Ag Data Commons
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Data from: Benzoxazinoids in roots and shoots of cereal rye (Secale cereale) and their fates in soil after cover crop termination

posted on 2024-02-16, 22:16 authored by Clifford P. Rice, Briana A. Otte, Matthew KramerMatthew Kramer, Harry H. Schomberg, Steven B. Mirsky, Katherine L. Tully

Cover crops provide many agroecosystem services, including weed suppression, which is partially exerted through release of allelopathic benzoxazinoid (BX) compounds. This research characterizes (1) changes in concentrations of BX compounds in shoots, roots, and soil at three growth stages (GS) of cereal rye (Secale cereale L.), and (2) their degradation over time following termination. Concentrations of shoot dominant BX compounds, DIBOA-glc and DIBOA, were least at GS 83 (boot). The root dominant BX compound, HMBOA-glc, concentration was least at GS 54 (elongation). Rhizosphere soil BX concentrations were 1000 times smaller than in root tissues. Dominant compounds in soil were HMBOA-glc and HMBOA. Concentrations of BX compounds were similar for soil near root crowns and between-rows. Soil BX concentrations following cereal rye termination declined exponentially over time in three of four treatments: incorporated shoots (S) and roots (R), no-till S+R (cereal rye rolled flat), and no-till R (shoots removed), but not in no-till S. On the day following cereal rye termination, soil concentrations of HMBOA-glc and HMBOA in these three treatments increased above initial concentrations. Concentrations of these two compounds decreased the fastest while DIBOA-glc declined the slowest (half-life of 4 d in no-till S+R soil). Placement of shoots on the surface of an area where cereal rye had not grown (no-till S) did not increase soil concentrations of BX compounds. The short duration and complex dynamics of BX compounds in soil prior to and following termination illustrate the limited window for enhancing weed suppression by cereal rye allelochemicals; valuable information for programs breeding for enhanced weed suppression.

In addition to the data analyzed for this article, we also include the R code.

Resources in this dataset:

  • Resource Title: BX data following termination.

    File Name: FinalBXsForMatt-20200908.csv

    Resource Description: For each sample, gives the time, depth, location, and plot treatment, and then the compound concentrations. This is the principal data set analyzed with the R (anal2-cleaned.r) code, see that code for use.

  • Resource Title: BX compounds from 3rd sampling time before termination.

    File Name: soil2-20201123.csv

    Resource Description: These data are for comparison with the post termination data. They were taken at the 3rd sampling time (pre-termination), a day prior to termination. Each sample is identified with a treatment, date, and plot location, in addition to the BX concentrations. See R code (anal2-cleaned.r) for how this file is used.

  • Resource Title: Soil location (within row versus between row) values of BX compounds.

    File Name: s2b.csv

    Resource Description: Each row gives the average BX compound for each soil location (within row versus between row) for the second sample for each plot. These data are combined with bx3 (the data set read in from the file , "FinalBXsForMatt-20200908.csv"). See R (anal2-cleaned.r) code for use.

  • Resource Title: R code for analysis of the decay (post-termination) BX data..

    File Name: anal2-cleaned.r

    Resource Description: This is the R code used to analyze the termination data. It also creates and writes out some data subsets (used for analysis and plots) that are later read in.

    Resource Software Recommended: R version 3.6.3,url:

  • Resource Title: Tissue BX compounds.

    File Name: tissues20210728b.csv

    Resource Description: Data file holding results from a tissue analysis for BX compounds, in ug, from shoots and roots, and at various sampling times. Read into the R file, anal1-cleaned.r where it is used in a statistical analysis and to create figures.

  • Resource Title: BX compounds from soil with a live rye cover crop.

    File Name: soil2-20201214.csv

    Resource Description: BX compounds (in ng/g dry wt), by treatment, sampling time, date, and plot ID. These are data are read into the R program, anal1-cleaned.r, for analysis and to create figures. These are soil samples taken from locations with a live rye plant cover crop.

  • Resource Title: R code for BX analyses of soil under rye and plant tissues.

    File Name: anal1-cleaned.r

    Resource Description: R code for analysis of the soil BX compounds under a live rye cover crop at different growing stages, and for the analysis of tissue BX compounds. In addition to statistical analyses, code in this file creates figures, also some statistical output that is used to create a file that is later read in for figure creation (s2-CLD20220730-Stage.csv).

    Resource Software Recommended: R version 3.6.3,url:

  • Resource Title: Description of data files for anal2-cleaned.r.

    File Name: readme2.txt

    Resource Description: Describes the input files used in the R code in anal2-cleaned.r, including descriptions and formats for each field. The file also describes some output (results) files that were uploaded to this site. This is a plain ASCII text file.

  • Resource Title: Estimates produced by anal2-cleaned.r from statistical modeling..

    File Name: Estimates20201110.csv

    Resource Description: Estimates produced by anal2-cleaned.r from statistical modeling (see readme2.txt)

  • Resource Title: Summary statistics from anal2-cleaned.r.

    File Name: CV20210412.csv

    Resource Description: Summary statistics from anal2-cleaned.r, used for plots

  • Resource Title: Data summaries (same as CV20210412.csv), rescaled.

    File Name: RESCALE-20210412.csv

    Resource Description: Same as "CV20210412.csv" except log of data have been rescaled to minimum at least zero and maximum one, see readme2.txt

  • Resource Title: Statistical summaries for different stages.

    File Name: s2-CLD20220730-Stage.csv

    Resource Description: Statistical summaries used for creating a figure (not used in paper), used in anal1-cleaned.r; data for soil BX under living rye.

  • Resource Title: Description of data files for anal1-cleaned.r.

    File Name: readme1.txt

    Resource Description: Contains general descriptions of data imported into anal1-cleaned.r, and a description of each field. Also contains some descriptions of files output by anal1-cleaned.r, used to create tables or figures.


USDA-ARS: CRIS 8042-22000-167-00D


Data contact name

Kramer, Matthew

Data contact email


Ag Data Commons

Intended use

Support the published manuscript and give others the opportunity to reanalyze the data. The data were collected to understand the fate of various cereal rye exudates in the soil.

Use limitations

There was some slight contamination across treatment areas within a plot, possibly due to foot traffic or roots from neighboring plots invading the area, as explained in the paper. Measures were not taken frequently enough at the study's beginning (following termination).

Temporal Extent Start Date


Temporal Extent End Date



  • periodic


  • Not specified

Geographic Coverage


Geographic location - description

Beltsville Agricultural Research Center, Beltsville, Maryland USA

ISO Topic Category

  • environment
  • farming

Ag Data Commons Group

  • Upper Chesapeake Bay
  • Long-Term Agroecosystem Research

National Agricultural Library Thesaurus terms

benzoxazinoids; roots; shoots; rye; Secale cereale; soil; cover crop termination; cover crops; agroecosystems; weed control; developmental stages; rhizosphere; tissues; root crown; no-tillage; half life; allelochemicals; breeding; computer software; bioactive compounds

OMB Bureau Code

  • 005:18 - Agricultural Research Service

OMB Program Code

  • 005:040 - National Research

ARS National Program Number

  • 304

Primary article PubAg Handle

Pending citation

  • No

Public Access Level

  • Public

Preferred dataset citation

Rice, Clifford P.; Otte, Briana A.; Kramer, Matthew; Schomberg, Harry H.; Mirsky, Steven B.; Tully, Katherine L. (2022). Data from: Benzoxazinoids in roots and shoots of cereal rye (Secale cereale) and their fates in soil after cover crop termination. Ag Data Commons.