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Yuan X, Jiang X, Zhang M, Wang L, Jiao W, Chen H, Mao J, Ye W, Song Q. Integrative omics analysis elucidates the genetic basis underlying seed weight and oil content in soybean. THE PLANT CELL 2024; 36:2160-2175. [PMID: 38412459 PMCID: PMC11132872 DOI: 10.1093/plcell/koae062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 01/29/2024] [Accepted: 02/22/2024] [Indexed: 02/29/2024]
Abstract
Synergistic optimization of key agronomic traits by traditional breeding has dramatically enhanced crop productivity in the past decades. However, the genetic basis underlying coordinated regulation of yield- and quality-related traits remains poorly understood. Here, we dissected the genetic architectures of seed weight and oil content by combining genome-wide association studies (GWAS) and transcriptome-wide association studies (TWAS) using 421 soybean (Glycine max) accessions. We identified 26 and 33 genetic loci significantly associated with seed weight and oil content by GWAS, respectively, and detected 5,276 expression quantitative trait loci (eQTLs) regulating expression of 3,347 genes based on population transcriptomes. Interestingly, a gene module (IC79), regulated by two eQTL hotspots, exhibited significant correlation with both seed weigh and oil content. Twenty-two candidate causal genes for seed traits were further prioritized by TWAS, including Regulator of Weight and Oil of Seed 1 (GmRWOS1), which encodes a sodium pump protein. GmRWOS1 was verified to pleiotropically regulate seed weight and oil content by gene knockout and overexpression. Notably, allelic variations of GmRWOS1 were strongly selected during domestication of soybean. This study uncovers the genetic basis and network underlying regulation of seed weight and oil content in soybean and provides a valuable resource for improving soybean yield and quality by molecular breeding.
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Affiliation(s)
- Xiaobo Yuan
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu 210095, China
| | - Xinyu Jiang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu 210095, China
| | - Mengzhu Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu 210095, China
| | - Longfei Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu 210095, China
| | - Wu Jiao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu 210095, China
| | - Huatao Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, No. 50 Zhongling, Nanjing, Jiangsu 210014, China
| | - Junrong Mao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu 210095, China
| | - Wenxue Ye
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu 210095, China
| | - Qingxin Song
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu 210095, China
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Yu G, Chen D, Ye M, Wu X, Zhu Z, Shen Y, Mehareb EM, Esh A, Raza G, Wang K, Wang Q, Jin JB. H3K27 demethylase SsJMJ4 negatively regulates drought-stress responses in sugarcane. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:3040-3053. [PMID: 38310636 DOI: 10.1093/jxb/erae037] [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: 11/29/2023] [Accepted: 02/02/2024] [Indexed: 02/06/2024]
Abstract
Sugarcane (Saccharum spp.), a leading sugar and energy crop, is seriously impacted by drought stress. However, the molecular mechanisms underlying sugarcane drought resistance, especially the functions of epigenetic regulators, remain elusive. Here, we show that a S. spontaneum KDM4/JHDM3 group JmjC protein, SsJMJ4, negatively regulates drought-stress responses through its H3K27me3 demethylase activity. Ectopic overexpression of SsJMJ4 in Arabidopsis reduced drought resistance possibly by promoting expression of AtWRKY54 and AtWRKY70, encoding two negative regulators of drought stress. SsJMJ4 directly bound to AtWRKY54 and AtWRKY70, and reduced H3K27me3 levels at these loci to ensure their proper transcription under normal conditions. Drought stress down-regulated both transcription and protein abundance of SsJMJ4, which was correlated with the reduced occupancy of SsJMJ4 at AtWRKY54 and AtWRKY70 chromatin, increased H3K27me3 levels at these loci, as well as reduced transcription levels of these genes. In S. spontaneum, drought stress-repressed transcription of SsWRKY122, an ortholog of AtWRKY54 and AtWRKY70, was associated with increased H3K27me3 levels at these loci. Transient overexpression of SsJMJ4 in S. spontaneum protoplasts raised transcription of SsWRKY122, paralleled with reduced H3K27me3 levels at its loci. These results suggest that the SsJMJ4-mediated dynamic deposition of H3K27me3 is required for an appropriate response to drought stress.
