DOI: 10.5061/dryad.4mw6m90b6
title: Data from: Genome-wide association mapping within a local Arabidopsis thaliana population more fully reveals the genetic architecture for defensive metabolite diversity

description: A paradoxical finding from genome-wide association studies (GWAS) in
 plants is that variation in metabolite profiles typically maps to a small
 number of loci, despite the complexity of underlying biosynthetic
 pathways. This discrepancy may partially arise from limitations presented
 by geographically diverse mapping panels. Properties of metabolic pathways
 that impede GWAS by diluting the additive effect of a causal variant, such
 as allelic and genic heterogeneity and epistasis, would be expected to
 increase in severity with the geographic range of the mapping panel. We
 hypothesized that a population from a single locality would reveal an
 expanded set of associated loci. We tested this in a French Arabidopsis
 thaliana population (&lt; 1 km transect) by profiling and conducting
 GWAS for glucosinolates, a suite of defensive metabolites that have been
 studied in depth through functional and genetic mapping approaches. For
 two distinct classes of glucosinolates, we discovered more associations at
 biosynthetic loci than previous GWAS with continental-scale mapping
 panels. Candidate genes underlying novel associations were supported by
 concordance between their observed effects in the TOU-A population and
 previous functional genetic and biochemical characterization. Local
 populations complement geographically diverse mapping panels to reveal a
 more complete genetic architecture for metabolic traits.
description: This dataset contains measurements of defensive metabolites in
 genotyped accessions of <em>Arabodopsis thaliana</em>, the
 genotypes used for genome-wide association (GWA) mapping of these
 metabolites, and the output of GWA analyses. For the TOU-A population,
 metabolites were extracted and quantified from full rosettes using high
 pressure liquid chromatography and mass spectrometry (HPLC-MS/MS). The raw
 HPLC-MS/MS output files have been deposited here, along with the output of
 linear mixed models of metabolite variation across accessions. For other
 populations, metabolite abundances were obtained from prior publications
 and associated repositories, as described here in the README file and in
 the methods section of the manuscript associated with this dataset
 (doi:10.1098/rstb.2020.0512). GWA mapping of each metabolite in each
 population was conducted using the GEMMA package (doi:10.1038/ng.2310),
 and all output files have been deposited here. Scripts used for the
 analysis of the current dataset are available at
 https://github.com/peterlaurin/TOUA_Glucosinolate_GWAS.
description: # Data from: Genome-wide association mapping within a local Arabidopsis
 thaliana population more fully reveals the genetic architecture for
 defensive metabolite diversity
 [https://doi.org/10.5061/dryad.4mw6m90b6](https://doi.org/10.5061/dryad.4mw6m90b6) Glucosinolate Metabolite Profiles from the TOU-A Population ``` Data Description Output of metabolite quantification for individual rosettes of each TOU-A Arabidopsis accession, generated by high pressure liquid chromatography and mass spectrometry (HPLC-MS/MS) Data Source Novel data generated in the present study (doi: 10.1098/rstb.2020.0512) File Structure and Organization Original_Chromatograms_QQQ_sets23: zipped folder that contains all files Set[num]_Plate[num]: subfolders that contain files from each 96-well extraction plate ("Plate") per experimental batch ("Set", N=2 replicates/plant accession/set) set[num]_plate[num]_P1_[position].mzML: HPLC-MS/MS output file in .mzML format for each sample, identified by set (as above), plate(as above), and position within the plate (range: A01-H12) ``` Quantification of Individual Glucosinolate Metabolite Abundances from the TOU-A Population ``` Data Description Abundances of metabolites of interest, calculated from the HPLC-MS/MS output Data Source Novel data generated in the present study (doi: 10.1098/rstb.2020.0512) using "glucosinolate_profiling" scripts at https://github.com/peterlaurin/TOUA_Glucosinolate_GWAS File Structure and Organization (with Definitions for Variables as Relevant) Metabolite_Peak_Integration.zip: zipped folder that contains all files Extraction[AB|CD]_ADG.csv: metadata for each plant sample for which metabolites were quantified in Set 2 (CD) or 3 (EF) ID_short: abbreviated TOU-A accession ID (i.e., 1_23 = TOU-A1_23) Day: Batch for plant harvesting (two blocks harvested per day) Block: Complete block for plant growth and harvesting TrayNum, Row, Col: Position (Row, Col) in the 98-cell tray (TrayNum) in which the plant was grown Weight: Wet weight of plant rosette (grams) Date, Heure: Date and time of sample collection (removal from soil, weighing, and initiation of extraction in methanol) Plaque, Ligne, Colonne: Sample position (Ligne, Colonne) within the 96-well plate (Plaque) for extraction and quantification of metabolites gsl.