DOI: 10.25338/b8jp8c
title: Vegetative biomass production under different inorganic nitrogen forms of the USDA rice (Oryza sativa L.) diversity panel 1

description: 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/.
description: We evaluated growth of rice seedlings under
 NO<sub>3</sub><sup>–</sup> versus
 NH<sub>4</sub><sup>+</sup> nutrition, and under
 different concentrations of
 NH<sub>4</sub><sup>+</sup> as sole nitrogen
 sources. We germinated seeds on a rolled germination paper soaked with 1
 mM CaSO<sub>4</sub> and placed the rolls in a controlled
 environment chamber at 28°/20°C light/dark, under 450
 <em>μmol</em><em>⋅s<sup>−1</sup></em><em>⋅m<sup>−2</sup></em> 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 dm<sup>3</sup> opaque, aerated hydroponic polyethylene containers, each filled with 16 dm<sup>3</sup> of nutrient solution. Each tub contained 48 seedlings of different genotypes. The nutrient solution was composed of 1 mM K<sub>2</sub>HPO<sub>4</sub>, 1 mM KH<sub>2</sub>PO<sub>4</sub>, 2 mM CaCl<sub>2</sub>, 2 mM MgSO<sub>4</sub>, and 0.06 g L<sup>−1</sup> Fe-NaDTPA, and micronutrients according to a modified Hoagland solution (Epstein & Bloom, 2005). Nitrogen treatments included 3 concentrations of (NH<sub>4</sub>)<sub>2</sub>SO<sub>4</sub> (0.3, 3, and 10 mM) and a single concentration of KNO<sub>3</sub> (3 mM). We adjusted the solution pH with H<sub>2</sub>SO<sub>4</sub> 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).
description: # Vegetative biomass production under different inorganic nitrogen forms
 of the USDA rice (Oryza sativa L.) diversity panel 1 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/](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.