Vegetative biomass production under different inorganic nitrogen forms of the USDA rice (Oryza sativa L.) diversity panel 1
Data files
Mar 17, 2025 version files 2.50 MB
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RDP1_Nform_data.csv
2.49 MB
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README.md
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Abstract
We characterized early vegetative biomass production in response to inorganic nitrogen source, ammonium (NH4+) or nitrate (NO3–), in 390 accessions from the USDA Rice Diversity Panel 1, which contains broad genetic diversity from the global germplasm. We grew these accessions under NO3– versus NH4+ nutrition, and under different concentrations of NH4+ as sole nitrogen sources in a greenhouse with day/night temperatures approximately 28°/24°C under natural sunlight in Davis, California (38°32'20.2"N 121°46'52.5"W) in 2018-2019. This dataset contains dry biomass (g) at three weeks after transplanting. We used the biomass data as inputs for Genome-Wide Association Analyses, with the genotype data publicly available from http://ricediversity.org/.
This dataset contains dry biomass at three weeks after transplanting of 390 rice accessions from The USDA Rice Diversity Panel 1 (RDP1) within the USDA/ARS Genetics Stocks-Oryza (GSOR) collection. The full RDP1 panel was registered and described by Eizenga et al (doi 10.3198/jpr2013.03.0013crmp).
We evaluated growth of these accessions under NO3– versus NH4+ nutrition, and under different concentrations of NH4+ as sole nitrogen sources in a greenhouse with day/night temperatures approximately 28°/24°C under natural sunlight in Davis, California (38°32’20.2”N 121°46’52.5”W) in 2018-2019. We used the biomass data as inputs for Genome-Wide Association Analyses, with the genotype data publicly available from http://ricediversity.org/.
Description of the data and file structure
“RDP1_Nform_data” (csv, 2437 KB) contains 19756 entries (rows) and 15 variables (columns). The first row is a variable name. Each row represents one part (either shoot or root) of an individual plant replicate (n=9878 plants). Data type, units, and descriptions of each variable are as followed:
- sampleset: character, no unit, All accessions are part of The USDA Rice Diversity Panel 1 (RDP1).
- accession: character (factor with 389 levels), no unit, Accession names.
- GSOR_ID: character (factor with 390 levels), no unit, Accession ID according to the USDA/ARS Genetics Stocks-Oryza (GSOR) collection.
- IRGC_ID: character (factor with 382 levels), no unit, Accession ID according to the International Rice Germplasm Collection of the International Rice Research Institute (IRRI).
- NSFTV_ID: character (factor with 390 levels), no unit, Accession ID according to NSF Rice Diversity Panel, renamed in Eizenga et al (doi 10.3198/jpr2013.03.0013crmp).
- HDRA_ID: character (factor with 368 levels), no unit, Accession ID according to High Density Rice Array (doi 10.1038/ncomms10532).
- GWAS_ID: character (factor with 390 levels), no unit, Accession ID according to the genotype data for Genome-Wide Association Analyses (doi 10.1038/ncomms10532).
- subpop: character (factor with 8 levels), no unit, Subpopulations of 390 accessions phenotyped in this experiment; classification according to the panel registration and previous studies (doi 10.1038/ncomms10532, doi 10.3198/jpr2013.03.0013crmp).
- varietal: character (factor with 3 levels), no unit, Varietal groups of 390 accessions phenotyped in this experiment.
- trt: character (factor with 4 levels), no unit, Nitrogen treatments (Inorganic nitrogen form and concentration in mM).
- exp: character (factor with 2 levels), no unit, Experiment replicate. We repeated the experiment twice consecutively. See the following variable.
- subexp: character (factor with 2 levels), no unit, Group within each experiment replicate. This is a nested variable in ‘exp’. The first experiment replicate examined accessions ID# 0001 – 0220 (last 4 digits of the USDA Genetic Stocks Oryza; GSOR_ID) on December 10, 2018 – January 3, 2019 and accessions ID#0220 – 2020 on January 10 – February 3, 2019); the second replicate examined accessions ID#0001 – 0220 on March 14 – April 7, 2019 and accessions ID#0220 – 2020 on April 12 – May 4, 2019).
- block: character (factor with 4 levels), no unit, Experimental block based on location within the greenhouse. We arranged the containers in a randomized block design with 4 biological plant replicates of each genotype in each experiment replicate.
- organ: character (factor with 2 levels), no unit, Harvestable plant parts as shoot or root.
- dw: numeric, g, Dry mass at three weeks after transplanting, following oven-dried at 65°C and weighed by Sartorius BL120S balance (Sartorius AG, Göttingen, Germany).
Sharing/Access information
Links to other publicly accessible locations of the data: None.
Data was derived from the following sources: Not applicable.
Code/Software
The submission does not contain any code or software.
We evaluated growth of rice seedlings under NO3– versus NH4+ nutrition, and under different concentrations of NH4+ as sole nitrogen sources. We germinated seeds on a rolled germination paper soaked with 1 mM CaSO4 and placed the rolls in a controlled environment chamber at 28°/20°C light/dark, under 450 μmol⋅s−1⋅m−2 photosynthetic photon flux density at plant height during the 12 hr light period.
At 7 d post germination, when seedlings had one true leaf, we transferred seedlings into 20 dm3 opaque, aerated hydroponic polyethylene containers, each filled with 16 dm3 of nutrient solution. Each tub contained 48 seedlings of different genotypes. The nutrient solution was composed of 1 mM K2HPO4, 1 mM KH2PO4, 2 mM CaCl2, 2 mM MgSO4, and 0.06 g L−1 Fe-NaDTPA, and micronutrients according to a modified Hoagland solution (Epstein & Bloom, 2005). Nitrogen treatments included 3 concentrations of (NH4)2SO4 (0.3, 3, and 10 mM) and a single concentration of KNO3 (3 mM). We adjusted the solution pH with H2SO4 to 5.95 and replaced the solution every few days when pH dropped below 5.30. We arranged the containers in a randomized block design with 4 biological plant replicates of each genotype.
We repeated the experiment twice in a greenhouse with day/night temperatures approximately 28°/24°C under natural sunlight in Davis, California (38°32'20.2"N 121°46'52.5"W): the first replicate examined accessions ID# 0001 – 0220 (last 4 digits of the USDA Genetic Stocks Oryza; GSOR ID) on December 10, 2018 – January 3, 2019 and accessions ID#0220 – 2020 on January 10 – February 3, 2019); the second replicate examined accessions ID#0001 – 0220 on March 14 – April 7, 2019 and accessions ID#0220 – 2020 on April 12 – May 4, 2019). We harvested shoot and root separately at three weeks after transplanting, dried them at 65°C and then weighed them with Sartorius BL120S balance (Sartorius AG, Göttingen, Germany).