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Lacrampe N, Lugan R, Dumont D, Nicot PC, Lecompte F, Colombié S. Modelling metabolic fluxes of tomato stems reveals that nitrogen shapes central metabolism for defence against Botrytis cinerea. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:4093-4110. [PMID: 38551810 PMCID: PMC11233421 DOI: 10.1093/jxb/erae140] [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: 09/12/2023] [Accepted: 03/28/2024] [Indexed: 07/11/2024]
Abstract
Among plant pathogens, the necrotrophic fungus Botrytis cinerea is one of the most prevalent, leading to severe crop damage. Studies related to its colonization of different plant species have reported variable host metabolic responses to infection. In tomato, high N availability leads to decreased susceptibility. Metabolic flux analysis can be used as an integrated method to better understand which metabolic adaptations lead to effective host defence and resistance. Here, we investigated the metabolic response of tomato infected by B. cinerea in symptomless stem tissues proximal to the lesions for 7 d post-inoculation, using a reconstructed metabolic model constrained by a large and consistent metabolic dataset acquired under four different N supplies. An overall comparison of 48 flux solution vectors of Botrytis- and mock-inoculated plants showed that fluxes were higher in Botrytis-inoculated plants, and the difference increased with a reduction in available N, accompanying an unexpected increase in radial growth. Despite higher fluxes, such as those involved in cell wall synthesis and other pathways, fluxes related to glycolysis, the tricarboxylic acid cycle, and amino acid and protein synthesis were limited under very low N, which might explain the enhanced susceptibility. Limiting starch synthesis and enhancing fluxes towards redox and specialized metabolism also contributed to defence independent of N supply.
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Affiliation(s)
- Nathalie Lacrampe
- PSH unit, INRAE, F-84914 Avignon, France
- UMR Qualisud, Avignon Université, F-84916 Avignon, France
| | | | | | | | | | - Sophie Colombié
- UMR 1332 BFP, INRAE, Univ Bordeaux, F-33883 Villenave d’Ornon, France
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2
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Nehela Y, Mazrou YSA, El_Gammal NA, Atallah O, Xuan TD, Elzaawely AA, El-Zahaby HM, Abdelrhim AS, Behiry SI, Hafez EM, Makhlouf AH, Hussain WAM. Non-proteinogenic amino acids mitigate oxidative stress and enhance the resistance of common bean plants against Sclerotinia sclerotiorum. FRONTIERS IN PLANT SCIENCE 2024; 15:1385785. [PMID: 38711604 PMCID: PMC11070507 DOI: 10.3389/fpls.2024.1385785] [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: 02/13/2024] [Accepted: 04/09/2024] [Indexed: 05/08/2024]
Abstract
White mold, caused by the necrotrophic fungus Sclerotinia sclerotiorum, is a challenging disease to common bean cultivation worldwide. In the current study, two non-proteinogenic amino acids (NPAAs), γ-aminobutyric acid (GABA) and ß-alanine, were suggested as innovative environmentally acceptable alternatives for more sustainable management of white mold disease. In vitro, GABA and ß-alanine individually demonstrated potent dose-dependent fungistatic activity and effectively impeded the radial growth and development of S. sclerotiorum mycelium. Moreover, the application of GABA or ß-alanine as a seed treatment followed by three root drench applications efficiently decreased the disease severity, stimulated plant growth, and boosted the content of photosynthetic pigments of treated S. sclerotiorum-infected plants. Furthermore, although higher levels of hydrogen peroxide (H2O2), superoxide anion (O2 •-), and malondialdehyde (MDA) indicated that S. sclerotiorum infection had markedly triggered oxidative stress in infected bean plants, the exogenous application of both NPAAs significantly reduced the levels of the three studied oxidative stress indicators. Additionally, the application of GABA and ß-alanine increased the levels of both non-enzymatic (total soluble phenolics and flavonoids), as well as enzymatic (catalase [CAT], peroxidases [POX], and polyphenol oxidase [PPO]) antioxidants in the leaves of S. sclerotiorum-infected plants and improved their scavenging activity and antioxidant efficiency. Applications of GABA and ß-alanine also raised the proline and total amino acid content of infected bean plants. Lastly, the application of both NPAAs upregulated the three antioxidant-related genes PvCAT1, PvCuZnSOD1, and PvGR. Collectively, the fungistatic activity of NPAAs, coupled with their ability to alleviate oxidative stress, enhance antioxidant defenses, and stimulate plant growth, establishes them as promising eco-friendly alternatives for white mold disease management for sustainable bean production.
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Affiliation(s)
- Yasser Nehela
- Department of Agricultural Botany, Faculty of Agriculture, Tanta University, Tanta, Egypt
| | - Yasser S. A. Mazrou
- Business Administration Department, Community College, King Khalid University, Abha, Saudi Arabia
| | - Nehad A. El_Gammal
- Plant Pathology Research Institute, Agricultural Research Center, Giza, Egypt
| | - Osama Atallah
- Department of Plant Pathology, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Tran Dang Xuan
- Transdisciplinary Science and Engineering Program, Graduate School of Advanced Science and Engineering, Hiroshima University, Higashi-Hiroshima, Japan
- Center for the Planetary Health and Innovation Science (PHIS), The International Development and Cooperation (IDEC) Institute, Hiroshima University, Higashi-Hiroshima, Japan
| | | | - Hassan M. El-Zahaby
- Department of Agricultural Botany, Faculty of Agriculture, Tanta University, Tanta, Egypt
| | | | - Said I. Behiry
- Agricultural Botany Department, Faculty of Agriculture (Saba Basha), Alexandria University, Alexandria, Egypt
| | - Emad M. Hafez
- Department of Agronomy, Faculty of Agriculture, Kafrelsheikh University, Kafr El-Sheikh, Egypt
| | - Abeer H. Makhlouf
- Department of Agricultural Botany, Faculty of Agriculture, Minufiya University, Shibin El-Kom, Egypt
| | - Warda A. M. Hussain
- Plant Pathology Research Institute, Agricultural Research Center, Giza, Egypt
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Lavoignat M, Cassan C, Pétriacq P, Gibon Y, Heumez E, Duque C, Momont P, Rincent R, Blancon J, Ravel C, Le Gouis J. Different wheat loci are associated to heritable free asparagine content in grain grown under different water and nitrogen availability. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:46. [PMID: 38332254 DOI: 10.1007/s00122-024-04551-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 01/07/2024] [Indexed: 02/10/2024]
Abstract
KEY MESSAGE Different wheat QTLs were associated to the free asparagine content of grain grown in four different conditions. Environmental effects are a key factor when selecting for low acrylamide-forming potential. The amount of free asparagine in grain of a wheat genotype determines its potential to form harmful acrylamide in derivative food products. Here, we explored the variation in the free asparagine, aspartate, glutamine and glutamate contents of 485 accessions reflecting wheat worldwide diversity to define the genetic architecture governing the accumulation of these amino acids in grain. Accessions were grown under high and low nitrogen availability and in water-deficient and well-watered conditions, and plant and grain phenotypes were measured. Free amino acid contents of grain varied from 0.01 to 1.02 mg g-1 among genotypes in a highly heritable way that did not correlate strongly with grain yield, protein content, specific weight, thousand-kernel weight or heading date. Mean free asparagine content was 4% higher under high nitrogen and 3% higher in water-deficient conditions. After genotyping the accessions, single-locus and multi-locus genome-wide association study models were used to identify several QTLs for free asparagine content located on nine chromosomes. Each QTL was associated with a single amino acid and growing environment, and none of the QTLs colocalised with genes known to be involved in the corresponding amino acid metabolism. This suggests that free asparagine content is controlled by several loci with minor effects interacting with the environment. We conclude that breeding for reduced asparagine content is feasible, but should be firmly based on multi-environment field trials. KEY MESSAGE Different wheat QTLs were associated to the free asparagine content of grain grown in four different conditions. Environmental effects are a key factor when selecting for low acrylamide-forming potential.
