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Zheng L, Gao S, Bai Y, Zeng H, Shi H. NF-YC15 transcription factor activates ethylene biosynthesis and improves cassava disease resistance. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:2424-2434. [PMID: 38600705 PMCID: PMC11331790 DOI: 10.1111/pbi.14355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 03/04/2024] [Accepted: 03/29/2024] [Indexed: 04/12/2024]
Abstract
The nuclear factor Y (NF-Y) transcription factors play important roles in plant development and physiological responses. However, the relationship between NF-Y, plant hormone and plant stress resistance in tropical crops remains unclear. In this study, we identified MeNF-YC15 gene in the NF-Y family that significantly responded to Xanthomonas axonopodis pv. manihotis (Xam) treatment. Using MeNF-YC15-silenced and -overexpressed cassava plants, we elucidated that MeNF-YC15 positively regulated disease resistance to cassava bacterial blight (CBB). Notably, we illustrated MeNF-YC15 downstream genes and revealed the direct genetic relationship between MeNF-YC15 and 1-aminocyclopropane-1-carboxylic acid (ACC) oxidase (MeACO1)-ethylene module in disease resistance, as evidenced by the rescued disease susceptibility of MeNF-YC15 silenced cassava plants with ethylene treatment or overexpressing MeACO1. In addition, the physical interaction between 2C-type protein phosphatase 1 (MePP2C1) and MeNF-YC15 inhibited the transcriptional activation of MeACO1 by MeNF-YC15. In summary, MePP2C1-MeNF-YC15 interaction modulates ethylene biosynthesis and cassava disease resistance, providing gene network for cassava genetic improvement.
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Affiliation(s)
- Liyan Zheng
- National Key Laboratory for Tropical Crop Breeding, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, School of Tropical Agriculture and ForestryHainan UniversitySanya and HaikouHainan provinceChina
| | - Shuai Gao
- National Key Laboratory for Tropical Crop Breeding, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, School of Tropical Agriculture and ForestryHainan UniversitySanya and HaikouHainan provinceChina
| | - Yujing Bai
- National Key Laboratory for Tropical Crop Breeding, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, School of Tropical Agriculture and ForestryHainan UniversitySanya and HaikouHainan provinceChina
| | - Hongqiu Zeng
- National Key Laboratory for Tropical Crop Breeding, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, School of Tropical Agriculture and ForestryHainan UniversitySanya and HaikouHainan provinceChina
| | - Haitao Shi
- National Key Laboratory for Tropical Crop Breeding, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, School of Tropical Agriculture and ForestryHainan UniversitySanya and HaikouHainan provinceChina
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Lin C, Lan C, Li X, Xie W, Lin F, Liang Y, Tao Z. A pair of nuclear factor Y transcription factors act as positive regulators in jasmonate signaling and disease resistance in Arabidopsis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024. [PMID: 38953749 DOI: 10.1111/jipb.13732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Accepted: 06/12/2024] [Indexed: 07/04/2024]
Abstract
The plant hormone jasmonate (JA) regulates plant growth and immunity by orchestrating a genome-wide transcriptional reprogramming. In the resting stage, JASMONATE-ZIM DOMAIN (JAZ) proteins act as main repressors to regulate the expression of JA-responsive genes in the JA signaling pathway. However, the mechanisms underlying de-repression of JA-responsive genes in response to JA treatment remain elusive. Here, we report two nuclear factor Y transcription factors NF-YB2 and NF-YB3 (thereafter YB2 and YB3) play key roles in such de-repression in Arabidopsis. YB2 and YB3 function redundantly and positively regulate plant resistance against the necrotrophic pathogen Botrytis cinerea, which are specially required for transcriptional activation of a set of JA-responsive genes following inoculation. Furthermore, YB2 and YB3 modulated their expression through direct occupancy and interaction with histone demethylase Ref6 to remove repressive histone modifications. Moreover, YB2 and YB3 physically interacted with JAZ repressors and negatively modulated their abundance, which in turn attenuated the inhibition of JAZ proteins on the transcription of JA-responsive genes, thereby activating JA response and promoting disease resistance. Overall, our study reveals the positive regulators of YB2 and YB3 in JA signaling by positively regulating transcription of JA-responsive genes and negatively modulating the abundance of JAZ proteins.
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Affiliation(s)
- Chuyu Lin
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Chenghao Lan
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Xiaoxiao Li
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Wei Xie
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Fucheng Lin
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Biotechnology, Zhejiang University, Hangzhou, 311400, China
| | - Yan Liang
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Zeng Tao
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
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Alam MM, Alam KM, Momotaz R, Arifunnahar M, Rahman Bhuyin Apu MM, Siddique SS. Botrytis gray mold of Lilium in Bangladesh: Diagnosis, basic study and control. Heliyon 2024; 10:e33165. [PMID: 39021951 PMCID: PMC11253255 DOI: 10.1016/j.heliyon.2024.e33165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 06/13/2024] [Accepted: 06/14/2024] [Indexed: 07/20/2024] Open
Abstract
Bangladesh Agricultural Research Institute (BARI) released two beautiful Lilium varieties in 2020. In the same year the farmers in Gazipur district reported a set of disease symptoms on these flowers and alerted the Plant Pathology Division of BARI. Subsequent investigation confirmed the symptoms as Botrytis gray mold (BGM), caused by Botrytis cinerea. The pathogen identity was confirmed through ITS gene sequencing. A series of in vitro and in planta experiments conducted to understand the symptoms, the optimal growth condition for the pathogen, potential resistant Lilium genotypes, effective chemical treatments and potential of biological control agents to combat the disease. B. cinerea exhibited the highest growth in V8 media (88.55 mm) at pH6 (85.32 mm) and temperature between 20 and 25 °C (89.56 mm), and pH6 (85.32 mm). Screening revealed that five oriental-originated genotypes provided lower disease incidence (31.66-41.66 %), and were categorized as moderately resistant to resistant in disease reaction. Six fungicides successfully reduced mycelial growth in vitro. Moreover, Ipridione provided the lowest % disease incidence (27.11) and % disease severity (5.33) in the in planta nethouse experiment. Therefore, this fungicide was recommended to the farmers initially. Additionally, two fungal biocontrol agents Epicoccum nigrum EJS002 and Trichoderma ThC003, demonstrated effectiveness in reducing leaf lesion size over control in a detach leaf assessment technique. In conclusion, this study presents BGM of Lilium as a farmers issue for the first time in Bangladesh. It also provides valuable insights into its management, recommending specific chemical fungicides for farmers to use, and two fungal antagonists (E. nigrum EJS002 and Trichoderma ThC003) as potential disease control agent.
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Affiliation(s)
- Md Mahfuz Alam
- Crops Division, Bangladesh Agricultural Research Council (BARC), Dhaka-1215, Bangladesh
| | - Khondoker Mohammad Alam
- Plant Pathology Division, Bangladesh Agricultural Research Institute (BARI), Gazipur-1701 Bangladesh
| | - Rumana Momotaz
- Plant Pathology Division, Bangladesh Agricultural Research Institute (BARI), Gazipur-1701 Bangladesh
| | - Most Arifunnahar
- Plant Pathology Division, Bangladesh Agricultural Research Institute (BARI), Gazipur-1701 Bangladesh
| | | | - Shaikh Sharmin Siddique
- Department of Plant Pathology, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Bangladesh
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Cui Z, Wang X, Dai Y, Li Y, Ban Y, Tian W, Zhang X, Feng X, Zhang X, Jia L, He G, Sang X. Transcription factor OsNF-YC1 regulates grain size by coordinating the transcriptional activation of OsMADS1 in Oryza sativa L. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38887937 DOI: 10.1111/tpj.16868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 04/23/2024] [Accepted: 05/23/2024] [Indexed: 06/20/2024]
Abstract
Grain weight, grain number per panicle, and the number of panicles are the three factors that determine rice (Oryza sativa L.) yield. Of these, grain weight, which not only directly determines rice yield but also influences appearance and quality, is often considered the most important for rice production. Here, we describe OsNF-YC1, a member of the NF-Y transcription factor family that regulates rice grain size. OsNF-YC1 knockout plants (osnf-yc1), obtained using CRISPR-Cas9 technology, showed reduced grain weight due to reduced width and thickness, with no change in grain length, leading to a slenderer grain shape. Downregulation of OsNF-YC1 using RNA interference resulted in similar grain phenotypes as osnf-yc1. OsNF-YC1 affects grain formation by regulating both cell proliferation and cell expansion. OsNF-YC1 localizes in both the nucleus and cytoplasm, has transcriptional activation activity at both the N-terminus and C-terminus, and is highly expressed in young panicles. OsNF-YC1 interacts with OsMADS1 both in vivo and in vitro. Further analysis showed that the histone-like structural CBFD-NFYB-HMF domain of OsNF-YC1 conserved in the OsNF-YC transcription factor family can directly interact with the MADS-box domain of OsMADS1 to enhance its transcriptional activation activity. This interaction positively regulates the expression of OsMADS55, the direct downstream target of OsMADS1. Therefore, this paper reveals a potential grain size regulation pathway controlled by an OsNF-YC1-OsMADS1-OsMADS55 module in rice.
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Affiliation(s)
- Zhibo Cui
- Chongqing Key Laboratory of Crop Molecular Improvement, Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Xiaowen Wang
- Chongqing Key Laboratory of Crop Molecular Improvement, Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Yongdong Dai
- Chongqing Key Laboratory of Crop Molecular Improvement, Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Yangyang Li
- Chongqing Key Laboratory of Crop Molecular Improvement, Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Yijie Ban
- Chongqing Key Laboratory of Crop Molecular Improvement, Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Weijiang Tian
- Chongqing Key Laboratory of Crop Molecular Improvement, Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Xiaobo Zhang
- Chongqing Key Laboratory of Crop Molecular Improvement, Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Xinyu Feng
- Chongqing Key Laboratory of Crop Molecular Improvement, Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Xuefei Zhang
- Chongqing Key Laboratory of Crop Molecular Improvement, Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Luqi Jia
- Chongqing Key Laboratory of Crop Molecular Improvement, Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Guanghua He
- Chongqing Key Laboratory of Crop Molecular Improvement, Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Xianchun Sang
- Chongqing Key Laboratory of Crop Molecular Improvement, Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, 400715, China
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Yang Y, Li Z, Zhang J. ZmNF-YA1 Contributes to Maize Thermotolerance by Regulating Heat Shock Response. Int J Mol Sci 2024; 25:6275. [PMID: 38892463 PMCID: PMC11173165 DOI: 10.3390/ijms25116275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 06/01/2024] [Accepted: 06/04/2024] [Indexed: 06/21/2024] Open
Abstract
Zea mays (maize) is a staple food, feed, and industrial crop. Heat stress is one of the major stresses affecting maize production and is usually accompanied by other stresses, such as drought. Our previous study identified a heterotrimer complex, ZmNF-YA1-YB16-YC17, in maize. ZmNF-YA1 and ZmNF-YB16 were positive regulators of the drought stress response and were involved in maize root development. In this study, we investigated whether ZmNF-YA1 confers heat stress tolerance in maize. The nf-ya1 mutant and overexpression lines were used to test the role of ZmNF-YA1 in maize thermotolerance. The nf-ya1 mutant was more temperature-sensitive than the wild-type (WT), while the ZmNF-YA1 overexpression lines showed a thermotolerant phenotype. Higher malondialdehyde (MDA) content and reactive oxygen species (ROS) accumulation were observed in the mutant, followed by WT and overexpression lines after heat stress treatment, while an opposite trend was observed for chlorophyll content. RNA-seq was used to analyze transcriptome changes in nf-ya1 and its wild-type control W22 in response to heat stress. Based on their expression profiles, the heat stress response-related differentially expressed genes (DEGs) in nf-ya1 compared to WT were grouped into seven clusters via k-means clustering. Gene Ontology (GO) enrichment analysis of the DEGs in different clades was performed to elucidate the roles of ZmNF-YA1-mediated transcriptional regulation and their contribution to maize thermotolerance. The loss function of ZmNF-YA1 led to the failure induction of DEGs in GO terms of protein refolding, protein stabilization, and GO terms for various stress responses. Thus, the contribution of ZmNF-YA1 to protein stabilization, refolding, and regulation of abscisic acid (ABA), ROS, and heat/temperature signaling may be the major reason why ZmNF-YA1 overexpression enhanced heat tolerance, and the mutant showed a heat-sensitive phenotype.