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Affiliation(s)
- Guangrun Yu
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
- School of Life Sciences, Nantong University, Nantong 226019, China
| | - Daoqian Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Meiling Ye
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Xiaoge Wu
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Zhiying Zhu
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Yan Shen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Eid M Mehareb
- Sugar Crops Research Institute, Agricultural Research Center, Giza 12619, Egypt
| | - Ayman Esh
- Sugar Crops Research Institute, Agricultural Research Center, Giza 12619, Egypt
| | - Ghulam Raza
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, 38000, Pakistan
| | - Kai Wang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
- School of Life Sciences, Nantong University, Nantong 226019, China
| | - Qiongli Wang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Jing Bo Jin
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
- Academician Workstation of Agricultural High-tech Industrial Area of the Yellow River Delta, National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Dongying, Shandong, China
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3
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Wang F, Miao H, Zhang S, Hu X, Chu Y, Yang W, Wang H, Wang J, Shan S, Chen J. Weighted gene co-expression network analysis reveals hub genes regulating response to salt stress in peanut. BMC PLANT BIOLOGY 2024; 24:425. [PMID: 38769518 PMCID: PMC11103959 DOI: 10.1186/s12870-024-05145-x] [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: 03/26/2024] [Accepted: 05/13/2024] [Indexed: 05/22/2024]
Abstract
Peanut (Arachis hypogaea L.) is an important oilseed crop worldwide. However, soil salinization becomes one of the main limiting factors of peanut production. Therefore, developing salt-tolerant varieties and understanding the molecular mechanisms of salt tolerance is important to protect peanut yield in saline areas. In this study, we selected four peanut varieties with contrasting response to salt challenges with T1 and T2 being tolerance and S1 and S2 being susceptible. High-throughput RNA sequencing resulted in more than 314.63 Gb of clean data from 48 samples. We identified 12,057 new genes, 7,971of which have functional annotations. KEGG pathway enrichment analysis of uniquely expressed genes in salt-tolerant peanut revealed that upregulated genes in the root are involved in the MAPK signaling pathway, fatty acid degradation, glycolysis/gluconeogenesis, and upregulated genes in the shoot were involved in plant hormone signal transduction and the MAPK signaling pathway. Na+ content, K+ content, K+/ Na+, and dry mass were measured in root and shoot tissues, and two gene co-expression networks were constructed based on weighted gene co-expression network analysis (WGCNA) in root and shoot. In this study, four key modules that are highly related to peanut salt tolerance in root and shoot were identified, plant hormone signal transduction, phenylpropanoid biosynthesis, starch and sucrose metabolism, flavonoid biosynthesis, carbon metabolism were identified as the key biological processes and metabolic pathways for improving peanut salt tolerance. The hub genes include genes encoding ion transport (such as HAK8, CNGCs, NHX, NCL1) protein, aquaporin protein, CIPK11 (CBL-interacting serine/threonine-protein kinase 11), LEA5 (late embryogenesis abundant protein), POD3 (peroxidase 3), transcription factor, and MAPKKK3. There were some new salt-tolerant genes identified in peanut, including cytochrome P450, vinorine synthase, sugar transport protein 13, NPF 4.5, IAA14, zinc finger CCCH domain-containing protein 62, beta-amylase, fatty acyl-CoA reductase 3, MLO-like protein 6, G-type lectin S-receptor-like serine/threonine-protein kinase, and kinesin-like protein KIN-7B. The identification of key modules, biological pathways, and hub genes in this study enhances our understanding of the molecular mechanisms underlying salt tolerance in peanuts. This knowledge lays a theoretical foundation for improving and innovating salt-tolerant peanut germplasm.
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Affiliation(s)
- Feifei Wang
- Shandong Peanut Research Institute, Qingdao, 266100, People's Republic of China
| | - Huarong Miao
- Shandong Peanut Research Institute, Qingdao, 266100, People's Republic of China
| | - Shengzhong Zhang
- Shandong Peanut Research Institute, Qingdao, 266100, People's Republic of China
| | - Xiaohui Hu
- Shandong Peanut Research Institute, Qingdao, 266100, People's Republic of China
| | - Ye Chu
- Department of Horticulture, University of Georgia Tifton Campus, Tifton, GA, 31793, USA
| | - Weiqiang Yang
- Shandong Peanut Research Institute, Qingdao, 266100, People's Republic of China
| | - Heng Wang
- Agricultural Technical Service Center, Rizhao, 276700, Shandong, China
| | - Jingshan Wang
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, People's Republic of China
| | - Shihua Shan
- Shandong Peanut Research Institute, Qingdao, 266100, People's Republic of China
| | - Jing Chen
- Shandong Peanut Research Institute, Qingdao, 266100, People's Republic of China.
