Method for Preparation of Nutrient-depleted Soil for Determination of Plant Nutrient Requirements

Sharma, Nikhil; Kuchi, Surekha; Singh, Vineet; Raghuram, Nandula

doi:10.1080/00103624.2019.1648492

Cited by 11 publications

(13 citation statements)

References 25 publications

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“…The two genotypes, namely, Nidhi and Panvel1 were previously characterized as contrasting for NUE ( Sharma et al, 2018 , Sharma et al, 2021 ). Their potted whole plants were grown in nutrient-depleted sand as described earlier ( Sharma et al, 2019 ) to ensure precise control of the N-form (nitrate) and N-dose (1.5 or 15 mM) and avoid uncertainties typical in the field soils. The differential N-response and NUE of both the genotypes ( Figures 1A,B ) was confirmed by RT-qPCR analysis of the expression of nitrate reductase and nitrite reductase ( Figures 1C,D ).…”

Section: Discussionmentioning

confidence: 99%

“…Seeds of Nidhi were procured from the Indian Institute of Rice Research, Hyderabad, India, whereas seeds of Panvel1 were from Panvel, Maharashtra, India. Seeds of modal weight were selected ( Sharma et al, 2018 ) and surface sterilized using 0.1% mercuric chloride for 50 s followed by several washes with ultrapure water and allowed to soak in it for 2 h. They were sown in pots filled with nutrient-depleted sand ( Sharma et al, 2019 ) saturated with Arnon-Hoagland medium ( Hoagland and Arnon, 1950 ) with normal (15 mM) or low nitrate concentration (1.5 mM) as control and test conditions as described earlier ( Sharma et al, 2021 ). The pots were replenished with media to saturation every few days and plants were grown for 21 days in the greenhouse at 28 ° C and 70% relative humidity with 270 μmol m –2 s –1 light intensity and 12/12 h photoperiod.…”

Section: Methodsmentioning

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: Methodsmentioning

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 experimental design minimized internal variation within each genotype by using seeds of modal weight ( Sharma et al, 2018 ). External variation was minimized by using: (a) nutrient-depleted sand ( Sharma et al, 2019 ) to eliminate the roles of soil nutrients and microbial N-transformations; (b) defined sterilized media with known concentrations of either nitrate or urea as the sole N source; (c) controlled temperature, humidity and light. This design enabled the identification of even subtle differences in the effect of N form and dose on various parameters and genotypes.…”

Section: Discussionmentioning

confidence: 99%

“…Seeds of the above six rice genotypes were weighed individually and only seeds of modal weight ( + 0.5 mg) were used for the green-house studies to control intra-varietal variation ( Sitaramam et al, 2008 ; Sharma et al, 2018 ). They were surface-sterilized with 0.1% mercuric chloride for 50 s, followed by 8–10 washes with deionized water and soaked in deionized water for 2 h. They were then sown in pots filled to two-thirds of their height with nutrient-depleted sand, prepared by repeated washing till it had no detectable N as described earlier ( Sharma et al, 2019 ). Prior to sowing, the pots were saturated for 2 days with Arnon–Hoagland medium ( Hoagland and Arnon, 1950 ) containing nitrate or urea as the sole source of N at normal (15 mM N) or low level (1.5 mM N).…”

Section: Methodsmentioning

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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“…Indica ) namely Nidhi and Panvel1 were chosen, based on contrasting germination, yield and NUE (Sharma et al, 2018, Sharma et al, 2021). Their seeds of modal weight were surface-sterilized and grown in pots containing nutrient-depleted soil exactly as described (Sharma et al, 2018, Sharma et al, 2019). The pots were saturated with modified Arnon-Hoagland medium containing urea as the sole N source at 15 mM (normal) or 1.5 mM (low) concentration as control and test conditions as described earlier (Sharma et al 2021).…”

Section: Methodsmentioning

confidence: 99%

Genomewide basis for nitrogen use efficiency in contrasting genotypes of rice

Sharma

Jaiswal

Kumari

et al. 2022

Preprint

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Rice is an ideal crop with huge germplasm diversity and post-genomic resources for improvement of nitrogen (N) use efficiency (NUE). There is a paucity of comparative studies on rice genotypes contrasting for NUE, especially with urea, the predominant fertilizer in rice growing countries. In this study, low urea-responsive transcriptomes of contrasting rice genotypes namely Nidhi (low NUE) and Panvel1 (high NUE) were compared. They were based on whole plants grown for 21 days in pots containing nutrient-depleted soil fertilized with normal (15 mM) and low urea (1.5 mM) media. There were 1497 and 2819 differentially expressed genes (DEGs) in Nidhi and Panvel1, respectively, of which 271 were common. Though 1226 DEGs were genotype-specific in Nidhi and 2548 in Panvel1, there was far higher commonality in underlying processes. High NUE is associated with the urea-responsive regulation of other nutrient transporters, miRNAs, transcription factors and better photosynthesis, water use efficiency and post translational modifications. Many of their genes co-localized to NUE QTLs on chromosomes 1, 3 and 9. Field evaluation of the contrasting genotypes under different doses of urea revealed better performance of Panvel1 in different agronomic parameters including grain yield, transport/uptake efficiencies and NUE. Comparison of our urea-based transcriptomes with our previous nitrate-based transcriptomes from the same contrasting rice genotypes revealed many common processes despite large differences in their expression profiles. Our model proposes that differential involvement of transporters and transcription factors among others contributes to better urea uptake, translocation, utilization, flower development and yield for high NUE.SummaryRice genotypes with contrasting urea use efficiency differ in the role of transporters, transcription factors, miRNAs, post-translational modifications, photosynthesis and water use efficiency

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Method for Preparation of Nutrient-depleted Soil for Determination of Plant Nutrient Requirements

Cited by 11 publications

References 25 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

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

Genomewide basis for nitrogen use efficiency in contrasting genotypes of rice

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