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Affiliation(s)
- Yaling Yang
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China;
| | - Zhaoxia Li
- Agronomy College, Qingdao Agricultural University, Qingdao 266109, China;
| | - Juren Zhang
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China;
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Tan X, Wang G, Cao C, Yang Z, Zhang H, Li Y, Wei Z, Chen J, Sun Z. Two different viral proteins suppress NUCLEAR FACTOR-YC-mediated antiviral immunity during infection in rice. PLANT PHYSIOLOGY 2024; 195:850-864. [PMID: 38330080 DOI: 10.1093/plphys/kiae070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 12/18/2023] [Accepted: 12/21/2023] [Indexed: 02/10/2024]
Abstract
Plant viruses have multiple strategies to counter and evade the host's antiviral immune response. However, limited research has been conducted on the antiviral defense mechanisms commonly targeted by distinct types of plant viruses. In this study, we discovered that NUCLEAR FACTOR-YC (NF-YC) and NUCLEAR FACTOR-YA (NF-YA), 2 essential components of the NF-Y complex, were commonly targeted by viral proteins encoded by 2 different rice (Oryza sativa L.) viruses, rice stripe virus (RSV, Tenuivirus) and southern rice black streaked dwarf virus (SRBSDV, Fijivirus). In vitro and in vivo experiments showed that OsNF-YCs associate with OsNF-YAs and inhibit their transcriptional activation activity, resulting in the suppression of OsNF-YA-mediated plant susceptibility to rice viruses. Different viral proteins RSV P2 and SRBSDV SP8 directly disrupted the association of OsNF-YCs with OsNF-YAs, thereby suppressing the antiviral defense mediated by OsNF-YCs. These findings suggest an approach for conferring broad-spectrum disease resistance in rice and reveal a common mechanism employed by viral proteins to evade the host's antiviral defense by hindering the antiviral capabilities of OsNF-YCs.
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Affiliation(s)
- Xiaoxiang Tan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Guoda Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Chen Cao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Zihang Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Hehong Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Yanjun Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Zhongyan Wei
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Jianping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Zongtao Sun
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
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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] [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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Bai J, Guo H, Xiong H, Xie Y, Gu J, Zhao L, Zhao S, Ding Y, Liu L. Strigolactone and abscisic acid synthesis and signaling pathways are enhanced in the wheat oligo-tillering mutant ot1. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2024; 44:12. [PMID: 38313680 PMCID: PMC10837411 DOI: 10.1007/s11032-024-01450-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 01/10/2024] [Indexed: 02/06/2024]
Abstract
Tiller number greatly contributes to grain yield in wheat. Using ethylmethanesulfonate mutagenesis, we previously discovered the oligo-tillering mutant ot1. The tiller number was significantly lower in ot1 than in the corresponding wild type from the early tillering stage until the heading stage. Compared to the wild type, the thousand-grain weight and grain length were increased by 15.41% and 31.44%, respectively, whereas the plant height and spike length were decreased by 26.13% and 37.25%, respectively. Transcriptomic analysis was conducted at the regreening and jointing stages to identify differential expressed genes (DEGs). Functional enrichment analysis with the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) databases showed differential expression of genes associated with ADP binding, transmembrane transport, and transcriptional regulation during tiller development. Differences in tiller number in ot1 led to the upregulation of genes in the strigolactone (SL) and abscisic acid (ABA) pathways. Specifically, the SL biosynthesis genes DWARF (D27), D17, D10, and MORE AXILLARY GROWTH 1 (MAX1) were upregulated by 3.37- to 8.23-fold; the SL signal transduction genes D14 and D53 were upregulated by 1.81- and 1.32-fold, respectively; the ABA biosynthesis genes 9-CIS-EPOXICAROTENOID DIOXIGENASE 3 (NCED3) and NCED5 were upregulated by 1.66- and 3.4-fold, respectively; and SNF1-REGULATED PROTEIN KINASE2 (SnRK2) and PROTEIN PHOSPHATASE 2C (PP2C) genes were upregulated by 1.30- to 4.79-fold. This suggested that the tiller number reduction in ot1 was due to alterations in plant hormone pathways. Genes known to promote tillering growth were upregulated, whereas those known to inhibit tillering growth were downregulated. For example, PIN-FORMED 9 (PIN9), which promotes tiller development, was upregulated by 8.23-fold in ot1; Ideal Plant Architecture 1 (IPA1), which inhibits tiller development, was downregulated by 1.74-fold. There were no significant differences in the expression levels of TILLER NUMBER 1 (TN1) or TEOSINTE BRANCHED 1 (TB1), indicating that the tiller reduction in ot1 was not controlled by known genes. Our findings provide valuable data for subsequent research into the genetic bases and regulatory mechanisms of wheat tillering. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-024-01450-3.
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Affiliation(s)
- Jiaxing Bai
- State Key Laboratory of Crop Gene Resources and Breeding, National Engineering Laboratory of Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huijun Guo
- State Key Laboratory of Crop Gene Resources and Breeding, National Engineering Laboratory of Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongchun Xiong
- State Key Laboratory of Crop Gene Resources and Breeding, National Engineering Laboratory of Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongdun Xie
- State Key Laboratory of Crop Gene Resources and Breeding, National Engineering Laboratory of Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiayu Gu
- State Key Laboratory of Crop Gene Resources and Breeding, National Engineering Laboratory of Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Linshu Zhao
- State Key Laboratory of Crop Gene Resources and Breeding, National Engineering Laboratory of Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shirong Zhao
- State Key Laboratory of Crop Gene Resources and Breeding, National Engineering Laboratory of Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuping Ding
- State Key Laboratory of Crop Gene Resources and Breeding, National Engineering Laboratory of Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Luxiang Liu
- State Key Laboratory of Crop Gene Resources and Breeding, National Engineering Laboratory of Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Yan X, Han M, Li S, Liang Z, Ouyang J, Wang X, Liao P. A member of NF-Y family, OsNF-YC5 negatively regulates salt tolerance in rice. Gene 2024; 892:147869. [PMID: 37797782 DOI: 10.1016/j.gene.2023.147869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/16/2023] [Accepted: 10/02/2023] [Indexed: 10/07/2023]
Abstract
NF-Y, a critical transcription factor, binds to the CCAAT-box in target gene promoters, playing a pivotal role in plant development and abiotic stress response. OsNF-YC5, encodes a putative subunit of the NF-Y transcription factor in rice, had an undetermined function. Our research revealed that OsNF-YC5 is induced by high salinity and exogenous abscisic acid (ABA). Subcellular localization studies showed that OsNF-YC5 is nuclear- and cytoplasm-localized. Using CRISPR-Cas9 to disrupt OsNF-YC5, we observed significantly enhanced rice salinity tolerance and ABA-hypersensitivity. Compared to the wild-type, osnf-yc5 mutants exhibited reduced H2O2 and malondialdehyde (MDA) levels, increased catalase (CAT) activity, and elevated OsCATA transcripts under salt stress. Moreover, ABA-dependent (OsABI2 and OsLEA3) and ABA-independent (OsDREB1A, OsDREB1B, and OsDREB2A) marker genes were upregulated in mutant lines in response to salinity. These results indicate that disrupting OsNF-YC5 enhances rice salinity tolerance, potentially by boosting CAT enzyme activity and modulating gene expression in both ABA-dependent and ABA-independent pathways. Therefore, this study provides a valuable theoretical foundation and genetic resources for developing novel salt-tolerant rice varieties.
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Affiliation(s)
- Xin Yan
- School of Life Sciences, Nanchang University, Nanchang 330031, Jiangxi, PR China
| | - Mengtian Han
- School of Life Sciences, Nanchang University, Nanchang 330031, Jiangxi, PR China
| | - Shuai Li
- School of Life Sciences, Nanchang University, Nanchang 330031, Jiangxi, PR China
| | - Zhiyan Liang
- School of Life Sciences, Nanchang University, Nanchang 330031, Jiangxi, PR China
| | - Jiexiu Ouyang
- School of Life Sciences, Nanchang University, Nanchang 330031, Jiangxi, PR China
| | - Xin Wang
- School of Life Sciences, Nanchang University, Nanchang 330031, Jiangxi, PR China
| | - Pengfei Liao
- School of Life Sciences, Nanchang University, Nanchang 330031, Jiangxi, PR China.
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10
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Li M, Li W, Zhao M, Li Z, Wang GL, Liu W, Liang C. Transcriptome analysis reveals a lncRNA-miRNA-mRNA regulatory network in OsRpp30-mediated disease resistance in rice. BMC Genomics 2023; 24:643. [PMID: 37884868 PMCID: PMC10604448 DOI: 10.1186/s12864-023-09748-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 10/17/2023] [Indexed: 10/28/2023] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) play critical roles in various biological processes in plants. Extensive studies utilizing high-throughput RNA sequencing have revealed that many lncRNAs are involved in plant disease resistance. Oryza sativa RNase P protein 30 (OsRpp30) has been identified as a positive regulator of rice immunity against fungal and bacterial pathogens. Nevertheless, the specific functions of lncRNAs in relation to OsRpp30-mediated disease resistance in rice remain elusive. RESULTS We conducted a comprehensive analysis of lncRNAs, miRNAs, and mRNAs expression patterns in wild type (WT), OsRpp30 overexpression (OsRpp30-OE), and OsRpp30 knockout (OsRpp30-KO) rice plants. In total, we identified 91 differentially expressed lncRNAs (DElncRNAs), 1671 differentially expressed mRNAs (DEmRNAs), and 41 differentially expressed miRNAs (DEmiRNAs) across the different rice lines. To gain further insights, we investigated the interaction between DElncRNAs and DEmRNAs, leading to the discovery of 10 trans- and 27 cis-targeting pairs specific to the OsRpp30-OE and OsRpp30-KO samples. In addition, we constructed a competing endogenous RNA (ceRNA) network comprising differentially expressed lncRNAs, miRNAs, and mRNAs to elucidate their intricate interplay in rice disease resistance. The ceRNA network analysis uncovered a set of gene targets regulated by lncRNAs and miRNAs, which were found to be involved in pathogen recognition, hormone pathways, transcription factor activation, and other biological processes related to plant immunity. CONCLUSIONS Our study provides a comprehensive expression profiling of lncRNAs, miRNAs, and mRNAs in a collection of defense mutants in rice. To decipher the putative functional significance of lncRNAs, we constructed trans- and cis-targeting networks involving differentially expressed lncRNAs and mRNAs, as well as a ceRNA network incorporating differentially expressed lncRNAs, miRNAs, and mRNAs. Together, the findings from this study provide compelling evidence supporting the pivotal roles of lncRNAs in OsRpp30-mediated disease resistance in rice.