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Zhang Y, Wu X, Wang X, Dai M, Peng Y. Crop root system architecture in drought response. J Genet Genomics 2024:S1673-8527(24)00100-0. [PMID: 38723744 DOI: 10.1016/j.jgg.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 04/26/2024] [Accepted: 05/01/2024] [Indexed: 07/27/2024]
Abstract
Drought is a natural disaster that profoundly impacts on global agricultural production, significantly reduces crop yields, and thereby poses a severe threat to worldwide food security. Addressing the challenge of effectively improving crop drought resistance (DR) to mitigate yield loss under drought conditions is a global issue. An optimal root system architecture (RSA) plays a pivotal role in enhancing crops' capacity to efficiently uptake water and nutrients, which consequently strengthens their resilience against environmental stresses. In this review, we discuss the compositions and roles of crop RSA and summarize the most recent developments in augmenting drought tolerance in crops by manipulating RSA-related genes. Based on the current research, we propose the potential optimal RSA configuration that could be helpful in enhancing crop DR. Lastly, we discussed the existing challenges and future directions for breeding crops with enhanced DR capabilities through genetic improvements targeting RSA.
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Affiliation(s)
- Yanjun Zhang
- College of Agronomy, Gansu Agricultural University, Lanzhou, Gansu 730070, China; State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, Gansu 730070, China; Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu 730070, China; Key Laboratory of Crop Gene Resources and Germplasm Innovation in Northwest Cold and Arid Regions, Ministry of Agriculture and Rural Affairs, Lanzhou, Gansu 730070, China
| | - Xi Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Wuhan, HuBei 430070, China
| | - Xingrong Wang
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu 730070, China; Key Laboratory of Crop Gene Resources and Germplasm Innovation in Northwest Cold and Arid Regions, Ministry of Agriculture and Rural Affairs, Lanzhou, Gansu 730070, China
| | - Mingqiu Dai
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Wuhan, HuBei 430070, China.
| | - Yunling Peng
- College of Agronomy, Gansu Agricultural University, Lanzhou, Gansu 730070, China; State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, Gansu 730070, China.
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Wang X, Li X, Zhao W, Hou X, Dong S. Current views of drought research: experimental methods, adaptation mechanisms and regulatory strategies. FRONTIERS IN PLANT SCIENCE 2024; 15:1371895. [PMID: 38638344 PMCID: PMC11024477 DOI: 10.3389/fpls.2024.1371895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 03/20/2024] [Indexed: 04/20/2024]
Abstract
Drought stress is one of the most important abiotic stresses which causes many yield losses every year. This paper presents a comprehensive review of recent advances in international drought research. First, the main types of drought stress and the commonly used drought stress methods in the current experiment were introduced, and the advantages and disadvantages of each method were evaluated. Second, the response of plants to drought stress was reviewed from the aspects of morphology, physiology, biochemistry and molecular progression. Then, the potential methods to improve drought resistance and recent emerging technologies were introduced. Finally, the current research dilemma and future development direction were summarized. In summary, this review provides insights into drought stress research from different perspectives and provides a theoretical reference for scholars engaged in and about to engage in drought research.
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Affiliation(s)
- Xiyue Wang
- College of Agriculture, Northeast Agricultural University, Heilongjiang, Harbin, China
| | - Xiaomei Li
- College of Agriculture, Heilongjiang Agricultural Engineering Vocational College, Heilongjiang, Harbin, China
| | - Wei Zhao
- College of Agriculture, Northeast Agricultural University, Heilongjiang, Harbin, China
| | - Xiaomin Hou
- Millet Research Institute, Qiqihar Sub-Academy of Heilongjiang Academy of Agricultural Sciences, Heilongjiang, Qiqihar, China
| | - Shoukun Dong
- College of Agriculture, Northeast Agricultural University, Heilongjiang, Harbin, China
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6
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Tang H, Yuan C, Shi H, Liu F, Shan S, Wang Z, Sun Q, Sun J. Genome-Wide Identification of Peanut B-Boxs and Functional Characterization of AhBBX6 in Salt and Drought Stresses. PLANTS (BASEL, SWITZERLAND) 2024; 13:955. [PMID: 38611484 PMCID: PMC11013918 DOI: 10.3390/plants13070955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 03/19/2024] [Accepted: 03/22/2024] [Indexed: 04/14/2024]
Abstract
The B-box (BBX) gene family includes zinc finger protein transcription factors that regulate a multitude of physiological and developmental processes in plants. While BBX gene families have been previously determined in various plants, the members and roles of peanut BBXs are largely unknown. In this research, on the basis of the genome-wide identification of BBXs in three peanut species (Arachis hypogaea, A. duranensis, and A. ipaensis), we investigated the expression profile of the BBXs in various tissues and in response to salt and drought stresses and selected AhBBX6 for functional characterization. We identified a total of 77 BBXs in peanuts, which could be grouped into five subfamilies, with the genes from the same branch of the same subgroup having comparable exon-intron structures. In addition, a significant number of cis-regulatory elements involved in the regulation of responses to light and hormones and abiotic stresses were found in the promoter region of peanut BBXs. Based on the analysis of transcriptome data and qRT-PCR, we identified AhBBX6, AhBBX11, AhBBX13, and AhBBX38 as potential genes associated with tolerance to salt and drought. Silencing AhBBX6 using virus-induced gene silencing compromised the tolerance of peanut plants to salt and drought stresses. The results of this study provide knowledge on peanut BBXs and establish a foundation for future research into their functional roles in peanut development and stress response.
