatory Pathways Underlying Drought Stress Response in Rice. Int J Mol Sci 2024; 25:1185. [PMID: 38256261 PMCID: PMC10817035 DOI: 10.3390/ijms25021185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 01/10/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
Rice is a staple food for 350 million people globally. Its yield thus affects global food security. Drought is a serious environmental factor affecting rice growth. Alleviating the inhibition of drought stress is thus an urgent challenge that should be solved to enhance rice growth and yield. This review details the effects of drought on rice morphology, physiology, biochemistry, and the genes associated with drought stress response, their biological functions, and molecular regulatory pathways. The review further highlights the main future research directions to collectively provide theoretical support and reference for improving drought stress adaptation mechanisms and breeding new drought-resistant rice varieties.
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Affiliation(s)
- Anjing Geng
- Institute of Quality Standard and Monitoring Technology for Agro-Products of Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Testing and Evaluation for Agro-Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Quality & Safety Risk Assessment for Agro-Products, Guangzhou 510640, China
| | - Wenli Lian
- Institute of Quality Standard and Monitoring Technology for Agro-Products of Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Testing and Evaluation for Agro-Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Quality & Safety Risk Assessment for Agro-Products, Guangzhou 510640, China
| | - Yihan Wang
- Institute of Quality Standard and Monitoring Technology for Agro-Products of Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Testing and Evaluation for Agro-Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Quality & Safety Risk Assessment for Agro-Products, Guangzhou 510640, China
| | - Minghao Liu
- Institute of Quality Standard and Monitoring Technology for Agro-Products of Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Testing and Evaluation for Agro-Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Quality & Safety Risk Assessment for Agro-Products, Guangzhou 510640, China
| | - Yue Zhang
- Institute of Quality Standard and Monitoring Technology for Agro-Products of Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Testing and Evaluation for Agro-Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Quality & Safety Risk Assessment for Agro-Products, Guangzhou 510640, China
| | - Xu Wang
- Institute of Quality Standard and Monitoring Technology for Agro-Products of Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Testing and Evaluation for Agro-Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Quality & Safety Risk Assessment for Agro-Products, Guangzhou 510640, China
| | - Guang Chen
- Institute of Quality Standard and Monitoring Technology for Agro-Products of Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Testing and Evaluation for Agro-Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Quality & Safety Risk Assessment for Agro-Products, Guangzhou 510640, China
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Seo JS, Kim SH, Shim JS, Um T, Oh N, Park T, Kim YS, Oh SJ, Kim JK. The rice NUCLEAR FACTOR-YA5 and MICRORNA169a module promotes nitrogen utilization during nitrogen deficiency. Plant Physiol 2023; 194:491-510. [PMID: 37723121 PMCID: PMC10756765 DOI: 10.1093/plphys/kiad504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 09/20/2023]
Abstract
Nitrogen (N) is essential for plant growth and development. Therefore, understanding its utilization is essential for improving crop productivity. However, much remains to be learned about plant N sensing and signaling. Here, rice (Oryza sativa) NUCLEAR FACTOR-YA5 (OsNF-YA5) expression was tightly regulated by N status and induced under N-deficient conditions. Overexpression (OE) of OsNF-YA5 in rice resulted in increased chlorophyll levels and delayed senescence compared to control plants under normal N conditions. Agronomic traits were significantly improved in OE plants and impaired in knockout mutants under N-deficient conditions. Using a dexamethasone-inducible system, we identified the putative targets of OsNF-YA5 that include amino acid, nitrate/peptide transporters, and NITRATE TRANSPORTER 1.1A (OsNRT1.1A), which functions as a key transporter in rice. OsNF-YA5 directly enhanced OsNRT1.1A expression and N uptake rate under N-deficient conditions. Besides, overexpression of OsNF-YA5 also enhanced the expression of GLUTAMINE SYNTHETASE 1/2 (GS1/2) and GLUTAMINE OXOGLUTARATE AMINOTRANSFERASE 1/2 (GOGAT1/2), increasing free amino acid contents under N-deficient conditions. Osa-miR169a expression showed an opposite pattern with OsNF-YA5 depending on N status. Further analysis revealed that osa-miR169a negatively regulates OsNF-YA5 expression and N utilization, demonstrating that an OsNF-YA5/osa-miR169a module tightly regulates rice N utilization for adaptation to N status.
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Affiliation(s)
- Jun Sung Seo
- GreenBio Science & Technology, Seoul National University, Pyeongchang 25354, Korea
| | - Sung Hwan Kim
- Crop Biotechnology Institute, Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang 25354, Korea
| | - Jae Sung Shim
- GreenBio Science & Technology, Seoul National University, Pyeongchang 25354, Korea
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Korea
| | - Taeyoung Um
- GreenBio Science & Technology, Seoul National University, Pyeongchang 25354, Korea
| | - Nuri Oh
- Crop Biotechnology Institute, Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang 25354, Korea
| | - Taehyeon Park
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Korea
| | - Youn Shic Kim
- GreenBio Science & Technology, Seoul National University, Pyeongchang 25354, Korea
| | - Se-Jun Oh
- LaSemilla Co. Ltd., Pyeongchang 25354, Korea
| | - Ju-Kon Kim
- GreenBio Science & Technology, Seoul National University, Pyeongchang 25354, Korea
- Crop Biotechnology Institute, Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang 25354, Korea
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Korea
- LaSemilla Co. Ltd., Pyeongchang 25354, Korea
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Wang T, Zou H, Ren S, Jin B, Lu Z. Genome-Wide Identification, Characterization, and Expression Analysis of NF-Y Gene Family in Ginkgo biloba Seedlings and GbNF-YA6 Involved in Heat-Stress Response and Tolerance. Int J Mol Sci 2023; 24:12284. [PMID: 37569658 PMCID: PMC10418864 DOI: 10.3390/ijms241512284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/22/2023] [Accepted: 07/30/2023] [Indexed: 08/13/2023] Open
Abstract
Nuclear factor Y (NF-Y) transcription factors play an essential role in regulating plant growth, development, and stress responses. Despite extensive research on the NF-Y gene family across various species, the knowledge regarding the NF-Y family in Ginkgo biloba remains unknown. In this study, we identified a total of 25 NF-Y genes (seven GbNF-YAs, 12 GbNF-YBs, and six GbNF-YCs) in the G. biloba genome. We characterized the gene structure, conserved motifs, multiple sequence alignments, and phylogenetic relationships with other species (Populus and Arabidopsis). Additionally, we conducted a synteny analysis, which revealed the occurrence of segment duplicated NF-YAs and NF-YBs. The promoters of GbNF-Y genes contained cis-acting elements related to stress response, and miRNA-mRNA analysis showed that some GbNF-YAs with stress-related cis-elements could be targeted by the conserved miRNA169. The expression of GbNF-YA genes responded to drought, salt, and heat treatments, with GbNF-YA6 showing significant upregulation under heat and drought stress. Subcellular localization indicated that GbNF-YA6 was located in both the nucleus and the membrane. Overexpressing GbNF-YA6 in ginkgo callus significantly induced the expression of heat-shock factors (GbHSFs), and overexpressing GbNF-YA6 in transgenic Arabidopsis enhanced its heat tolerance. Additionally, Y2H assays demonstrated that GbNF-YA6 could interact with GbHSP at the protein level. Overall, our findings offer novel insights into the role of GbNF-YA in enhancing abiotic stress tolerance and warrant further functional research of GbNF-Y genes.
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Affiliation(s)
| | | | | | - Biao Jin
- College of Horticulture and Landscape, Yangzhou University, Yangzhou 225009, China; (T.W.); (H.Z.); (S.R.)
| | - Zhaogeng Lu
- College of Horticulture and Landscape, Yangzhou University, Yangzhou 225009, China; (T.W.); (H.Z.); (S.R.)
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Zhang Y, Xu J, Li R, Ge Y, Li Y, Li R. Plants' Response to Abiotic Stress: Mechanisms and Strategies. Int J Mol Sci 2023; 24:10915. [PMID: 37446089 DOI: 10.3390/ijms241310915] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/24/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
Abiotic stress is the adverse effect of any abiotic factor on a plant in a given environment, impacting plants' growth and development. These stress factors, such as drought, salinity, and extreme temperatures, are often interrelated or in conjunction with each other. Plants have evolved mechanisms to sense these environmental challenges and make adjustments to their growth in order to survive and reproduce. In this review, we summarized recent studies on plant stress sensing and its regulatory mechanism, emphasizing signal transduction and regulation at multiple levels. Then we presented several strategies to improve plant growth under stress based on current progress. Finally, we discussed the implications of research on plant response to abiotic stresses for high-yielding crops and agricultural sustainability. Studying stress signaling and regulation is critical to understand abiotic stress responses in plants to generate stress-resistant crops and improve agricultural sustainability.
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Affiliation(s)
- Yan Zhang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing 100083, China
| | - Jing Xu
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing 100083, China
| | - Ruofan Li
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing 100083, China
| | - Yanrui Ge
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing 100083, China
| | - Yufei Li
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing 100083, China
| | - Ruili Li
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing 100083, China
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9
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Rani V, Joshi DC, Joshi P, Singh R, Yadav D. "Millet Models" for harnessing nuclear factor-Y transcription factors to engineer stress tolerance in plants: current knowledge and emerging paradigms. Planta 2023; 258:29. [PMID: 37358736 DOI: 10.1007/s00425-023-04186-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 06/17/2023] [Indexed: 06/27/2023]
Abstract
MAIN CONCLUSION The main purpose of this review is to shed light on the role of millet models in imparting climate resilience and nutritional security and to give a concrete perspective on how NF-Y transcription factors can be harnessed for making cereals more stress tolerant. Agriculture faces significant challenges from climate change, bargaining, population, elevated food prices, and compromises with nutritional value. These factors have globally compelled scientists, breeders, and nutritionists to think of some options that can combat the food security crisis and malnutrition. To address these challenges, mainstreaming the climate-resilient and nutritionally unparalleled alternative crops like millet is a key strategy. The C4 photosynthetic pathway and adaptation to low-input marginal agricultural systems make millets a powerhouse of important gene and transcription factor families imparting tolerance to various kinds of biotic and abiotic stresses. Among these, the nuclear factor-Y (NF-Y) is one of the prominent transcription factor families that regulate diverse genes imparting stress tolerance. The primary purpose of this article is to shed light on the role of millet models in imparting climate resilience and nutritional security and to give a concrete perspective on how NF-Y transcription factors can be harnessed for making cereals more stress tolerant. Future cropping systems could be more resilient to climate change and nutritional quality if these practices were implemented.
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Affiliation(s)
- Varsha Rani
- Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, Uttar Pradesh, 273009, India
| | - D C Joshi
- ICAR-Vivekananda Institute of Hill Agriculture, Almora, Uttarakhand, 263601, India
| | - Priyanka Joshi
- Plant and Environmental Sciences, 113 Biosystems Research Complex, Clemson University, Clemson, South Carolina, 29634, USA
| | - Rajesh Singh
- Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India
| | - Dinesh Yadav
- Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, Uttar Pradesh, 273009, India.
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Zhao M, Du C, Zeng J, Gao Z, Zhu Y, Wang J, Zhang Y, Zhu Z, Wang Y, Chen M, Wang Y, Chang J, Yang G, He G, Li Y, Chen X. Integrated omic analysis provides insights into the molecular regulation of stress tolerance by partial root-zone drying in rice. Front Plant Sci 2023; 14:1156514. [PMID: 37360728 PMCID: PMC10288491 DOI: 10.3389/fpls.2023.1156514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/26/2023] [Indexed: 06/28/2023]
Abstract
Partial root-zone drying (PRD) is an effective water-saving irrigation strategy that improves stress tolerance and facilitates efficient water use in several crops. It has long been considered that abscisic acid (ABA)-dependent drought resistance may be involved during partial root-zone drying. However, the molecular mechanisms underlying PRD-mediated stress tolerance remain unclear. It's hypothesized that other mechanisms might contribute to PRD-mediated drought tolerance. Here, rice seedlings were used as a research model and the complex transcriptomic and metabolic reprogramming processes were revealed during PRD, with several key genes involved in osmotic stress tolerance identified by using a combination of physiological, transcriptome, and metabolome analyses. Our results demonstrated that PRD induces transcriptomic alteration mainly in the roots but not in the leaves and adjusts several amino-acid and phytohormone metabolic pathways to maintain the balance between growth and stress response compared to the polyethylene glycol (PEG)-treated roots. Integrated analysis of the transcriptome and metabolome associated the co-expression modules with PRD-induced metabolic reprogramming. Several genes encoding the key transcription factors (TFs) were identified in these co-expression modules, highlighting several key TFs, including TCP19, WRI1a, ABF1, ABF2, DERF1, and TZF7, involved in nitrogen metabolism, lipid metabolism, ABA signaling, ethylene signaling, and stress regulation. Thus, our work presents the first evidence that molecular mechanisms other than ABA-mediated drought resistance are involved in PRD-mediated stress tolerance. Overall, our results provide new insights into PRD-mediated osmotic stress tolerance, clarify the molecular regulation induced by PRD, and identify genes useful for further improving water-use efficiency and/or stress tolerance in rice.