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Affiliation(s)
- Mélanie Lavoignat
- Université Clermont Auvergne, INRAE, UMR1095 GDEC, 63000, Clermont-Ferrand, France
- AgroParisTech, 75005, Paris, France
| | - Cédric Cassan
- Université Bordeaux, INRAE, UMR 1332 BFP, 33883, Villenave d'Ornon, France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 33140, Villenave d'Ornon, France
| | - Pierre Pétriacq
- Université Bordeaux, INRAE, UMR 1332 BFP, 33883, Villenave d'Ornon, France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 33140, Villenave d'Ornon, France
| | - Yves Gibon
- Université Bordeaux, INRAE, UMR 1332 BFP, 33883, Villenave d'Ornon, France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 33140, Villenave d'Ornon, France
| | | | | | | | - Renaud Rincent
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190, Gif-sur-Yvette, France
| | - Justin Blancon
- Université Clermont Auvergne, INRAE, UMR1095 GDEC, 63000, Clermont-Ferrand, France
| | - Catherine Ravel
- Université Clermont Auvergne, INRAE, UMR1095 GDEC, 63000, Clermont-Ferrand, France
| | - Jacques Le Gouis
- Université Clermont Auvergne, INRAE, UMR1095 GDEC, 63000, Clermont-Ferrand, France.
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Díaz FP, Dussarrat T, Carrasco-Puga G, Colombié S, Prigent S, Decros G, Bernillon S, Cassan C, Flandin A, Guerrero PC, Gibon Y, Rolin D, Cavieres LA, Pétriacq P, Latorre C, Gutiérrez RA. Ecological and metabolic implications of the nurse effect of Maihueniopsis camachoi in the Atacama Desert. THE NEW PHYTOLOGIST 2024; 241:1074-1087. [PMID: 37984856 DOI: 10.1111/nph.19415] [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: 07/06/2023] [Accepted: 10/31/2023] [Indexed: 11/22/2023]
Abstract
Plant-plant positive interactions are key drivers of community structure. Yet, the underlying molecular mechanisms of facilitation processes remain unexplored. We investigated the 'nursing' effect of Maihueniopsis camachoi, a cactus that thrives in the Atacama Desert between c. 2800 and 3800 m above sea level. We hypothesised that an important protective factor is thermal amelioration of less cold-tolerant species with a corresponding impact on molecular phenotypes. To test this hypothesis, we compared plant cover and temperatures within the cactus foliage with open areas and modelled the effect of temperatures on plant distribution. We combined eco-metabolomics and machine learning to test the molecular consequences of this association. Multiple species benefited from the interaction with M. camachoi. A conspicuous example was the extended distribution of Atriplex imbricata to colder elevations in association with M. camachoi (400 m higher as compared to plants in open areas). Metabolomics identified 93 biochemical markers predicting the interaction status of A. imbricata with 79% accuracy, independently of year. These findings place M. camachoi as a key species in Atacama plant communities, driving local biodiversity with an impact on molecular phenotypes of nursed species. Our results support the stress-gradient hypothesis and provide pioneer insights into the metabolic consequences of facilitation.
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Affiliation(s)
- Francisca P Díaz
- Instituto de Geografía, Pontificia Universidad Católica de Valparaíso, 2362807, Valparaíso, Chile
- Institute of Ecology and Biodiversity, Chile (IEB), Las Palmeras 3425, Ñuñoa, 7800003, Santiago, Chile
- ANID Millennium Institute Center for Genome Regulation and ANID Millennium Institute for Integrative Biology (iBio), Libertador Bernardo O'Higgins 340, 8331150, Santiago, Chile
| | - Thomas Dussarrat
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Libertador Bernardo O'Higgins 340, 8331150, Santiago, Chile
- Univ. Bordeaux, INRAE, UMR1332 BFP, 33882, Villenave d'Ornon, France
| | - Gabriela Carrasco-Puga
- ANID Millennium Institute Center for Genome Regulation and ANID Millennium Institute for Integrative Biology (iBio), Libertador Bernardo O'Higgins 340, 8331150, Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Libertador Bernardo O'Higgins 340, 8331150, Santiago, Chile
| | - Sophie Colombié
- Univ. Bordeaux, INRAE, UMR1332 BFP, 33882, Villenave d'Ornon, France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 33140, Villenave d'Ornon, France
| | - Sylvain Prigent
- Univ. Bordeaux, INRAE, UMR1332 BFP, 33882, Villenave d'Ornon, France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 33140, Villenave d'Ornon, France
| | - Guillaume Decros
- Univ. Bordeaux, INRAE, UMR1332 BFP, 33882, Villenave d'Ornon, France
| | - Stéphane Bernillon
- Univ. Bordeaux, INRAE, UMR1332 BFP, 33882, Villenave d'Ornon, France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 33140, Villenave d'Ornon, France
| | - Cédric Cassan
- Univ. Bordeaux, INRAE, UMR1332 BFP, 33882, Villenave d'Ornon, France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 33140, Villenave d'Ornon, France
| | - Amélie Flandin
- Univ. Bordeaux, INRAE, UMR1332 BFP, 33882, Villenave d'Ornon, France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 33140, Villenave d'Ornon, France
| | - Pablo C Guerrero
- Institute of Ecology and Biodiversity, Chile (IEB), Las Palmeras 3425, Ñuñoa, 7800003, Santiago, Chile
- Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, 7800003, Concepción, Chile
- Instituto Milenio Biodiversidad de Ecosistemas Antárticos y Subantárticos, 8331150, Santiago, Chile
| | - Yves Gibon
- Univ. Bordeaux, INRAE, UMR1332 BFP, 33882, Villenave d'Ornon, France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 33140, Villenave d'Ornon, France
| | - Dominique Rolin
- Univ. Bordeaux, INRAE, UMR1332 BFP, 33882, Villenave d'Ornon, France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 33140, Villenave d'Ornon, France
| | - Lohengrin A Cavieres
- Institute of Ecology and Biodiversity, Chile (IEB), Las Palmeras 3425, Ñuñoa, 7800003, Santiago, Chile
- Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, 7800003, Concepción, Chile
| | - Pierre Pétriacq
- Univ. Bordeaux, INRAE, UMR1332 BFP, 33882, Villenave d'Ornon, France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 33140, Villenave d'Ornon, France
| | - Claudio Latorre
- Institute of Ecology and Biodiversity, Chile (IEB), Las Palmeras 3425, Ñuñoa, 7800003, Santiago, Chile
- Departamento de Ecología, Pontificia Universidad Católica de Chile, Libertador Bernardo O'Higgins 340, 8331150, Santiago, Chile
| | - Rodrigo A Gutiérrez
- Institute of Ecology and Biodiversity, Chile (IEB), Las Palmeras 3425, Ñuñoa, 7800003, Santiago, Chile
- ANID Millennium Institute Center for Genome Regulation and ANID Millennium Institute for Integrative Biology (iBio), Libertador Bernardo O'Higgins 340, 8331150, Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Libertador Bernardo O'Higgins 340, 8331150, Santiago, Chile
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Boulogne I, Petit P, Desfontaines L, Durambur G, Deborde C, Mirande-Ney C, Arnaudin Q, Plasson C, Grivotte J, Chamot C, Bernard S, Loranger-Merciris G. Biological and Chemical Characterization of Musa paradisiaca Leachate. BIOLOGY 2023; 12:1326. [PMID: 37887036 PMCID: PMC10604775 DOI: 10.3390/biology12101326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 10/07/2023] [Accepted: 10/09/2023] [Indexed: 10/28/2023]
Abstract
There is a growing demand for molecules of natural origin for biocontrol and biostimulation, given the current trend away from synthetic chemical products. Leachates extracted from plantain stems were obtained after biodegradation of the plant material. To characterize the leachate, quantitative determinations of nitrogen, carbon, phosphorus, and cations (K+, Ca2+, Mg2+, Na+), Q2/4, Q2/6, and Q4/6 absorbance ratios, and metabolomic analysis were carried out. The potential role of plantain leachates as fungicide, elicitor of plant defense, and/or plant biostimulant was evaluated by agar well diffusion method, phenotypic, molecular, and imaging approaches. The plant extracts induced a slight inhibition of fungal growth of an aggressive strain of Colletotrichum gloeosporioides, which causes anthracnose. Organic compounds such as cinnamic, ellagic, quinic, and fulvic acids and indole alkaloid such as ellipticine, along with some minerals such as potassium, calcium, and phosphorus, may be responsible for the inhibition of fungal growth. In addition, jasmonic, benzoic, and salicylic acids, which are known to play a role in plant defense and as biostimulants in tomato, were detected in leachate extract. Indeed, foliar application of banana leachate induced overexpression of LOXD, PPOD, and Worky70-80 genes, which are involved in phenylpropanoid metabolism, jasmonic acid biosynthesis, and salicylic acid metabolism, respectively. Leachate also activated root growth in tomato seedlings. However, the main impact of the leachate was observed on mature plants, where it caused a reduction in leaf area and fresh weight, the remodeling of stem cell wall glycopolymers, and an increase in the expression of proline dehydrogenase.
