DOI: 10.5061/dryad.rbnzs7hnp
title: Data from: Uncovering the genetic basis of competitiveness, and the potential for cooperation, in plant groups

description: Crop productivity was transformed by incorporating dwarfing genes that
 made plants smaller and less competitive (more cooperative). Beyond such
 major shifts in plant size, however, it is not clear how much variation in
 competitiveness remains and how to find its genetic basis. We performed
 plant density experiments, using 484 lines of the Arabidopsis thaliana
 Multi-parent Advanced Generation Inter-Cross (MAGIC) population, to
 compare methods for mapping the genetic basis of plant competitiveness. We
 first found that a major dwarfing gene, the erecta allele, caused reduced
 competitiveness and higher group productivity. Then, measuring
 competitiveness more generally, we found: (i) extensive variation in
 generic measures of competitiveness that extended beyond the effects of
 the erecta allele; (ii) a novel genomic region underlying variation in
 competitiveness; and (iii) that some measures of competitiveness were more
 useful than others. Our results show how modern genomic resources,
 including multi-parent populations, could uncover hidden genes for more
 cooperative crop plants.
description: We collected data from greenhouse experiments with the
 <em>Arabidopsis</em> MAGIC lines in an automated greenhouse at
 the National Plant Phenomics Centre (University of Aberystwyth,
 UK). We present raw data and least-squares mean trait
 values calculated for each MAGIC line.  The
 'full' dataset includes all 484 lines included in the study.
  The 'reduced' dataset excludes some replicates, as explained in
 the paper. 
description: # Data from: Uncovering the genetic basis of competitiveness, and the
 potential for cooperation, in plant groups
 [https://doi.org/10.5061/dryad.rbnzs7hnp](https://doi.org/10.5061/dryad.rbnzs7hnp) ## Description of the data and file structure Greenhouse experiments at the National Plant Phenomics Centre. The experiment was performed in 3 Batches, and each batch contained 3 blocks. The experiment involved 484 lines of the Arabidopsis MAGIC population. There were two treatment groups: Isolation, where single plants grew alone, and Group, where 4 plants (from the same MAGIC line) grew together in a pot. Each line-treatment level combination was replicated 3 times.  ### Files and variables #### File: LeastSquaresMeans\_full\_dataset.txt and .xlsx **Description:**   Least squares means were calculated to account for variation in experimental effects (batch, block), as described in the paper.  This gives an adjusted mean value for each MAGIC line. #### Variables * Line:  Identifies the MAGIC line * erecta?:   Yes or No, whether the Line carries the *erecta* dwarfing allele * LSM branch number Isolation:  Least squares mean branch number/plant in Isolation (count) * LSM branch number Groups: Least squares mean branch number/plant in Groups (count) * LSM height Isolation:  Least squares mean height of plants in Isolation (cm) * LSM height Groups: Least squares mean height of plants in groups (cm) * LSM siliques/plant Isolation: Least squares mean number of fertile fruits (siliques) per plant in Isolation (count) * LSM siliques/plant Group: Least squares mean number of fertile fruits (siliques) per plant in Group (count) * LSM total siliques/pot Groups: Least squares mean total number of fertile fruits (siliques) per pot in Group (count) * tradeoff_siliques: Values for the individual-group tradeoff score * RII_siliques: Values for the Relative Interaction Intensity * RC_siliques: Values for Response to Competition index * ADI_siliques: Values for Adaptation to Density Index #### File: LeastSquaresMeans\_reduced\_dataset.txt and .xlsx **Description:** Least squares means were calculated to account for variation in experimental effects (batch, block), as described in the paper.  This gives an adjusted mean value for each MAGIC line. Variables are the same as in the 'full' dataset. ##### Variables * line:  Identifies the MAGIC line * erecta?: Yes or No, whether the Line carries the *erecta* dwarfing allele * LSM branch number/plant Isolation: Least squares mean branch number/plant in Isolation (count) * LSM branch number/plant Groups: Least squares mean branch number/plant in Groups (count) * LSM height/plant Isolation: Least squares mean height of plants in Isolation (cm) * LSM height Groups: Least squares mean height of plants in groups (cm) * LSM siliques/plant Isolation: Least squares mean number of fertile fruits (siliques) per plant in Isolation (count) * LSM siliques/plant Groups: Least squares mean number of fertile fruits (siliques) per plant in Group (count) * LSM total siliques/pot Groups: Least squares mean total number of fertile fruits (siliques) per pot in Group (count) * tradeoff_siliques: Values for the individual-group tradeoff score * RII_siliques: Values for the Relative Interaction Intensity * RC_siliques: Values for Response to Competition index * ADI_siliques: Values for Adaptation to Density Index #### File: All\_raw\_MAGIC\_data.txt and .xlsx **Description:**  All data collected for each pot in the MAGIC experiment. Each line is a pot in the experiment.  ##### Variables * Line:  Identifies the MAGIC line * ID: Unique identifier for each pot in the experiment * batch: Identifies the batch (A, B, or C) * block: Identifies the block within a batch (1, 2, or 3) * erecta?: Yes or No, whether the Line carries the *erecta* dwarfing allele * treatment:    Individual treatment (1)  or group treatment (4) * flowering time: flowering time, in days after sowing * height/plant: plant height in cm * branch number/plant: number of branches per plant (count) * siliques/plant: number of fertile fruits (siliques) per plant (count) * total siliques/pot: total number of fertile siliques counted in the pot * exclude?:   Yes or No, whether the pot was classified as having aborted siliques, leading to exclusion in the reduced dataset * Height_1:  Height of plant 1 in the pot (cm) * Height_2:  Height of plant 2 in the pot (cm), or NA * Height_3: Height of plant 3 in the pot (cm), or NA * Height_4: Height of plant 4 in the pot (cm), or NA * Average_height: average height (cm) of plants in the pot * Branch_1: Number of branches on plant 1 in the pot * Branch_2:  Number of branches on plant 2 in the pot, or NA * Branch_3: Number of branches on plant 3 in the pot, or NA * Branch_4: Number of branches on plant 4 in the pot, or NA * Average_branches: Average number of branches/plant in the pot * total branches: Total number of branches in the pot * Siliques_1:  Number of fertile siliques on Plant 1 in the pot * Siliques_2: Number of fertile siliques on Plant 2 in the pot, or NA * Siliques_3: Number of fertile siliques on Plant 3 in the pot, or NA * Siliques_4: Number of fertile siliques on Plant 4 in the pot, or NA ## Code/software N/A