AUTHOR=Sunseri Francesco , Aci Meriem Miyassa , Mauceri Antonio , Caldiero Ciro , Puccio Guglielmo , Mercati Francesco , Abenavoli Maria Rosa 

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

JOURNAL=Frontiers in Plant Science

VOLUME=Volume 14 - 2023

YEAR=2023

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2023.1125378

DOI=10.3389/fpls.2023.1125378

ISSN=1664-462X

ABSTRACT=Understanding the complex regulatory network underlying plant nitrogen (N) responses associated with high Nitrogen Use Efficiency (NUE) is one of the main challenges for sustainable cropping systems. Nitrate (NO3-), acting as both N source and signal molecule, provokes a very fast transcriptome reprogramming allowing plants to adapt to its availability. These changes are genotype and tissue-specific, thus the comparison between contrasting genotypes is crucial to uncover high NUE mechanisms. Here, we compared, for the first time, the spatio-temporal transcriptome changes in both root and shoot of two NUE contrasting tomato genotypes, Regina Ostuni (high-NUE) and UC82 (low-NUE) in response to short-term (within 24h) low (LN) and high (HN) NO3- resupply. Using time-series transcriptome data (0, 8 and 24h), we identified 395 and 482 N-responsive genes differentially expressed (DEGs) between RO and UC82, in shoot and root, respectively. Protein kinase signaling pathway, plant hormone signal transduction and phenylpropanoid biosynthesis pathway resulted the main enriched metabolic pathways in shoot and root, respectively, up regulated in RO compared to UC82. Interestingly, several N transporters belonging to NRT and NPF families, such as NRT2.3, NRT2.4, NPF1.2 and NPF8.3, were found differential expressed between RO and UC82 genotypes, which might explain the contrasting NUE performances. Transcription factors (TFs) belonging to several families, such as ERF, LOB, GLK, NFYB, ARF, Zinc-finger, and MYB, were differentially expressed between genotypes in response to LN. A complementary Weighted Gene Co-expression Network Analysis (WGCNA) allowed to the identification of LN-responsive co-expression modules in RO shoot and root. The regulatory network analysis revealed the candidate genes that might have key function in short-term LN regulation. In particular, an Asparagine synthetase (ASNS), a CBL-interacting serine/threonine-protein kinase 1 (CIPK1), a Cytokinin riboside 5'-monophosphate phosphoribohydrolase (LOG8), a Glycosyltransferase (UGT73C4) and an ERF2 were identified in shoot, while a LRR receptor-like serine/threonine-protein kinase (FEI1) and two TFs NF-YB5 and LOB37 were identified in root. Our results revealed the potential candidate genes that independently and/or concurrently may regulate short-term low-N response, suggesting a key role played by cytokinin and ROS balancing in early LN regulation mechanisms adopted by the N-use efficient genotype RO.