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Affiliation(s)
- Isabelle Boulogne
- Université de Rouen Normandie, Normandie Univ, GlycoMEV UR 4358, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, IRIB, GDR CNRS Chemobiologie, RMT BESTIM, F-76000 Rouen, France; (I.B.); (G.D.); (C.M.-N.); (Q.A.); (C.P.); (J.G.); (S.B.)
| | - Philippe Petit
- Université des Antilles, UMR ISYEB-MNHN-CNRS-Sorbonne Université-EPHE, UFR Sciences Exactes et Naturelles, Campus de Fouillole, F-97157 Pointe-à-Pitre, Guadeloupe, France;
| | | | - Gaëlle Durambur
- Université de Rouen Normandie, Normandie Univ, GlycoMEV UR 4358, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, IRIB, GDR CNRS Chemobiologie, RMT BESTIM, F-76000 Rouen, France; (I.B.); (G.D.); (C.M.-N.); (Q.A.); (C.P.); (J.G.); (S.B.)
| | - Catherine Deborde
- INRAE, PROBE Research Infrastructure, BIBS Facility, F-44300 Nantes, France;
- INRAE, UR1268 BIA Biopolymères Interactions Assemblages F-44300 Nantes, France
| | - Cathleen Mirande-Ney
- Université de Rouen Normandie, Normandie Univ, GlycoMEV UR 4358, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, IRIB, GDR CNRS Chemobiologie, RMT BESTIM, F-76000 Rouen, France; (I.B.); (G.D.); (C.M.-N.); (Q.A.); (C.P.); (J.G.); (S.B.)
| | - Quentin Arnaudin
- Université de Rouen Normandie, Normandie Univ, GlycoMEV UR 4358, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, IRIB, GDR CNRS Chemobiologie, RMT BESTIM, F-76000 Rouen, France; (I.B.); (G.D.); (C.M.-N.); (Q.A.); (C.P.); (J.G.); (S.B.)
| | - Carole Plasson
- Université de Rouen Normandie, Normandie Univ, GlycoMEV UR 4358, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, IRIB, GDR CNRS Chemobiologie, RMT BESTIM, F-76000 Rouen, France; (I.B.); (G.D.); (C.M.-N.); (Q.A.); (C.P.); (J.G.); (S.B.)
| | - Julie Grivotte
- Université de Rouen Normandie, Normandie Univ, GlycoMEV UR 4358, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, IRIB, GDR CNRS Chemobiologie, RMT BESTIM, F-76000 Rouen, France; (I.B.); (G.D.); (C.M.-N.); (Q.A.); (C.P.); (J.G.); (S.B.)
| | - Christophe Chamot
- Université de Rouen Normandie, Normandie Univ, INSERM, CNRS, HeRacLeS US 51 UAR 2026, PRIMACEN, F-76000 Rouen, France;
| | - Sophie Bernard
- Université de Rouen Normandie, Normandie Univ, GlycoMEV UR 4358, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, IRIB, GDR CNRS Chemobiologie, RMT BESTIM, F-76000 Rouen, France; (I.B.); (G.D.); (C.M.-N.); (Q.A.); (C.P.); (J.G.); (S.B.)
- Université de Rouen Normandie, Normandie Univ, INSERM, CNRS, HeRacLeS US 51 UAR 2026, PRIMACEN, F-76000 Rouen, France;
| | - Gladys Loranger-Merciris
- Université des Antilles, UMR ISYEB-MNHN-CNRS-Sorbonne Université-EPHE, UFR Sciences Exactes et Naturelles, Campus de Fouillole, F-97157 Pointe-à-Pitre, Guadeloupe, France;
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β-Cyclocitral-Mediated Metabolic Changes Optimize Growth and Defense Responses in Solanum lycopersicum L. Metabolites 2023; 13:metabo13030329. [PMID: 36984769 PMCID: PMC10053473 DOI: 10.3390/metabo13030329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 02/14/2023] [Accepted: 02/18/2023] [Indexed: 02/25/2023] Open
Abstract
β-cyclocitral (βCC) is one of the significant oxidative products of β-carotene. It primes plants for multiple stress acclimation without compromising plant growth. Metabolic reorganization is necessary to maintain a balance between growth and defense. However, the βCC-mediated changes in a plant’s metabolic network are unknown. Here, we demonstrate how βCC-induced metabolic changes enable Solanum lycopersicum L. (tomato) plants to promote defense and maintain growth under stress. An analysis of early (0–240 min) and late (72 h) changes in the tomato metabolome after βCC-treatment using liquid chromatography and tandem mass spectrometry identified 57 compounds. A principal coordinate analysis suggested that βCC treatment significantly changes the metabolite profile. A variable importance in projection (VIP) analysis revealed 16 and 19 discriminant metabolites from early and late samples, respectively (VIP ≥ 1.0). Upregulated metabolites were mainly amino acids and phytophenols. Pathway enrichment analysis showed that βCC treatment influenced amino acid metabolism at early and later times; however, phenylpropanoid and isoquinoline biosynthesis were influenced only at the later time. A 66.6% similarity in the upregulated metabolites of βCC- and simulated-herbivory-treated plants confirmed βCC’s role against herbivores. We conclude that βCC steers a temporal separation in amino acids and defense metabolite accumulation that optimizes resource allocation to growth and defense.
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Genomics, Proteomics, and Metabolomics Approaches to Improve Abiotic Stress Tolerance in Tomato Plant. Int J Mol Sci 2023; 24:ijms24033025. [PMID: 36769343 PMCID: PMC9918255 DOI: 10.3390/ijms24033025] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 02/09/2023] Open
Abstract
To explore changes in proteins and metabolites under stress circumstances, genomics, proteomics, and metabolomics methods are used. In-depth research over the previous ten years has gradually revealed the fundamental processes of plants' responses to environmental stress. Abiotic stresses, which include temperature extremes, water scarcity, and metal toxicity brought on by human activity and urbanization, are a major cause for concern, since they can result in unsustainable warming trends and drastically lower crop yields. Furthermore, there is an emerging reliance on agrochemicals. Stress is responsible for physiological transformations such as the formation of reactive oxygen, stomatal opening and closure, cytosolic calcium ion concentrations, metabolite profiles and their dynamic changes, expression of stress-responsive genes, activation of potassium channels, etc. Research regarding abiotic stresses is lacking because defense feedbacks to abiotic factors necessitate regulating the changes that activate multiple genes and pathways that are not properly explored. It is clear from the involvement of these genes that plant stress response and adaptation are complicated processes. Targeting the multigenicity of plant abiotic stress responses caused by genomic sequences, transcripts, protein organization and interactions, stress-specific and cellular transcriptome collections, and mutant screens can be the first step in an integrative approach. Therefore, in this review, we focused on the genomes, proteomics, and metabolomics of tomatoes under abiotic stress.