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Affiliation(s)
- Minghua Li
- Department of Biology, Miami University, Oxford, OH, 45056, USA
| | - Wei Li
- Department of Plant Pathology, Ohio State University, Columbus, OH, 43210, USA
| | - Meixia Zhao
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA
| | - Zhiqiang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Guo-Liang Wang
- Department of Plant Pathology, Ohio State University, Columbus, OH, 43210, USA.
| | - Wende Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Chun Liang
- Department of Biology, Miami University, Oxford, OH, 45056, USA.
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11
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Leitão ST, Mendes FA, Rubiales D, Vaz Patto MC. Oligogenic Control of Quantitative Resistance Against Powdery Mildew Revealed in Portuguese Common Bean Germplasm. PLANT DISEASE 2023; 107:3113-3122. [PMID: 37102726 DOI: 10.1094/pdis-02-23-0313-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Common bean (Phaseolus vulgaris L.) is one of the most important food legumes worldwide, and its production is severely affected by fungal diseases such as powdery mildew. Portugal has a diverse germplasm, with accessions of Andean, Mesoamerican, and admixed origin, making it a valuable resource for common bean genetic studies. In this work, we evaluated the response of a Portuguese collection of 146 common bean accessions to Erysiphe diffusa infection, observing a wide range of disease severity and different levels of compatible and incompatible reactions, revealing the presence of different resistance mechanisms. We identified 11 incompletely hypersensitive resistant and 80 partially resistant accessions. We performed a genome-wide association study to clarify its genetic control, resulting in the identification of eight disease severity-associated single-nucleotide polymorphisms, spread across chromosomes Pv03, Pv09, and Pv10. Two of the associations were unique to partial resistance and one to incomplete hypersensitive resistance. The proportion of variance explained by each association varied between 15 and 86%. The absence of a major locus, together with the relatively small number of loci controlling disease severity, suggested an oligogenic inheritance of both types of resistance. Seven candidate genes were proposed, including a disease resistance protein (toll interleukin 1 receptor-nucleotide binding site-leucine-rich repeat class), an NF-Y transcription factor complex component, and an ABC-2 type transporter family protein. This work contributes with new resistance sources and genomic targets valuable to develop selection molecular tools and support powdery mildew resistance precision breeding in common bean.
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Li Y, Nan Z, Matthew C, Wang Y, Duan T. Arbuscular mycorrhizal fungus changes alfalfa (Medicago sativa) metabolites in response to leaf spot (Phoma medicaginis) infection, with subsequent effects on pea aphid (Acyrthosiphon pisum) behavior. THE NEW PHYTOLOGIST 2023; 239:286-300. [PMID: 37010085 DOI: 10.1111/nph.18924] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 03/27/2023] [Indexed: 06/02/2023]
Abstract
Plant disease occurs simultaneously with insect attack. Arbuscular mycorrhizal fungi (AMF) modify plant biotic stress response. Arbuscular mycorrhizal fungi and pathogens may modify plant volatile organic compound (VOC) production and insect behavior. Nevertheless, such effects are rarely studied, particularly for mesocosms where component organisms interact with each other. Plant-mediated effects of leaf pathogen (Phoma medicaginis) infection on aphid (Acyrthosiphon pisum) infestation, and role of AMF (Rhizophagus intraradices) in modifying these interactions were elucidated in a glasshouse experiment. We evaluated alfalfa disease occurrence, photosynthesis, phytohormones, trypsin inhibitor (TI) and total phenol response to pathogen and aphid attack, with or without AMF, and aphid behavior towards VOCs from AMF inoculated and non-mycorrhizal alfalfa, with or without pathogen infection. AM fungus enhanced alfalfa resistance to pathogen and aphid infestation. Plant biomass, root : shoot ratio, net photosynthetic rate, transpiration rate, stomatal conductance, salicylic acid, and TI were significantly increased in AM-inoculated alfalfa. Arbuscular mycorrhizal fungi and pathogen significantly changed alfalfa VOCs. Aphids preferred VOCs of AM-inoculated and nonpathogen-infected to nonmycorrhizal and pathogen-infected alfalfa. We propose that AMF alter plant response to multiple biotic stresses in ways both beneficial and harmful to the plant host, providing a basis for strategies to manage pathogens and herbivore pests.
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Affiliation(s)
- Yingde Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Lanzhou University, Lanzhou, 730020, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou, 730020, China
| | - Zhibiao Nan
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Lanzhou University, Lanzhou, 730020, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou, 730020, China
| | - Cory Matthew
- School of Agriculture and Environment, College of Sciences, Massey University, Private Bag 11-222, Palmerston North, 4442, New Zealand
| | - Yajie Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Lanzhou University, Lanzhou, 730020, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou, 730020, China
| | - Tingyu Duan
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Lanzhou University, Lanzhou, 730020, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou, 730020, China
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13
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Yu J, Zhu C, Xuan W, An H, Tian Y, Wang B, Chi W, Chen G, Ge Y, Li J, Dai Z, Liu Y, Sun Z, Xu D, Wang C, Wan J. Genome-wide association studies identify OsWRKY53 as a key regulator of salt tolerance in rice. Nat Commun 2023; 14:3550. [PMID: 37321989 PMCID: PMC10272163 DOI: 10.1038/s41467-023-39167-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 06/01/2023] [Indexed: 06/17/2023] Open
Abstract
Salinity stress progressively reduces plant growth and productivity, while plant has developed complex signaling pathways to confront salt stress. However, only a few genetic variants have been identified to mediate salt tolerance in the major crop rice, and the molecular mechanism remains poorly understood. Here, we identify ten candidate genes associated with salt-tolerance (ST) traits by performing a genome-wide association analysis in rice landraces. We characterize two ST-related genes, encoding transcriptional factor OsWRKY53 and Mitogen-activated protein Kinase Kinase OsMKK10.2, that mediate root Na+ flux and Na+ homeostasis. We further find that OsWRKY53 acts as a negative modulator regulating expression of OsMKK10.2 in promoting ion homeostasis. Furthermore, OsWRKY53 trans-represses OsHKT1;5 (high-affinity K+ transporter 1;5), encoding a sodium transport protein in roots. We show that the OsWRKY53-OsMKK10.2 and OsWRKY53-OsHKT1;5 module coordinate defenses against ionic stress. The results shed light on the regulatory mechanisms underlying plant salt tolerance.
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Affiliation(s)
- Jun Yu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Centre for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
- Southern Japonica Rice R&D Corporation Ltd, Key Laboratory of Biology, Genetics and Breeding of Japonica Rice in the Mid-lower Yangtze River, Ministry of Agriculture, Nanjing, 210095, China
| | - Chengsong Zhu
- Department of Immunology, The University of Texas Southwestern Medical Centre, Dallas, TX, 75390, USA
| | - Wei Xuan
- MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hongzhou An
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Centre for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
- Southern Japonica Rice R&D Corporation Ltd, Key Laboratory of Biology, Genetics and Breeding of Japonica Rice in the Mid-lower Yangtze River, Ministry of Agriculture, Nanjing, 210095, China
| | - Yunlu Tian
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Centre for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
- Southern Japonica Rice R&D Corporation Ltd, Key Laboratory of Biology, Genetics and Breeding of Japonica Rice in the Mid-lower Yangtze River, Ministry of Agriculture, Nanjing, 210095, China
| | - Baoxiang Wang
- Lianyungang Academy of Agricultural Science, Lianyungang, Jiangsu, 222006, China
| | - Wenchao Chi
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Centre for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
- Southern Japonica Rice R&D Corporation Ltd, Key Laboratory of Biology, Genetics and Breeding of Japonica Rice in the Mid-lower Yangtze River, Ministry of Agriculture, Nanjing, 210095, China
| | - Gaoming Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Centre for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
- Southern Japonica Rice R&D Corporation Ltd, Key Laboratory of Biology, Genetics and Breeding of Japonica Rice in the Mid-lower Yangtze River, Ministry of Agriculture, Nanjing, 210095, China
| | - Yuwei Ge
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Centre for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
- Southern Japonica Rice R&D Corporation Ltd, Key Laboratory of Biology, Genetics and Breeding of Japonica Rice in the Mid-lower Yangtze River, Ministry of Agriculture, Nanjing, 210095, China
| | - Jin Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Centre for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
- Southern Japonica Rice R&D Corporation Ltd, Key Laboratory of Biology, Genetics and Breeding of Japonica Rice in the Mid-lower Yangtze River, Ministry of Agriculture, Nanjing, 210095, China
| | - Zhaoyang Dai
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Centre for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
- Southern Japonica Rice R&D Corporation Ltd, Key Laboratory of Biology, Genetics and Breeding of Japonica Rice in the Mid-lower Yangtze River, Ministry of Agriculture, Nanjing, 210095, China
| | - Yan Liu
- Lianyungang Academy of Agricultural Science, Lianyungang, Jiangsu, 222006, China
| | - Zhiguang Sun
- Lianyungang Academy of Agricultural Science, Lianyungang, Jiangsu, 222006, China
| | - Dayong Xu
- Lianyungang Academy of Agricultural Science, Lianyungang, Jiangsu, 222006, China
| | - Chunming Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Centre for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China.
- Southern Japonica Rice R&D Corporation Ltd, Key Laboratory of Biology, Genetics and Breeding of Japonica Rice in the Mid-lower Yangtze River, Ministry of Agriculture, Nanjing, 210095, China.
| | - Jianmin Wan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Centre for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China.