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Affiliation(s)
- Minhua Zhao
- Henry Fok School of Biology and Agriculture, Guangdong Engineering Technology Research Center for Efficient Utilization of Water and Soil Resources in North Region, Shaoguan University, Shaoguan, Guangdong, China
| | - Canghao Du
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jian Zeng
- Henry Fok School of Biology and Agriculture, Guangdong Engineering Technology Research Center for Efficient Utilization of Water and Soil Resources in North Region, Shaoguan University, Shaoguan, Guangdong, China
| | - Zhihong Gao
- Henry Fok School of Biology and Agriculture, Guangdong Engineering Technology Research Center for Efficient Utilization of Water and Soil Resources in North Region, Shaoguan University, Shaoguan, Guangdong, China
| | - Yongyong Zhu
- Henry Fok School of Biology and Agriculture, Guangdong Engineering Technology Research Center for Efficient Utilization of Water and Soil Resources in North Region, Shaoguan University, Shaoguan, Guangdong, China
| | - Jinfei Wang
- Henry Fok School of Biology and Agriculture, Guangdong Engineering Technology Research Center for Efficient Utilization of Water and Soil Resources in North Region, Shaoguan University, Shaoguan, Guangdong, China
| | - Yupeng Zhang
- Henry Fok School of Biology and Agriculture, Guangdong Engineering Technology Research Center for Efficient Utilization of Water and Soil Resources in North Region, Shaoguan University, Shaoguan, Guangdong, China
| | - Zetao Zhu
- Henry Fok School of Biology and Agriculture, Guangdong Engineering Technology Research Center for Efficient Utilization of Water and Soil Resources in North Region, Shaoguan University, Shaoguan, Guangdong, China
| | - Yaqiong Wang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Mingjie Chen
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yuesheng Wang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Junli Chang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Guangxiao Yang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Guangyuan He
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yin Li
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xiaoyuan Chen
- Henry Fok School of Biology and Agriculture, Guangdong Engineering Technology Research Center for Efficient Utilization of Water and Soil Resources in North Region, Shaoguan University, Shaoguan, Guangdong, China
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11
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Peng M, Gan F, Lin X, Yang R, Li S, Li W, Wu L, Fan X, Chen K. Overexpression of OsNF-YB4 leads to flowering early, improving photosynthesis and better grain yield in hybrid rice. Plant Sci 2023; 331:111661. [PMID: 36813243 DOI: 10.1016/j.plantsci.2023.111661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/17/2023] [Accepted: 02/19/2023] [Indexed: 06/18/2023]
Abstract
For cereal crops, such as rice, the grain yield mainly comes from the accumulation of carbohydrates in the seed, which depends ultimately on photosynthesis during the growth period. To create early ripen variety, higher efficiency of photosynthesis is thus necessary to get higher grain yield with shorter growth period. In this study, flowering early was observed in the hybrid rice with overexpression of OsNF-YB4. Along with the flowering early, the hybrid rice also was shorter in plant height with less of leaves and internodes, but no changes of panicle length and leaf emergence. The grain yield was kept or even increased in the hybrid rice with shorter growth period. Transcription analysis revealed that Ghd7-Ehd1-Hd3a/RFT1 was activated early to promote the flowering transition in the overexpression hybrids. RNA-Seq study further showed that carbohydrate-related pathways were significantly altered in addition to circadian pathway. Notably, up-regulation of three pathways related to plant photosynthesis was observed, as well. Increased carbon assimilation with alteration of chlorophyll contents was subsequently detected in the following physiological experiments. All these results demonstrate that overexpression of OsNF-YB4 in the hybrid rice activates flowering early and improves photosynthesis resulting in better grain yield with shorter growth period.
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Affiliation(s)
- Meifang Peng
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, 106 Shizishan Road, Chengdu 610061, Sichuan, China
| | - Feng Gan
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, 106 Shizishan Road, Chengdu 610061, Sichuan, China
| | - Xiaomin Lin
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, 106 Shizishan Road, Chengdu 610061, Sichuan, China
| | - Run Yang
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, 106 Shizishan Road, Chengdu 610061, Sichuan, China
| | - Shaoyi Li
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, 106 Shizishan Road, Chengdu 610061, Sichuan, China
| | - Wei Li
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, 106 Shizishan Road, Chengdu 610061, Sichuan, China
| | - Lan Wu
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, 106 Shizishan Road, Chengdu 610061, Sichuan, China
| | - Xiaoli Fan
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, 106 Shizishan Road, Chengdu 610061, Sichuan, China
| | - Kegui Chen
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, 106 Shizishan Road, Chengdu 610061, Sichuan, China.
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12
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Swathik Clarancia P, Naveenarani M, Ashwin Narayan J, Krishna SS, Thirugnanasambandam PP, Valarmathi R, Suresha GS, Gomathi R, Kumar RA, Manickavasagam M, Jegadeesan R, Arun M, Hemaprabha G, Appunu C. Genome-Wide Identification, Characterization and Expression Analysis of Plant Nuclear Factor (NF-Y) Gene Family Transcription Factors in Saccharum spp. Genes (Basel) 2023; 14:1147. [PMID: 37372327 DOI: 10.3390/genes14061147] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 05/16/2023] [Accepted: 05/20/2023] [Indexed: 06/29/2023] Open
Abstract
Plant nuclear factor (NF-Y) is a transcriptional activating factor composed of three subfamilies: NF-YA, NF-YB, and NF-YC. These transcriptional factors are reported to function as activators, suppressors, and regulators under different developmental and stress conditions in plants. However, there is a lack of systematic research on the NF-Y gene subfamily in sugarcane. In this study, 51 NF-Y genes (ShNF-Y), composed of 9 NF-YA, 18 NF-YB, and 24 NF-YC genes, were identified in sugarcane (Saccharum spp.). Chromosomal distribution analysis of ShNF-Ys in a Saccharum hybrid located the NF-Y genes on all 10 chromosomes. Multiple sequence alignment (MSA) of ShNF-Y proteins revealed conservation of core functional domains. Sixteen orthologous gene pairs were identified between sugarcane and sorghum. Phylogenetic analysis of NF-Y subunits of sugarcane, sorghum, and Arabidopsis showed that ShNF-YA subunits were equidistant while ShNF-YB and ShNF-YC subunits clustered distinctly, forming closely related and divergent groups. Expression profiling under drought treatment showed that NF-Y gene members were involved in drought tolerance in a Saccharum hybrid and its drought-tolerant wild relative, Erianthus arundinaceus. ShNF-YA5 and ShNF-YB2 genes had significantly higher expression in the root and leaf tissues of both plant species. Similarly, ShNF-YC9 had elevated expression in the leaf and root of E. arundinaceus and in the leaf of a Saccharum hybrid. These results provide valuable genetic resources for further sugarcane crop improvement programs.
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Affiliation(s)
- Peter Swathik Clarancia
- Division of Crop Improvement, Indian Council of Agricultural Research-Sugarcane Breeding Institute, Coimbatore 641007, India
| | - Murugan Naveenarani
- Division of Crop Improvement, Indian Council of Agricultural Research-Sugarcane Breeding Institute, Coimbatore 641007, India
- Bharathidasan University, Tiruchirappalli 620024, India
| | - Jayanarayanan Ashwin Narayan
- Division of Crop Improvement, Indian Council of Agricultural Research-Sugarcane Breeding Institute, Coimbatore 641007, India
| | - Sakthivel Surya Krishna
- Division of Crop Improvement, Indian Council of Agricultural Research-Sugarcane Breeding Institute, Coimbatore 641007, India
| | | | - Ramanathan Valarmathi
- Division of Crop Improvement, Indian Council of Agricultural Research-Sugarcane Breeding Institute, Coimbatore 641007, India
| | | | - Raju Gomathi
- Division of Crop Improvement, Indian Council of Agricultural Research-Sugarcane Breeding Institute, Coimbatore 641007, India
| | - Raja Arun Kumar
- Division of Crop Improvement, Indian Council of Agricultural Research-Sugarcane Breeding Institute, Coimbatore 641007, India
| | - Markandan Manickavasagam
- Department of Biotechnology, School of Life Sciences, Bharathidasan University, Tiruchirappalli 620024, India
| | - Ramalingam Jegadeesan
- Centre for Plant Molecular Biology and Bioinformatics, Tamil Nadu Agricultural University, Coimbatore 641003, India
| | - Muthukrishnan Arun
- Department of Biotechnology, Bharathiar University, Coimbatore 641046, India
| | - Govindakurup Hemaprabha
- Division of Crop Improvement, Indian Council of Agricultural Research-Sugarcane Breeding Institute, Coimbatore 641007, India
| | - Chinnaswamy Appunu
- Division of Crop Improvement, Indian Council of Agricultural Research-Sugarcane Breeding Institute, Coimbatore 641007, India
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13
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Jin X, Zhang Y, Li X, Huang J. OsNF-YA3 regulates plant growth and osmotic stress tolerance by interacting with SLR1 and SAPK9 in rice. Plant J 2023; 114:914-933. [PMID: 36906910 DOI: 10.1111/tpj.16183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 02/27/2023] [Accepted: 03/07/2023] [Indexed: 05/27/2023]
Abstract
The antagonism between gibberellin (GA) and abscisic acid (ABA) signaling pathways is vital to balance plant growth and stress response. Nevertheless, the mechanism by which plants determine the balance remains to be elucidated. Here, we report that rice NUCLEAR FACTOR-Y A3 (OsNF-YA3) modulates GA- and ABA-mediated balance between plant growth and osmotic stress tolerance. OsNF-YA3 loss-of-function mutants exhibit stunted growth, compromised GA biosynthetic gene expression, and decreased GA levels, while its overexpression lines have promoted growth and enhanced GA content. Chromatin immunoprecipitation-quantitative polymerase chain reaction analysis and transient transcriptional regulation assays demonstrate that OsNF-YA3 activates GA biosynthetic gene OsGA20ox1 expression. Furthermore, the DELLA protein SLENDER RICE1 (SLR1) physically interacts with OsNF-YA3 and thus inhibits its transcriptional activity. On the other side, OsNF-YA3 negatively regulates plant osmotic stress tolerance by repressing ABA response. OsNF-YA3 reduces ABA levels by transcriptionally regulating ABA catabolic genes OsABA8ox1 and OsABA8ox3 by binding to their promoters. Furthermore, OSMOTIC STRESS/ABA-ACTIVATED PROTEIN KINASE 9 (SAPK9), the positive component in ABA signaling, interacts with OsNF-YA3 and mediates OsNF-YA3 phosphorylation, resulting in its degradation in plants. Collectively, our findings establish OsNF-YA3 as an important transcription factor that positively modulates GA-regulated plant growth and negatively controls ABA-mediated water-deficit and salt tolerance. These findings shed light on the molecular mechanism underlying the balance between the growth and stress response of the plant.
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Affiliation(s)
- Xinkai Jin
- Key Laboratory of Biorheological Science and Technology of Ministry of Education, Bioengineering College, Chongqing University, Chongqing, 400044, China
| | - Yifan Zhang
- Key Laboratory of Biorheological Science and Technology of Ministry of Education, Bioengineering College, Chongqing University, Chongqing, 400044, China
| | - Xingxing Li
- Key Laboratory of Biorheological Science and Technology of Ministry of Education, Bioengineering College, Chongqing University, Chongqing, 400044, China
| | - Junli Huang
- Key Laboratory of Biorheological Science and Technology of Ministry of Education, Bioengineering College, Chongqing University, Chongqing, 400044, China
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14
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Ashalatha KL, Arunkumar KP, Gowda M. Genomic and transcriptomic analysis of sacred fig (Ficus religiosa). BMC Genomics 2023; 24:197. [PMID: 37046210 PMCID: PMC10100241 DOI: 10.1186/s12864-023-09270-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 03/23/2023] [Indexed: 04/14/2023] Open
Abstract
BACKGROUND Peepal/Bodhi tree (Ficus religiosa L.) is an important, long-lived keystone ecological species. Communities on the Indian subcontinent have extensively employed the plant in Ayurveda, traditional medicine, and spiritual practices. The Peepal tree is often thought to produce oxygen both during the day and at night by Indian folks. The goal of our research was to produce molecular resources using whole-genome and transcriptome sequencing techniques. RESULTS The complete genome of the Peepal tree was sequenced using two next-generation sequencers Illumina HiSeq1000 and MGISEQ-2000. We assembled the draft genome of 406 Mb, using a hybrid assembly workflow. The genome annotation resulted in 35,093 protein-coding genes; 53% of its genome consists of repetitive sequences. To understand the physiological pathways in leaf tissues, we analyzed photosynthetically distinct conditions: bright sunny days and nights. The RNA-seq analysis supported the expression of 26,479 unigenes. The leaf transcriptomic analysis of the diurnal and nocturnal periods revealed the expression of the significant number of genes involved in the carbon-fixation pathway. CONCLUSIONS This study presents a draft hybrid genome assembly for F. religiosa and its functional annotated genes. The genomic and transcriptomic data-derived pathways have been analyzed for future studies on the Peepal tree.
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Affiliation(s)
- K L Ashalatha
- The University of Trans-Disciplinary Health Sciences and Technology (TDU), Yelahanka, Bengaluru, 560064, India
| | - Kallare P Arunkumar
- Central Silk Board, Central Muga Eri Research and Training Institute (CMER&TI), Ministry of Textiles Lahdoigarh, Jorhat, Assam, 785700, India
| | - Malali Gowda
- The University of Trans-Disciplinary Health Sciences and Technology (TDU), Yelahanka, Bengaluru, 560064, India.
- The University of Trans-Disciplinary Health Sciences and Technology (TDU), DNA Life Organization, Yelahanka, Bengaluru, 560064, India.