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Singh RR, Ameye M, Haesaert G, Deveux M, Spanoghe P, Audenaert K, Rabasse JM, Kyndt T. β-Aminobutyric acid induced phytotoxicity and effectiveness against nematode is stereomer-specific and dose-dependent in tomato. PHYSIOLOGIA PLANTARUM 2023; 175:e13862. [PMID: 36690578 DOI: 10.1111/ppl.13862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 11/10/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
β-Aminobutyric acid (BABA) induces resistance to a/biotic stress but is associated with phytotoxicity in some plant species. There are two enantiomers of BABA, the R and S enantiomers. We evaluated the phytotoxicity caused by the RS BABA (racemic mixture of R and S BABA), evaluating the dose-response effect and different modes of application on tomato. Results show that RS BABA-induced phytotoxicity in tomato is dose-dependent and stronger with foliar applications than with soil drench. We further evaluated the phytotoxicity of the two enantiomers separately and observed that BABA-induced phytotoxicity is stereomer-specific. In comparison with less phytotoxic effects induced by S BABA, R BABA induces dose-dependent and systemic phytotoxic symptoms. To investigate the possible physiological causes of this phytotoxicity, we measured levels of oxidative stress and anthocyanins and validated the findings with gene expression analyses. Our results show that high doses of RS and R BABA induce hydrogen peroxide, lipid peroxidation, and anthocyanin accumulation in tomato leaves, while this response is milder and more transient upon S BABA application. Next, we evaluated BABA induced resistance against root-knot nematode Meloidogyne incognita in tomato. BABA-induced resistance was found to be stereomer-specific and dependent on dose and mode of application. R or RS BABA multiple soil drench application at low doses induces resistance to nematodes with less phytotoxic effects. Taken together, our data provide useful knowledge on how BABA can be applied in crop production by enhancing stress tolerance and limiting phytotoxicity.
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Affiliation(s)
| | - Maarten Ameye
- Department of Plants and Crops, Ghent University, Ghent, Belgium
| | - Geert Haesaert
- Department of Plants and Crops, Ghent University, Ghent, Belgium
| | - Melissa Deveux
- Department of Plants and Crops, Ghent University, Ghent, Belgium
| | - Pieter Spanoghe
- Department of Plants and Crops, Ghent University, Ghent, Belgium
| | - Kris Audenaert
- Department of Plants and Crops, Ghent University, Ghent, Belgium
| | | | - Tina Kyndt
- Department of Biotechnology, Ghent University, Ghent, Belgium
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9
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Desmedt W, Kudjordjie EN, Chavan SN, Desmet S, Nicolaisen M, Vanholme B, Vestergård M, Kyndt T. Distinct chemical resistance-inducing stimuli result in common transcriptional, metabolic, and nematode community signatures in rice root and rhizosphere. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:7564-7581. [PMID: 36124630 DOI: 10.1093/jxb/erac375] [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: 01/28/2022] [Accepted: 09/15/2022] [Indexed: 06/15/2023]
Abstract
Induced resistance (IR), a phenotypic state induced by an exogenous stimulus and characterized by enhanced resistance to future (a)biotic challenge, is an important component of plant immunity. Numerous IR-inducing stimuli have been described in various plant species, but relatively little is known about 'core' systemic responses shared by these distinct IR stimuli and the effects of IR on plant-associated microbiota. In this study, rice (Oryza sativa) leaves were treated with four distinct IR stimuli (β-aminobutyric acid, acibenzolar-S-methyl, dehydroascorbic acid, and piperonylic acid) capable of inducing systemic IR against the root-knot nematode Meloidogyne graminicola and evaluated their effect on the root transcriptome and exudome, and root-associated nematode communities. Our results reveal shared transcriptional responses-notably induction of jasmonic acid and phenylpropanoid metabolism-and shared alterations to the exudome that include increased amino acid, benzoate, and fatty acid exudation. In rice plants grown in soil from a rice field, IR stimuli significantly affected the composition of rhizosphere nematode communities 3 d after treatment, but by 14 d after treatment these changes had largely reverted. Notably, IR stimuli did not reduce nematode diversity, which suggests that IR might offer a sustainable option for managing plant-parasitic nematodes.
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Affiliation(s)
- Willem Desmedt
- Department of Biotechnology, Ghent University, 9000 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Enoch Narh Kudjordjie
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, 4200 Slagelse, Denmark
| | - Satish Namdeo Chavan
- Department of Biotechnology, Ghent University, 9000 Ghent, Belgium
- ICAR-Indian Institute of Rice Research, Rajendranagar, 500030 Hyderabad, India
| | - Sandrien Desmet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
- VIB Metabolomics Core Ghent, 9052 Ghent, Belgium
| | - Mogens Nicolaisen
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, 4200 Slagelse, Denmark
| | - Bartel Vanholme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Mette Vestergård
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, 4200 Slagelse, Denmark
| | - Tina Kyndt
- Department of Biotechnology, Ghent University, 9000 Ghent, Belgium
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10
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Poucet T, Beauvoit B, González‐Moro MB, Cabasson C, Pétriacq P, Flandin A, Gibon Y, Marino D, Dieuaide‐Noubhani M. Impaired cell growth under ammonium stress explained by modeling the energy cost of vacuole expansion in tomato leaves. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:1014-1028. [PMID: 36198049 PMCID: PMC9828129 DOI: 10.1111/tpj.15991] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 09/20/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
Ammonium (NH4 + )-based fertilization efficiently mitigates the adverse effects of nitrogen fertilization on the environment. However, high concentrations of soil NH4 + provoke growth inhibition, partly caused by the reduction of cell enlargement and associated with modifications of cell composition, such as an increase of sugars and a decrease in organic acids. Cell expansion depends largely on the osmotic-driven enlargement of the vacuole. However, the involvement of subcellular compartmentation in the adaptation of plants to ammonium nutrition has received little attention, until now. To investigate this, tomato (Solanum lycopersicum) plants were cultivated under nitrate and ammonium nutrition and the fourth leaf was harvested at seven developmental stages. The vacuolar expansion was monitored and metabolites and inorganic ion contents, together with intracellular pH, were determined. A data-constrained model was constructed to estimate subcellular concentrations of major metabolites and ions. It was first validated at the three latter developmental stages by comparison with subcellular concentrations obtained experimentally using non-aqueous fractionation. Then, the model was used to estimate the subcellular concentrations at the seven developmental stages and the net vacuolar uptake of solutes along the developmental series. Our results showed ammonium nutrition provokes an acidification of the vacuole and a reduction in the flux of solutes into the vacuoles. Overall, analysis of the subcellular compartmentation reveals a mechanism behind leaf growth inhibition under ammonium stress linked to the higher energy cost of vacuole expansion, as a result of alterations in pH, the inhibition of glycolysis routes and the depletion of organic acids.