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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14
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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 SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 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] [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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15
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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. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:914-933. [PMID: 36906910 DOI: 10.1111/tpj.16183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [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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16
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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] [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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17
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Nishiguchi M, Ali ME, Kaya T, Kobayashi K. Plant virus disease control by vaccination and transgenic approaches: Current status and perspective. PLANT RNA VIRUSES 2023:373-424. [DOI: 10.1016/b978-0-323-95339-9.00028-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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18
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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:ijms232415778. [PMID: 36555422 PMCID: PMC9778975 DOI: 10.3390/ijms232415778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [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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Ma J, Wei H, Yu X, Lv Y, Zhang Y, Qian Q, Shang L, Guo L. Compared analysis with a high-quality genome of weedy rice reveals the evolutionary game of de-domestication. FRONTIERS IN PLANT SCIENCE 2022; 13:1065449. [PMID: 36466225 PMCID: PMC9716140 DOI: 10.3389/fpls.2022.1065449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 11/03/2022] [Indexed: 06/17/2023]
Abstract
The weedy rice (Oryza sativa f. spontanea) harbors large numbers of excellent traits and genetic diversities, which serves as a valuable germplasm resource and has been considered as a typical material for research about de-domestication. However, there are relatively few reference genomes on weedy rice that severely limit exploiting these genetic resources and revealing more details about de-domestication events. In this study, a high-quality genome (~376.4 Mb) of weedy rice A02 was assembled based on Nanopore ultra-long platform with a coverage depth of about 79.3× and 35,423 genes were predicted. Compared to Nipponbare genome, 5,574 structural variations (SVs) were found in A02. Based on super pan-genome graph, population SVs of 238 weedy rice and cultivated rice accessions were identified using public resequencing data. Furthermore, the de-domestication sites of weedy rice and domestication sites of wild rice were analyzed and compared based on SVs and single-nucleotide polymorphisms (SNPs). Interestingly, an average of 2,198 genes about de-domestication could only be found by F ST analysis based on SVs (SV-F ST) while not by F ST analysis based on SNPs (SNP-F ST) in divergent region. Additionally, there was a low overlap between domestication and de-domestication intervals, which demonstrated that two different mechanisms existed in these events. Our finding could facilitate pinpointing of the evolutionary events that had shaped the genomic architecture of wild, cultivated, and weedy rice, and provide a good foundation for cloning of the superior alleles for breeding.
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Affiliation(s)
- Jie Ma
- State Key Lab for Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Hua Wei
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Xiaoman Yu
- State Key Lab for Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Yang Lv
- State Key Lab for Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Yu Zhang
- State Key Lab for Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Qian Qian
- State Key Lab for Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Lianguang Shang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Longbiao Guo
- State Key Lab for Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
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Zhao Y, Zhang Y, Li T, Ni C, Bai X, Lin R, Xiao K. TaNF-YA7-5B, a gene encoding nuclear factor Y (NF-Y) subunit A in Triticum aestivum, confers plant tolerance to PEG-inducing dehydration simulating drought through modulating osmotic stress-associated physiological processes. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 188:81-96. [PMID: 35988390 DOI: 10.1016/j.plaphy.2022.07.036] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 07/20/2022] [Accepted: 07/23/2022] [Indexed: 05/27/2023]
Abstract
Members of nuclear factor-Y (NF-Y) transcription factors play important roles in regulating physiological processes associated with abiotic stress responses. In this study, we characterized TaNF-YA7-5B, a gene encoding wheat NY-YA subunit, in mediating plant adaptation to PEG-inducing dehydration stress. TaNF-YA7-5B shares high similarities to its homologs across various plant species. The TaNF-YA7-5B protein is specified by its conserved domains as plant NF-YA members and targets onto nucleus after endoplasmic reticulum assortment. Yeast two-hybrid assays indicated that TaNF-YA7-5B interacts with TaNF-YB2 and TaNF-YC7, two members of NF-YB and NF-YC subfamilies, suggesting a heterotrimer constituted by TaNF-YA7-5B and above NF-YB and -YC partners. TaNF-YA7-5B displayed induced expression upon drought and whose PEG-inducing dehydration-elevated transcripts were restored under normal recovery condition, suggesting its involvement in plant PEG-inducing dehydration response through modifying transcription efficiency. Overexpressing TaNF-YA7-5B conferred plant improved growth under PEG-inducing dehydration, which was ascribed largely to the gene function in regulating stomata closing and leaf water retention, osmolyte biosynthesis, and cellular ROS homeostasis. The expression of P5CS gene TaP5CS2 and antioxidant enzyme (AE) genes, namely, TaSOD3, TaCAT1, and TaPOD4, was upregulated and downregulated in lines with overexpression and knockdown of TaNF-YA7-5B, respectively; transgene analysis on them validated their functions in positively regulating proline accumulation and ROS scavenging under PEG-inducing dehydration. RNA-seq analysis revealed modified transcription of numerous genes underlying TaNF-YA7-5B enriched by GO terms 'biological process', 'cellular components', and 'molecular function'. Therefore, TaNF-YA7-5B is a crucial regulator for plant drought adaptation through comprehensively integrating diverse physiological processes associated with drought acclimation.
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Affiliation(s)
- Yingjia Zhao
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, 071001, China; College of Agronomy, Agricultural University of Hebei, Baoding, 071001, China
| | - Yanyang Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, 071001, China; College of Agronomy, Agricultural University of Hebei, Baoding, 071001, China
| | - Tianjiao Li
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, 071001, China; College of Agronomy, Agricultural University of Hebei, Baoding, 071001, China
| | - Chenyang Ni
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, 071001, China; College of Agronomy, Agricultural University of Hebei, Baoding, 071001, China
| | - Xinyang Bai
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, 071001, China; College of Agronomy, Agricultural University of Hebei, Baoding, 071001, China
| | - Ruize Lin
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, 071001, China; College of Agronomy, Agricultural University of Hebei, Baoding, 071001, China
| | - Kai Xiao
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, 071001, China; College of Agronomy, Agricultural University of Hebei, Baoding, 071001, China.
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Yang Y, Wang B, Wang J, He C, Zhang D, Li P, Zhang J, Li Z. Transcription factors ZmNF-YA1 and ZmNF-YB16 regulate plant growth and drought tolerance in maize. PLANT PHYSIOLOGY 2022; 190:1506-1525. [PMID: 35861438 PMCID: PMC9516732 DOI: 10.1093/plphys/kiac340] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 06/25/2022] [Indexed: 05/26/2023]
Abstract
The identification of drought stress regulatory genes is crucial for the genetic improvement of maize (Zea mays L.) yield. Nuclear factors Y (NF-Ys) are important transcription factors, but their roles in the drought stress tolerance of plants and underlying molecular mechanisms are largely unknown. In this work, we used yeast two-hybrid screening to identify potential interactors of ZmNF-YB16 and confirmed the interaction between ZmNF-YA1 and ZmNF-YB16-YC17 and between ZmNF-YA7 and ZmNF-YB16-YC17. ZmNF-YB16 interacted with ZmNF-YC17 via its histone fold domain to form a heterodimer in the cytoplasm and then entered the nucleus to form a heterotrimer with ZmNF-YA1 or ZmNF-YA7 under osmotic stress. Overexpression of ZmNF-YA1 improved drought and salt stress tolerance and root development of maize, whereas zmnf-ya1 mutants exhibited drought and salt stress sensitivity. ZmNF-YA1-mediated transcriptional regulation, especially in JA signaling, histone modification, and chromatin remodeling, could underlie the altered stress tolerance of zmnf-ya1 mutant plants. ZmNF-YA1 bound to promoter CCAAT motifs and directly regulated the expression of multiple genes that play important roles in stress responses and plant development. Comparison of ZmNF-YB16- and ZmNF-YA1-regulated genes showed that ZmNF-YA1 and ZmNF-YB16 have similar biological functions in stress responses but varied functions in other biological processes. Taken together, ZmNF-YA1 is a positive regulator of plant drought and salt stress responses and is involved in the root development of maize, and ZmNF-Y complexes with different subunits may have discrepant functions.
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Affiliation(s)
| | | | | | - Chunmei He
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, Shandong, China
| | - Dengfeng Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Peng Li
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Juren Zhang
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, 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] [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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NF-YA transcription factors suppress jasmonic acid-mediated antiviral defense and facilitate viral infection in rice. PLoS Pathog 2022; 18:e1010548. [PMID: 35560151 PMCID: PMC9132283 DOI: 10.1371/journal.ppat.1010548] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [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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Panzade KP, Kale SS, Manoj ML, Kothawale SP, Damse DN. Genome-Wide Analysis and Expression Profile of Nuclear Factor Y (NF-Y) Gene Family in Z. jujuba. Appl Biochem Biotechnol 2022; 194:1373-1389. [PMID: 34731431 DOI: 10.1007/s12010-021-03730-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 10/21/2021] [Indexed: 10/19/2022]
Abstract
Nuclear factor-Y (NF-Y) is an important transcription factor in the plant species, which potentially provides a higher level of functional diversity including for abiotic stress tolerance. The genome-wide study and expression analysis of NF-Y gene family in Ziziphus, an elite abiotic stress-tolerant species, assist bioprospecting of genes. Here, a total of 32 NF-Y (8 NF-YA, 15 NF-YB, and 9 NF-YC) genes were identified in genome-wide search of Z. jujuba genome. Physicochemical properties, cellular localization, gene structure, chromosomal location, and protein motifs were analyzed for structural and functional understanding. Identified 12 NF-Ys were responsible for the expansion of NF-Y gene family by tandem duplication in Z. jujuba. Phylogenetic and comparative physical mapping of Z. jujuba NF-Ys with its orthologs illustrated evolutionary and functional insights into NF-Y gene family. A total of 45 perfect microsatellites (20bp to 40bp) were extracted across the ZjNF-Y genes. The promoter and gene ontology study suggested that Z. jujuba NF-Y gene family is functionally diverse and could play a wide-ranging role in plant abiotic stress, development, and cellular processes. An expression study revealed that large numbers of the NF-Ys are differentially expressed in response to drought and salinity. The total 15 and 18 ZjNF-Y genes that are upregulated under drought and salinity stress, respectively, are the potential candidates for further functional analysis for development of climate-resilient crops. The present study established a base for understanding the role of NF-Ys in Z. jujuba under abiotic stress conditions and paved a way for further research.
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Affiliation(s)
- Kishor Prabhakar Panzade
- Department of Plant Biotechnology, SDMVM College of Agricultural Biotechnology, Georai Tanda, Maharashtra, 431002, India.
| | - Sonam S Kale
- Department of Plant Biotechnology, MGM College of Agricultural Biotechnology, Aurangabad, Maharashtra, 431007, India
| | | | | | - Dipak N Damse
- Central Sugarcane Research Station, Padegaon, Mahatma Phule Agriculture University, Rahuri, Maharashtra, 415521, India
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Wang H, Bi Y, Gao Y, Yan Y, Yuan X, Xiong X, Wang J, Liang J, Li D, Song F. A Pathogen-Inducible Rice NAC Transcription Factor ONAC096 Contributes to Immunity Against Magnaprothe oryzae and Xanthomonas oryzae pv. oryzae by Direct Binding to the Promoters of OsRap2.6, OsWRKY62, and OsPAL1. FRONTIERS IN PLANT SCIENCE 2021; 12:802758. [PMID: 34956298 PMCID: PMC8702954 DOI: 10.3389/fpls.2021.802758] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 11/15/2021] [Indexed: 06/14/2023]
Abstract
The rice NAC transcriptional factor family harbors 151 members, and some of them play important roles in rice immunity. Here, we report the function and molecular mechanism of a pathogen-inducible NAC transcription factor, ONAC096, in rice immunity against Magnaprothe oryzae and Xanthomonas oryzae pv. oryzae. Expression of ONAC096 was induced by M. oryzae and by abscisic acid and methyl jasmonate. ONAC096 had the DNA binding ability to NAC recognition sequence and was found to be a nucleus-localized transcriptional activator whose activity depended on its C-terminal. CRISPR/Cas9-mediated knockout of ONAC096 attenuated rice immunity against M. oryzae and X. oryzae pv. oryzae as well as suppressed chitin- and flg22-induced reactive oxygen species burst and expression of PTI marker genes OsWRKY45 and OsPAL4; by contrast, overexpression of ONAC096 enhanced rice immunity against these two pathogens and strengthened chitin- or flg22-induced PTI. RNA-seq transcriptomic profiling and qRT-PCR analysis identified a small set of defense and signaling genes that are putatively regulated by ONAC096, and further biochemical analysis validated that ONAC096 could directly bind to the promoters of OsRap2.6, OsWRKY62, and OsPAL1, three known defense and signaling genes that regulate rice immunity. ONAC096 interacts with ONAC066, which is a positive regulator of rice immunity. These results demonstrate that ONAC096 positively contributes to rice immunity against M. oryzae and X. oryzae pv. oryzae through direct binding to the promoters of downstream target genes including OsRap2.6, OsWRKY62, and OsPAL1.