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15
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Li M, Du Q, Li J, Wang H, Xiao H, Wang J. Genome-Wide Identification and Chilling Stress Analysis of the NF-Y Gene Family in Melon. Int J Mol Sci 2023; 24:ijms24086934. [PMID: 37108097 PMCID: PMC10138816 DOI: 10.3390/ijms24086934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/16/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
The nuclear factor Y (NF-Y) transcription factor contains three subfamilies: NF-YA, NF-YB, and NF-YC. The NF-Y family have been reported to be key regulators in plant growth and stress responses. However, little attention has been given to these genes in melon (Cucumis melo L.). In this study, twenty-five NF-Ys were identified in the melon genome, including six CmNF-YAs, eleven CmNF-YBs, and eight CmNF-YCs. Their basic information (gene location, protein characteristics, and subcellular localization), conserved domains and motifs, and phylogeny and gene structure were subsequently analyzed. Results showed highly conserved motifs exist in each subfamily, which are distinct between subfamilies. Most CmNF-Ys were expressed in five tissues and exhibited distinct expression patterns. However, CmNF-YA6, CmNF-YB1/B2/B3/B8, and CmNF-YC6 were not expressed and might be pseudogenes. Twelve CmNF-Ys were induced by cold stress, indicating the NF-Y family plays a key role in melon cold tolerance. Taken together, our findings provide a comprehensive understanding of CmNF-Y genes in the development and stress response of melon and provide genetic resources for solving the practical problems of melon production.
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Affiliation(s)
- Meng Li
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Qingjie Du
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Juanqi Li
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Hu Wang
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Huaijuan Xiao
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Jiqing Wang
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
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16
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Bhattacharjee B, Hallan V. NF-YB family transcription factors in Arabidopsis: Structure, phylogeny, and expression analysis in biotic and abiotic stresses. Front Microbiol 2023; 13:1067427. [PMID: 36733773 PMCID: PMC9887194 DOI: 10.3389/fmicb.2022.1067427] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 12/22/2022] [Indexed: 01/18/2023] Open
Abstract
Nuclear factor-Y (NF-Y) transcription factors (TFs) are conserved heterotrimeric complexes present and widespread across eukaryotes. Three main subunits make up the structural and functional aspect of the NF-Y TFs: NF-YA, NF-YB and NF-YC, which bind to the conserved CCAAT- box of the promoter region of specific genes, while also interacting with each other, thereby forming myriad combinations. The NF-YBs are expressed differentially in various tissues and plant development stages, likely impacting many of the cellular processes constitutively and under stress conditions. In this study, ten members of NF-YB family from Arabidopsis thaliana were identified and expression profiles were mined from microarray data under different biotic and abiotic conditions, revealing key insights into the involvement of this class of proteins in the cellular and biological processes in Arabidopsis. Analysis of cis-acting regulatory elements (CAREs) indicated the presence of abiotic and biotic stress-related transcription factor binding sites (TFBs), shedding light on the multifaceted roles of these TFs. Microarray data analysis inferred distinct patterns of expression in various tissues under differing treatments such as drought, cold and heat stress as well as bacterial, fungal, and viral stress, indicating their likelihood of having an expansive range of regulatory functions under native and stressed conditions; while quantitative real-time PCR (qRT-PCR) based expression analysis revealed that these TFs get real-time-modulated in a stress dependent manner. This study, overall, provides an understanding of the AtNF-YB family of TFs in their regulation and participation in various morphogenetic and defense- related pathways and can provide insights for development of transgenic plants for trait dependent studies.
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Affiliation(s)
- Bipasha Bhattacharjee
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India,Plant Virology Laboratory, Division of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, India
| | - Vipin Hallan
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India,Plant Virology Laboratory, Division of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, India,*Correspondence: Vipin Hallan, ✉
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17
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Ji J, Zeng Y, Zhang S, Chen F, Hou X, Li Q. The miR169b/NFYA1 module from the halophyte Halostachys caspica endows salt and drought tolerance in Arabidopsis through multi-pathways. Front Plant Sci 2023; 13:1026421. [PMID: 36726670 PMCID: PMC9886095 DOI: 10.3389/fpls.2022.1026421] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 12/01/2022] [Indexed: 06/18/2023]
Abstract
Salt and drought are the major abiotic stress factors plaguing plant growth, development and crop yields. Certain abiotic-stress tolerant plants have developed special mechanisms for adapting to adverse environments in the long process of evolution. Elucidating the molecular mechanisms by which they can exert resistance to abiotic stresses is beneficial for breeding new cultivars to guide agricultural production. Halostachys caspica, a perennial halophyte belonging to Halostachys in Amaranthaceae, is extremely tolerant to harsh environments, which is commonly grown in the saline-alkali arid desert area of Northwest, China. However, the molecular mechanism of stress tolerance is unclear. Nuclear Factor Y-A (NFYA) is a transcription factor that regulates the expression of downstream genes in plant response to adverse environments. It has also been reported that some members of the NFYA family are the main targets of miR169 in plants. In this study, we mainly focused on exploring the functions and preliminary mechanism of the miR169b/NFYA1 module from H. caspica to abiotic stress. The main results showed that RLM-RACE technology validated that HcNFYA1 was targeted by HcmiR169b, qRT-PCR revealed that HcmiR169b was repressed and HcNFYA1 was induced in the H. caspica branches under various abiotic stress as well ABA treatment and Arabidopsis stable transformation platform with molecular methods was applied to elucidate that the HcmiR169b/HcNFYA1 module conferred the salt and drought tolerance to plants by enhancing ABA synthesis and ABA signal transduction pathways, maintaining ROS homeostasis and the stability of cell membrane. HcNFYA1 is expected to be a candidate gene to improve plant resistance to salt and drought stresses.
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Affiliation(s)
- Jieyun Ji
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, sChina
| | - Youling Zeng
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, sChina
| | - Suwei Zhang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, sChina
| | - Fangyuan Chen
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, sChina
| | - Xianfei Hou
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Qiang Li
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
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18
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Jiang S, Wang H, Wen Y, Liang J, Li D, Song F. The NF-Y Transcription Factor Family in Watermelon: Re-Characterization, Assembly of ClNF-Y Complexes, Hormone- and Pathogen-Inducible Expression and Putative Functions in Disease Resistance. Int J Mol Sci 2022; 23. [PMID: 36555422 DOI: 10.3390/ijms232415778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/04/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022] Open
Abstract
Nuclear factor Y (NF-Y) is a heterotrimeric transcription factor that binds to the CCAAT cis-element in the promoters of target genes and plays critical roles in plant growth, development, and stress responses. In the present study, we aimed to re-characterize the ClNF-Y family in watermelon, examine the assembly of ClNF-Y complexes, and explore their possible involvement in disease resistance. A total of 25 ClNF-Y genes (7 ClNF-YAs, 10 ClNF-YBs, and 8 ClNF-YCs) were identified in the watermelon genome. The ClNF-Y family was comprehensively characterized in terms of gene and protein structures, phylogenetic relationships, and evolution events. Different types of cis-elements responsible for plant growth and development, phytohormones, and/or stress responses were identified in the promoters of the ClNF-Y genes. ClNF-YAs and ClNF-YCs were mainly localized in the nucleus, while most of the ClNF-YBs were localized in the cytoplasm of cells. ClNF-YB5, -YB6, -YB7, -YB8, -YB9, and -YB10 interacted with ClNF-YC2, -YC3, -YC4, -YC5, -YC6, -YC7, and -YC8, while ClNF-YB1 and -YB3 interacted with ClNF-YC1. A total of 37 putative ClNF-Y complexes were identified, e.g., ClNF-YA1, -YA2, -YA3, and -YA7 assembled into 13, 8, 8, and 8 ClNF-Y complexes with different ClNF-YB/-YC heterodimers. Most of the ClNF-Y genes responded with distinct expression patterns to defense hormones such as salicylic acid, methyl jasmonate, abscisic acid, and ethylene precursor 1-aminocyclopropane-1-carboxylate, and to infection by the vascular infecting fungus Fusarium oxysporum f. sp. niveum. Overexpression of ClNF-YB1, -YB8, -YB9, ClNF-YC2, and -YC7 in transgenic Arabidopsis resulted in an earlier flowering phenotype. Overexpression of ClNF-YB8 in Arabidopsis led to enhanced resistance while overexpression of ClNF-YA2 and -YC2 resulted in decreased resistance against Botrytis cinerea. Similarly, overexpression of ClNF-YA3, -YB1, and -YC4 strengthened resistance while overexpression of ClNF-YA2 and -YB8 attenuated resistance against Pseudomonas syringae pv. tomato DC3000. The re-characterization of the ClNF-Y family provides a basis from which to investigate the biological functions of ClNF-Y genes in respect of growth, development, and stress response in watermelon, and the identification of the functions of some ClNF-Y genes in disease resistance enables further exploration of the molecular mechanism of ClNF-Ys in the regulation of watermelon immunity against diverse pathogens.
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Liu X, Yang Y, Hou S, Men Y, Han Y. The Integration of Genome-Wide Association Study and Homology Analysis to Explore the Genomic Regions and Candidate Genes for Panicle-Related Traits in Foxtail Millet. Int J Mol Sci 2022; 23. [PMID: 36499063 DOI: 10.3390/ijms232314735] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 10/26/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022] Open
Abstract
Panicle traits are important factors affecting yield, and their improvement has long been a critical goal in foxtail millet breeding. In order to understand the genetic basis of panicle formation, a large-scale genome-wide association study (GWAS) was performed in this study for six panicle-related traits based on 706,646 high-polymorphism SNP loci in 407 accessions. As a result, 87 quantitative trait loci (QTL) regions with a physical distance of less than 100 kb were detected to be associated with these traits in three environments. Among them, 27 core regions were stably detected in at least two environments. Based on rice-foxtail millet homologous comparison, expression, and haplotype analysis, 27 high-confidence candidate genes in the QTL regions, such as Si3g11200 (OsDER1), Si1g27910 (OsMADS6), Si7g27560 (GS5), etc., affected panicle-related traits by involving multiple plant growth regulator pathways, a photoperiod response, as well as panicle and grain development. Most of these genes showed multiple effects on different panicle-related traits, such as Si3g11200 affecting all six traits. In summary, this study clarified a strategy based on the integration of GWAS, a homologous comparison, and haplotype analysis to discover the genomic regions and candidate genes for important traits in foxtail millet. The detected QTL regions and candidate genes could be further used for gene clone and marker-assisted selection in foxtail millet breeding.
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Lv M, Cao H, Wang X, Zhang K, Si H, Zang J, Xing J, Dong J. Identification and expression analysis of maize NF-YA subunit genes. PeerJ 2022; 10:e14306. [PMID: 36389434 PMCID: PMC9648346 DOI: 10.7717/peerj.14306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 10/05/2022] [Indexed: 11/09/2022] Open
Abstract
NF-YAs encode subunits of the nuclear factor-Y (NF-Y) gene family. NF-YAs represent a kind of conservative transcription factor in plants and are involved in plant growth and development, as well as resistance to biotic and abiotic stress. In this study, 16 maize (Zea mays) NF-YA subunit genes were identified using bioinformatics methods, and they were divided into three categories by a phylogenetic analysis. A conserved domain analysis showed that most contained a CCAAT-binding transcription factor (CBFB) _NF-YA domain. Maize NF-YA subunit genes showed very obvious tissue expression characteristics. The expression level of the NF-YA subunit genes significantly changed under different abiotic stresses, including Fusarium graminearum infection and salicylic acid (SA) or jasmonic acid (JA) treatments. After inoculation with Setosphaeria turcica and Cochliobolus heterostrophus, the lesion areas of nfya01 and nfya06 were significantly larger than that of B73, indicating that ZmNFYA01 and ZmNFYA06 positively regulated maize disease resistance. ZmNFYA01 and ZmNFYA06 may regulated maize disease resistance by affecting the transcription levels of ZmPRs. Thus, NF-YA subunit genes played important roles in promoting maize growth and development and resistance to stress. The results laid a foundation for clarifying the functions and regulatory mechanisms of NF-YA subunit genes in maize.
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Affiliation(s)
- Mingyue Lv
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultrual University, Baoding, Hebei, China,Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, Hebei, China
| | - Hongzhe Cao
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultrual University, Baoding, Hebei, China,Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, Hebei, China
| | - Xue Wang
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, Hebei, China
| | - Kang Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultrual University, Baoding, Hebei, China,Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, Hebei, China
| | - Helong Si
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultrual University, Baoding, Hebei, China,Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, Hebei, China
| | - Jinping Zang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultrual University, Baoding, Hebei, China,Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, Hebei, China
| | - Jihong Xing
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultrual University, Baoding, Hebei, China,Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, Hebei, China
| | - Jingao Dong
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultrual University, Baoding, Hebei, China,Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, Hebei, China
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Ou S, Xu Z, Mai C, Li B, Wang J. Ectopic expression of GmNF-YA8 in Arabidopsis delays flowering via modulating the expression of gibberellic acid biosynthesis- and flowering-related genes and promotes lateral root emergence in low phosphorus conditions. Front Plant Sci 2022; 13:1033938. [PMID: 36340418 PMCID: PMC9630906 DOI: 10.3389/fpls.2022.1033938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
NUCLEAR FACTOR Y subunit alpha (NF-YA), together with NF-YB and NF-YC, regulates plant growth and development, as well as plant responses to biotic and abiotic stresses. Although extensive studies have examined the functions of NF-YAs in Arabidopsis thaliana, the roles of NF- YAs in Glycinme max are poorly understood. In this study, we identified a phosphorus (P) starvation-responsive NF-YA8 in soybean. The expression of GmNF-YA8 is induced by low P or low nitrogen in leaves, but not by potassium or iron starvation, respectively. GmNF-YA8 is localized in the nucleus and plasma membrane. Ectopic expression of GmNF-YA8 inhibits plant growth and delayed flowering in Arabidopsis. Exogenous application of gibberellic acid (GA) rescues the delayed flowering phenotype in Arabidopsis overexpressing GmNF-YA8 lines GmNF-YA8OE-05 and GmNF-YA8OE-20. Moreover, quantitative real time PCR (qRT-PCR) verified that overexpression of GmNF-YA8 downregulates GA20ox2 and GA3ox2 expression, but upregulates GA2ox2 and GA2ox3 that encode enzymes, which inactive bioactive GAs. Consistent with the late flowering phenotype of Arabidopsis trangenic lines that overexpress GmNF-YA8, the transcript levels of flowering-promoting genes AP1, CO, LFY, and SOC1 are reduced. In addition, overexpression of GmNF-YA8 promotes the emergence of lateral root (LR) primordium from epidermis rather than the initiation of LR in low P, and increases the LR density in low nitrogen. Our results provide insights into the roles of GmNF-YA8.