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Affiliation(s)
- Théo Poucet
- Department of Plant Biology and EcologyUniversity of the Basque Country (UPV/EHU)E‐48940LeioaSpain
- Université de Bordeaux, INRAE, UMR Biologie du Fruit et PathologieVillenave d'Ornon33140France
| | - Bertrand Beauvoit
- Université de Bordeaux, INRAE, UMR Biologie du Fruit et PathologieVillenave d'Ornon33140France
| | | | - Cécile Cabasson
- Université de Bordeaux, INRAE, UMR Biologie du Fruit et PathologieVillenave d'Ornon33140France
- Bordeaux Metabolome, MetaboHUBPHENOME‐EMPHASISVillenave d'Ornon33140France
| | - Pierre Pétriacq
- Université de Bordeaux, INRAE, UMR Biologie du Fruit et PathologieVillenave d'Ornon33140France
- Bordeaux Metabolome, MetaboHUBPHENOME‐EMPHASISVillenave d'Ornon33140France
| | - Amélie Flandin
- Université de Bordeaux, INRAE, UMR Biologie du Fruit et PathologieVillenave d'Ornon33140France
- Bordeaux Metabolome, MetaboHUBPHENOME‐EMPHASISVillenave d'Ornon33140France
| | - Yves Gibon
- Université de Bordeaux, INRAE, UMR Biologie du Fruit et PathologieVillenave d'Ornon33140France
- Bordeaux Metabolome, MetaboHUBPHENOME‐EMPHASISVillenave d'Ornon33140France
| | - Daniel Marino
- Department of Plant Biology and EcologyUniversity of the Basque Country (UPV/EHU)E‐48940LeioaSpain
- Ikerbasque, Basque Foundation for ScienceE‐48011BilbaoSpain
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11
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Dynamic Change of Carbon and Nitrogen Sources in Colonized Apples by Penicillium expansum. Foods 2022; 11:foods11213367. [PMID: 36359980 PMCID: PMC9657820 DOI: 10.3390/foods11213367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/19/2022] [Accepted: 10/22/2022] [Indexed: 12/03/2022] Open
Abstract
Penicillium expansum is a necrotrophic pathogen, which actively kills host cells and obtains nutrients from dead cells to achieve infection. However, few reports have elucidated the differential levels of carbon and nitrogen sources over increasing distances of the leading edge in fungal colonized fruit tissues during colonization. Our results showed that the highest consumption of sucrose and fructose, as well as the accumulation of glucose, were found in the decayed region of P. expansum-colonized ‘Delicious’ apple fruit compared with the healthy region at the leading edge and the healthy region 6 mm away from the leading edge. As nitrogen sources, the contents of methionine, glutamate, leucine, valine, isoleucine and serine were the lowest in the decayed region compared with the healthy regions during colonization. In addition, the titratable acidity, oxalic acid, citric acid, succinic acid and malic acid showed the highest accumulation in the decayed region compared with the healthy regions. P. expansum colonization induced the accumulation of saturated fatty acids in the decayed region, while the level of unsaturated fatty acids was the lowest. These changes were not observed in the healthy regions. These results indicated that P. expansum kills cells in advance of its colonization in order to obtain the nutrients of the apple tissue from the distal leading tissue of the colonized apple. It is understood that more carbon and nitrogen sources are required for fungal colonization, and a stronger defense response against colonization occurred in the fruit, causing the transit of nutrients from the distal tissue to the infected sites.
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12
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Singh DP, Bisen MS, Shukla R, Prabha R, Maurya S, Reddy YS, Singh PM, Rai N, Chaubey T, Chaturvedi KK, Srivastava S, Farooqi MS, Gupta VK, Sarma BK, Rai A, Behera TK. Metabolomics-Driven Mining of Metabolite Resources: Applications and Prospects for Improving Vegetable Crops. Int J Mol Sci 2022; 23:ijms232012062. [PMID: 36292920 PMCID: PMC9603451 DOI: 10.3390/ijms232012062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/13/2022] [Accepted: 09/23/2022] [Indexed: 11/16/2022] Open
Abstract
Vegetable crops possess a prominent nutri-metabolite pool that not only contributes to the crop performance in the fields, but also offers nutritional security for humans. In the pursuit of identifying, quantifying and functionally characterizing the cellular metabolome pool, biomolecule separation technologies, data acquisition platforms, chemical libraries, bioinformatics tools, databases and visualization techniques have come to play significant role. High-throughput metabolomics unravels structurally diverse nutrition-rich metabolites and their entangled interactions in vegetable plants. It has helped to link identified phytometabolites with unique phenotypic traits, nutri-functional characters, defense mechanisms and crop productivity. In this study, we explore mining diverse metabolites, localizing cellular metabolic pathways, classifying functional biomolecules and establishing linkages between metabolic fluxes and genomic regulations, using comprehensive metabolomics deciphers of the plant’s performance in the environment. We discuss exemplary reports covering the implications of metabolomics, addressing metabolic changes in vegetable plants during crop domestication, stage-dependent growth, fruit development, nutri-metabolic capabilities, climatic impacts, plant-microbe-pest interactions and anthropogenic activities. Efforts leading to identify biomarker metabolites, candidate proteins and the genes responsible for plant health, defense mechanisms and nutri-rich crop produce are documented. With the insights on metabolite-QTL (mQTL) driven genetic architecture, molecular breeding in vegetable crops can be revolutionized for developing better nutritional capabilities, improved tolerance against diseases/pests and enhanced climate resilience in plants.
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Affiliation(s)
- Dhananjaya Pratap Singh
- ICAR-Indian Institute of Vegetable Research, Jakhini, Shahanshahpur, Varanasi 221305, India
- Correspondence:
| | - Mansi Singh Bisen
- ICAR-Indian Institute of Vegetable Research, Jakhini, Shahanshahpur, Varanasi 221305, India
| | - Renu Shukla
- Indian Council of Agricultural Research (ICAR), Krishi Bhawan, Dr. Rajendra Prasad Road, New Delhi 110001, India
| | - Ratna Prabha
- ICAR-Indian Agricultural Statistics Research Institute, Centre for Agricultural Bioinformatics, Library Avenue, Pusa, New Delhi 110012, India
| | - Sudarshan Maurya
- ICAR-Indian Institute of Vegetable Research, Jakhini, Shahanshahpur, Varanasi 221305, India
| | - Yesaru S. Reddy
- ICAR-Indian Institute of Vegetable Research, Jakhini, Shahanshahpur, Varanasi 221305, India
| | - Prabhakar Mohan Singh
- ICAR-Indian Institute of Vegetable Research, Jakhini, Shahanshahpur, Varanasi 221305, India
| | - Nagendra Rai
- ICAR-Indian Institute of Vegetable Research, Jakhini, Shahanshahpur, Varanasi 221305, India
| | - Tribhuwan Chaubey
- ICAR-Indian Institute of Vegetable Research, Jakhini, Shahanshahpur, Varanasi 221305, India
| | - Krishna Kumar Chaturvedi
- ICAR-Indian Agricultural Statistics Research Institute, Centre for Agricultural Bioinformatics, Library Avenue, Pusa, New Delhi 110012, India
| | - Sudhir Srivastava
- ICAR-Indian Agricultural Statistics Research Institute, Centre for Agricultural Bioinformatics, Library Avenue, Pusa, New Delhi 110012, India
| | - Mohammad Samir Farooqi
- ICAR-Indian Agricultural Statistics Research Institute, Centre for Agricultural Bioinformatics, Library Avenue, Pusa, New Delhi 110012, India
| | - Vijai Kumar Gupta
- Biorefining and Advanced Materials Research Centre, Scotland’s Rural College, Kings Buildings, West Mains Road, Edinburgh EH9 3JG, UK
| | - Birinchi K. Sarma
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Anil Rai
- ICAR-Indian Agricultural Statistics Research Institute, Centre for Agricultural Bioinformatics, Library Avenue, Pusa, New Delhi 110012, India
| | - Tusar Kanti Behera
- ICAR-Indian Institute of Vegetable Research, Jakhini, Shahanshahpur, Varanasi 221305, India
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13
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Dussarrat T, Prigent S, Latorre C, Bernillon S, Flandin A, Díaz FP, Cassan C, Van Delft P, Jacob D, Varala K, Joubes J, Gibon Y, Rolin D, Gutiérrez RA, Pétriacq P. Predictive metabolomics of multiple Atacama plant species unveils a core set of generic metabolites for extreme climate resilience. THE NEW PHYTOLOGIST 2022; 234:1614-1628. [PMID: 35288949 PMCID: PMC9324839 DOI: 10.1111/nph.18095] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
Current crop yield of the best ideotypes is stagnating and threatened by climate change. In this scenario, understanding wild plant adaptations in extreme ecosystems offers an opportunity to learn about new mechanisms for resilience. Previous studies have shown species specificity for metabolites involved in plant adaptation to harsh environments. Here, we combined multispecies ecological metabolomics and machine learning-based generalized linear model predictions to link the metabolome to the plant environment in a set of 24 species belonging to 14 families growing along an altitudinal gradient in the Atacama Desert. Thirty-nine common compounds predicted the plant environment with 79% accuracy, thus establishing the plant metabolome as an excellent integrative predictor of environmental fluctuations. These metabolites were independent of the species and validated both statistically and biologically using an independent dataset from a different sampling year. Thereafter, using multiblock predictive regressions, metabolites were linked to climatic and edaphic stressors such as freezing temperature, water deficit and high solar irradiance. These findings indicate that plants from different evolutionary trajectories use a generic metabolic toolkit to face extreme environments. These core metabolites, also present in agronomic species, provide a unique metabolic goldmine for improving crop performances under abiotic pressure.