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Affiliation(s)
- Hui Wang
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Yan Bi
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Yizhou Gao
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Yuqing Yan
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Xi Yuan
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, China
| | - Xiaohui Xiong
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Jiajing Wang
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Jiayu Liang
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Dayong Li
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Fengming Song
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
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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] [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] [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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Liu Z, Li Y, Zhu J, Ma W, Li Z, Bi Z, Sun C, Bai J, Zhang J, Liu Y. Genome-Wide Identification and Analysis of the NF-Y Gene Family in Potato ( Solanum tuberosum L.). Front Genet 2021; 12:739989. [PMID: 34603398 PMCID: PMC8484916 DOI: 10.3389/fgene.2021.739989] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 08/20/2021] [Indexed: 11/15/2022] Open
Abstract
Nuclear factor Y (NF-Y) is a ubiquitous transcription factor in eukaryotes, which is composed of three subunits (NF-YA, NF-YB, and NF-YC). NF-Y has been identified as a key regulator of multiple pathways in plants. Although the NF-Y gene family has been identified in many plants, it has not been reported in potato (Solanum tuberosum). In the present study, a total of 41 NF-Y proteins in potato (StNF-Ys) were identified, including 10 StNF-YA, 22 StNF-YB, and nine StNF-YC subunits, and their distribution on chromosomes, gene structure, and conserved motif was analyzed. A synteny analysis indicated that 14 and 38 pairs of StNF-Y genes were orthologous to Arabidopsis and tomato (Solanum lycopersicum), respectively, and these gene pairs evolved under strong purifying selection. In addition, we analyzed the expression profiles of NF-Y genes in different tissues of double haploid (DM) potato, as well as under abiotic stresses and hormone treatments by RNA-seq downloaded from the Potato Genome Sequencing Consortium (PGSC) database. Furthermore, we performed RNA-seq on white, red, and purple tuber skin and flesh of three potato cultivars at the tuber maturation stage to identify genes that might be involved in anthocyanin biosynthesis. These results provide valuable information for improved understanding of StNF-Y gene family and further functional analysis of StNF-Y genes in fruit development, abiotic stress tolerance, and anthocyanin biosynthesis in potato.
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Affiliation(s)
- Zhen Liu
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
| | - Yuanming Li
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Jinyong Zhu
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Wenjing Ma
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Zhitao Li
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Zhenzhen Bi
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Chao Sun
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Jiangping Bai
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Junlian Zhang
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Yuhui Liu
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
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Engineering cereal crops for enhanced abiotic stress tolerance. PROCEEDINGS OF THE INDIAN NATIONAL SCIENCE ACADEMY 2021. [DOI: 10.1007/s43538-021-00006-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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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. FRONTIERS IN PLANT SCIENCE 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] [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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Pabuayon ICM, Kitazumi A, Gregorio GB, Singh RK, de los Reyes BG. Contributions of Adaptive Plant Architecture to Transgressive Salinity Tolerance in Recombinant Inbred Lines of Rice: Molecular Mechanisms Based on Transcriptional Networks. Front Genet 2020; 11:594569. [PMID: 33193743 PMCID: PMC7644915 DOI: 10.3389/fgene.2020.594569] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 10/05/2020] [Indexed: 11/30/2022] Open
Abstract
Genetic novelties are important nucleators of adaptive speciation. Transgressive segregation is a major mechanism that creates genetic novelties with morphological and developmental attributes that confer adaptive advantages in certain environments. This study examined the morpho-developmental and physiological profiles of recombinant inbred lines (RILs) from the salt-sensitive IR29 and salt-tolerant Pokkali rice, representing the total range of salt tolerance including the outliers at both ends of the spectrum. Morpho-developmental and physiological profiles were integrated with a hypothesis-driven interrogation of mRNA and miRNA transcriptomes to uncover the critical genetic networks that have been rewired for novel adaptive architecture. The transgressive super-tolerant FL510 had a characteristic small tiller angle and wider, more erect, sturdier, and darker green leaves. This unique morphology resulted in lower transpiration rate, which also conferred a special ability to retain water more efficiently for osmotic avoidance. The unique ability for water retention conferred by such adaptive morphology appeared to enhance the efficacy of defenses mediated by Na+ exclusion mechanism (SalTol-effects) inherited from Pokkali. The super-tolerant FL510 and super-sensitive FL499 had the smallest proportions of differentially expressed genes with little overlaps. Genes that were steadily upregulated in FL510 comprised a putative cytokinin-regulated genetic network that appeared to maintain robust growth under salt stress through well-orchestrated cell wall biogenesis and cell expansion, likely through major regulatory (OsRR23, OsHK5) and biosynthetic (OsIPT9) genes in the cytokinin signaling pathway. Meanwhile, a constitutively expressed cluster in FL510 prominently featured two transcription factors (OsIBH1, TAC3) that control tiller angle and growth habit through the brassinosteroid signaling pathway. Both the putative cytokinin-mediated and brassinosteroid-mediated clusters appeared to function as highly coordinated network synergies in FL510. In contrast, both networks appeared to be sub-optimal and inferior in the other RILs and parents as they were disjointed and highly fragmented. Transgressively expressed miRNAs (miR169, miR397, miR827) were also identified as prominent signatures of FL510, with functional implications to mechanisms that support robust growth, homeostasis, and osmotic stress avoidance. Results of this study demonstrate how genetic recombination creates novel morphology that complements inducible defenses hence transgressive adaptive phenotypes.
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Affiliation(s)
| | - Ai Kitazumi
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, United States
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Huang HE, Ho MH, Chang H, Chao HY, Ger MJ. Overexpression of plant ferredoxin-like protein promotes salinity tolerance in rice (Oryza sativa). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 155:136-146. [PMID: 32750653 DOI: 10.1016/j.plaphy.2020.07.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 06/18/2020] [Accepted: 07/13/2020] [Indexed: 05/02/2023]
Abstract
High-salinity stress is one of the major limiting factors on crop productivity. Physiological strategies against high-salinity stress include generation of reactive oxygen species (ROS), induction of stress-related genes expression, accumulation of abscisic acid (ABA) and up-regulation of antiporters. ROS are metabolism by-products and involved in signal transduction pathway. Constitutive expression of plant ferrodoxin-like protein (PFLP) gene enhances pathogen-resistance activities and root-hair growth through promoting ROS generation. However, the function of PFLP in abiotic stress responses is unclear. In this study, PFLP-1 and PFLP-2-transgenic rice plants were generated to elucidate the role of PFLP under salinity stress. PFLP overexpression significantly increased salt tolerance in PFLP-transgenic rice plants compared with non-transgenic plants (Oryza sativa japonica cv. Tainung 67, designated as TNG67). In high-salinity conditions, PFLP-transgenic plants exhibited earlier ROS production, higher antioxidant enzyme activities, higher ABA accumulation, up-regulated expression of stress-related genes (OsRBOHa, Cu/Zn SOD, OsAPX, OsNCED2, OsSOS1, OsCIPK24, OsCBL4, and OsNHX2), and leaf sodium ion content was lower compared with TNG67 plant. In addition, transgenic lines maintained electron transport rates and contained lower malondialdhyde (MDA) content than TNG67 plant did under salt-stress conditions. Overall results indicated salinity tolerance was improved by PFLP overexpression in transgenic rice plant. The PFLP gene is a potential candidate for improving salinity tolerance for valuable agricultural crops.
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Affiliation(s)
- Hsiang-En Huang
- Department of Life Sciences, National Taitung University, Taitung, 95002, Taiwan.
| | - Mei-Hsuan Ho
- Institute of Biotechnology, National University of Kaohsiung, Kaohsiung, 81148, Taiwan.
| | - Hsiang Chang
- Department of Biotechnology and Pharmaceutical Technology, Yuanpei University of Medical Technology, Hsinchu, 30015, Taiwan.
| | - Hsien-Yu Chao
- Institute of Biotechnology, National University of Kaohsiung, Kaohsiung, 81148, Taiwan.
| | - Mang-Jye Ger
- Department of Life Sciences, National University of Kaohsiung, Kaohsiung, 81148, Taiwan.
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Zuluaga AP, Bidzinski P, Chanclud E, Ducasse A, Cayrol B, Gomez Selvaraj M, Ishitani M, Jauneau A, Deslandes L, Kroj T, Michel C, Szurek B, Koebnik R, Morel JB. The Rice DNA-Binding Protein ZBED Controls Stress Regulators and Maintains Disease Resistance After a Mild Drought. FRONTIERS IN PLANT SCIENCE 2020; 11:1265. [PMID: 33013945 PMCID: PMC7461821 DOI: 10.3389/fpls.2020.01265] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 07/31/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Identifying new sources of disease resistance and the corresponding underlying resistance mechanisms remains very challenging, particularly in Monocots. Moreover, the modification of most disease resistance pathways made so far is detrimental to tolerance to abiotic stresses such as drought. This is largely due to negative cross-talks between disease resistance and abiotic stress tolerance signaling pathways. We have previously described the role of the rice ZBED protein containing three Zn-finger BED domains in disease resistance against the fungal pathogen Magnaporthe oryzae. The molecular and biological functions of such BED domains in plant proteins remain elusive. RESULTS Using Nicotiana benthamiana as a heterologous system, we show that ZBED localizes in the nucleus, binds DNA, and triggers basal immunity. These activities require conserved cysteine residues of the Zn-finger BED domains that are involved in DNA binding. Interestingly, ZBED overexpressor rice lines show increased drought tolerance. More importantly, the disease resistance response conferred by ZBED is not compromised by drought-induced stress. CONCLUSIONS Together our data indicate that ZBED might represent a new type of transcriptional regulator playing simultaneously a positive role in both disease resistance and drought tolerance. We demonstrate that it is possible to provide disease resistance and drought resistance simultaneously.