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Affiliation(s)
- Siyan Ou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, China
- Root Biology Center & College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory of Lingnan Modern Agricultural Science and Technology, Guangzhou, China
| | - Zhihao Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, China
- Root Biology Center & College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory of Lingnan Modern Agricultural Science and Technology, Guangzhou, China
| | - Cuishan Mai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, China
- Root Biology Center & College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory of Lingnan Modern Agricultural Science and Technology, Guangzhou, China
| | - Bodi Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, China
- Root Biology Center & College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory of Lingnan Modern Agricultural Science and Technology, Guangzhou, China
| | - Jinxiang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, China
- Root Biology Center & College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory of Lingnan Modern Agricultural Science and Technology, Guangzhou, China
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Huang Y, Ma H, Wang X, Cui T, Han G, Zhang Y, Wang C. Expression patterns of the poplar NF-Y gene family in response to Alternaria alternata and hormone treatment and the role of PdbNF-YA11 in disease resistance. Front Bioeng Biotechnol 2022; 10:956271. [PMID: 36185440 PMCID: PMC9523018 DOI: 10.3389/fbioe.2022.956271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 08/16/2022] [Indexed: 11/13/2022] Open
Abstract
Plant nuclear factor-Y (NF-Y) transcription factors (TFs) are key regulators of growth and stress resistance. However, the role of NF-Y TFs in poplar in response to biotic stress is still unclear. In this study, we cloned 26 PdbNF-Y encoding genes in the hybrid poplar P. davidiana × P. bollena, including 12 PdbNF-YAs, six PdbNF-YBs, and eight PdbNF-YCs. Their physical and chemical parameters, conserved domains, and phylogeny were subsequently analyzed. The protein–protein interaction (PPI) network showed that the three PdbNF-Y subunits may interact with NF-Y proteins belonging to two other subfamilies and other TFs. Tissue expression analysis revealed that PdbNF-Ys exhibited three distinct expression patterns in three tissues. Cis-elements related to stress-responsiveness were found in the promoters of PdbNF-Ys, and most PdbNF-Ys were shown to be differentially expressed under Alternaria alternata and hormone treatments. Compared with the PdbNF-YB and PdbNF-YC subfamilies, more PdbNF-YAs were significantly induced under the two treatments. Moreover, loss- and gain-of-function analyses showed that PdbNF-YA11 plays a positive role in poplar resistance to A. alternata. Additionally, RT‒qPCR analyses showed that overexpression and silencing PdbNF-YA11 altered the transcript levels of JA-related genes, including LOX, AOS, AOC, COI, JAZ, ORCA, and MYC, suggesting that PdbNF-YA11-mediated disease resistance is related to activation of the JA pathway. Our findings will contribute to functional analysis of NF-Y genes in woody plants, especially their roles in response to biotic stress.
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Xu H, Li S, Kazeem BB, Ajadi AA, Luo J, Yin M, Liu X, Chen L, Ying J, Tong X, Wang Y, Niu B, Chen C, Zeng X, Zhang J. Five Rice Seed-Specific NF-YC Genes Redundantly Regulate Grain Quality and Seed Germination via Interfering Gibberellin Pathway. Int J Mol Sci 2022; 23:ijms23158382. [PMID: 35955515 PMCID: PMC9368926 DOI: 10.3390/ijms23158382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 07/24/2022] [Accepted: 07/26/2022] [Indexed: 12/05/2022] Open
Abstract
NF-YCs are important transcription factors with diverse functions in the plant kingdoms including seed development. NF-YC8, 9, 10, 11 and 12 are close homologs with similar seed-specific expression patterns. Despite the fact that some of the NF-YCs are functionally known; their biological roles have not been systematically explored yet, given the potential functional redundancy. In this study, we generated pentuple mutant pnfyc of NF-YC8-12 and revealed their functions in the regulation of grain quality and seed germination. pnfyc grains displayed significantly more chalkiness with abnormal starch granule packaging. pnfyc seed germination and post-germination growth are much slower than the wild-type NIP, largely owing to the GA-deficiency as exogenous GA was able to fully recover the germination phenotype. The RNA-seq experiment identified a total of 469 differentially expressed genes, and several GA-, ABA- and grain quality control-related genes might be transcriptionally regulated by the five NF-YCs, as revealed by qRT-PCR analysis. The results demonstrated the redundant functions of NF-YC8-12 in regulating GA pathways that underpin rice grain quality and seed germination, and shed a novel light on the functions of the seed-specific NF-YCs.
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Affiliation(s)
- Huayu Xu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (H.X.); (S.L.); (B.B.K.); (A.A.A.); (J.L.); (M.Y.); (X.L.); (L.C.); (J.Y.); (X.T.); (Y.W.)
| | - Shufan Li
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (H.X.); (S.L.); (B.B.K.); (A.A.A.); (J.L.); (M.Y.); (X.L.); (L.C.); (J.Y.); (X.T.); (Y.W.)
| | - Bello Babatunde Kazeem
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (H.X.); (S.L.); (B.B.K.); (A.A.A.); (J.L.); (M.Y.); (X.L.); (L.C.); (J.Y.); (X.T.); (Y.W.)
| | - Abolore Adijat Ajadi
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (H.X.); (S.L.); (B.B.K.); (A.A.A.); (J.L.); (M.Y.); (X.L.); (L.C.); (J.Y.); (X.T.); (Y.W.)
| | - Jinjin Luo
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (H.X.); (S.L.); (B.B.K.); (A.A.A.); (J.L.); (M.Y.); (X.L.); (L.C.); (J.Y.); (X.T.); (Y.W.)
| | - Man Yin
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (H.X.); (S.L.); (B.B.K.); (A.A.A.); (J.L.); (M.Y.); (X.L.); (L.C.); (J.Y.); (X.T.); (Y.W.)
| | - Xinyong Liu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (H.X.); (S.L.); (B.B.K.); (A.A.A.); (J.L.); (M.Y.); (X.L.); (L.C.); (J.Y.); (X.T.); (Y.W.)
| | - Lijuan Chen
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (H.X.); (S.L.); (B.B.K.); (A.A.A.); (J.L.); (M.Y.); (X.L.); (L.C.); (J.Y.); (X.T.); (Y.W.)
| | - Jiezheng Ying
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (H.X.); (S.L.); (B.B.K.); (A.A.A.); (J.L.); (M.Y.); (X.L.); (L.C.); (J.Y.); (X.T.); (Y.W.)
| | - Xiaohong Tong
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (H.X.); (S.L.); (B.B.K.); (A.A.A.); (J.L.); (M.Y.); (X.L.); (L.C.); (J.Y.); (X.T.); (Y.W.)
| | - Yifeng Wang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (H.X.); (S.L.); (B.B.K.); (A.A.A.); (J.L.); (M.Y.); (X.L.); (L.C.); (J.Y.); (X.T.); (Y.W.)
| | - Baixiao Niu
- College of Agriculture, Yangzhou University, Yangzhou 225009, China; (B.N.); (C.C.)
| | - Chen Chen
- College of Agriculture, Yangzhou University, Yangzhou 225009, China; (B.N.); (C.C.)
| | - Xiaoshan Zeng
- Hunan Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
- Correspondence: (X.Z.); (J.Z.); Tel./Fax: +86-731-86491768 (X.Z.); +86-571-63370277 (J.Z.)
| | - Jian Zhang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (H.X.); (S.L.); (B.B.K.); (A.A.A.); (J.L.); (M.Y.); (X.L.); (L.C.); (J.Y.); (X.T.); (Y.W.)
- Correspondence: (X.Z.); (J.Z.); Tel./Fax: +86-731-86491768 (X.Z.); +86-571-63370277 (J.Z.)
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Tan X, Zhang H, Yang Z, Wei Z, Li Y, Chen J, Sun Z. NF-YA transcription factors suppress jasmonic acid-mediated antiviral defense and facilitate viral infection in rice. PLoS Pathog 2022; 18:e1010548. [PMID: 35560151 DOI: 10.1371/journal.ppat.1010548] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 05/25/2022] [Accepted: 04/25/2022] [Indexed: 12/22/2022] Open
Abstract
NF-Y transcription factors are known to play many diverse roles in the development and physiological responses of plants but little is known about their role in plant defense. Here, we demonstrate the negative roles of rice NF-YA family genes in antiviral defense against two different plant viruses, Rice stripe virus (RSV, Tenuivirus) and Southern rice black-streaked dwarf virus (SRBSDV, Fijivirus). RSV and SRBSDV both induced the expression of OsNF-YA family genes. Overexpression of OsNF-YAs enhanced rice susceptibility to virus infection, while OsNF-YAs RNAi mutants were more resistant. Transcriptome sequencing showed that the expression of jasmonic acid (JA)-related genes was significantly decreased in plants overexpressing OsNF-YA when they were infected by viruses. qRT-PCR and JA sensitivity assays confirmed that OsNF-YAs play negative roles in regulating the JA pathway. Further experiments showed that OsNF-YAs physically interact with JA signaling transcription factors OsMYC2/3 and interfere with JA signaling by dissociating the OsMYC2/3-OsMED25 complex, which inhibits the transcriptional activation activity of OsMYC2/3. Together, our results reveal that OsNF-YAs broadly inhibit plant antiviral defense by repressing JA signaling pathways, and provide new insight into how OsNF-YAs are directly associated with the JA pathway.
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Wang T, Wei Q, Wang Z, Liu W, Zhao X, Ma C, Gao J, Xu Y, Hong B. CmNF-YB8 affects drought resistance in chrysanthemum by altering stomatal status and leaf cuticle thickness. J Integr Plant Biol 2022; 64:741-755. [PMID: 34889055 DOI: 10.1111/jipb.13201] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 12/08/2021] [Indexed: 06/13/2023]
Abstract
Drought is a major abiotic stress that limits plant growth and development. Adaptive mechanisms have evolved to mitigate drought stress, including the capacity to adjust water loss rate and to modify the morphology and structure of the epidermis. Here, we show that the expression of CmNF-YB8, encoding a nuclear factor Y (NF-Y) B-type subunit, is lower under drought conditions in chrysanthemum (Chrysanthemum morifolium). Transgenic chrysanthemum lines in which transcript levels of CmNF-YB8 were reduced by RNA interference (CmNF-YB8-RNAi) exhibited enhanced drought resistance relative to control lines, whereas lines overexpressing CmNF-YB8 (CmNF-YB8-OX) were less tolerant to drought. Compared to wild type (WT), CmNF-YB8-RNAi plants showed reduced stomatal opening and a thicker epidermal cuticle that correlated with their water loss rate. We also identified genes involved in stomatal adjustment (CBL-interacting protein kinase 6, CmCIPK6) and cuticle biosynthesis (CmSHN3) that are more highly expressed in CmNF-YB8-RNAi lines than in WT, CmCIPK6 being a direct downstream target of CmNF-YB8. Virus-induced gene silencing of CmCIPK6 or CmSHN3 in the CmNF-YB8-RNAi background abolished the effects of CmNF-YB8-RNAi on stomatal closure and cuticle deposition, respectively. CmNF-YB8 thus regulates CmCIPK6 and CmSHN3 expression to alter stomatal movement and cuticle thickness in the leaf epidermis, thereby affecting drought resistance.
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Affiliation(s)
- Tianle Wang
- State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Qian Wei
- State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Zhiling Wang
- State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Wenwen Liu
- State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Xin Zhao
- State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Chao Ma
- State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Junping Gao
- State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Yanjie Xu
- State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Bo Hong
- State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China
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Xuanyuan G, Lian Q, Jia R, Du M, Kang L, Pu Y, Zhang Z, Qi J, Zhao J. Genome-wide screening and identification of nuclear Factor-Y family genes and exploration their function on regulating abiotic and biotic stress in potato (Solanum tuberosum L.). Gene 2021; 812:146089. [PMID: 34896520 DOI: 10.1016/j.gene.2021.146089] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 10/21/2021] [Accepted: 11/16/2021] [Indexed: 12/30/2022]
Abstract
The Nuclear Factor-Y (NF-Y) transcription factor (TF), which includes three distinct subunits (NF-YA, NF-YB and NF-YC), is known to manipulate various aspects of plant growth, development, and stress responses. Although the NF-Y gene family was well studied in many species, little is known about their functions in potato. In this study, a total of 37 potato NF-Y genes were identified, including 11 StNF-YAs, 20 StNF-YBs, and 6 StNF-YCs. The genetic features of these StNF-Y genes were investigated by comparing their evolutionary relationship, intron/exon organization and motif distribution pattern. Multiple alignments showed that all StNF-Y proteins possessed clearly conserved core regions that were flanked by non-conserved sequences. Gene duplication analysis indicated that nine StNF-Y genes were subjected to tandem duplication and eight StNF-Ys arose from segmental duplication events. Synteny analysis suggested that most StNF-Y genes (33 of 37) were orthologous to potato's close relative tomato (Solanum lycopersicum L.). Tissue-specific expression of the StNF-Y genes suggested their potential roles in controlling potato growth and development. The role of StNF-Ys in regulating potato responses to abiotic stress (ABA, drought and salinity) was also confirmed: twelve StNF-Y genes were up-regulated and another two were down-regulated under different abiotic treatments. In addition, genes responded differently to pathogen challenges, suggesting that StNF-Y genes may play distinct roles under certain biotic stress. In summary, insights into the evolution of NF-Y family members and their functions in potato development and stress responses are provided.