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Affiliation(s)
- Haohong Tang
- Key Laboratory of Oasis Eco-Agriculture, College of Agriculture, Shihezi University, Shihezi 832000, China; (H.T.); (H.S.); (F.L.)
| | - Cuiling Yuan
- Shandong Peanut Research Institute, Qingdao 266100, China; (C.Y.); (S.S.)
| | - Haonan Shi
- Key Laboratory of Oasis Eco-Agriculture, College of Agriculture, Shihezi University, Shihezi 832000, China; (H.T.); (H.S.); (F.L.)
| | - Feng Liu
- Key Laboratory of Oasis Eco-Agriculture, College of Agriculture, Shihezi University, Shihezi 832000, China; (H.T.); (H.S.); (F.L.)
| | - Shihua Shan
- Shandong Peanut Research Institute, Qingdao 266100, China; (C.Y.); (S.S.)
| | - Zhijun Wang
- Biotechnology Research Institute, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi 832000, China;
| | - Quanxi Sun
- Shandong Peanut Research Institute, Qingdao 266100, China; (C.Y.); (S.S.)
| | - Jie Sun
- Key Laboratory of Oasis Eco-Agriculture, College of Agriculture, Shihezi University, Shihezi 832000, China; (H.T.); (H.S.); (F.L.)
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Liang X, Li J, Yang Y, Jiang C, Guo Y. Designing salt stress-resilient crops: Current progress and future challenges. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:303-329. [PMID: 38108117 DOI: 10.1111/jipb.13599] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 12/10/2023] [Accepted: 12/15/2023] [Indexed: 12/19/2023]
Abstract
Excess soil salinity affects large regions of land and is a major hindrance to crop production worldwide. Therefore, understanding the molecular mechanisms of plant salt tolerance has scientific importance and practical significance. In recent decades, studies have characterized hundreds of genes associated with plant responses to salt stress in different plant species. These studies have substantially advanced our molecular and genetic understanding of salt tolerance in plants and have introduced an era of molecular design breeding of salt-tolerant crops. This review summarizes our current knowledge of plant salt tolerance, emphasizing advances in elucidating the molecular mechanisms of osmotic stress tolerance, salt-ion transport and compartmentalization, oxidative stress tolerance, alkaline stress tolerance, and the trade-off between growth and salt tolerance. We also examine recent advances in understanding natural variation in the salt tolerance of crops and discuss possible strategies and challenges for designing salt stress-resilient crops. We focus on the model plant Arabidopsis (Arabidopsis thaliana) and the four most-studied crops: rice (Oryza sativa), wheat (Triticum aestivum), maize (Zea mays), and soybean (Glycine max).
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Affiliation(s)
- Xiaoyan Liang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
| | - Jianfang Li
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100194, China
| | - Yongqing Yang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100094, China
| | - Caifu Jiang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100094, China
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
| | - Yan Guo
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100094, China
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
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Yu B, Chao DY, Zhao Y. How plants sense and respond to osmotic stress. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:394-423. [PMID: 38329193 DOI: 10.1111/jipb.13622] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/12/2024] [Accepted: 01/18/2024] [Indexed: 02/09/2024]
Abstract
Drought is one of the most serious abiotic stresses to land plants. Plants sense and respond to drought stress to survive under water deficiency. Scientists have studied how plants sense drought stress, or osmotic stress caused by drought, ever since Charles Darwin, and gradually obtained clues about osmotic stress sensing and signaling in plants. Osmotic stress is a physical stimulus that triggers many physiological changes at the cellular level, including changes in turgor, cell wall stiffness and integrity, membrane tension, and cell fluid volume, and plants may sense some of these stimuli and trigger downstream responses. In this review, we emphasized water potential and movements in organisms, compared putative signal inputs in cell wall-containing and cell wall-free organisms, prospected how plants sense changes in turgor, membrane tension, and cell fluid volume under osmotic stress according to advances in plants, animals, yeasts, and bacteria, summarized multilevel biochemical and physiological signal outputs, such as plasma membrane nanodomain formation, membrane water permeability, root hydrotropism, root halotropism, Casparian strip and suberin lamellae, and finally proposed a hypothesis that osmotic stress responses are likely to be a cocktail of signaling mediated by multiple osmosensors. We also discussed the core scientific questions, provided perspective about the future directions in this field, and highlighted the importance of robust and smart root systems and efficient source-sink allocations for generating future high-yield stress-resistant crops and plants.