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Affiliation(s)
- Thomas Dussarrat
- Departamento de Genética Molecular y MicrobiologíaPontificia Universidad Católica de ChileFONDAP Center for Genome Regulation and Millenium Institute for Integrative Biology (iBio)Av Libertador Bernardo O'Higgins 340SantiagoChile
- Univ. BordeauxINRAEUMR1332 BFP, 33882Villenave d'OrnonFrance
| | - Sylvain Prigent
- Univ. BordeauxINRAEUMR1332 BFP, 33882Villenave d'OrnonFrance
- Bordeaux MetabolomeMetaboHUBPHENOME‐EMPHASIS33140Villenave d'OrnonFrance
| | - Claudio Latorre
- Departamento de EcologíaPontificia Universidad Católica de ChileAv Libertador Bernardo O'Higgins 340SantiagoChile
- Institute of Ecology and Biodiversity (IEB)Las Palmeras3425ÑuñoaSantiagoChile
| | - Stéphane Bernillon
- Univ. BordeauxINRAEUMR1332 BFP, 33882Villenave d'OrnonFrance
- Bordeaux MetabolomeMetaboHUBPHENOME‐EMPHASIS33140Villenave d'OrnonFrance
| | - Amélie Flandin
- Univ. BordeauxINRAEUMR1332 BFP, 33882Villenave d'OrnonFrance
- Bordeaux MetabolomeMetaboHUBPHENOME‐EMPHASIS33140Villenave d'OrnonFrance
| | - Francisca P. Díaz
- Departamento de Genética Molecular y MicrobiologíaPontificia Universidad Católica de ChileFONDAP Center for Genome Regulation and Millenium Institute for Integrative Biology (iBio)Av Libertador Bernardo O'Higgins 340SantiagoChile
| | - Cédric Cassan
- Univ. BordeauxINRAEUMR1332 BFP, 33882Villenave d'OrnonFrance
- Bordeaux MetabolomeMetaboHUBPHENOME‐EMPHASIS33140Villenave d'OrnonFrance
| | - Pierre Van Delft
- Bordeaux MetabolomeMetaboHUBPHENOME‐EMPHASIS33140Villenave d'OrnonFrance
- Laboratoire de Biogenèse Membranaire, CNRSUniv. Bordeaux, UMR 5200Villenave d'OrnonFrance
| | - Daniel Jacob
- Univ. BordeauxINRAEUMR1332 BFP, 33882Villenave d'OrnonFrance
- Bordeaux MetabolomeMetaboHUBPHENOME‐EMPHASIS33140Villenave d'OrnonFrance
| | - Kranthi Varala
- Department of Horticulture and Landscape ArchitecturePurdue UniversityWest LafayetteIN47907USA
- Center for Plant BiologyPurdue UniversityWest LafayetteIN47907USA
| | - Jérôme Joubes
- Laboratoire de Biogenèse Membranaire, CNRSUniv. Bordeaux, UMR 5200Villenave d'OrnonFrance
| | - Yves Gibon
- Univ. BordeauxINRAEUMR1332 BFP, 33882Villenave d'OrnonFrance
- Bordeaux MetabolomeMetaboHUBPHENOME‐EMPHASIS33140Villenave d'OrnonFrance
| | - Dominique Rolin
- Univ. BordeauxINRAEUMR1332 BFP, 33882Villenave d'OrnonFrance
- Bordeaux MetabolomeMetaboHUBPHENOME‐EMPHASIS33140Villenave d'OrnonFrance
| | - Rodrigo A. Gutiérrez
- Departamento de Genética Molecular y MicrobiologíaPontificia Universidad Católica de ChileFONDAP Center for Genome Regulation and Millenium Institute for Integrative Biology (iBio)Av Libertador Bernardo O'Higgins 340SantiagoChile
| | - Pierre Pétriacq
- Univ. BordeauxINRAEUMR1332 BFP, 33882Villenave d'OrnonFrance
- Bordeaux MetabolomeMetaboHUBPHENOME‐EMPHASIS33140Villenave d'OrnonFrance
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14
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Catoni M, Alvarez-Venegas R, Worrall D, Holroyd G, Barraza A, Luna E, Ton J, Roberts MR. Long-Lasting Defence Priming by β-Aminobutyric Acid in Tomato Is Marked by Genome-Wide Changes in DNA Methylation. FRONTIERS IN PLANT SCIENCE 2022; 13:836326. [PMID: 35498717 PMCID: PMC9051511 DOI: 10.3389/fpls.2022.836326] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 03/23/2022] [Indexed: 05/26/2023]
Abstract
Exposure of plants to stress conditions or to certain chemical elicitors can establish a primed state, whereby responses to future stress encounters are enhanced. Stress priming can be long-lasting and likely involves epigenetic regulation of stress-responsive gene expression. However, the molecular events underlying priming are not well understood. Here, we characterise epigenetic changes in tomato plants primed for pathogen resistance by treatment with β-aminobutyric acid (BABA). We used whole genome bisulphite sequencing to construct tomato methylomes from control plants and plants treated with BABA at the seedling stage, and a parallel transcriptome analysis to identify genes primed for the response to inoculation by the fungal pathogen, Botrytis cinerea. Genomes of plants treated with BABA showed a significant reduction in global cytosine methylation, especially in CHH sequence contexts. Analysis of differentially methylated regions (DMRs) revealed that CHH DMRs were almost exclusively hypomethylated and were enriched in gene promoters and in DNA transposons located in the chromosome arms. Genes overlapping CHH DMRs were enriched for a small number of stress response-related gene ontology terms. In addition, there was significant enrichment of DMRs in the promoters of genes that are differentially expressed in response to infection with B. cinerea. However, the majority of genes that demonstrated priming did not contain DMRs, and nor was the overall distribution of methylated cytosines in primed genes altered by BABA treatment. Hence, we conclude that whilst BABA treatment of tomato seedlings results in characteristic changes in genome-wide DNA methylation, CHH hypomethylation appears only to target a minority of genes showing primed responses to pathogen infection. Instead, methylation may confer priming via in-trans regulation, acting at a distance from defence genes, and/or by targeting a smaller group of regulatory genes controlling stress responses.
