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Article

Integrative Transcriptomic and Metabolomic Analysis at Organ Scale Reveals Gene Modules Involved in the Responses to Suboptimal Nitrogen Supply in Tomato

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Departamento de Biología Vegetal, Universitat de València, 46022 València, Spain
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Departamento de Producción Vegetal, Universitat Politècnica de València, 46022 València, Spain
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Joint Research Unit UJI-UPV Improvement of Agri-Food Quality, COMAV, Universitat Politècnica de València, 46022 València, Spain
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Centro de Biotecnología y Genómica de Plantas, INIA-CSIC-Universidad Politécnica de Madrid, 28223 Madrid, Spain
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Bioinformatic and Genomic Group, COMAV-UPV, Universitat Politècnica de València, 28223 València, Spain
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Institute of Biochemistry and Microbiology, Faculty of Sciences, Universidad Austral de Chile, Valdivia 5110566, Chile
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ANID–Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile
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Authors to whom correspondence should be addressed.
Academic Editor: Agnieszka Golicz
Agronomy 2021, 11(7), 1320; https://doi.org/10.3390/agronomy11071320
Received: 6 May 2021 / Revised: 14 June 2021 / Accepted: 24 June 2021 / Published: 29 June 2021
(This article belongs to the Special Issue Functional Genomics Research of Crops)
The development of high nitrogen use efficiency (NUE) cultivars under low N inputs is required for sustainable agriculture. To this end, in this study, we analyzed the impact of long-term suboptimal N conditions on the metabolome and transcriptome of tomato to identify specific molecular processes and regulators at the organ scale. Physiological and metabolic analysis revealed specific responses to maintain glutamate, asparagine, and sucrose synthesis in leaves for partition to sustain growth, while assimilated C surplus is stored in the roots. The transcriptomic analyses allowed us to identify root and leaf sets of genes whose expression depends on N availability. GO analyses of the identified genes revealed conserved biological functions involved in C and N metabolism and remobilization as well as other specifics such as the mitochondrial alternative respiration and chloroplastic cyclic electron flux. In addition, integrative analyses uncovered N regulated genes in root and leaf clusters, which are positively correlated with changes in the levels of different metabolites such as organic acids, amino acids, and formate. Interestingly, we identified transcription factors with high identity to TGA4, ARF8, HAT22, NF-YA5, and NLP9, which play key roles in N responses in Arabidopsis. Together, this study provides a set of nitrogen-responsive genes in tomato and new putative targets for tomato NUE and fruit quality improvement under limited N supply. View Full-Text
Keywords: nitrogen; suboptimal conditions; metabolome; transcriptome; growth; leaves; roots; Solanum lycopersicum; tomato nitrogen; suboptimal conditions; metabolome; transcriptome; growth; leaves; roots; Solanum lycopersicum; tomato
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MDPI and ACS Style

Renau-Morata, B.; Molina, R.-V.; Minguet, E.G.; Cebolla-Cornejo, J.; Carrillo, L.; Martí, R.; García-Carpintero, V.; Jiménez-Benavente, E.; Yang, L.; Cañizares, J.; Canales, J.; Medina, J.; Nebauer, S.G. Integrative Transcriptomic and Metabolomic Analysis at Organ Scale Reveals Gene Modules Involved in the Responses to Suboptimal Nitrogen Supply in Tomato. Agronomy 2021, 11, 1320. https://doi.org/10.3390/agronomy11071320

AMA Style

Renau-Morata B, Molina R-V, Minguet EG, Cebolla-Cornejo J, Carrillo L, Martí R, García-Carpintero V, Jiménez-Benavente E, Yang L, Cañizares J, Canales J, Medina J, Nebauer SG. Integrative Transcriptomic and Metabolomic Analysis at Organ Scale Reveals Gene Modules Involved in the Responses to Suboptimal Nitrogen Supply in Tomato. Agronomy. 2021; 11(7):1320. https://doi.org/10.3390/agronomy11071320

Chicago/Turabian Style

Renau-Morata, Begoña, Rosa-Victoria Molina, Eugenio G. Minguet, Jaime Cebolla-Cornejo, Laura Carrillo, Raúl Martí, Víctor García-Carpintero, Eva Jiménez-Benavente, Lu Yang, Joaquín Cañizares, Javier Canales, Joaquín Medina, and Sergio G. Nebauer 2021. "Integrative Transcriptomic and Metabolomic Analysis at Organ Scale Reveals Gene Modules Involved in the Responses to Suboptimal Nitrogen Supply in Tomato" Agronomy 11, no. 7: 1320. https://doi.org/10.3390/agronomy11071320

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