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Affiliation(s)
- Bo Yu
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, The Chinese Academy of Sciences, Shanghai, 200032, China
- Key Laboratory of Plant Carbon Capture, The Chinese Academy of Sciences, Shanghai, 200032, China
| | - Dai-Yin Chao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, The Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yang Zhao
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, The Chinese Academy of Sciences, Shanghai, 200032, China
- Key Laboratory of Plant Carbon Capture, The Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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9
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Song S, Wang Y, Wang J, Liu Y, Zhang X, Yang A, Li F. Low H3K27me3 deposition at CYP82E4 determines the nicotinic conversion rate in Nicotiana tabacum. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108234. [PMID: 38056040 DOI: 10.1016/j.plaphy.2023.108234] [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: 06/12/2023] [Revised: 10/22/2023] [Accepted: 11/22/2023] [Indexed: 12/08/2023]
Abstract
Nicotine conversion is the process by which nornicotine is synthesized from nicotine. The capacity of a plant to carry out this process is represented by the nicotine conversion rate (NCR), which is defined as the percentage of nornicotine content out of the total nicotine + nornicotine content. Nicotine conversion in tobacco is mediated by CYP82E4. Although there are cultivar-specific differences in NCR, these do not correspond to differences in the CYP82E4 promoter or gene body sequences, and little is known about the underlying regulatory mechanism. Here, we found that histone H3 Lysine 27 trimethylation (H3K27me3) was involved in CYP82E4 expression, functioning as a transcriptional repressor. Compared to a high-NCR near-isogenic line, a low-NCR cultivar showed increased levels of the repressive histone modification markers H3K27me3 and H3K9me3 at CYP82E4. Comparison of histone markers between several cultivars with varying NCRs showed that H3K27me3 and H3K9me3 levels were significantly associated with cultivar-specific differences in NCR. Treatment with the H3K27me3 demethylase inhibitor GSK-J4 increased total H3K27me3 levels and enriched H3K27me3 at the CYP82E4 locus; the increased levels of H3K27me3 further inhibited CYP82E4 expression. Knocking out E(z), an indispensable gene for H3K27me3 formation, decreased H3K27me3 levels at CYP82E4, leading to a more than three-fold increase in CYP82E4 expression. Changes in CYP82E4 expression during leaf senescence and chilling stress were also strongly correlated with H3K27me3 levels. These findings reveal a strong correlation between CYP82E4 expression and histone modifications, and demonstrate an instance of histone-mediated alkaloid regulation for the first time.
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Affiliation(s)
- Shiyang Song
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China; Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081, China
| | - Yaqi Wang
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China; Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081, China
| | - Jin Wang
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China; Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081, China
| | - Yanfang Liu
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China; Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081, China
| | - Xingzi Zhang
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China; Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081, China
| | - Aiguo Yang
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China.
| | - Fengxia Li
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China.
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10
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Hu Y, Liu Y, Wei JJ, Zhang WK, Chen SY, Zhang JS. Regulation of seed traits in soybean. ABIOTECH 2023; 4:372-385. [PMID: 38106437 PMCID: PMC10721594 DOI: 10.1007/s42994-023-00122-8] [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: 08/01/2023] [Accepted: 10/18/2023] [Indexed: 12/19/2023]
Abstract
Soybean (Glycine max) is an essential economic crop that provides vegetative oil and protein for humans, worldwide. Increasing soybean yield as well as improving seed quality is of great importance. Seed weight/size, oil and protein content are the three major traits determining seed quality, and seed weight also influences soybean yield. In recent years, the availability of soybean omics data and the development of related techniques have paved the way for better research on soybean functional genomics, providing a comprehensive understanding of gene functions. This review summarizes the regulatory genes that influence seed size/weight, oil content and protein content in soybean. We also provided a general overview of the pleiotropic effect for the genes in controlling seed traits and environmental stresses. Ultimately, it is expected that this review will be beneficial in breeding improved traits in soybean.