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Kulkarni SR, Balachandran SM, Ulaganathan K, Balakrishnan D, Prasad ASH, Rekha G, Kousik MBVN, Hajira SK, Kale RR, Aleena D, Anila M, Punniakoti E, Dilip T, Pranathi K, Das MA, Shaik M, Chaitra K, Sinha P, Sundaram RM. Mapping novel QTLs for yield related traits from a popular rice hybrid KRH-2 derived doubled haploid (DH) population. 3 Biotech 2021; 11:513. [PMID: 34926111 DOI: 10.1007/s13205-021-03045-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 10/29/2021] [Indexed: 11/30/2022] Open
Abstract
A doubled haploid (DH) population consisting of 125 DHLs derived from the popular rice hybrid, KRH-2 (IR58025A/KMR3R) was utilized for Quantitative Trait Loci (QTL) mapping to identify novel genomic regions associated with yield related traits. A genetic map was constructed with 126 polymorphic SSR and EST derived markers, which were distributed across rice genome. QTL analysis using inclusive composite interval mapping (ICIM) method identified a total of 24 major and minor effect QTLs. Among them, twelve major effect QTLs were identified for days to fifty percent flowering (qDFF12-1), total grain yield/plant (qYLD3-1 and qYLD6-1), test (1,000) grain weight (qTGW6-1 and qTGW7-1), panicle weight (qPW9-1), plant height (qPH12-1), flag leaf length (qFLL6-1), flag leaf width (qFLW4-1), panicle length (qPL3-1 and qPL6-1) and biomass (qBM4-1), explaining 29.95-56.75% of the phenotypic variability with LOD scores range of 2.72-16.51. Chromosomal regions with gene clusters were identified on chromosome 3 for total grain yield/plant (qYLD3-1) and panicle length (qPL3-1) and on chromosome 6 for total grain yield/plant (qYLD6-1), flag leaf length (qFLL6-1) and panicle length (qPL6-1). Majority of the QTLs identified were observed to be co-localized with the previously reported QTL regions. Five novel, major effect QTLs associated with panicle weight (qPW9-1), plant height (qPH12-1), flag leaf width (qFLW4-1), panicle length (qPL3-1) and biomass (qBM4-1) and three novel minor effect QTLs for panicle weight (qPW3-1 and qPW8-1) and fertile grains per panicle (qFGP5-1) were identified. These QTLs can be used in breeding programs aimed to yield improvement after their validation in alternative populations. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-03045-7.
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Affiliation(s)
- Swapnil Ravindra Kulkarni
- Biotechnology Department, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State (TS) 500030 India
| | - S M Balachandran
- Biotechnology Department, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State (TS) 500030 India
| | - K Ulaganathan
- Centre for Plant Molecular Biology (CPMB), Osmania University, Hyderabad, 500007 India
| | - Divya Balakrishnan
- Biotechnology Department, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State (TS) 500030 India
| | - A S Hari Prasad
- Biotechnology Department, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State (TS) 500030 India
| | - G Rekha
- Biotechnology Department, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State (TS) 500030 India
| | - M B V N Kousik
- Biotechnology Department, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State (TS) 500030 India
| | - S K Hajira
- Biotechnology Department, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State (TS) 500030 India
| | - Ravindra Ramarao Kale
- Biotechnology Department, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State (TS) 500030 India
| | - D Aleena
- Biotechnology Department, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State (TS) 500030 India
| | - M Anila
- Biotechnology Department, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State (TS) 500030 India
| | - E Punniakoti
- Biotechnology Department, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State (TS) 500030 India
| | - T Dilip
- Biotechnology Department, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State (TS) 500030 India
| | - K Pranathi
- Biotechnology Department, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State (TS) 500030 India
| | - M Ayyappa Das
- Biotechnology Department, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State (TS) 500030 India
| | - Mastanbee Shaik
- Biotechnology Department, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State (TS) 500030 India
| | - K Chaitra
- Biotechnology Department, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State (TS) 500030 India
| | - Pragya Sinha
- Biotechnology Department, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State (TS) 500030 India
| | - R M Sundaram
- Biotechnology Department, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State (TS) 500030 India
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Li S, Zhang N, Zhu X, Ma R, Liu S, Wang X, Yang J, Si H. Genome-Wide Analysis of NF-Y Genes in Potato and Functional Identification of StNF-YC9 in Drought Tolerance. Front Plant Sci 2021; 12:749688. [PMID: 34858457 PMCID: PMC8631771 DOI: 10.3389/fpls.2021.749688] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/21/2021] [Indexed: 06/03/2023]
Abstract
The nuclear factor Y (NF-Y) family is comprised of transcription factors that have been implicated in multiple plant biological processes. However, little is known about this family in potato. In the present study, a total of 41 StNF-Y genes were identified in the potato genome. In addition, the phylogenetic, gene structure, motif, and chromosomal location of this family were analyzed. The tissue expression profiles based on RNA-seq data showed that 27 StNF-Y genes had tissue-specific expression, while the remaining 14 had low expression in all tissues. Publicly available transcriptomics data from various abiotic stresses revealed several stress-responsive StNF-Y genes, which were further verified via quantitative real-time polymerase chain reaction experiments. Furthermore, the StNF-YC9 gene was highly induced by dehydration and drought treatments. StNF-YC9 protein was mainly localized in the nucleus and cytoplasmic membrane. Overexpressing StNF-YC9 potato lines (OxStNF-YC9) had significantly increased in root length and exhibited stronger stomatal closure in potato treated by polyethylene-glycol and abscisic acid. In addition, OxStNF-YC9 lines had higher photosynthetic rates and decreased water loss under short-term drought stress compared to wild-type plants. During long-term drought stress, OxStNF-YC9 lines had higher proline levels, lower malondialdehyde content, and increased activity of several antioxidant enzymes, including superoxide dismutase, catalase, and peroxidase. This study increased our understanding of the StNF-Y gene and suggested that StNF-YC9 played an important role in drought tolerance by increased the photosynthesis rate, antioxidant enzyme activity, and proline accumulation coupled to lowered malondialdehyde accumulation in potato.
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Affiliation(s)
- Shigui Li
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Ning Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xi Zhu
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Rui Ma
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Shengyan Liu
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Xiao Wang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jiangwei Yang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Huaijun Si
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
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Zheng X, Zhang H, Zhang L, Xu F, Shi L, Wang S, Hong J, Ding G. Identification and Comprehensive Analysis of the Nuclear Factor-Y Family Genes Reveal Their Multiple Roles in Response to Nutrient Deficiencies in Brassica napus. Int J Mol Sci 2021; 22:10354. [PMID: 34638695 DOI: 10.3390/ijms221910354] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 09/22/2021] [Accepted: 09/23/2021] [Indexed: 12/11/2022] Open
Abstract
Nuclear Factor-Y (NF-Y) transcription factors play vital roles in plant abiotic stress response. Here, the NF-Y family in Brassica napus, which is hyper-sensitive to nitrogen (N) deprivation, was comprehensively identified and systematically characterized. A total of 108 NF-Y family members were identified in B. napus and categorized into three subfamilies (38 NF-YA, 46 NF-YB and 24 NF-YC; part of the Arabidopsis NF-YC homologous genes had been lost during B. napus evolution). In addition, the expansion of the NF-Y family in B. napus was driven by whole-genome duplication and segmental duplication. Differed expression patterns of BnaNF-Ys were observed in response to multiple nutrient starvations. Thirty-four genes were regulated only in one nutrient deficient condition. Moreover, more BnaNF-YA genes were differentially expressed under nutrient limited environments compared to the BnaNF-YB and BnaNF-YC subfamilies. Sixteen hub genes responded diversely to N deprivation in five rapeseed tissues. In summary, our results laid a theoretical foundation for the follow-up functional study of the key NF-Y genes in B. napus in regulating nutrient homeostasis, especially N.
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Jung SE, Bang SW, Kim SH, Seo JS, Yoon HB, Kim YS, Kim JK. Overexpression of OsERF83, a Vascular Tissue-Specific Transcription Factor Gene, Confers Drought Tolerance in Rice. Int J Mol Sci 2021; 22:7656. [PMID: 34299275 DOI: 10.3390/ijms22147656] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/12/2021] [Accepted: 07/14/2021] [Indexed: 11/17/2022] Open
Abstract
Abiotic stresses severely affect plant growth and productivity. To cope with abiotic stresses, plants have evolved tolerance mechanisms that are tightly regulated by reprogramming transcription factors (TFs). APETALA2/ethylene-responsive factor (AP2/ERF) transcription factors are known to play an important role in various abiotic stresses. However, our understanding of the molecular mechanisms remains incomplete. In this study, we identified the role of OsERF83, a member of the AP2/ERF transcription factor family, in response to drought stress. OsERF83 is a transcription factor localized to the nucleus and induced in response to various abiotic stresses, such as drought and abscisic acid (ABA). Overexpression of OsERF83 in transgenic plants (OsERF83OX) significantly increased drought tolerance, with higher photochemical efficiency in rice. OsERF83OX was also associated with growth retardation, with reduced grain yields under normal growth conditions. OsERF83 is predominantly expressed in the vascular tissue of all organs. Transcriptome analysis revealed that OsERF83 regulates drought response genes, which are related to the transporter (OsNPF8.10, OsNPF8.17, OsLH1), lignin biosynthesis (OsLAC17, OsLAC10, CAD8D), terpenoid synthesis (OsTPS33, OsTPS14, OsTPS3), cytochrome P450 family (Oscyp71Z4, CYP76M10), and abiotic stress-related genes (OsSAP, OsLEA14, PCC13-62). OsERF83 also up-regulates biotic stress-associated genes, including PATHOGENESIS-RELATED PROTEIN (PR), WALL-ASSOCIATED KINASE (WAK), CELLULOSE SYNTHASE-LIKE PROTEIN E1 (CslE1), and LYSM RECEPTOR-LIKE KINASE (RLK) genes. Our results provide new insight into the multiple roles of OsERF83 in the cross-talk between abiotic and biotic stress signaling pathways.
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Singroha G, Sharma P, Sunkur R. Current status of microRNA-mediated regulation of drought stress responses in cereals. Physiol Plant 2021; 172:1808-1821. [PMID: 33956991 DOI: 10.1111/ppl.13451] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 04/20/2021] [Accepted: 05/04/2021] [Indexed: 05/03/2023]
Abstract
Drought is one of the most important abiotic stress factors impeding crop productivity. With the uncovering of their role as potential regulators of gene expression, microRNAs (miRNAs) have been recognized as new targets for developing stress resistance. MicroRNAs are small noncoding RNAs whose abundance is significantly altered under stress conditions. Interestingly, plant miRNAs predominantly targets transcription factors (TFs), and some of which are also the most critical drought-responsive genes that in turn could regulate the expression of numerous loci with drought-adaptive potential. The phytohormone ABA plays important roles in regulating stomatal conductance and in initiating an adaptive response to drought stress. miRNAs are implicated in regulating ABA-(abscisic acid) and non-ABA-mediated drought resistance pathways. For instance, miR159-MYB module and miR169-NFYA module participates in an ABA-dependent pathway, whereas several other ABA-independent miRNA-target modules (miR156-SPL; miR393-TIR1; miR160-ARF10, ARF16, ARF17; miR167-ARF6 and ARF8; miR390/TAS3siRNA-ARF2, ARF3, ARF4) collectively regulate drought responses in plants. Overall, miRNA-mediated drought response manifests diverse molecular, biochemical and physiological processes. Because of their immense role in controlling gene expression, miRNA manipulation has significant potential to augment plant tolerance to drought stress. This review compiles the current understanding of drought-responsive miRNAs in major cereals. Also, potential miRNA manipulation strategies currently in use along with the challenges and future perspectives are discussed.
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Affiliation(s)
- Garima Singroha
- Crop Improvement Division, ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Pradeep Sharma
- Crop Improvement Division, ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Ramanjulu Sunkur
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, Oklahoma, USA
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Shim JS, Park SH, Lee DK, Kim YS, Park SC, Redillas MCFR, Seo JS, Kim JK. The Rice GLYCINE-RICH PROTEIN 3 Confers Drought Tolerance by Regulating mRNA Stability of ROS Scavenging-Related Genes. Rice (N Y) 2021; 14:31. [PMID: 33742286 PMCID: PMC7979854 DOI: 10.1186/s12284-021-00473-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 03/10/2021] [Indexed: 05/08/2023]
Abstract
BACKGROUND Plant glycine-rich proteins are categorized into several classes based on their protein structures. The glycine-rich RNA binding proteins (GRPs) are members of class IV subfamily possessing N-terminus RNA-recognition motifs (RRMs) and proposed to be involved in post-transcriptional regulation of its target transcripts. GRPs are involved in developmental process and cellular stress responses, but the molecular mechanisms underlying these regulations are still elusive. RESULTS Here, we report the functional characterization of rice GLYCINE-RICH PROTEIN 3 (OsGRP3) and its physiological roles in drought stress response. Both drought stress and ABA induce the expression of OsGRP3. Transgenic plants overexpressing OsGRP3 (OsGRP3OE) exhibited tolerance while knock-down plants (OsGRP3KD) were susceptible to drought compared to the non-transgenic control. In vivo, subcellular localization analysis revealed that OsGRP3-GFP was transported from cytoplasm/nucleus into cytoplasmic foci following exposure to ABA and mannitol treatments. Comparative transcriptomic analysis between OsGRP3OE and OsGRP3KD plants suggests that OsGRP3 is involved in the regulation of the ROS related genes. RNA-immunoprecipitation analysis revealed the associations of OsGRP3 with PATHOGENESIS RELATED GENE 5 (PR5), METALLOTHIONEIN 1d (MT1d), 4,5-DOPA-DIOXYGENASE (DOPA), and LIPOXYGENASE (LOX) transcripts. The half-life analysis showed that PR5 transcripts decayed slower in OsGRP3OE but faster in OsGRP3KD, while MT1d and LOX transcripts decayed faster in OsGRP3OE but slower in OsGRP3KD plants. H2O2 accumulation was reduced in OsGRP3OE and increased in OsGRP3KD plants compared to non-transgenic plants (NT) under drought stress. CONCLUSION OsGRP3 plays a positive regulator in rice drought tolerance and modulates the transcript level and mRNA stability of stress-responsive genes, including ROS-related genes. Moreover, OsGRP3 contributes to the reduction of ROS accumulation during drought stress. Our results suggested that OsGRP3 alleviates ROS accumulation by regulating ROS-related genes' mRNA stability under drought stress, which confers drought tolerance.