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Affiliation(s)
- A. Paola Zuluaga
- BGPI, INRA, CIRAD, SupAgro, Univ. Montpellier, Montpellier, France
| | | | - Emilie Chanclud
- BGPI, INRA, CIRAD, SupAgro, Univ. Montpellier, Montpellier, France
| | - Aurelie Ducasse
- BGPI, INRA, CIRAD, SupAgro, Univ. Montpellier, Montpellier, France
| | - Bastien Cayrol
- BGPI, INRA, CIRAD, SupAgro, Univ. Montpellier, Montpellier, France
| | | | | | - Alain Jauneau
- Institut Fédératif de Recherche 3450, Université de Toulouse, CNRS, UPS, Plateforme Imagerie TRI-Genotoul, Castanet-Tolosan, France
| | | | - Thomas Kroj
- BGPI, INRA, CIRAD, SupAgro, Univ. Montpellier, Montpellier, France
| | - Corinne Michel
- BGPI, INRA, CIRAD, SupAgro, Univ. Montpellier, Montpellier, France
| | - Boris Szurek
- UMR Interactions Plantes-Microorganismes-Environnement (IPME), IRD-Cirad-Université Montpellier, Institut de Recherche pour le Développement, Montpellier, France
| | - Ralf Koebnik
- UMR Interactions Plantes-Microorganismes-Environnement (IPME), IRD-Cirad-Université Montpellier, Institut de Recherche pour le Développement, Montpellier, France
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34
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Kulkarni SR, Balachandran SM, Ulaganathan K, Balakrishnan D, Praveen M, Prasad ASH, Fiyaz RA, Senguttuvel P, Sinha P, Kale RR, Rekha G, Kousik MBVN, Harika G, Anila M, Punniakoti E, Dilip T, Hajira SK, Pranathi K, Das MA, Shaik M, Chaitra K, Rao PK, Gangurde SS, Pandey MK, Sundaram RM. Molecular mapping of QTLs for yield related traits in recombinant inbred line (RIL) population derived from the popular rice hybrid KRH-2 and their validation through SNP genotyping. Sci Rep 2020; 10:13695. [PMID: 32792551 PMCID: PMC7427098 DOI: 10.1038/s41598-020-70637-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 07/10/2020] [Indexed: 01/27/2023] Open
Abstract
The study was undertaken to identify the quantitative trait loci (QTLs) governing yield and its related traits using a recombinant inbred line (RIL) population derived from the popular rice hybrid, KRH-2 (IR58025A/KMR3R). A genetic map spanning 294.2 cM was constructed with 126 simple sequence repeats (SSR) loci uniformly distributed across the rice genome. QTL analysis using phenotyping and genotyping information identified a total of 22 QTLs. Of these, five major effect QTLs were identified for the following traits: total grain yield/plant (qYLD3-1), panicle weight (qPW3-1), plant height (qPH12-1), flag leaf width (qFLW4-1) and panicle length (qPL3-1), explaining 20.23–22.76% of the phenotypic variance with LOD scores range of 6.5–10.59. Few genomic regions controlling several traits (QTL hotspot) were identified on chromosome 3 for total grain yield/plant (qYLD3-1) and panicle length (qPL3-1). Significant epistatic interactions were also observed for total grain yield per plant (YLD) and panicle length (PL). While most of these QTLs were observed to be co-localized with the previously reported QTL regions, a novel, major QTL associated with panicle length (qPL3-1) was also identified. SNP genotyping of selected high and low yielding RILs and their QTL mapping with 1,082 SNPs validated most of the QTLs identified through SSR genotyping. This facilitated the identification of novel major effect QTLs with much better resolution and precision. In-silico analysis of novel QTLs revealed the biological functions of the putative candidate gene (s) associated with selected traits. Most of the high-yielding RILs possessing the major yield related QTLs were identified to be complete restorers, indicating their possible utilization in development of superior rice hybrids.
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Affiliation(s)
- Swapnil Ravindra Kulkarni
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - S M Balachandran
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India.
| | - K Ulaganathan
- Centre for Plant Molecular Biology (CPMB), Osmania University, Hyderabad, India
| | - Divya Balakrishnan
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - M Praveen
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - A S Hari Prasad
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - R A Fiyaz
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - P Senguttuvel
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - Pragya Sinha
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - Ravindra R Kale
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - G Rekha
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - M B V N Kousik
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - G Harika
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - M Anila
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - E Punniakoti
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - T Dilip
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - S K Hajira
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - K Pranathi
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - M Ayyappa Das
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - Mastanbee Shaik
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - K Chaitra
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - P Koteswara Rao
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - Sunil S Gangurde
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Manish K Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - R M Sundaram
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India.
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Sruthilaxmi CB, Babu S. Proteome Responses to Individual Pathogens and Abiotic Conditions in Rice Seedlings. PHYTOPATHOLOGY 2020; 110:1326-1341. [PMID: 32175828 DOI: 10.1094/phyto-11-19-0425-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Rice plants under field conditions experience various biotic and abiotic stresses and are adapted to survive using a molecular cross-talk of genes and their protein products based on the severity of a given stress. Seedlings of cultivated variety ASD16 (resistant to fungal disease, blast; tolerant to abiotic stress, salinity) were subjected to salt, drought, high temperature and low temperature stress as well as infection by Rhizoctonia solani and Xanthomonas oryzae pv. oryzae (causing reemerging diseases such as sheath blight and leaf blight), respectively, the sheath blight and bacterial leaf blight pathogens. Leaf proteome was analyzed using two-dimensional electrophoresis and differentially expressed proteins were identified using mass spectrometry. In addition to many other differentially expressed proteins, acidic endochitinase was found to be upregulated during fungal infection and drought treatment, and a germin-like protein upregulated during fungal infection and high temperature stress. These two proteins were further validated at the gene expression level using reverse transcription-PCR in dual stress experiments. Pot culture plants were subjected to fungal infection followed by drought and drought followed by fungal infection to validate chitinase gene expression. Similarly, plants subjected to fungal infections followed by high temperature stress and vice versa were used to validate the expression of germin-like protein-coding gene. The results of the present study indicate that chitinase and germin-like protein are potential targets for further exploration to develop rice plants resistant or tolerant to biotic and abiotic stresses.
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Affiliation(s)
| | - Subramanian Babu
- VIT School of Agricultural Innovations and Advanced Learning, Vellore Institute of Technology, Vellore 632014, India
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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 BIOLOGY 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] [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 (BASEL, SWITZERLAND) 2020; 9:E336. [PMID: 32155874 PMCID: PMC7154908 DOI: 10.3390/plants9030336] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [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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Affiliation(s)
- Qian Wei
- 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; (Q.W.); (S.W.); (C.L.); (Y.Y.)
| | - Shiyun Wen
- 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; (Q.W.); (S.W.); (C.L.); (Y.Y.)
| | - Chuying Lan
- 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; (Q.W.); (S.W.); (C.L.); (Y.Y.)
| | - Yixun Yu
- 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; (Q.W.); (S.W.); (C.L.); (Y.Y.)
| | - Guoju Chen
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
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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. ANNALS OF BOTANY 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] [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
| | - 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
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Marmisolle FE, Arizmendi A, Ribone A, Rivarola M, García ML, Reyes CA. Up-regulation of microRNA targets correlates with symptom severity in Citrus sinensis plants infected with two different isolates of citrus psorosis virus. PLANTA 2019; 251:7. [PMID: 31776669 DOI: 10.1007/s00425-019-03294-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 10/11/2019] [Indexed: 06/10/2023]
Abstract
MAIN CONCLUSION: miRNA targets from Citrus sinensis are predicted and validated using degradome data. They show an up-regulation upon infection with CPsV, with a positive correlation between target expression and symptom severity. Sweet orange (Citrus sinensis) may suffer from disease symptoms induced by virus infections, thus resulting in drastic economic losses. Infection of sweet orange plants with two isolates of citrus psorosis virus (CPsV), expressing different symptomatologies, alters the accumulation of a set of endogenous microRNAs (miRNAs). Here, we predicted ten putative targets from four down-regulated miRNAs: three belonging to the CCAAT-binding transcription factor family (CBFAs); an Ethylene-responsive transcription factor (RAP2-7); an Integrase-type DNA-binding superfamily protein (AP2B); Transport inhibitor response 1 (TIR1); GRR1-like protein 1-related (GRR1); Argonaute 2-related (AGO2), Argonaute 7 (AGO7), and a long non-coding RNA (ncRNA). We validated six of them through analysis of leaf degradome data. Expressions of the validated targets increase in infected samples compared to healthy tissue, showing a more striking up-regulation those samples with higher symptom severity. This study contributes to the understanding of the miRNA-mediated regulation of important transcripts in Citrus sinensis through target validation and shed light in the manner a virus can alter host regulatory mechanisms leading to symptom expression.
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Affiliation(s)
- Facundo E Marmisolle
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET-UNLP, Calles 47 y 115, 1900 La Plata, Buenos Aires, Argentina
| | - Ailín Arizmendi
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET-UNLP, Calles 47 y 115, 1900 La Plata, Buenos Aires, Argentina
| | - Andrés Ribone
- IABiMo, Conicet-INTA, CICVyA-INTA, Hurlingham, Buenos Aires, Argentina
| | - Máximo Rivarola
- IABiMo, Conicet-INTA, CICVyA-INTA, Hurlingham, Buenos Aires, Argentina
| | - María L García
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET-UNLP, Calles 47 y 115, 1900 La Plata, Buenos Aires, Argentina
| | - Carina A Reyes
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET-UNLP, Calles 47 y 115, 1900 La Plata, Buenos Aires, Argentina.
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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] [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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Maheshwari P, Kummari D, Palakolanu SR, Nagasai Tejaswi U, Nagaraju M, Rajasheker G, Jawahar G, Jalaja N, Rathnagiri P, Kavi Kishor PB. Genome-wide identification and expression profile analysis of nuclear factor Y family genes in Sorghum bicolor L. (Moench). PLoS One 2019; 14:e0222203. [PMID: 31536532 PMCID: PMC6752760 DOI: 10.1371/journal.pone.0222203] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 08/24/2019] [Indexed: 01/28/2023] Open
Abstract
Members of the plant Heme Activator Protein (HAP) or NUCLEAR FACTOR Y (NF-Y) are trimeric transcription factor complexes composed of the NF-YA, NF-YB and NF-YC subfamilies. They bind to the CCAAT box in the promoter regions of the target genes and regulate gene expressions. Plant NF-Ys were reported to be involved in adaptation to several abiotic stresses as well as in development. In silico analysis of Sorghum bicolor genome resulted in the identification of a total of 42 NF-Y genes, among which 8 code for the SbNF-YA, 19 for SbNF-YB and 15 for the SbNF-YC subunits. Analysis was also performed to characterize gene structures, chromosomal distribution, duplication status, protein subcellular localizations, conserved motifs, ancestral protein sequences, miRNAs and phylogenetic tree construction. Phylogenetic relationships and ortholog predictions displayed that sorghum has additional NF-YB genes with unknown functions in comparison with Arabidopsis. Analysis of promoters revealed that they harbour many stress-related cis-elements like ABRE and HSE, but surprisingly, DRE and MYB elements were not detected in any of the subfamilies. SbNF-YA1, 2, and 6 were found upregulated under 200 mM salt and 200 mM mannitol stresses. While NF-YA7 appeared associated with high temperature (40°C) stress, NF-YA8 was triggered by both cold (4°C) and high temperature stresses. Among NF-YB genes, 7, 12, 15, and 16 were induced under multiple stress conditions such as salt, mannitol, ABA, cold and high temperatures. Likewise, NF-YC 6, 11, 12, 14, and 15 were enhanced significantly in a tissue specific manner under multiple abiotic stress conditions. Majority of the mannitol (drought)-inducible genes were also induced by salt, high temperature stresses and ABA. Few of the high temperature stress-induced genes are also induced by cold stress (NF-YA2, 4, 6, 8, NF-YB2, 7, 10, 11, 12, 14, 16, 17, NF-YC4, 6, 12, and 13) thus suggesting a cross talk among them. This work paves the way for investigating the roles of diverse sorghum NF-Y proteins during abiotic stress responses and provides an insight into the evolution of diverse NF-Y members.
