Biological Determinants of Crop Nitrogen Use Efficiency and Biotechnological Avenues for Improvement

Sinha, Vimlendu Bhushan; Jangam, Annie Prasanna; Raghuram, Nandula

doi:10.1007/978-3-030-58065-0_11

Cited by 14 publications

(8 citation statements)

References 58 publications

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“…This knowledge is critical to dissecting the regulatory networks of this complex trait. 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.…”

Section: Discussionmentioning

confidence: 99%

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

Sunseri

Aci²,

Mauceri³

et al. 2023

Front. Plant Sci.

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BackgroundUnderstanding 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 an N source and a signal molecule, provokes 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 uncovering high NUE mechanisms.MethodsHere, 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 24 h) low (LN) and high (HN) NO3- resupply. ResultsUsing time-series transcriptome data (0, 8, and 24 h), we identified 395 and 482 N-responsive genes differentially expressed (DEGs) between RO and UC82 in shoot and root, respectively. Protein kinase signaling plant hormone signal transduction, and phenylpropanoid biosynthesis were the main enriched metabolic pathways in shoot and root, respectively, and were upregulated 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 differentially 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 the identification of LN-responsive co-expression modules in RO shoot and root. The regulatory network analysis revealed candidate genes that might have key functions 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 the shoot, while an LRR receptor-like serine/threonine-protein kinase (FEI1) and two TFs NF-YB5 and LOB37 were identified in the root. DiscussionOur results revealed 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.

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Section: Discussionmentioning

confidence: 99%

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

Sunseri

Aci²,

Mauceri³

et al. 2023

Front. Plant Sci.

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“…All other metabolites containing N are generated by transamination of amino acids, which also provide the main organic N-pool for translocation and secondary remobilization during senescence, which is particularly important in cereals ( Snyder and Tegeder, 2021 ). All these processes have been targeted for understanding and improving NUE with varying results ( Mandal et al, 2018 ; Raghuram and Sharma, 2019 ; Sinha et al, 2016 , 2020 ; Madan et al, 2022 ).…”

Section: Introductionmentioning

confidence: 99%

Comparative Transcriptomic Analyses of Nitrate-Response in Rice Genotypes With Contrasting Nitrogen Use Efficiency Reveals Common and Genotype-Specific Processes, Molecular Targets and Nitrogen Use Efficiency-Candidates

et al. 2022

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The genetic basis for nitrogen (N)-response and N use efficiency (NUE) must be found in N-responsive gene expression or protein regulation. Our transcriptomic analysis of nitrate response in two contrasting rice genotypes of Oryza sativa ssp. Indica (Nidhi with low NUE and Panvel1 with high NUE) revealed the processes/functions underlying differential N-response/NUE. The microarray analysis of low nitrate response (1.5 mM) relative to normal nitrate control (15 mM) used potted 21-days old whole plants. It revealed 1,327 differentially expressed genes (DEGs) exclusive to Nidhi and 666 exclusive to Panvel1, apart from 70 common DEGs, of which 10 were either oppositely expressed or regulated to different extents. Gene ontology analyses revealed that photosynthetic processes were among the very few processes common to both the genotypes in low N response. Those unique to Nidhi include cell division, nitrogen utilization, cytoskeleton, etc. in low N-response, whereas those unique to Panvel1 include signal transduction, protein import into the nucleus, and mitochondria. This trend of a few common but mostly unique categories was also true for transporters, transcription factors, microRNAs, and post-translational modifications, indicating their differential involvement in Nidhi and Panvel1. Protein-protein interaction networks constructed using DEG-associated experimentally validated interactors revealed subnetworks involved in cytoskeleton organization, cell wall, etc. in Nidhi, whereas in Panvel1, it was chloroplast development. NUE genes were identified by selecting yield-related genes from N-responsive DEGs and their co-localization on NUE-QTLs revealed the differential distribution of NUE-genes between genotypes but on the same chromosomes 1 and 3. Such hotspots are important for NUE breeders.

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“…While some improvement in agronomic NUE can be attained through slow-release fertilizers ( Li T. et al, 2018 ), bio-fertilizers ( Bargaz et al, 2018 ; Quevedo-Amaya et al, 2020 ) and crop management practices ( Guo et al, 2017 ; Cui et al, 2018 ; Santiago-Arenas et al, 2020 ), the improvement of inherent plant NUE has to be tackled biologically. The lack of a well-defined phenotype for N response and NUE has hampered biological interventions for crop improvement ( Mandal et al, 2018 ; Raghuram and Sharma, 2019 ; Sinha et al, 2020 ). However, there has been some recent progress in identifying phenotypic parameters for N-response/NUE in model plants ( Li et al, 2017 ).…”

Section: Introductionmentioning

confidence: 99%

“…There have been several attempts to find genes involved in N-response through functional genomics ( Pathak et al, 2020 ). Single gene transgenics were used to improve N-uptake, assimilation or remobilization, but with little improvement of NUE, if any ( Mandal et al, 2018 ; Raghuram and Sharma, 2019 ; Sinha et al, 2020 ). Recent attempts in rice have been more encouraging ( Fang et al, 2013 ; Fan et al, 2014 ; Sun et al, 2014 ), especially when NAR2.1 and NRT2.3a were co-overexpressed ( Chen et al, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

Nitrogen Use Efficiency Phenotype and Associated Genes: Roles of Germination, Flowering, Root/Shoot Length and Biomass

et al. 2021

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Crop improvement for Nitrogen Use Efficiency (NUE) requires a well-defined phenotype and genotype, especially for different N-forms. As N-supply enhances growth, we comprehensively evaluated 25 commonly measured phenotypic parameters for N response using 4 N treatments in six indica rice genotypes. For this, 32 replicate potted plants were grown in the green-house on nutrient-depleted sand. They were fertilized to saturation with media containing either nitrate or urea as the sole N source at normal (15 mM N) or low level (1.5 mM N). The variation in N-response among genotypes differed by N form/dose and increased developmentally from vegetative to reproductive parameters. This indicates survival adaptation by reinforcing variation in every generation. Principal component analysis segregated vegetative parameters from reproduction and germination. Analysis of variance revealed that relative to low level, normal N facilitated germination, flowering and vegetative growth but limited yield and NUE. Network analysis for the most connected parameters, their correlation with yield and NUE, ranking by Feature selection and validation by Partial least square discriminant analysis enabled shortlisting of eight parameters for NUE phenotype. It constitutes germination and flowering, shoot/root length and biomass parameters, six of which were common to nitrate and urea. Field-validation confirmed the NUE differences between two genotypes chosen phenotypically. The correspondence between multiple approaches in shortlisting parameters for NUE makes it a novel and robust phenotyping methodology of relevance to other plants, nutrients or other complex traits. Thirty-Four N-responsive genes associated with the phenotype have also been identified for genotypic characterization of NUE.

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Biological Determinants of Crop Nitrogen Use Efficiency and Biotechnological Avenues for Improvement

Cited by 14 publications

References 58 publications

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

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

Comparative Transcriptomic Analyses of Nitrate-Response in Rice Genotypes With Contrasting Nitrogen Use Efficiency Reveals Common and Genotype-Specific Processes, Molecular Targets and Nitrogen Use Efficiency-Candidates

Nitrogen Use Efficiency Phenotype and Associated Genes: Roles of Germination, Flowering, Root/Shoot Length and Biomass

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