Nitrate-responsive transcriptome analysis reveals additional genes/processes and associated traits viz. height, tillering, heading date, stomatal density and yield in japonica rice

Mandal, Vikas Kumar; Jangam, Annie Prasanna; Chakraborty, Navjyoti; Raghuram, Nandula

doi:10.1007/s00425-021-03816-9

Cited by 15 publications

(39 citation statements)

References 72 publications

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“…Our previous transcriptomic analyses revealed many unreported genes/processes involved in nitrate-response in Indica rice ( Pathak et al, 2020 ) as well as in Japonica ( Mandal et al, 2022 ). Further, a meta-analysis of all N-responsive transcriptomes together with yield-related genes predicted and shortlisted some NUE-related genes ( Kumari et al, 2021 ).…”

Section: Discussionmentioning

confidence: 99%

“…Photosynthesis is considered to be a key process that determines N response and NUE in crops ( Long, 2020 ), through the regulation of associated genes in rice ( Kumari et al, 2021 ; Sharma et al, 2021 ; Mandal et al, 2022 ). We sought to further validate these findings using contrasting genotypes in this study.…”

Section: Discussionmentioning

confidence: 99%

“…It is the third most-produced and second most consumed crop in the world, apart from being a post-genomic model crop. This is evidenced by genome sequences of 3000 rice genotypes ( Li et al, 2014 ) and growing functional genomics of N ( Li et al, 2018 ; Pathak et al, 2020 ; Mandal et al, 2022 ). Further, the recent NUE phenotype ( Sharma et al, 2018 , 2021 ; Pathak et al, 2021 ) growing quantitative trait loci (QTL) and genotyping ( Kumari et al, 2021 ) make rice an ideal target crop for NUE improvement.…”

Section: Introductionmentioning

confidence: 99%

“…This is one of the reasons why nitrate-transcriptomes are predominant even in the rice functional genomics literature (listed in Kumari et al, 2021 ). They are also available for subspecies Indica ( Pathak et al, 2020 ) and Japonica ( Mandal et al, 2022 ).…”

Section: Introductionmentioning

confidence: 99%

“…In addition to these genes, some interesting QTLs have been identified as linked to NUE ( Sinha et al, 2018 ; Waqas et al, 2018 ; Kumari et al, 2021 ). Transcriptomic studies in rice revealed thousands of nitrate-responsive genes totaling 23,626 numbers ( Mandal et al, 2022 ) but they were all limited to single genotypes. This limits the utility of functional genomic studies in the genetic dissection of NUE.…”

Section: Introductionmentioning

confidence: 99%

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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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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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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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Reactive Nitrogen in Climate Change, Crop Stress, and Sustainable Agriculture

Raghuram

2023

Global Climate Change and Plant Stress Management

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Nitrate-responsive transcriptome analysis of rice RGA1 mutant reveals the role of G-protein alpha subunit in negative regulation of nitrogen-sensitivity and use efficiency

Prasanna,

Mandal,

Kumar

et al. 2023

Plant Cell Rep

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Nitrogen (N) use e ciency (NUE) is important for sustainable agriculture. G-protein signalling was implicated in N-response/NUE in rice, but needs genetic characterization of the role of α subunit (RGA1). We found that RGA1 knock-out mutant in japonica rice exhibited lesser nitrate-dose sensitivity, higher yield and NUE relative to the wild type (WT). We investigated its genomewide basis using nitrateresponsive rga1 transcriptome relative to WT. It revealed 3,416 differentially expressed genes (DEGs), including 719 associated with development, grain yield and phenotypic traits for NUE. The upregulated DEGs were related to photosynthesis, chlorophyll, tetrapyrrole and porphyrin biosynthesis, while the downregulated DEGs belonged to cellular protein metabolism and transport, small GTPase signalling, cell redox homeostasis etc. RT-qPCR validated 26 nitrate-responsive DEGs across functional categories. Physiological validation of nitrate-response in the mutant and WT at 1.5 and 15 mM doses revealed higher chlorophyll and stomatal length but decreased stomatal density, conductance and transpiration.The consequent increase in photosynthesis and water use e ciency may contribute to higher yield and NUE in the mutant, whereas the WT was N-dose sensitive. The mutant was not as N dose-responsive as WT in shoot/root growth, productive tillers and heading date, but equally responsive as WT in total N and protein content. RGA1mutant is less impacted by higher N-dose or salt stress in terms of yield, protein content, photosynthetic performance, relative water content, water use e ciency and catalase activity. PPI-network analyses revealed known NUE-related proteins as RGA1 interactors. Therefore, RGA1 regulates N-dose sensitivity and NUE in rice. Key MessageNitrate-responsive transcriptomic, phenotypic and physiological analyses of rice RGA1 mutant revealed many novel RGA1-regulated genes/processes/traits related to nitrogen use e ciency, and provided robust genetic evidence of RGA1-regulation of NUE.

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Nitrate-responsive transcriptome analysis reveals additional genes/processes and associated traits viz. height, tillering, heading date, stomatal density and yield in japonica rice

Cited by 15 publications

References 72 publications

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

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

Reactive Nitrogen in Climate Change, Crop Stress, and Sustainable Agriculture

Nitrate-responsive transcriptome analysis of rice RGA1 mutant reveals the role of G-protein alpha subunit in negative regulation of nitrogen-sensitivity and use efficiency

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