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Affiliation(s)
- P. Maheshwari
- Department of Genetics, Osmania University, Hyderabad, India
| | - Divya Kummari
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
| | - Sudhakar Reddy Palakolanu
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
| | - U. Nagasai Tejaswi
- Department of Biotechnology, Vignan’s Foundation for Science, Technology and Research, Vadlamudi, Guntur, Andhra Pradesh, India
| | - M. Nagaraju
- Department of Genetics, Osmania University, Hyderabad, India
- Department of Biochemistry, ICMR-National Institute of Nutrition, Hyderabad, India
| | - G. Rajasheker
- Department of Genetics, Osmania University, Hyderabad, India
| | - G. Jawahar
- Department of Genetics, Osmania University, Hyderabad, India
| | - N. Jalaja
- Department of Biotechnology, Vignan’s Foundation for Science, Technology and Research, Vadlamudi, Guntur, Andhra Pradesh, India
| | - P. Rathnagiri
- Genomix CARL Pvt. Ltd. Rayalapuram Road, Pulivendula, Kadapa, Andhra Pradesh, India
- Genomix Molecular Diagnostics Pvt Ltd., Kukatpally, Hyderabad, India
- Genomix Biotech Inc., Atlanta, GA, United States of America
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Li Y, Duan T, Nan Z, Li Y. Arbuscular mycorrhizal fungus alleviates alfalfa leaf spots caused by Phoma medicaginis revealed by RNA-seq analysis. J Appl Microbiol 2019; 130:547-560. [PMID: 31310670 DOI: 10.1111/jam.14387] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 06/28/2019] [Accepted: 07/11/2019] [Indexed: 01/10/2023]
Abstract
AIMS One of the major limitations to the production of alfalfa (Medicago sativa) is the fungus Phoma medicaginis, which infects alfalfa and causes leaf spots. This study aims to understand alfalfa's response to P. medicaginis infection, the colonization of arbuscular mycorrhizal fungus (AMF) and the effect of AMF on plant-pathogen interactions. METHODS AND RESULTS Transcriptome analysis (RNA-seq) was used to identify differentially expressed genes (DEGs) in alfalfa infected by P. medicaginis and colonized by AMF Rhizophagus intraradices. AMF ameliorated the effects of P. medicaginis infection on alfalfa by reducing leaf spot incidence and disease index by 39·48 and 56·18% respectively. Inoculation with pathogen and AMF induced the activity of defence pathways, including peroxidase (POD), polyphenol oxidase activities and jasmonic acid (JA), salicylic acid concentration. Plants showed differential expression of P. medicaginis resistance-related genes, including genes belonging to pathogenesis-related (PR) proteins, chitinase activity, flavonoid biosynthesis, phenylpropanoid biosynthesis, glutathione metabolism, phenylalanine metabolism and photosynthesis. Inoculation with AMF led to changes in the expression of genes involved in PR proteins, chitinase activity, phenylalanine metabolism and photosynthesis. CONCLUSION The physiological and transcriptional changes caused by P. medicaginis infection in non-mycorrhizal and mycorrhizal alfalfa provides crucial information for understanding AMF's association with pathogenic systems. SIGNIFICANCE AND IMPACT OF THE STUDY This study showed that AMF alleviated alfalfa leaf spots demonstrating that AMF can serve as a biocontrol strategy for alfalfa disease management.
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Affiliation(s)
- Y Li
- State Key Laboratory of Grassland Agro-Ecosystems Lanzhou Unviersity, Lanzhou, China.,Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou University, Lanzhou, China.,College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - T Duan
- State Key Laboratory of Grassland Agro-Ecosystems Lanzhou Unviersity, Lanzhou, China.,Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou University, Lanzhou, China.,College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Z Nan
- State Key Laboratory of Grassland Agro-Ecosystems Lanzhou Unviersity, Lanzhou, China.,Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou University, Lanzhou, China.,College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Y Li
- State Key Laboratory of Grassland Agro-Ecosystems Lanzhou Unviersity, Lanzhou, China.,Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou University, Lanzhou, China.,College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
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Jiang S, Wang D, Yan S, Liu S, Liu B, Kang H, Wang GL. Dissection of the Genetic Architecture of Rice Tillering using a Genome-wide Association Study. RICE (NEW YORK, N.Y.) 2019; 12:43. [PMID: 31222528 PMCID: PMC6586736 DOI: 10.1186/s12284-019-0302-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 05/27/2019] [Indexed: 05/25/2023]
Abstract
BACKGROUND Rice tiller number (TN) is one of the most important components associated with rice grain yield. Around one hundred rice TN genes have been identified, but dissecting the genetic architecture of rice TN variations remains difficult because of its complex trait and control by both major genes and quantitative trait loci (QTLs). RESULTS In this study, we used a subset of the rice diversity population II (S-RDP-II), genotyped with 700,000 single nucleotide polymorphisms (SNPs), to identify the loci associated with tiller number variations (LATNs) through a genome-wide association study (GWAS). The analysis revealed that 23 LATNs are significantly associated with TN variations. Among the 23 LATNs, eight are co-localized with previously cloned TN genes, and the remaining 15 LATNs are novel. DNA sequence analysis of the 15 novel LATNs led to the identification of five candidate genes using the accessions with extreme TN phenotypes. Genetic variations in two of the genes are mainly located in the promoter regions. qRT-PCR analysis showed that the expression levels of these two genes are also closely associated with TN variations. CONCLUSIONS We identified 15 novel LATNs that contribute significantly to the genetic variation of rice TN. Of these 15, the five identified TN-associated candidate genes will enhance our understanding of rice tillering and can be used as molecular markers for improving rice yield.
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Affiliation(s)
- Su Jiang
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pest, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Dan Wang
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Shuangyong Yan
- Tian Jin Key Laboratory of crop genetic breeding, Tianjin Crop Research Institute, Tianjin Academy of Agriculture Sciences, Tianjin, 300112, China
| | - Shiming Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pest, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Bin Liu
- Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Houxiang Kang
- State Key Laboratory for Biology of Plant Diseases and Insect Pest, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Guo-Liang Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pest, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
- Department of Plant Pathology, Ohio State University, Columbus, OH, 43210, USA.
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Mohammed S, Samad AA, Rahmat Z. Agrobacterium-Mediated Transformation of Rice: Constraints and Possible Solutions. RICE SCIENCE 2019; 26:133-146. [DOI: 10.1016/j.rsci.2019.04.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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Li N, Zheng H, Cui J, Wang J, Liu H, Sun J, Liu T, Zhao H, Lai Y, Zou D. Genome-wide association study and candidate gene analysis of alkalinity tolerance in japonica rice germplasm at the seedling stage. RICE (NEW YORK, N.Y.) 2019; 12:24. [PMID: 30976929 PMCID: PMC6459459 DOI: 10.1186/s12284-019-0285-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 04/02/2019] [Indexed: 05/22/2023]
Abstract
BACKGROUND Salinity-alkalinity stress is one of the major factors limiting rice production. The damage caused by alkaline salt stress to rice growth is more severe than that caused by neutral salt stress. At present, the genetic resources (quantitative trait loci (QTLs) and genes) that can be used by rice breeders to improve alkalinity tolerance are limited. Here, we assessed the alkalinity tolerance of rice at the seedling stage and performed a genome-wide association study (GWAS) based on genotypic data including 788,396 single-nucleotide polymorphisms (SNPs) developed by re-sequencing 295 japonica rice varieties. RESULTS We used the score of alkalinity tolerance (SAT), the concentrations of Na+ and K+ in the shoots (SNC and SKC, respectively) and the Na+/K+ ratio of shoots (SNK) as indices to assess alkalinity tolerance at the seedling stage in rice. Based on population structure analysis, the japonica rice panel was divided into three subgroups. Linkage disequilibrium (LD) analysis showed that LD decay occurred at 109.77 kb for the whole genome and varied between 13.79 kb and 415.77 kb across the 12 chromosomes, at which point the pairwise squared correlation coefficient (r2) decreased to half of its maximum value. A total of eight QTLs significantly associated with the SAT, SNC and SNK were identified by genome-wide association mapping. A common QTL associated with the SAT, SNC and SNK on chromosome 3 at the position of 15.0 Mb, which explaining 13.36~13.64% of phenotypic variation, was selected for further analysis. The candidate genes were filtered based on LD decay, Gene Ontology (GO) enrichment, RNA sequencing data, and quantitative real-time PCR (qRT-PCR) analysis. Moreover, sequence analysis revealed one 7-bp insertion/deletion (indel) difference in LOC_Os03g26210 (OsIRO3) between the alkalinity-tolerant and alkalinity-sensitive rice varieties. OsIRO3 encodes a bHLH-type transcription factor and has been shown to be a negative regulator of the Fe-deficiency response in rice. CONCLUSION Based on these results, OsIRO3 maybe a novel functional gene associated with alkalinity tolerance in japonica rice. This study provides resources for improving alkalinity tolerance in rice, and the functional molecular marker could be verified to breed new rice varieties with alkalinity tolerance via marker-assisted selection (MAS).
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Affiliation(s)
- Ning Li
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Hongliang Zheng
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
- Heilongjiang Academy of Agricultural Sciences Postdoctoral Programme, Harbin, 150030, China
| | - Jingnan Cui
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Jingguo Wang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Hualong Liu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Jian Sun
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Tongtong Liu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Hongwei Zhao
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Yongcai Lai
- Heilongjiang Academy of Agricultural Sciences Postdoctoral Programme, Harbin, 150030, China
| | - Detang Zou
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China.
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Dubey H, Kiran K, Jaswal R, Jain P, Kayastha AM, Bhardwaj SC, Mondal TK, Sharma TR. Discovery and profiling of small RNAs from Puccinia triticina by deep sequencing and identification of their potential targets in wheat. Funct Integr Genomics 2019; 19:391-407. [PMID: 30618015 DOI: 10.1007/s10142-018-00652-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 11/30/2018] [Accepted: 12/18/2018] [Indexed: 12/18/2022]
Abstract
Cross-kingdom RNAi is a well-documented phenomenon where sRNAs generated by host and pathogens may govern resistance or susceptible phenotypes during host-pathogen interaction. With the first example of the direct involvement of fungal generated sRNAs in virulence of plant pathogenic fungi Botrytis cinerea and recently from Puccinia striiformis f. sp. tritici, we attempted to identify sRNAs in Puccinia triticina (P. triticina). Four sRNA libraries were prepared and sequenced using Illumina sequencing technology and a total of ~ 1-1.28 million potential sRNAs and two microRNA-like small RNA (mil-RNAs) candidates were identified. Computational prediction of targets using a common set of sRNAs and P. triticina mil-RNAs (pt-mil-RNAs) within P. triticina and wheat revealed the majority of the targets as repetitive elements in P. triticina whereas in wheat, the target genes were identified to be involved in many biological processes including defense-related pathways. We found 9 receptor-like kinases (RLKs) and 14 target genes of each related to reactive oxygen species (ROS) pathway and transcription factors respectively, including significant numbers of target genes from various other categories. Expression analysis of twenty selected sRNAs, targeting host genes pertaining to ROS related, disease resistance, metabolic processes, transporter, apoptotic inhibitor, and transcription factors along with two pt-mil-RNAs by qRT-PCR showed distinct patterns of expression of the sRNAs in urediniospore-specific libraries. In this study, for the first time, we report identification of novel sRNAs identified in P. triticina including two pt-mil-RNAs that may play an important role in biotrophic growth and pathogenicity.