[mol_name]_samples_[range]_table.csv: table summarizing output of quantification for a given metabolite (mol_name) for a specified range of plant samples in the dataset mzr, rtr: range of m/z and retention time parameters for the focal metabolite numPts: number of data points detected in HPLC-MS/MS output file for the focal sample in the given mzr and rtr parameter range baseline: inferred baseline intensity used for zeroing out background intensity rtmin, rtmax: minimum and maximum retention time interval into, intb, maxo: three peak intensity metrics (integrated peak intensity, baseline corrected integrated peak intensity, and maximum peak intensity) reported from peak detection by xcms sn: single to noise ratio cutoff used for peak detection by by xcms numPeaks: number of peaks detected by xcms peakwidth, snthresh, prefilter: peak picking parameters required by xcms (see software documentation) slice_intb: integrated peak area by slice integration method developed for this study slice_prop: proportion of slices integrated within the user-specified rtr summit_intb: peak intensity by summit integration method developed for this study summit_numPts: number of largest slices within the user-specified window summed to give peak summit intensity gsl.[mol_name]_samples_[range]_plot.pdf: chromatogram images for parameters corresponding to a given metabolite (mol_name). The blue shaded area shows the peak identified by xcms; the yellow lines indicate the area integrated by our slice method, and the black lines indicate the intensities used for our summit method ``` Glucosinolate Metabolite Phenotypes for All Populations ``` Data Description Per-accession genotypic effects on glucosinolate molecule abundances or ratios (phenotypes), estimated for each Arabidopsis accession from biological replicates Data Source Glucosinolate metabolite quantifications from individual plants were drawn from four studies, and per-accession phenotypes were estimated from these datasets for the present study (doi: 10.1098/rstb.2020.0512) using "phenotypic_analyses_and_gwas_prep" scripts at https://github.com/peterlaurin/TOUA_Glucosinolate_GWAS Brachi: doi:10.1073/pnas.1421416112 Katz: doi:10.7554/eLife.67784 Wu: doi:10.1016/j.molp.2017.08.012 TOU: doi: 10.1098/rstb.2020.0512 (this study) File Structure and Organization (with Definitions for Variables as Relevant) Phenotypes.zip: a zipped folder that contains all files Brachi/Katz/TOU/Wu: subfolder that contains files for a given study phen_glucosinolates[means|BLUPs]_[date].csv: best linear unbiased prediction values (BLUPs,estimated from linear mixed models (LMMs)) or means conveying the effect of each Arabidopsis accession's genotypic effect (row) on the abundance of each glucosinolate molecule (column) ID: identifier for each Arabidopsis accession, using standardized nomenclature from the appropriate mapping panel Additional columns: means or BLUPs per accession model_info.txt: output from LMMs of glucosinolate metabolite abundance using data from each of the four studies molecule: glucosinolate molecule used as dependent variable intercept: model intercept p: p value for the effect of plant accession pve_id: percent variance explained by plant accession ratios_to_calculate.csv: list of molecule pairs for which log2(precursor:product abundance) were calculated, in numbered order corresponding to the names (e.g., ratio1, ratio2, ...) of the GWAS output files molecule_1: precursor molecule molecule_2: product molecule ``` Genome-Wide Association Mapping for All Populations ``` Data Description Output from genome-wide association studies (GWAS) of glucosinolate molecule abundances or ratios implemented using GEMMA Data Source All GWAS were conducted in the present study (doi: 10.1098/rstb.2020.0512), using per-accession glucosinolate phenotypes obtained described in the preceding section File Structure and Organization (with Definitions for Variables as Relevant) \[study].tar.gz: zipped directory containing GWAS output from analysis of a given dataset (Brachi, Katz, Wu, TOU; see preceding section); N192 indicates that a subset of 192 accessions was analyzed \[blup|ratio]_[aliphatic|indolic]: subdirectory indicating if the enclosed GWAS were for aliphatic or indolic glucosinolate molecules and for BLUPs/means of individual abundances or precursor:product ratios lmm_maf03_[trait].assoc.fixed.txt: GWAS output for a given glucosinolate molecule abundance or ratio (trait) chr, ps: SNP location by chromosome and position rs: unique SNP identifier n_miss: number of individuals with missing genotype information for the SNP allele1, allele0: nucleotide identity of the two alleles af: frequency of the minor allele beta, se: SNP effect size (beta) and standard error (se) p_wald: Wald Test p-value for SNP snp_table_all_pvals.csv: compilation of p-values per SNP for all GWAS contained within the focal category (i.e., within the GWAS contained in a given subdirectory) rs,chr,ps,af: SNP identifier information as in lmm_maf03_[trait].assoc.fixed.txt above p_[trait]: Wald Test p-value for SNP from GWAS of a given molecule abundance or ratio (trait) p_wald_min: Lowest Wald Test p-value for the SNP across all GWAS in the focal category (subdirectory) ``` Further descriptions or resources can be found in the following locations: ``` Accompanying manuscript: doi 10.1098/rstb.2020.0512 GitHub: https://github.com/peterlaurin/TOUA_Glucosinolate_GWAS ```