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Affiliation(s)
- Marco Catoni
- School of Bioscience, University of Birmingham, Birmingham, United Kingdom
| | - Raul Alvarez-Venegas
- Departamento de Ingeniería Genética, CINVESTAV-IPN, Unidad Irapuato, Guanajuato, Mexico
| | - Dawn Worrall
- Lancaster Environment Centre, Lancaster University, Lancaster, United Kingdom
| | - Geoff Holroyd
- Lancaster Environment Centre, Lancaster University, Lancaster, United Kingdom
| | - Aarón Barraza
- CONACYT-CIBNOR, Centro de Investigaciones Biológicas del Noroeste, La Paz, Mexico
| | - Estrella Luna
- School of Bioscience, University of Birmingham, Birmingham, United Kingdom
| | - Jurriaan Ton
- School of Biosciences, Institute of Sustainable Food, University of Sheffield, Sheffield, United Kingdom
| | - Michael R. Roberts
- Lancaster Environment Centre, Lancaster University, Lancaster, United Kingdom
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15
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16
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Martins J, Pétriacq P, Flandin A, Gómez-Cadenas A, Monteiro P, Pinto G, Canhoto J. Genotype determines Arbutus unedo L. physiological and metabolomic responses to drought and recovery. FRONTIERS IN PLANT SCIENCE 2022; 13:1011542. [PMID: 36483964 PMCID: PMC9723149 DOI: 10.3389/fpls.2022.1011542] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 10/24/2022] [Indexed: 05/13/2023]
Abstract
Strawberry tree (Arbutus unedo) is a small resilient species with a circum-Mediterranean distribution, high ecological relevance in southern European forests and with several economical applications. As most orchards are usually installed on marginal lands where plants usually face severe drought, selecting plants that can better cope with water restriction is critical, and a better understanding of the tolerance mechanisms is required. Strawberry tree plants under drought follow a typical isohydric strategy, by limiting transpiration through stomata closure. However, the contribution of genotype and its bio-geographic origin on plant performance needs clarification, as well as the involvement of a specific metabolic reactions associated with the mechanical response. To test this hypothesis, several eco-physiological and biochemical parameters were assessed on different genotypes, and the metabolic profiles studied, including important stress-related phytohormones, on plants under different water regimes (plants watered to 70% and 18% field capacity) and a recovery assay. A contrasting drought tolerance was found in plants from different genotypes, associated with physiological and metabolic responses. Metabolomics revealed more than 500 metabolic features were differentially accumulated, including abscisic and salicylic acids, for the genotype with better performance under drought (A4). This genotype also recovered faster when the imposed stress was interrupted, thus indicating the relevance of metabolic adaptation under water deficit conditions. By correlating carbon assimilation with identified metabolites, some proved to be satisfactory predictors of plant performance under drought and might be used for marker assisted breeding. Therefore, our study proves the importance of genotype as a major selection criterion of resistant plants to drought and provides empirical knowledge of the metabolic response involved. We also hypothesized the involvement of phenolics on response mechanisms under drought, which is worth to be explored to shed light on the metabolic pathways involved in plant response to water stress.
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Affiliation(s)
- João Martins
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, Coimbra, Portugal
- *Correspondence: João Martins,
| | - Pierre Pétriacq
- UMR BFP, University Bordeaux, INRAE, Villenave d’Ornon, France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, Villenave d’Ornon, France
| | - Amélie Flandin
- UMR BFP, University Bordeaux, INRAE, Villenave d’Ornon, France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, Villenave d’Ornon, France
| | - Aurelio Gómez-Cadenas
- Departamento de Ciencias Agrarias y del Medio Natural, Universitat Jaume I, Castelló, Spain
| | - Pedro Monteiro
- Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, Aveiro, Portugal
| | - Glória Pinto
- Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, Aveiro, Portugal
| | - Jorge Canhoto
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, Coimbra, Portugal
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17
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Allwood JW, Williams A, Uthe H, van Dam NM, Mur LAJ, Grant MR, Pétriacq P. Unravelling Plant Responses to Stress-The Importance of Targeted and Untargeted Metabolomics. Metabolites 2021; 11:558. [PMID: 34436499 PMCID: PMC8398504 DOI: 10.3390/metabo11080558] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/10/2021] [Accepted: 08/16/2021] [Indexed: 12/19/2022] Open
Abstract
Climate change and an increasing population, present a massive global challenge with respect to environmentally sustainable nutritious food production. Crop yield enhancements, through breeding, are decreasing, whilst agricultural intensification is constrained by emerging, re-emerging, and endemic pests and pathogens, accounting for ~30% of global crop losses, as well as mounting abiotic stress pressures, due to climate change. Metabolomics approaches have previously contributed to our knowledge within the fields of molecular plant pathology and plant-insect interactions. However, these remain incredibly challenging targets, due to the vast diversity in metabolite volatility and polarity, heterogeneous mixtures of pathogen and plant cells, as well as rapid rates of metabolite turn-over. Unravelling the systematic biochemical responses of plants to various individual and combined stresses, involves monitoring signaling compounds, secondary messengers, phytohormones, and defensive and protective chemicals. This demands both targeted and untargeted metabolomics approaches, as well as a range of enzymatic assays, protein assays, and proteomic and transcriptomic technologies. In this review, we focus upon the technical and biological challenges of measuring the metabolome associated with plant stress. We illustrate the challenges, with relevant examples from bacterial and fungal molecular pathologies, plant-insect interactions, and abiotic and combined stress in the environment. We also discuss future prospects from both the perspective of key innovative metabolomic technologies and their deployment in breeding for stress resistance.
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Affiliation(s)
- James William Allwood
- Environmental and Biochemical Sciences, James Hutton Institute, Errol Road, Invergowrie, Dundee DD2 5DA, UK
| | - Alex Williams
- School of Earth and Environmental Sciences, The University of Manchester, Oxford Road, Manchester M13 9PT, UK;
- Department of Animal and Plant Sciences, Biosciences, The University of Sheffield Western Bank, Sheffield S10 2TN, UK
| | - Henriette Uthe
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Molecular Interaction Ecology Group, Friedrich-Schiller University Jena, Puschstr. 4, 04103 Leipzig, Germany; (H.U.); (N.M.v.D.)
| | - Nicole M. van Dam
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Molecular Interaction Ecology Group, Friedrich-Schiller University Jena, Puschstr. 4, 04103 Leipzig, Germany; (H.U.); (N.M.v.D.)
| | - Luis A. J. Mur
- Institute of Biological, Environmental and Rural Sciences (IBERS), Edward Llwyd Building, Aberystwyth University, Aberystwyth SY23 3DA, UK;
| | - Murray R. Grant
- Gibbet Hill Campus, School of Life Sciences, The University of Warwick, Coventry CV4 7AL, UK;
| | - Pierre Pétriacq
- UMR 1332 Fruit Biology and Pathology, Centre INRAE de Nouvelle Aquitaine Bordeaux, University of Bordeaux, 33140 Villenave d’Ornon, France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, Centre INRAE de Nouvelle Aquitaine-Bordeaux, 33140 Villenave d’Ornon, France
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Singh RR, Pajar JA, Audenaert K, Kyndt T. Induced Resistance by Ascorbate Oxidation Involves Potentiating of the Phenylpropanoid Pathway and Improved Rice Tolerance to Parasitic Nematodes. FRONTIERS IN PLANT SCIENCE 2021; 12:713870. [PMID: 34456953 PMCID: PMC8386471 DOI: 10.3389/fpls.2021.713870] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 07/08/2021] [Indexed: 05/07/2023]
Abstract
Anticipating an increased ecological awareness, scientists have been exploring new strategies to reduce the use of chemical pesticides to control pests and diseases. Triggering the intrinsic plant defense system is one of the promising strategies to reduce yield loss by pathogenic organisms, such as nematodes. Ascorbate oxidase (AO) enzyme plays an important role in plant defense by regulating the apoplastic ascorbate/dehydroascorbate (DHA) ratio via the ascorbate oxidation process. Ascorbate oxidation is known to induce systemic resistance in rice against parasitic root-knot nematodes (RKN). Here, we sought to evaluate if AO- or DHA-induced resistance (IR) against RKN M. graminicola involves activation of the phenylpropanoid pathway and whether this IR phenotype has potential effects on growth of rice seedlings under stressed and unstressed conditions. Our results show that AO/DHA-IR against these parasitic nematodes is dependent on activation of phenylalanine ammonia lyase (PAL). However, application of reduced ascorbic acid (AA) did not induce this response. Gene expression analysis via qRT-PCR showed that OsPAL2 and OsPAL4 are highly expressed in AO/DHA-sprayed nematode-infected roots and PAL-activity measurements confirmed that AO/DHA spraying triggers the plants for primed activation of this enzyme upon nematode infection. AO/DHA-IR is not effective in plants sprayed with a chemical PAL inhibitor confirming that AO/DHA-induced resistance is dependent on PAL activity. Improved plant growth and low nematode infection in AO/DHA-sprayed plants was found to be correlated with an increase in shoot chlorophyll fluorescence (Fv/Fm), chlorophyll index (ChlIdx), and modified anthocyanin reflection index which were proven to be good above-ground parameters for nematode infestation. A detailed growth analysis confirmed the improved growth of AO/DHA-treated plants under nematode-infected conditions. Taken together, our results indicate that ascorbate oxidation enhances the phenylpropanoid-based response to nematode infection and leads to a tolerance phenotype in treated rice plants.