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Affiliation(s)
- Jae Sung Shim
- Crop Biotechnology Institute, GreenBio Science and Technology, Seoul National University, Pyeongchang, 25354, South Korea
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, South Korea
| | - Su-Hyun Park
- Crop Biotechnology Institute, GreenBio Science and Technology, Seoul National University, Pyeongchang, 25354, South Korea
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Dong-Keun Lee
- Crop Biotechnology Institute, GreenBio Science and Technology, Seoul National University, Pyeongchang, 25354, South Korea
- E GREEN GLOBAL, Gunpo, 15843, South Korea
| | - Youn Shic Kim
- Crop Biotechnology Institute, GreenBio Science and Technology, Seoul National University, Pyeongchang, 25354, South Korea
- Agriculture and Life Sciences Research Institute, Kangwon National University, Chuncheon, 24341, South Korea
| | - Soo-Chul Park
- Crop Biotechnology Institute, GreenBio Science and Technology, Seoul National University, Pyeongchang, 25354, South Korea
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Jeonju, 54874, South Korea
| | | | - Jun Sung Seo
- Crop Biotechnology Institute, GreenBio Science and Technology, Seoul National University, Pyeongchang, 25354, South Korea.
| | - Ju-Kon Kim
- Crop Biotechnology Institute, GreenBio Science and Technology, Seoul National University, Pyeongchang, 25354, South Korea.
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Liu R, Wu M, Liu HL, Gao YM, Chen J, Yan HW, Xiang Y. Genome-wide identification and expression analysis of the NF-Y transcription factor family in Populus. Physiol Plant 2021; 171:309-327. [PMID: 32134494 DOI: 10.1111/ppl.13084] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 10/18/2019] [Accepted: 11/01/2019] [Indexed: 06/10/2023]
Abstract
In the past few years, many studies have reported that the transcription factor Nuclear Factor Y (NF-Y) gene family plays important roles in embryonic development, photosynthesis, flowering time regulation and stress response, in various plants. Although the NF-Y gene family has been systematically studied in many species, little is known about NF-Y genes in Populus. In this study, the NF-Y gene family in the Populus genome was identified and its structural characteristics were described. Fifty-two NF-Y genes were authenticated in the Populus trichocarpa genome and categorized into three subfamilies (NF-YA/B/C) by phylogenetic analysis. Chromosomal localization of these genes revealed that they were distributed randomly across 17 of the 19 chromosomes. Segmental duplication played a vital role in the amplification of Populus NF-Y gene family. Moreover, microsynteny analysis indicated that, among Populus trichocarpa, Arabidopsis thaliana, Vitis vinifera and Carica papaya, NF-Y duplicated regions were more conserved between Populus trichocarpa and Vitis vinifera. Redundant stress-related cis-elements were also found in the promoters of most 13 NF-YA genes and their expression levels varied widely following drought, salt, ABA and cold treatments. Subcellular localization experiments in tobacco showed that PtNF-YA3 was localized in nucleus and cytomembrane, while PtNF-YA4 was only in the nucleus in tobacco. According to the transcriptional activity experiments, neither of them had transcriptional activity in yeast. In summary, a comprehensive analysis of the Populus NF-Y gene family was performed to establish a theoretical basis for further functional studies on this family.
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Affiliation(s)
- Rui Liu
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Min Wu
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Huan-Long Liu
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Ya-Meng Gao
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Jun Chen
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Han-Wei Yan
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Yan Xiang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
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Xie Y, Bao C, Chen P, Cao F, Liu X, Geng D, Li Z, Li X, Hou N, Zhi F, Niu C, Zhou S, Zhan X, Ma F, Guan Q. Abscisic acid homeostasis is mediated by feedback regulation of MdMYB88 and MdMYB124. J Exp Bot 2021; 72:592-607. [PMID: 32995885 DOI: 10.1093/jxb/eraa449] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 09/24/2020] [Indexed: 06/11/2023]
Abstract
The phytohormone abscisic acid (ABA) is involved in various plant processes. In response to drought stress, plants quickly accumulate ABA, but the regulatory mechanism of ABA accumulation is largely unknown, especially in woody plants. In this study, we report that MdMYB88 and MdMYB124 are myeloblastosis (MYB) transcription factors critical for ABA accumulation in apple trees (Malus x domestica) following drought, and this regulation is negatively controlled by ABA. MdMYB88 and MdMYB124 positively regulate leaf water transpiration, photosynthetic capacity, and stress endurance in apple trees under drought conditions. MdMYB88 and MdMYB124 regulate the expression of biosynthetic and catabolic genes of ABA, as well as drought- and ABA- responsive genes. MdMYB88 associates with promoter regions of the ABA biosynthetic gene 9-cis-epoxycarotenoid dioxygenase 3 (NCED3). Finally, expression of MdMYB88 and MdMYB124 is repressed by ABA. Our results identify a feedback regulation of MdMYB88 and MdMYB124 in modulating ABA homeostasis in apple trees.
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Affiliation(s)
- Yinpeng Xie
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P.R. China
- Institute for Advanced Studies, Wuhan University, Wuhan, P.R. China
| | - Chana Bao
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P.R. China
| | - Pengxiang Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P.R. China
| | - Fuguo Cao
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P.R. China
| | - Xiaofang Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P.R. China
| | - Dali Geng
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P.R. China
| | - Zhongxing Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P.R. China
| | - Xuewei Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P.R. China
| | - Nan Hou
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P.R. China
| | - Fang Zhi
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P.R. China
| | - Chundong Niu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P.R. China
| | - Shuangxi Zhou
- The New Zealand Institute for Plant and Food Research Ltd., Hawke's Bay, New Zealand
| | - Xiangqiang Zhan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P.R. China
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P.R. China
| | - Qingmei Guan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P.R. China
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Qu Y, Wang Y, Zhu J, Zhang Y, Hou H. Genomic Organization, Phylogenetic Comparison, and Differential Expression of the Nuclear Factor-Y Gene Family in Apple ( Malus Domestica). Plants (Basel) 2020; 10:plants10010016. [PMID: 33374140 PMCID: PMC7824617 DOI: 10.3390/plants10010016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 12/16/2020] [Accepted: 12/22/2020] [Indexed: 01/23/2023]
Abstract
The nuclear factor Y (NF-Y) as a transcription factor plays an important role in plants growth and development, and response to stress. However, few genome-wide analyzes and functional research of the NF-Y family has been undertaken in apple (Malus domestica Borkh.) so far. In this study, we comprehensively identified the 43 MdNF-Y genes in apple, which dispersedly distributed among the three subgroups based on their sequence alignment analysis, including 11 MdNF-YAs, 22 MdNF-YBs and 10 MdNF-YCs. The members in the same subgroups had similar evolution relationships, gene structures, and conserved motifs. The gene duplication analysis suggested that all the genes were dispersed followed by 27 segmental duplication. Moreover, based on synteny analysis of MdNF-Ys with eight plant species results suggested that some ortholog genes were preserved during the evolution of these species. Cis-element analysis showed potential functions of MdNF-Ys in apple growth and development and responded to abiotic stress. Furthermore, the interaction among MdNF-Ys protein were investigated in yeast two-hybrid assays. The expression patterns of MdNF-Ys in tissue-specific response reveled divergence and might play important role in apple growth and development. Subsequently, whole MdNF-Y genes family was carried out for RT-PCR in response to five abiotic stress (ABA, drought, heat, cold, and salinity) to identify their expression patterns. Taken together, our study will provide a foundation for the further study to the molecular mechanism of apple in growing development and response to abiotic stresses.
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Affiliation(s)
- Yanjie Qu
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, Shandong, China; (Y.Q.); (Y.W.); (J.Z.); (Y.Z.)
- Qingdao Key Laboratory of Genetic Development and Breeding in Horticultural Plants, Qingdao Agricultural University, Qingdao 266109, Shandong, China
| | - Yaping Wang
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, Shandong, China; (Y.Q.); (Y.W.); (J.Z.); (Y.Z.)
- Qingdao Key Laboratory of Genetic Development and Breeding in Horticultural Plants, Qingdao Agricultural University, Qingdao 266109, Shandong, China
| | - Jun Zhu
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, Shandong, China; (Y.Q.); (Y.W.); (J.Z.); (Y.Z.)
- Qingdao Key Laboratory of Genetic Development and Breeding in Horticultural Plants, Qingdao Agricultural University, Qingdao 266109, Shandong, China
| | - Yugang Zhang
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, Shandong, China; (Y.Q.); (Y.W.); (J.Z.); (Y.Z.)
- Qingdao Key Laboratory of Genetic Development and Breeding in Horticultural Plants, Qingdao Agricultural University, Qingdao 266109, Shandong, China
| | - Hongmin Hou
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, Shandong, China; (Y.Q.); (Y.W.); (J.Z.); (Y.Z.)
- Qingdao Key Laboratory of Genetic Development and Breeding in Horticultural Plants, Qingdao Agricultural University, Qingdao 266109, Shandong, China
- Correspondence: ; Tel.: +86-0532-860-80752
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Aslam M, Sugita K, Qin Y, Rahman A. Aux/IAA14 Regulates microRNA-Mediated Cold Stress Response in Arabidopsis Roots. Int J Mol Sci 2020; 21:E8441. [PMID: 33182739 DOI: 10.3390/ijms21228441] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/04/2020] [Accepted: 11/04/2020] [Indexed: 12/16/2022] Open
Abstract
The phytohormone auxin and microRNA-mediated regulation of gene expressions are key regulators of plant growth and development at both optimal and under low-temperature stress conditions. However, the mechanistic link between microRNA and auxin in regulating plant cold stress response remains elusive. To better understand the role of microRNA (miR) in the crosstalk between auxin and cold stress responses, we took advantage of the mutants of Arabidopsis thaliana with altered response to auxin transport and signal. Screening of the mutants for root growth recovery after cold stress at 4 °C revealed that the auxin signaling mutant, solitary root 1 (slr1; mutation in Aux/IAA14), shows a hypersensitive response to cold stress. Genome-wide expression analysis of miRs in the wild-type and slr1 mutant roots using next-generation sequencing revealed 180 known and 71 novel cold-responsive microRNAs. Cold stress also increased the abundance of 26–31 nt small RNA population in slr1 compared with wild type. Comparative analysis of microRNA expression shows significant differential expression of 13 known and 7 novel miRs in slr1 at 4 °C compared with wild type. Target gene expression analysis of the members from one potential candidate miR, miR169, revealed the possible involvement of miR169/NF-YA module in the Aux/IAA14-mediated cold stress response. Taken together, these results indicate that SLR/IAA14, a transcriptional repressor of auxin signaling, plays a crucial role in integrating miRs in auxin and cold responses.
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Ma XJ, Fu JD, Tang YM, Yu TF, Yin ZG, Chen J, Zhou YB, Chen M, Xu ZS, Ma YZ. GmNFYA13 Improves Salt and Drought Tolerance in Transgenic Soybean Plants. Front Plant Sci 2020; 11:587244. [PMID: 33193539 PMCID: PMC7644530 DOI: 10.3389/fpls.2020.587244] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 09/25/2020] [Indexed: 05/31/2023]
Abstract
NF-YA transcription factors function in modulating tolerance to abiotic stresses that are serious threats to crop yields. In this study, GmNFYA13, an NF-YA gene in soybean, was strongly induced by salt, drought, ABA, and H2O2, and suppressed by tungstate, an ABA synthesis inhibitor. The GmNFYA13 transcripts were detected in different tissues in seedling and flowering stages, and the expression levels in roots were highest. GmNFYA13 is a nuclear localization protein with self-activating activity. Transgenic Arabidopsis plants overexpressing GmNFYA13 with higher transcript levels of stress-related genes showed ABA hypersensitivity and enhanced tolerance to salt and drought stresses compared with WT plants. Moreover, overexpression of GmNFYA13 resulted in higher salt and drought tolerance in OE soybean plants, while suppressing it produced the opposite results. In addition, GmNFYA13 could bind to the promoters of GmSALT3, GmMYB84, GmNCED3, and GmRbohB to regulate their expression abundance in vivo. The data in this study suggested that GmNFYA13 enhanced salt and drought tolerance in soybean plants.