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Affiliation(s)
- Yang Hu
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101 China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Yue Liu
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101 China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Jun-Jie Wei
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101 China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Wan-Ke Zhang
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101 China
| | - Shou-Yi Chen
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101 China
| | - Jin-Song Zhang
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101 China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
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Wang R, Li J, Zhang F, Miao X. Non-Tandem CCCH-Type Zinc-Finger Protein CpZF_CCCH1 Improves Fatty Acid Desaturation and Stress Tolerance in Chlamydomonas reinhardtii. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37910392 DOI: 10.1021/acs.jafc.3c05511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
The properties and nutritional value of microalgal bioproducts depend significantly on fatty acid desaturation, which is generally modulated by manipulating the culture conditions or associated gene expressions. Here, we investigated the role of CpZF_CCCH1, a non-tandem CCCH-type zinc-finger (non-TZF) protein, in elevating polyunsaturated fatty acid (PUFA) content (11.00-16.36%) in Chlamydomonas reinhardtii. Through lipidomic and flow cytometry analyses, we observed reduced triacylglycerol accumulation (7.01-21.15%) and elevated levels of membrane lipids containing PUFAs (7.81-46.18%) in C. reinhardtii overexpressing CpZF_CCCH1. Additionally, overexpression of nucleus-located CpZF_CCCH1 downregulated genes associated with triacylglycerol assembly and lipid turnover from 2.00- to 2.90-fold, likely by binding to GCN4 motif and promoter of 3-phosphate-glycerol acyltransferase. Furthermore, overexpression of CpZF_CCCH1 alleviated reactive oxygen species levels by 59.28-73.26% and enhanced stress tolerance under adverse conditions. These findings expanded the roles of non-TZF proteins in lipid metabolism, opening new avenues for metabolic engineering to enhance the nutritional value and stress tolerance of microalgae and agricultural crops.
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Affiliation(s)
- Rui Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- Biomass Energy Research Center, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Junhao Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- Biomass Energy Research Center, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Feng Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- Biomass Energy Research Center, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaoling Miao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- Biomass Energy Research Center, Shanghai Jiao Tong University, Shanghai 200240, China
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12
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Chu D, Zhang Z, Hu Y, Fang C, Xu X, Yuan J, Zhang J, Tian Z, Wang G. Genome-wide scan for oil quality reveals a coregulation mechanism of tocopherols and fatty acids in soybean seeds. PLANT COMMUNICATIONS 2023; 4:100598. [PMID: 37029487 PMCID: PMC10504561 DOI: 10.1016/j.xplc.2023.100598] [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: 10/31/2022] [Revised: 03/24/2023] [Accepted: 04/04/2023] [Indexed: 06/01/2023]
Abstract
Tocopherols (vitamin E) play essential roles in human health because of their antioxidant activity, and plant-derived oils are the richest sources of tocopherols in the human diet. Although soybean (Glycine max) is one of the main sources of plant-derived oil and tocopherol in the world, the relationship between tocopherol and oil in soybean seeds remains unclear. Here, we focus on dissecting tocopherol metabolism with the long-term goal of increasing α-tocopherol content and soybean oil quality. We first collected tocopherol and fatty acid profiles in a soybean population (>800 soybean accessions) and found that tocopherol content increased during soybean domestication. A strong positive correlation between tocopherol and oil content was also detected. Five tocopherol pathway-related loci were identified using a metabolite genome-wide association study strategy. Genetic variations in three tocopherol pathway genes were responsible for total tocopherol content and composition in the soybean population through effects on enzyme activity, mainly caused by non-conserved amino acid substitution or changes in gene transcription level. Moreover, the fatty acid regulatory transcription factor GmZF351 directly activated tocopherol pathway gene expression, increasing both fatty acid and tocopherol contents in soybean seeds. Our study reveals the functional differentiation of tocopherol pathway genes in soybean populations and provides a framework for development of new soybean varieties with high α-tocopherol content and oil quality in seeds.
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Affiliation(s)
- Danni Chu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100039, China
| | - Zhifang Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yang Hu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100039, China
| | - Chao Fang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Xindan Xu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Jia Yuan
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Jinsong Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100039, China
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100039, China.
| | - Guodong Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100039, China.
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