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Affiliation(s)
- Richard Raj Singh
- Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Jessil Ann Pajar
- Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Kris Audenaert
- Department of Plants and Crops, Ghent University, Ghent, Belgium
| | - Tina Kyndt
- Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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19
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Rubio B, Fernandez O, Cosson P, Berton T, Caballero M, Lion R, Roux F, Bergelson J, Gibon Y, Schurdi-Levraud V. Metabolic Profile Discriminates and Predicts Arabidopsis Susceptibility to Virus under Field Conditions. Metabolites 2021; 11:metabo11040230. [PMID: 33918649 PMCID: PMC8069729 DOI: 10.3390/metabo11040230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/27/2021] [Accepted: 04/02/2021] [Indexed: 12/13/2022] Open
Abstract
As obligatory parasites, plant viruses alter host cellular metabolism. There is a lack of information on the variability of virus-induced metabolic responses among genetically diverse plants in a natural context with daily changing conditions. To decipher the metabolic landscape of plant-virus interactions in a natural setting, twenty-six and ten accessions of Arabidopsis thaliana were inoculated with Turnip mosaic virus (TuMV), in two field experiments over 2 years. The accessions were measured for viral accumulation, above-ground biomass, targeted and untargeted metabolic profiles. The phenotypes of the accessions ranged from susceptibility to resistance. Susceptible and resistant accessions were shown to have different metabolic routes after inoculation. Susceptible genotypes accumulate primary and secondary metabolites upon infection, at the cost of hindered growth. Twenty-one metabolic signatures significantly accumulated in resistant accessions whereas they maintained their growth as mock-inoculated plants without biomass penalty. Metabolic content was demonstrated to discriminate and be highly predictive of the susceptibility of inoculated Arabidopsis. This study is the first to describe the metabolic landscape of plant-virus interactions in a natural setting and its predictive link to susceptibility. It provides new insights on plant-virus interactions. In this undomesticated species and in ecologically realistic conditions, growth and resistance are in a permanent conversation.
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Affiliation(s)
- Bernadette Rubio
- Université de Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, F-33140 Villenave d’Ornon, France; (B.R.); (O.F.); (P.C.); (T.B.); (M.C.); (R.L.); (Y.G.)
| | - Olivier Fernandez
- Université de Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, F-33140 Villenave d’Ornon, France; (B.R.); (O.F.); (P.C.); (T.B.); (M.C.); (R.L.); (Y.G.)
| | - Patrick Cosson
- Université de Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, F-33140 Villenave d’Ornon, France; (B.R.); (O.F.); (P.C.); (T.B.); (M.C.); (R.L.); (Y.G.)
| | - Thierry Berton
- Université de Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, F-33140 Villenave d’Ornon, France; (B.R.); (O.F.); (P.C.); (T.B.); (M.C.); (R.L.); (Y.G.)
| | - Mélodie Caballero
- Université de Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, F-33140 Villenave d’Ornon, France; (B.R.); (O.F.); (P.C.); (T.B.); (M.C.); (R.L.); (Y.G.)
| | - Roxane Lion
- Université de Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, F-33140 Villenave d’Ornon, France; (B.R.); (O.F.); (P.C.); (T.B.); (M.C.); (R.L.); (Y.G.)
| | - Fabrice Roux
- CNRS, INRAE, Université de Toulouse, LIPM, F-31320 Castanet-Tolosan, France;
| | - Joy Bergelson
- Ecology & Evolution, University of Chicago, 1101 E 57th St, Chicago, IL 60637, USA;
| | - Yves Gibon
- Université de Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, F-33140 Villenave d’Ornon, France; (B.R.); (O.F.); (P.C.); (T.B.); (M.C.); (R.L.); (Y.G.)
| | - Valérie Schurdi-Levraud
- Université de Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, F-33140 Villenave d’Ornon, France; (B.R.); (O.F.); (P.C.); (T.B.); (M.C.); (R.L.); (Y.G.)
- Correspondence:
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20
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Redox status regulates subcelluar localization of PpTGA1 associated with a BABA-induced priming defence against Rhizopus rot in peach fruit. Mol Biol Rep 2020; 47:6657-6668. [PMID: 32794133 DOI: 10.1007/s11033-020-05719-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 08/02/2020] [Indexed: 12/29/2022]
Abstract
This study attempted to characterize the involvement of a change in the redox status and subcellular localization in the BABA-induced priming resistance of peach fruit against Rhizopus rot. Specifically, 50 mM BABA primed the peaches for the enhanced disease resistance against R. stolonifer, as demonstrated by suppression of the disease development upon pathogen challenge accompanied by the clearly elevated level of TGA transcription factor (PpTGA1) and NPR1 gene (PpNPR1). In addition, the BABA elicitation enhanced the activities of a series of critical enzymes in the PPP and AsA-GSH cycle, and eventually promoted the NADPH and GSH pools, which altered the intracellular redox state towards a highly reductive condition. Additionally, PpTGA1-GFP was localized in the cytoplasm in the absence of BABA treatment or R. stolonifer inoculation, while BABA elicitation plus R. stolonifer inoculation caused PpTGA1-GFP to specifically translocate to the nucleus, where it interacted with PpNPR1 and regulated the positive expression of PR genes. Therefore, the observations implied that BABA could promote the reduction of the redox state, resulting in the translocation of PpTGA1 to the nucleus, which was a prerequisite for the induction of a priming defence against Rhizopus rot in peach.
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Special Issue on "Fruit Metabolism and Metabolomics". Metabolites 2020; 10:metabo10060230. [PMID: 32503284 PMCID: PMC7344593 DOI: 10.3390/metabo10060230] [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: 05/29/2020] [Accepted: 06/01/2020] [Indexed: 12/19/2022] Open
Abstract
Over the past 10 years, knowledge about several aspects of fruit metabolism has been greatly improved. Notably, high-throughput metabolomic technologies have allowed quantifying metabolite levels across various biological processes, and identifying the genes that underly fruit development and ripening. This Special Issue is designed to exemplify the current use of metabolomics studies of temperate and tropical fruit for basic research as well as practical applications. It includes articles about different aspects of fruit biochemical phenotyping, fruit metabolism before and after harvest, including primary and specialized metabolisms, and bioactive compounds involved in growth and environmental responses. The effect of genotype, stages of development or fruit tissue on metabolomic profiles and corresponding metabolism regulations are addressed, as well as the combination of other omics with metabolomics for fruit metabolism studies.
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