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Affiliation(s)
- Xiao-Jun Ma
- Institute of Crop Science/Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Jin-Dong Fu
- Institute of Crop Science/Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Yi-Miao Tang
- Beijing Engineering Research Center for Hybrid Wheat, The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Tai-Fei Yu
- Institute of Crop Science/Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Zhen-Gong Yin
- Institute of Crop Resources, Heilongjiang Academy of Agricultural Sciences, Heilongjiang, China
| | - Jun Chen
- Institute of Crop Science/Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Yong-Bin Zhou
- Institute of Crop Science/Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Ming Chen
- Institute of Crop Science/Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Zhao-Shi Xu
- Institute of Crop Science/Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - You-Zhi Ma
- Institute of Crop Science/Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
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Valandro F, Menguer PK, Cabreira-Cagliari C, Margis-Pinheiro M, Cagliari A. Programmed cell death (PCD) control in plants: New insights from the Arabidopsis thaliana deathosome. Plant Sci 2020; 299:110603. [PMID: 32900441 DOI: 10.1016/j.plantsci.2020.110603] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 05/28/2020] [Accepted: 07/14/2020] [Indexed: 06/11/2023]
Abstract
Programmed cell death (PCD) is a genetically controlled process that leads to cell suicide in both eukaryotic and prokaryotic organisms. In plants PCD occurs during development, defence response and when exposed to adverse conditions. PCD acts controlling the number of cells by eliminating damaged, old, or unnecessary cells to maintain cellular homeostasis. Unlike in animals, the knowledge about PCD in plants is limited. The molecular network that controls plant PCD is poorly understood. Here we present a review of the current mechanisms involved with the genetic control of PCD in plants. We also present an updated version of the AtLSD1 deathosome, which was previously proposed as a network controlling HR-mediated cell death in Arabidopsis thaliana. Finally, we discuss the unclear points and open questions related to the AtLSD1 deathosome.
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Affiliation(s)
- Fernanda Valandro
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil; Universidade Federal do Rio Grande do Sul (UFRGS), RS, Brazil.
| | - Paloma Koprovski Menguer
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil; Universidade Federal do Rio Grande do Sul (UFRGS), RS, Brazil.
| | | | - Márcia Margis-Pinheiro
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil; Universidade Federal do Rio Grande do Sul (UFRGS), RS, Brazil.
| | - Alexandro Cagliari
- Programa de Pós-Graduação em Ambiente e Sustentabilidade, Universidade Estadual do Rio Grande do Sul, RS, Brazil; Universidade Estadual do Rio Grande do Sul (UERGS), RS, Brazil.
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Wang Y, Wang J, Zhai L, Liang C, Chen K, Xu J. Identify QTLs and candidate genes underlying source-, sink-, and grain yield-related traits in rice by integrated analysis of bi-parental and natural populations. PLoS One 2020; 15:e0237774. [PMID: 32797075 DOI: 10.1371/journal.pone.0237774] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 08/03/2020] [Indexed: 12/18/2022] Open
Abstract
The source-sink relationship determines the ultimate grain yield of rice. In this study, we used a set of reciprocal introgression lines (ILs) derived from Xuishui09 × IR2061 to map quantitative trait loci (QTLs) that were associated with sink-, source-, and grain yield-related traits. A total of 95 QTLs influencing eight measured traits were identified using 6181 high-quality single nucleotide polymorphism markers. Nine background-independent QTLs were consistently detected in seven chromosomal regions in different genetic backgrounds. Seven QTLs clusters simultaneously affected sink-, source-, and grain yield-related traits, probably due to the genetic basis of significant correlations of grain yield with source and sink traits. We selected 15 candidate genes in the four QTLs consistently identified in the two populations by performing gene-based association and haplotype analyses using 2288 accessions from the 3K project. Among these, LOC_Os03g48970 for qTSN3b, LOC_Os06g04710 for qFLL6a, and LOC_Os07g32510 for qTGW7 were considered as the most likely candidate genes based on functional annotations. These results provide a basis for further study of candidate genes and for the development of high-yield rice varieties by balancing source–sink relationships using marker-assisted selection.
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Xu J, Trainotti L, Li M, Varotto C. Overexpression of Isoprene Synthase Affects ABA- and Drought-Related Gene Expression and Enhances Tolerance to Abiotic Stress. Int J Mol Sci 2020; 21:E4276. [PMID: 32560078 PMCID: PMC7352718 DOI: 10.3390/ijms21124276] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/10/2020] [Accepted: 06/13/2020] [Indexed: 01/08/2023] Open
Abstract
Isoprene is the most abundant single biogenic volatile compound emitted by plants. Despite the relevance of this molecule to plant abiotic resistance and its impact on global atmospheric chemistry, little is known about the details of its mechanism of action. Here, we characterized through both physiological and molecular methods the mechanisms of action of isoprene using model transgenic arabidopsis lines overexpressing a monocot isoprene synthase gene. Our results demonstrated the effect that isoprene had on ABA signaling at different tissue-specific, spatial, and temporal scales. In particular, we found that isoprene enhanced stomatal sensitivity to ABA through upregulation of RD29B signaling gene. By contrast, isoprene decreased sensitivity to ABA in germinating seeds and roots, suggesting tissue-specific mechanisms of action. In leaves, isoprene caused the downregulation of COR15A and P5CS genes, suggesting that the enhanced tolerance to water-deprivation stress observed in isoprene-emitting plants may be mediated chiefly by an enhanced membrane integrity and tolerance to osmotic stress.
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Affiliation(s)
- Jia Xu
- Department of Biodiversity and Molecular Ecology, Fondazione Edmund Mach, Research and Innovation Centre, via Mach 1, 38010 San Michele all’Adige (TN), Italy;
- Dipartimento di Biologia, Università degli Studi di Padova, viale Giuseppe Colombo, 3, 35131 Padova, Italy;
| | - Livio Trainotti
- Dipartimento di Biologia, Università degli Studi di Padova, viale Giuseppe Colombo, 3, 35131 Padova, Italy;
| | - Mingai Li
- Department of Biodiversity and Molecular Ecology, Fondazione Edmund Mach, Research and Innovation Centre, via Mach 1, 38010 San Michele all’Adige (TN), Italy;
| | - Claudio Varotto
- Department of Biodiversity and Molecular Ecology, Fondazione Edmund Mach, Research and Innovation Centre, via Mach 1, 38010 San Michele all’Adige (TN), Italy;
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Anwar A, Kim JK. Transgenic Breeding Approaches for Improving Abiotic Stress Tolerance: Recent Progress and Future Perspectives. Int J Mol Sci 2020; 21:E2695. [PMID: 32295026 PMCID: PMC7216248 DOI: 10.3390/ijms21082695] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 04/08/2020] [Accepted: 04/09/2020] [Indexed: 12/13/2022] Open
Abstract
The recent rapid climate changes and increasing global population have led to an increased incidence of abiotic stress and decreased crop productivity. Environmental stresses, such as temperature, drought, nutrient deficiency, salinity, and heavy metal stresses, are major challenges for agriculture, and they lead to a significant reduction in crop growth and productivity. Abiotic stress is a very complex phenomenon, involving a variety of physiological and biochemical changes in plant cells. Plants exposed to abiotic stress exhibit enhanced levels of ROS (reactive oxygen species), which are highly reactive and toxic and affect the biosynthesis of chlorophyll, photosynthetic capacity, and carbohydrate, protein, lipid, and antioxidant enzyme activities. Transgenic breeding offers a suitable alternative to conventional breeding to achieve plant genetic improvements. Over the last two decades, genetic engineering/transgenic breeding techniques demonstrated remarkable developments in manipulations of the genes for the induction of desired characteristics into transgenic plants. Transgenic approaches provide us with access to identify the candidate genes, miRNAs, and transcription factors (TFs) that are involved in specific plant processes, thus enabling an integrated knowledge of the molecular and physiological mechanisms influencing the plant tolerance and productivity. The accuracy and precision of this phenomenon assures great success in the future of plant improvements. Hence, transgenic breeding has proven to be a promising tool for abiotic stress improvement in crops. This review focuses on the potential and successful applications, recent progress, and future perspectives of transgenic breeding for improving abiotic stress tolerance and productivity in plants.
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Affiliation(s)
| | - Ju-Kon Kim
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science & Technology, Seoul National University, Pyeongchang 25354, Korea;
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Wang R, Cheng Y, Ke X, Zhang X, Zhang H, Huang J. Comparative analysis of salt responsive gene regulatory networks in rice and Arabidopsis. Comput Biol Chem 2020; 85:107188. [DOI: 10.1016/j.compbiolchem.2019.107188] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 11/25/2019] [Accepted: 12/05/2019] [Indexed: 11/25/2022]
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Ma XJ, Yu TF, Li XH, Cao XY, Ma J, Chen J, Zhou YB, Chen M, Ma YZ, Zhang JH, Xu ZS. Overexpression of GmNFYA5 confers drought tolerance to transgenic Arabidopsis and soybean plants. BMC Plant Biol 2020; 20:123. [PMID: 32192425 PMCID: PMC7082914 DOI: 10.1186/s12870-020-02337-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 03/10/2020] [Indexed: 05/27/2023]
Abstract
BACKGROUND Crop productivity is challenged by abiotic stresses, among which drought stress is the most common. NF-Y genes, especially NF-YA genes, regulate tolerance to abiotic stress. RESULTS Soybean NF-Y gene GmNFYA5 was identified to have the highest transcript level among all 21 NF-YA genes in soybean (Glycine max L.) under drought stress. Drought-induced transcript of GmNFYA5 was suppressed by the ABA synthesis inhibitor naproxen (NAP). GmNFYA5 transcript was detected in various tissues at vegetative and reproductive growth stages with higher levels in roots and leaves than in other tissues, which was consist with the GmNFYA5 promoter: GUS fusion assay. Overexpression of GmNFYA5 in transgenic Arabidopsis plants caused enhanced drought tolerance in seedlings by decreasing stomatal aperture and water loss from leaves. Overexpression and suppression of GmNFYA5 in soybean resulted in increased and decreased drought tolerance, respectively, relative to plants with an empty vector (EV). Transcript levels of ABA-dependent genes (ABI2, ABI3, NCED3, LEA3, RD29A, P5CS1, GmWRKY46, GmNCED2 and GmbZIP1) and ABA-independent genes (DREB1A, DREB2A, DREB2B, GmDREB1, GmDREB2 and GmDREB3) in transgenic plants overexpressing GmNFYA5 were higher than those of wild-type plants under drought stress; suppression of GmNFYA5 transcript produced opposite results. GmNFYA5 probably regulated the transcript abundance of GmDREB2 and GmbZIP1 by binding to the promoters in vivo. CONCLUSIONS Our results suggested that overexpression of GmNFYA5 improved drought tolerance in soybean via both ABA-dependent and ABA-independent pathways.
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Affiliation(s)
- Xiao-Jun Ma
- College of Agronomy, Northeast Agricultural University, Harbin, 150030 China
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081 China
| | - Tai-Fei Yu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081 China
| | - Xiao-Hui Li
- Crop Germplasm Resources Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, 136100 China
| | - Xin-You Cao
- Crop Research Institute, Shandong Academy of Agricultural Sciences, National Engineering Laboratory for Wheat and Maize, Key Laboratory of Wheat Biology and Genetic Improvement, Jinan, 250100 China
| | - Jian Ma
- College of Agronomy, Jilin Agricultural University, Changchun, 130118 China
| | - Jun Chen
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081 China
| | - Yong-Bin Zhou
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081 China
| | - Ming Chen
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081 China
| | - You-Zhi Ma
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081 China
| | - Jun-Hua Zhang
- College of Agronomy, Northeast Agricultural University, Harbin, 150030 China
| | - Zhao-Shi Xu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081 China
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Wei Q, Wen S, Lan C, Yu Y, Chen G. Genome-Wide Identification and Expression Profile Analysis of the NF-Y Transcription Factor Gene Family in Petunia hybrida. Plants 2020; 9:336. [PMID: 32155874 PMCID: PMC7154908 DOI: 10.3390/plants9030336] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 02/28/2020] [Accepted: 03/03/2020] [Indexed: 11/17/2022]
Abstract
Nuclear Factor Ys (NF-Ys) are a class of heterotrimeric transcription factors that play key roles in many biological processes, such as abiotic stress responses, flowering time, and root development. The petunia (Petunia hybrida) is a model ornamental plant, and its draft genome has been published. However, no details regarding the NF-Y gene family in petunias are available. Here, 27 NF-Y members from the petunia genome were identified, including 10 PhNF-YAs, 13 PhNF-YBs, and 4 PhNF-YCs. Multiple alignments showed that all PhNF-Y proteins had clear conserved core regions flanked by non-conserved sequences. Phylogenetic analyses identified five pairs of orthologues NF-YB proteins from Petunia and Arabidopsis, and six pairs of paralogues NF-Y proteins in Petunia. Analysis of the gene structure and conserved motifs further confirmed the closer relationship in each subfamily. Bioinformatics analysis revealed that 16 PhNF-Ys could be targeted by 18 miRNA families. RNA-seq results showed that expression patterns of PhNF-Ys among four major organs (leaf, stem, flower, and root) were clustered into six major groups. The stress response pattern of PhNF-Ys was identified under cold, heat, drought, and salinity treatments. Based on the RNA-seq data, we found that 3 genes responded to drought, 4 genes responded to salt, 10 genes responded to cold, and 9 genes responded to hot. In conclusion, this study provides useful information for further studying the functions of NF-Ys in stress response.
