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Chen H, Lv W, Zhang W, Zhao J, Zhang Q, Zhang Z. Integrated comparative transcriptome and physiological analysis reveals the metabolic responses underlying genotype variations in NH 4+ tolerance. FRONTIERS IN PLANT SCIENCE 2023; 14:1286174. [PMID: 38192699 PMCID: PMC10773859 DOI: 10.3389/fpls.2023.1286174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 11/16/2023] [Indexed: 01/10/2024]
Abstract
Several mechanisms have been proposed to explain NH4 + toxicity. However, the core information about the biochemical regulation of plants in response to NH4 + toxicity is still lacking. In this study, the tissue NH4 + concentration is an important factor contributing to variations in plant growth even under nitrate nutrition and NH4 + tolerance under ammonium nutrition. Furthermore, NH4 + led to the reprogramming of the transcriptional profile, as genes related to trehalose-6-phosphate and zeatin biosynthesis were downregulated, whereas genes related to nitrogen metabolism, camalexin, stilbenoid and phenylpropanoid biosynthesis were upregulated. Further analysis revealed that a large number of genes, which enriched in phenylpropanoid and stilbenoid biosynthesis, were uniquely upregulated in the NH4 +- tolerant ecotype Or-1. These results suggested that the NH4 +-tolerant ecotype showed a more intense response to NH4 + by activating defense processes and pathways. Importantly, the tolerant ecotype had a higher 15NH4 + uptake and nitrogen utilization efficiency, but lower NH4 +, indicating the tolerant ecotype maintained a low NH4 + level, mainly by promoting NH4 + assimilation rather than inhibiting NH4 + uptake. The carbon and nitrogen metabolism analysis revealed that the tolerant ecotype had a stronger carbon skeleton production capacity with higher levels of hexokinase, pyruvate kinase, and glutamate dehydrogenase activity to assimilate free NH4 +, Taken together, the results revealed the core mechanisms utilized by plants in response to NH4 +, which are consequently of ecological and agricultural importance.
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Affiliation(s)
- Haifei Chen
- College of Resources, Hunan Agricultural University, Changsha, China
| | - Wei Lv
- College of Resources, Hunan Agricultural University, Changsha, China
| | - Wenqi Zhang
- College of Resources, Hunan Agricultural University, Changsha, China
| | - Jie Zhao
- College of Resources, Hunan Agricultural University, Changsha, China
| | - Quan Zhang
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Zhenhua Zhang
- College of Resources, Hunan Agricultural University, Changsha, China
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Ray R, Halitschke R, Gase K, Leddy SM, Schuman MC, Rodde N, Baldwin IT. A persistent major mutation in canonical jasmonate signaling is embedded in an herbivory-elicited gene network. Proc Natl Acad Sci U S A 2023; 120:e2308500120. [PMID: 37607232 PMCID: PMC10466192 DOI: 10.1073/pnas.2308500120] [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: 05/21/2023] [Accepted: 07/19/2023] [Indexed: 08/24/2023] Open
Abstract
When insect herbivores attack plants, elicitors from oral secretions and regurgitants (OS) enter wounds during feeding, eliciting defense responses. These generally require plant jasmonate (JA) signaling, specifically, a jasmonoyl-L-isoleucine (JA-Ile) burst, for their activation and are well studied in the native tobacco Nicotiana attenuata. We used intraspecific diversity captured in a 26-parent MAGIC population planted in nature and an updated genome assembly to impute natural variation in the OS-elicited JA-Ile burst linked to a mutation in the JA-Ile biosynthetic gene NaJAR4. Experiments revealed that NaJAR4 variants were associated with higher fitness in the absence of herbivores but compromised foliar defenses, with two NaJAR homologues (4 and 6) complementing each other spatially and temporally. From decade-long seed collections of natural populations, we uncovered enzymatically inactive variants occurring at variable frequencies, consistent with a balancing selection regime maintaining variants. Integrative analyses of OS-induced transcriptomes and metabolomes of natural accessions revealed that NaJAR4 is embedded in a nonlinear complex gene coexpression network orchestrating responses to OS, which we tested by silencing four hub genes in two connected coexpressed networks and examining their OS-elicited metabolic responses. Lines silenced in two hub genes (NaGLR and NaFB67) co-occurring in the NaJAR4/6 module showed responses proportional to JA-Ile accumulations; two from an adjacent module (NaERF and NaFB61) had constitutively expressed defenses with high resistance. We infer that mutations with large fitness consequences can persist in natural populations due to compensatory responses from gene networks, which allow for diversification in conserved signaling pathways and are generally consistent with predictions of an omnigene model.
