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

Abstract

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.

Short-term transcriptomic analysis at organ scale reveals candidate genes involved in low N responses in NUE-contrasting tomato genotypes

“…In this study, the early molecular responses to low NO 3 -(LN) at tissue scale in two NUE contrasting tomato genotypes, RO (N-use efficient) and UC82 (N-use inefficient) (Abenavoli et al, 2016;Aci et al, 2021), were evaluated. The tissue-specific transcriptome timecourse analysis revealed the highest LN-sensitivity of the root compared to the shoot, in contrast with other findings revealing the shoot as the more responsible tissue for low N (Renau-Morata et al, 2021). These results were confirmed by the number of Nresponsive genes (3,000 vs. 2,000), among which 482 and 395 were differentially expressed between genotypes in root and shoot, respectively (Table S3).…”

“…The transcriptomic approach contributed to understanding the changes regulating crop responses to abiotic stress such as low N availability as well as to identifying key genes related to N-stress tolerance comparing NUE-contrasting genotypes (Goel et al, 2018;Sinha et al, 2018;Subudhi et al, 2020;Sultana et al, 2020;Mauceri et al, 2021;Puccio et al, 2022). In tomato, transcriptomic analyses led to the identification of genes differentially regulated by N availability (Wang et al, 2001;Renau-Morata et al, 2021), while no comparative transcriptome profiling between NUE-contrasting genotypes in response to N starvation and resupply has been reported so far.…”

“…In tomato, an array analysis of the root revealed N-induced genes that play a role in N nutrition, including transport and assimilation genes related to C and N metabolism as well as water channels, phosphate, and potassium transporters (Wang et al, 2001). More recently, an integrative transcriptomic and metabolomic approach was able to identify pathways and key regulatory genes in response to low N, again in tomato (Renau-Morata et al, 2021). Currently, a comparative transcriptome analysis of NUE contrasting genotypes in response to early LN resupply is not yet available.…”

Nitrogen-mediated metabolic patterns of susceptibility to Botrytis cinerea infection in tomato (Solanum lycopersicum) stems

“…S3. At up to 10 mM NO 3 − , higher N resulted in higher growth, measured by plant height and stem mass, suggesting a probable limitation in the photosynthetic capacity (Renau-Morata et al 2021 ). The stem water content was also significantly higher at 10 and 20 mM NO 3 − than at lower N supply levels, possibly related to the control of root hydraulic conductance through NO 3 − transporters and aquaporins (Cramer et al 2009 ; Tyerman et al 2017 ).…”

Uncovering Pathways Highly Correlated to NUE through a Combined Metabolomics and Transcriptomics Approach in Eggplant

“…Finally, after a long-term N-limiting condition (T 2 ), AM222 showed a higher accumulation in D-glucose and sucrose (starch and sucrose metabolism), while 67-3 evidenced a reduction in all the metabolites in the alanine, aspartate, and glutamate metabolism, but a slight L-glutamine accumulation. Sugars frequently play an important role as osmoprotectors, as membrane stabilizers, in stress buffering [ 24 ], as well as in the regulation of growth, photosynthesis, carbon partitioning, carbohydrate and lipid metabolism, protein synthesis, and gene expression [ 25 ]. Interestingly, the most N-use-efficient genotype AM222 compared to the other genotypes showed higher accumulation of phenylalanine and citric acid that were reported to confer tolerance to abiotic stress, improving growth and yield in many crop species [ 26 ].…”