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Affiliation(s)
- Himanshu Dubey
- ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012, India.,School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Kanti Kiran
- ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Rajdeep Jaswal
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, 160071, India
| | - Priyanka Jain
- ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Arvind M Kayastha
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Subhash C Bhardwaj
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Flowerdale, Shimla, 171009, India
| | - Tapan Kumar Mondal
- ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Tilak Raj Sharma
- ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012, India. .,National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, 160071, India.
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Yadav SK, Khatri K, Rathore MS, Jha B. Introgression of UfCyt c 6, a thylakoid lumen protein from a green seaweed Ulva fasciata Delile enhanced photosynthesis and growth in tobacco. Mol Biol Rep 2018; 45:1745-1758. [PMID: 30159639 DOI: 10.1007/s11033-018-4318-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 08/16/2018] [Indexed: 01/02/2023]
Abstract
Cytochromes are important components of photosynthetic electron transport chain. Here we report on genetic transformation of Cytochrome c6 (UfCyt c6) gene from Ulva fasciata Delile in tobacco for enhanced photosynthesis and growth. UfCyt c6 cDNA had an open reading frame of 330 bp encoding a polypeptide of 109 amino acids with a predicted molecular mass of 11.65 kDa and an isoelectric point of 5.21. UfCyt c6 gene along with a tobacco petE transit peptide sequence under control of CaMV35S promoter was transformed in tobacco through Agrobacterium mediated genetic transformation. Transgenic tobacco grew normal and exhibited enhanced growth as compared to wild type (WT) and vector control (VC) tobacco. Transgenic tobacco had higher contents of photosynthetic pigments and better ratios of photosynthetic pigments. The tobacco expressing UfCyt c6 gene exhibited higher photosynthetic rate and improved water use efficiency. Further activity of the water-splitting complex, photosystem II quantum yield, photochemical quenching, electron transfer rate, and photosynthetic yield were found comparatively higher in transgenic tobacco as compared to WT and VC tobacco. Alternatively basal quantum yield of non-photochemical processes in PSII and non-photochemical quenching were estimated lower in tobacco expressing UfCyt c6 gene. As a result of improved photosynthetic performance the transgenic tobacco had higher contents of sugar and starch, and exhibited comparatively better growth. To the best of our knowledge this is the first report on expression of UfCyt c6 gene from U. fasciata for improved photosynthesis and growth in tobacco.
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Affiliation(s)
- Sweta K Yadav
- Academy of Scientific and Innovative Research, CSIR, New Delhi, India
| | - Kusum Khatri
- Academy of Scientific and Innovative Research, CSIR, New Delhi, India
| | - Mangal S Rathore
- Academy of Scientific and Innovative Research, CSIR, New Delhi, India.
- Division of Biotechnology and Phycology, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), G.B. Marg, Bhavnagar, Gujarat, 364002, India.
| | - Bhavanath Jha
- Academy of Scientific and Innovative Research, CSIR, New Delhi, India.
- Division of Biotechnology and Phycology, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), G.B. Marg, Bhavnagar, Gujarat, 364002, India.
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Quan S, Niu J, Zhou L, Xu H, Ma L, Qin Y. Identification and characterization of NF-Y gene family in walnut (Juglans regia L.). BMC PLANT BIOLOGY 2018; 18:255. [PMID: 30352551 PMCID: PMC6199752 DOI: 10.1186/s12870-018-1459-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 10/03/2018] [Indexed: 05/19/2023]
Abstract
BACKGROUND The eukaryotic transcription factor NF-Y (which consists of NF-YA, NF-YB and NF-YC subunits) is involved in many important plant development processes. There are many reports about the NF-Y family in Arabidopsis and other plant species. However, there are no reports about the NF-Y family in walnut (Juglans regia L.). RESULTS Thirty-three walnut NF-Y genes (JrNF-Ys) were identified and mapped on the walnut genome. The JrNF-Y gene family consisted of 17 NF-YA genes, 9 NF-YB genes, and 7 NF-YC genes. The structural features of the JrNF-Y genes were investigated by comparing their evolutionary relationship and motif distributions. The comparisons indicated the NF-Y gene structure was both conserved and altered during evolution. Functional prediction and protein interaction analysis were performed by comparing the JrNF-Y protein structure with that in Arabidopsis. Two differentially expressed JrNF-Y genes were identified. Their expression was compared with that of three JrCOs and two JrFTs using quantitative real-time PCR (qPCR). The results revealed that the expression of JrCO2 was positively correlated with the expression of JrNF-YA11 and JrNF-YA12. In contrast, JrNF-CO1 and JrNF-YA12 were negatively correlated. CONCLUSIONS Thirty-three JrNF-Ys were identified and their evolutionary, structure, biological function and expression pattern were analyzed. Two of the JrNF-Ys were screened out, their expression was differentially expressed in different development periods of female flower buds, and in different tissues (female flower buds and leaf buds). Based on prediction and experimental data, JrNF-Ys may be involved in flowering regulation by co-regulate the expression of flowering genes with other transcription factors (TFs). The results of this study may make contribution to the further investigation of JrNF-Y family.
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Affiliation(s)
- Shaowen Quan
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, Xinjiang, 832003 China
- Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi, Xinjiang, 832003 China
| | - Jianxin Niu
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, Xinjiang, 832003 China
- Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi, Xinjiang, 832003 China
| | - Li Zhou
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, Xinjiang, 832003 China
- Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi, Xinjiang, 832003 China
| | - Hang Xu
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, Xinjiang, 832003 China
- Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi, Xinjiang, 832003 China
| | - Li Ma
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, Xinjiang, 832003 China
- Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi, Xinjiang, 832003 China
| | - Yang Qin
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, Xinjiang, 832003 China
- Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi, Xinjiang, 832003 China
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Myers ZA, Holt BF. NUCLEAR FACTOR-Y: still complex after all these years? CURRENT OPINION IN PLANT BIOLOGY 2018; 45:96-102. [PMID: 29902675 DOI: 10.1016/j.pbi.2018.05.015] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 04/11/2018] [Accepted: 05/22/2018] [Indexed: 06/08/2023]
Abstract
The NUCLEAR FACTOR-Y (NF-Y) families of transcription factors are important regulators of plant development and physiology. Though NF-Y regulatory roles have recently been suggested for numerous aspects of plant biology, their roles in flowering time, early seedling development, stress responses, hormone signaling, and nodulation are the best characterized. The past few years have also seen significant advances in our understanding of the mechanistic function of the NF-Y, and as such, increasingly complex and interesting questions are now more approachable. This review will primarily focus on these developmental, physiological, and mechanistic roles of the NF-Y in recent research.
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Affiliation(s)
- Zachary A Myers
- University of Oklahoma, Department of Microbiology and Plant Biology, 770 Van Vleet Oval, Norman, OK 73019, United States.
| | - Ben F Holt
- University of Oklahoma, Department of Microbiology and Plant Biology, 770 Van Vleet Oval, Norman, OK 73019, United States.
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50
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Zotova L, Kurishbayev A, Jatayev S, Khassanova G, Zhubatkanov A, Serikbay D, Sereda S, Sereda T, Shvidchenko V, Lopato S, Jenkins C, Soole K, Langridge P, Shavrukov Y. Genes Encoding Transcription Factors TaDREB5 and TaNFYC-A7 Are Differentially Expressed in Leaves of Bread Wheat in Response to Drought, Dehydration and ABA. FRONTIERS IN PLANT SCIENCE 2018; 9:1441. [PMID: 30319682 PMCID: PMC6171087 DOI: 10.3389/fpls.2018.01441] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 09/10/2018] [Indexed: 05/18/2023]
Abstract
Two groups of six spring bread wheat varieties with either high or low grain yield under the dry conditions of Central and Northern Kazakhstan were selected for analysis. Experiments were set up with the selected wheat varieties in controlled environments as follows: (1) slowly progressing drought imposed on plants in soil, (2) rapid dehydration of whole plants grown in hydroponics, (3) dehydration of detached leaves, and (4) ABA treatment of whole plants grown in hydroponics. Representatives of two different families of transcription factors (TFs), TaDREB5 and TaNFYC-A7, were found to be linked to yield-under-drought using polymorphic Amplifluor-like SNP marker assays. qRT-PCR revealed differing patterns of expression of these genes in the leaves of plants subjected to the above treatments. Under drought, TaDREB5 was significantly up-regulated in leaves of all high-yielding varieties tested and down-regulated in all low-yielding varieties, and the level of expression was independent of treatment type. In contrast, TaNFYC-A7 expression levels showed different responses in the high- and low-yield groups of wheat varieties. TaNFYC-A7 expression under dehydration (treatments 2 and 3) was higher than under drought (treatment 1) in all high-yielding varieties tested, while in all low-yielding varieties the opposite pattern was observed: the expression levels of this gene under drought were higher than under dehydration. Rapid dehydration of detached leaves and intact wheat plants grown in hydroponics produced similar changes in gene expression. ABA treatment of whole plants caused rapid stomatal closure and a rise in the transcript level of both genes during the first 30 min, which decreased 6 h after treatment. At this time-point, expression of TaNFYC-A7 was again significantly up-regulated compared to untreated controls, while TaDREB5 returned to its initial level of expression. These findings reveal significant differences in the transcriptional regulation of two drought-responsive and ABA-dependent TFs under slowly developing drought and rapid dehydration of wheat plants. The results obtained suggest that correlation between grain yield in dry conditions and TaNFYC-A7 expression levels in the examined wheat varieties is dependent on the length of drought development and/or strength of drought; while in the case of TaDREB5, no such dependence is observed.
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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
| | - Gulmira Khassanova
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan
| | - Askar Zhubatkanov
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan
| | - Dauren Serikbay
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan
| | - Sergey Sereda
- Karaganda Research Institute of Plant Industry and Breeding, Karaganda, Kazakhstan
| | - Tatiana Sereda
- Karaganda Research Institute of Plant Industry and Breeding, Karaganda, Kazakhstan
| | - Vladimir Shvidchenko
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan
| | - Sergiy Lopato
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, Australia
| | - Colin Jenkins
- College of Science and Engineering, Biological Sciences, Flinders University, Bedford Park, SA, Australia
| | - Kathleen Soole
- College of Science and Engineering, Biological Sciences, Flinders University, Bedford Park, SA, Australia
| | - Peter Langridge
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, Australia
| | - Yuri Shavrukov
- College of Science and Engineering, Biological Sciences, Flinders University, Bedford Park, SA, Australia
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