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Affiliation(s)
- Rishav Ray
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, 07745Jena, Germany
| | - Rayko Halitschke
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, 07745Jena, Germany
| | - Klaus Gase
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, 07745Jena, Germany
| | - Sabrina M. Leddy
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY14850
| | - Meredith C. Schuman
- Department of Geography, University of Zurich, 8006Zurich, Switzerland
- Department of Chemistry, University of Zurich, 8006Zurich, Switzerland
| | - Nathalie Rodde
- Institut national de recherche pour l’agriculture, l’alimentation et l’environnement, Centre National de Resources Génomiques Végétales, French Plant Genomic Resource Center, Castanet TolosanF-31326, France
| | - Ian T. Baldwin
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, 07745Jena, Germany
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Li C, Aluko OO, Shi S, Mo Z, Nong T, Shi C, Li Z, Wang Q, Liu H. Determination of optimal NH 4+/K + concentration and corresponding ratio critical for growth of tobacco seedlings in a hydroponic system. FRONTIERS IN PLANT SCIENCE 2023; 14:1152817. [PMID: 37496856 PMCID: PMC10368480 DOI: 10.3389/fpls.2023.1152817] [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: 01/28/2023] [Accepted: 05/19/2023] [Indexed: 07/28/2023]
Abstract
Inherently, ammonium (NH4 +) is critical for plant growth; however, its toxicity suppresses potassium (K+) uptake and vice-versa. Hence, attaining a nutritional balance between these two ions (NH4 + and K+) becomes imperative for the growth of tobacco seedlings. Therefore, we conducted a 15-day experimental study on tobacco seedlings exposed to different concentrations (47 treatments) of NH4 +/K+ at different corresponding 12 ratios simultaneously in a hydroponic system. Our study aimed at establishing the optimal NH4 +-K+ concentration and the corresponding ratio required for optimal growth of different tobacco plant organs during the seedling stage. The controls were the baseline for comparison in this study. Plants with low or excessive NH4 +-K+ concentration had leaf chlorosis or dark greenish colouration, stunted whole plant part biomass, and thin roots. We found that adequate K+ supply is a pragmatic way to mitigate NH4 +-induced toxicity in tobacco plants. The optimal growth for tobacco leaf and root was attained at NH4 +-K+ concentrations 2-2 mM (ratio 1:1), whereas stem growth was optimal at NH4 +-K+ 1-2 mM (1:2). The study provided an insight into the right combination of NH4 +/K+ that could mitigate or prevent NH4 + or K+ stress in the tobacco seedlings.
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Affiliation(s)
- Chuanzong Li
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Oluwaseun Olayemi Aluko
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
- State Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Sujuan Shi
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
- Technology Center, Shanghai Tobacco Company, Ltd, Beijing, China
| | - Zhijie Mo
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
- Yichang City Company, Hubei Tobacco Company, Yichang, China
| | - Tongjia Nong
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Chuhan Shi
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Zhihao Li
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
- Yichang City Company, Hubei Tobacco Company, Yichang, China
| | - Qian Wang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Haobao Liu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
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Kasemsap P, Bloom AJ. Breeding for Higher Yields of Wheat and Rice through Modifying Nitrogen Metabolism. PLANTS (BASEL, SWITZERLAND) 2022; 12:85. [PMID: 36616214 PMCID: PMC9823454 DOI: 10.3390/plants12010085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/21/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
Wheat and rice produce nutritious grains that provide 32% of the protein in the human diet globally. Here, we examine how genetic modifications to improve assimilation of the inorganic nitrogen forms ammonium and nitrate into protein influence grain yield of these crops. Successful breeding for modified nitrogen metabolism has focused on genes that coordinate nitrogen and carbon metabolism, including those that regulate tillering, heading date, and ammonium assimilation. Gaps in our current understanding include (1) species differences among candidate genes in nitrogen metabolism pathways, (2) the extent to which relative abundance of these nitrogen forms across natural soil environments shape crop responses, and (3) natural variation and genetic architecture of nitrogen-mediated yield improvement. Despite extensive research on the genetics of nitrogen metabolism since the rise of synthetic fertilizers, only a few projects targeting nitrogen pathways have resulted in development of cultivars with higher yields. To continue improving grain yield and quality, breeding strategies need to focus concurrently on both carbon and nitrogen assimilation and consider manipulating genes with smaller effects or that underlie regulatory networks as well as genes directly associated with nitrogen metabolism.
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Frungillo L. Mapping the genomic basis of developmental and metabolic responses to nitrogen. THE PLANT CELL 2022; 34:4663-4664. [PMID: 36194104 PMCID: PMC9709960 DOI: 10.1093/plcell/koac291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
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Knapp A, Stefani J, Katz E, Bloom AJ. Novel method for the quantification of rosette area from images of Arabidopsis seedlings grown on agar plates. APPLICATIONS IN PLANT SCIENCES 2022; 10:e11504. [PMID: 36518946 PMCID: PMC9742823 DOI: 10.1002/aps3.11504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 09/15/2022] [Accepted: 09/16/2022] [Indexed: 06/17/2023]
Abstract
PREMISE The agar-based culture of Arabidopsis seedlings is widely used for quantifying root traits. Shoot traits are generally overlooked in these studies, probably because the rosettes are often askew. A technique to assess the shoot surface area of seedlings grown inside agar culture dishes would facilitate simultaneous root and shoot phenotyping. METHODS We developed an image processing workflow in Python that estimates rosette area of Arabidopsis seedlings on agar culture dishes. We validated this method by comparing its output with other metrics of seedling growth. As part of a larger study on genetic variation in plant responses to nitrogen form and concentration, we measured the rosette areas from more than 2000 plate images. RESULTS The rosette area measured from plate images was strongly correlated with the rosette area measured from directly overhead and moderately correlated with seedling mass. Rosette area in the large image set was significantly influenced by genotype and nitrogen treatment. The broad-sense heritability of leaf area measured using this method was 0.28. DISCUSSION These results indicated that this approach for estimating rosette area produces accurate shoot phenotype data. It can be used with image sets for which other methods of leaf area quantification prove unsuitable.
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Affiliation(s)
- Anna Knapp
- Department of Plant SciencesUniversity of CaliforniaDavis, One Shields Ave.DavisCalifornia95616USA
| | - Jordan Stefani
- Department of Plant SciencesUniversity of CaliforniaDavis, One Shields Ave.DavisCalifornia95616USA
| | - Ella Katz
- Department of Plant SciencesUniversity of CaliforniaDavis, One Shields Ave.DavisCalifornia95616USA
| | - Arnold J. Bloom
- Department of Plant SciencesUniversity of CaliforniaDavis, One Shields Ave.DavisCalifornia95616USA
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