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He X, Liu G, Li B, Xie Y, Wei Y, Shang S, Tian L, Shi H. Functional analysis of the heterotrimeric NF-Y transcription factor complex in cassava disease resistance. Ann Bot 2020; 124:1185-1198. [PMID: 31282544 PMCID: PMC6943695 DOI: 10.1093/aob/mcz115] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 07/01/2019] [Indexed: 05/22/2023]
Abstract
BACKGROUND AND AIMS The nuclear factor Y (NF-Y) transcription factor complex is important in plant growth, development and stress response. Information regarding this transcription factor complex is limited in cassava (Manihot esculenta). In this study, 15 MeNF-YAs, 21 MeNF-YBs and 15 MeNF-YCs were comprehensively characterized during plant defence. METHODS Gene expression in MeNF-Ys was examined during interaction with the bacterial pathogen Xanthomonas axonopodis pv. manihotis (Xam). The yeast two-hybrid system was employed to investigate protein-protein interactions in the heterotrimeric NF-Y transcription factor complex. The in vivo roles of MeNF-Ys were revealed by virus-induced gene silencing (VIGS) in cassava. KEY RESULTS The regulation of MeNF-Ys in response to Xam indicated their possible roles in response to cassava bacterial blight. Protein-protein interaction assays identified the heterotrimeric NF-Y transcription factor complex (MeNF-YA1/3, MeNF-YB11/16 and MeNF-YC11/12). Moreover, the members of the heterotrimeric NF-Y transcription factor complex were located in the cell nucleus and conferred transcriptional activation activity to the CCAAT motif. Notably, the heterotrimeric NF-Y transcription factor complex positively regulated plant disease resistance to Xam, confirmed by a disease phenotype in overexpressing plants in Nicotiana benthamiana and VIGS in cassava. Consistently, the heterotrimeric NF-Y transcription factor complex positively regulated the expression of pathogenesis-related genes (MePRs). CONCLUSIONS The NF-Y transcription factor complex (MeNF-YA1/3, MeNF-YB11/16 and MeNF-YC11/12) characterized here was shown to play a role in transcriptional activation of MePR promoters, contributing to the plant defence response in cassava.
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Affiliation(s)
- Xinyi He
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
| | - Guoyin Liu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
| | - Bing Li
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
| | - Yanwei Xie
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
| | - Yunxie Wei
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
| | - Sang Shang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
- For correspondence. E-mail or
| | - Libo Tian
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
| | - Haitao Shi
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
- For correspondence. E-mail or
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46
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Wang P, Zheng Y, Guo Y, Chen X, Sun Y, Yang J, Ye N. Identification, expression, and putative target gene analysis of nuclear factor-Y (NF-Y) transcription factors in tea plant (Camellia sinensis). Planta 2019; 250:1671-1686. [PMID: 31410553 DOI: 10.1007/s00425-019-03256-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 08/06/2019] [Indexed: 05/03/2023]
Abstract
Genome-wide identification and characterization of nuclear factor-Y family in tea plants, and their expression profiles and putative targets provide the basis for further elucidation of their biological functions. The nuclear factor-Y (NF-Y) transcription factors (TFs) are crucial regulators of plant growth and physiology. However, the NF-Y TFs in tea plant (Camellia sinensis) have not yet been elucidated, and its biological functions, especially the putative target genes within the genome range, are still unclear. In this study, we identified 35 CsNF-Y encoding genes in the tea plant genome, including 10 CsNF-YAs, 15 CsNF-YBs and 10 CsNF-YCs. Their conserved domains and motifs, phylogeny, duplication event, gene structure, and promoter were subsequently analyzed. Tissue expression analysis revealed that CsNF-Ys exhibited three distinct expression patterns in eight tea tree tissues, among which CsNF-YAs were moderately expressed. Drought and abscisic acid (ABA) treatment indicated that CsNF-YAs may have a greater impact than other subunit members. Furthermore, through the genome-wide investigation of the presence of the CCAAT box, we found that CsNF-Ys may participate in the development of tea plants by regulating target genes of multiple physiological pathways, including photosynthesis, chlorophyll metabolism, fatty acid biosynthesis, and amino acid metabolism pathways. Our findings will contribute to the functional analysis of NF-Y genes in woody plants and the cultivation of high-quality tea plant cultivars.
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Affiliation(s)
- Pengjie Wang
- College of Horticulture, Key Laboratory of Tea Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Yucheng Zheng
- College of Horticulture, Key Laboratory of Tea Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Yongchun Guo
- College of Horticulture, Key Laboratory of Tea Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Xuejin Chen
- College of Horticulture, Key Laboratory of Tea Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Yun Sun
- College of Horticulture, Key Laboratory of Tea Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Jiangfan Yang
- College of Horticulture, Key Laboratory of Tea Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
| | - Naixing Ye
- College of Horticulture, Key Laboratory of Tea Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
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Abstract
As a semi-aquatic plant, rice requires water for proper growth, development, and orientation of physiological processes. Stress is induced at the cellular and molecular level when rice is exposed to drought or periods of low water availability. Plants have existing defense mechanisms in planta that respond to stress. In this review we examine the role played by miRNAs in the regulation and control of drought stress in rice through a summary of molecular studies conducted on miRNAs with emphasis on their contribution to drought regulatory networks in comparison to other plant systems. The interaction between miRNAs, target genes, transcription factors and their respective roles in drought-induced stresses is elaborated. The cross talk involved in controlling drought stress responses through the up and down regulation of targets encoding regulatory and functional proteins is highlighted. The information contained herein can further be explored to identify targets for crop improvement in the future.
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Affiliation(s)
- Kalaivani Nadarajah
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Malaysia.
| | - Ilakiya Sharanee Kumar
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Malaysia
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Bello BK, Hou Y, Zhao J, Jiao G, Wu Y, Li Z, Wang Y, Tong X, Wang W, Yuan W, Wei X, Zhang J. NF-YB1-YC12-bHLH144 complex directly activates Wx to regulate grain quality in rice (Oryza sativa L.). Plant Biotechnol J 2019; 17:1222-1235. [PMID: 30552799 PMCID: PMC6576074 DOI: 10.1111/pbi.13048] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 11/20/2018] [Accepted: 11/21/2018] [Indexed: 05/14/2023]
Abstract
Identification of seed development regulatory genes is the key for the genetic improvement in rice grain quality. NF-Ys are the important transcription factors, but their roles in rice grain quality control and the underlying molecular mechanism remain largely unknown. Here, we report the functional characterization a rice NF-Y heterotrimer complex NF-YB1-YC12-bHLH144, which is formed by the binding of NF-YB1 to NF-YC12 and then bHLH144 in a sequential order. Knock-out of each of the complex genes resulted in alteration of grain qualities in all the mutants as well as reduced grain size in crnf-yb1 and crnf-yc12. RNA-seq analysis identified 1496 genes that were commonly regulated by NF-YB1 and NF-YC12, including the key granule-bound starch synthase gene Wx. NF-YC12 and bHLH144 maintain NF-YB1 stability from the degradation mediated by ubiquitin/26S proteasome, while NF-YB1 directly binds to the 'G-box' domain of Wx promoter and activates Wx transcription, hence to regulate rice grain quality. Finally, we revealed a novel grain quality regulatory pathway controlled by NF-YB1-YC12-bHLH144 complex, which has great potential for rice genetic improvement.
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Affiliation(s)
| | - Yuxuan Hou
- State Key Lab of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Juan Zhao
- State Key Lab of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Guiai Jiao
- State Key Lab of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Yawen Wu
- State Key Lab of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Zhiyong Li
- State Key Lab of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Yifeng Wang
- State Key Lab of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Xiaohong Tong
- State Key Lab of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Wei Wang
- State Key Lab of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Wenya Yuan
- State Key Lab of Biocatalysis and Enzyme EngineeringHubei Collaborative Innovation Center for Green Transformation of Bio‐ResourcesHubei Key Laboratory of Industrial BiotechnologyCollege of Life SciencesHubei UniversityWuhanChina
| | - Xiangjin Wei
- State Key Lab of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Jian Zhang
- State Key Lab of Rice BiologyChina National Rice Research InstituteHangzhouChina
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49
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Zotova L, Kurishbayev A, Jatayev S, Goncharov NP, Shamambayeva N, Kashapov A, Nuralov A, Otemissova A, Sereda S, Shvidchenko V, Lopato S, Schramm C, Jenkins C, Soole K, Langridge P, Shavrukov Y. The General Transcription Repressor TaDr1 Is Co-expressed With TaVrn1 and TaFT1 in Bread Wheat Under Drought. Front Genet 2019; 10:63. [PMID: 30800144 PMCID: PMC6375888 DOI: 10.3389/fgene.2019.00063] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 01/24/2019] [Indexed: 12/31/2022] Open
Abstract
The general transcription repressor, TaDr1 gene, was identified during screening of a wheat SNP database using the Amplifluor-like SNP marker KATU-W62. Together with two genes described earlier, TaDr1A and TaDr1B, they represent a set of three homeologous genes in the wheat genome. Under drought, the total expression profiles of all three genes varied between different bread wheat cultivars. Plants of four high-yielding cultivars exposed to drought showed a 2.0-2.4-fold increase in TaDr1 expression compared to controls. Less strong, but significant 1.3-1.8-fold up-regulation of the TaDr1 transcript levels was observed in four low-yielding cultivars. TaVrn1 and TaFT1, which controls the transition to flowering, revealed similar profiles of expression as TaDr1. Expression levels of all three genes were in good correlation with grain yields of evaluated cultivars growing in the field under water-limited conditions. The results could indicate the involvement of all three genes in the same regulatory pathway, where the general transcription repressor TaDr1 may control expression of TaVrn1 and TaFT1 and, consequently, flowering time. The strength of these genes expression can lead to phenological changes that affect plant productivity and hence explain differences in the adaptation of the examined wheat cultivars to the dry environment of Northern and Central Kazakhstan. The Amplifluor-like SNP marker KATU-W62 used in this work can be applied to the identification of wheat cultivars differing in alleles at the TaDr1 locus and in screening hybrids.
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Affiliation(s)
- Lyudmila Zotova
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan
| | - Akhylbek Kurishbayev
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan
| | - Satyvaldy Jatayev
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan
| | - Nikolay P. Goncharov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Nazgul Shamambayeva
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan
| | - Azamat Kashapov
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan
| | - Arystan Nuralov
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan
| | - Ainur Otemissova
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan
| | - Sergey Sereda
- A.F.Khristenko Karaganda Agricultural Experimental Station, Karaganda, Kazakhstan
| | - Vladimir Shvidchenko
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan
| | - Sergiy Lopato
- Biological Sciences, College of Science and Engineering, Flinders University, Bedford Park, SA, Australia
| | - Carly Schramm
- Biological Sciences, College of Science and Engineering, Flinders University, Bedford Park, SA, Australia
| | - Colin Jenkins
- Biological Sciences, College of Science and Engineering, Flinders University, Bedford Park, SA, Australia
| | - Kathleen Soole
- Biological Sciences, College of Science and Engineering, Flinders University, Bedford Park, SA, Australia
| | - Peter Langridge
- School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
- Wheat Initiative, Julius Kühn-Institut, Berlin, Germany
| | - Yuri Shavrukov
- Biological Sciences, College of Science and Engineering, Flinders University, Bedford Park, SA, Australia
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50
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Bang SW, Lee D, Jung H, Chung PJ, Kim YS, Choi YD, Suh J, Kim J. Overexpression of OsTF1L, a rice HD-Zip transcription factor, promotes lignin biosynthesis and stomatal closure that improves drought tolerance. Plant Biotechnol J 2019; 17:118-131. [PMID: 29781573 PMCID: PMC6330637 DOI: 10.1111/pbi.12951] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 05/08/2018] [Accepted: 05/10/2018] [Indexed: 05/19/2023]
Abstract
Drought stress seriously impacts on plant development and productivity. Improvement of drought tolerance without yield penalty is a great challenge in crop biotechnology. Here, we report that the rice (Oryza sativa) homeodomain-leucine zipper transcription factor gene, OsTF1L (Oryza sativa transcription factor 1-like), is a key regulator of drought tolerance mechanisms. Overexpression of the OsTF1L in rice significantly increased drought tolerance at the vegetative stages of growth and promoted both effective photosynthesis and a reduction in the water loss rate under drought conditions. Importantly, the OsTF1L overexpressing plants showed a higher drought tolerance at the reproductive stage of growth with a higher grain yield than nontransgenic controls under field-drought conditions. Genomewide analysis of OsTF1L overexpression plants revealed up-regulation of drought-inducible, stomatal movement and lignin biosynthetic genes. Overexpression of OsTF1L promoted accumulation of lignin in shoots, whereas the RNAi lines showed opposite patterns of lignin accumulation. OsTF1L is mainly expressed in outer cell layers including the epidermis, and the vasculature of the shoots, which coincides with areas of lignification. In addition, OsTF1L overexpression enhances stomatal closure under drought conditions resulted in drought tolerance. More importantly, OsTF1L directly bound to the promoters of lignin biosynthesis and drought-related genes involving poxN/PRX38, Nodulin protein, DHHC4, CASPL5B1 and AAA-type ATPase. Collectively, our results provide a new insight into the role of OsTF1L in enhancing drought tolerance through lignin biosynthesis and stomatal closure in rice.
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Affiliation(s)
- Seung Woon Bang
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science and TechnologySeoul National UniversityPyeongchangKorea
- Center for Nutraceutical and Pharmaceutical MaterialsDivision of BioinformaticsMyongji UniversityYongin, GyeonggiKorea
| | - Dong‐Keun Lee
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science and TechnologySeoul National UniversityPyeongchangKorea
| | - Harin Jung
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science and TechnologySeoul National UniversityPyeongchangKorea
- Present address:
NUS Synthetic Biology for Clinical and Technological InnovationDepartment of BiochemistryYong Loo Lin School of MedicineNational University of SingaporeSingapore117596Singapore
| | - Pil Joong Chung
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science and TechnologySeoul National UniversityPyeongchangKorea
| | - Youn Shic Kim
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science and TechnologySeoul National UniversityPyeongchangKorea
| | - Yang Do Choi
- Department of Agricultural BiotechnologySeoul National UniversitySeoulKorea
| | - Joo‐Won Suh
- Center for Nutraceutical and Pharmaceutical MaterialsDivision of BioinformaticsMyongji UniversityYongin, GyeonggiKorea
| | - Ju‐Kon Kim
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science and TechnologySeoul National UniversityPyeongchangKorea
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