DOI: 10.5061/dryad.pg4f4qrvg
title: Genome-wide association study of aphid abundance highlights a locus affecting plant growth and flowering in Arabidopsis thaliana

description: Plant life-history traits, such as size and flowering, contribute to
 shaping variation in herbivore abundance. Although plant genes involved in
 physical and chemical traits have been well studied, less is known about
 the loci linking plant life-history traits and herbivore abundance. Here,
 we conducted a genome-wide association study (GWAS) of aphid abundance in
 a field population of Arabidopsis thaliana. This GWAS of aphid abundance
 detected a relatively rare but significant variant on the third chromosome
 of A. thaliana, which was also suggestively but non-significantly
 associated with the presence or absence of inflorescence. Out of candidate
 genes near this significant variant, a mutant of a ribosomal gene
 (AT3G13882) exhibited slower growth and later flowering than a wild type
 under laboratory conditions. A no-choice assay with the turnip aphid,
 Lipaphis erysimi, found that aphids were unable to successfully establish
 on the mutant. Our genome-wide association study of aphid abundance
 unexpectedly found a locus affecting plant growth and flowering.
description: # AraAphidGWAS Data and source codes for GWAS of aphid abundance on
 *Arabidopsis thaliana*. GWAS is done using the GWA-portal
 (). ## Directory ### data This
 directory includes GWAS phenotypes and *Arabidopsis* mutant data. Other
 intermediate files will be created during the analysis with GWA-portal and
 R. * aphid_No_per_day.csv\ Aphid monitoring data. The headers include:
 Date: Survey date (yyyy.mm.dd); IndivID: Individual plant ID; gwasID:
 Accession ID for GWAS; aphid_wing: No. of winged aphids; aphid_wingless:
 No. of wingless aphids; aphid_total: total no. of aphids. * AphidsNo.txt\
 The number of aphids per plant in the laboratory experiment. The headers
 include: Gene and Mutant: The wild type (WT) or the mutant of AT3G13882;
 No.: Plant ID; size: Initial size (cm) just before aphid release;
 Flowering: Days until flowering; t1-4: No. of aphids at t1, 2, 3, and 4 =
 3, 7, 10 and 14 days after the release, respectively. *
 AtZurich2018aphidsGWAportal_data.csv\ The input phenotype data for the
 GWA-portal. The headers include: gwasID: Accession ID for GWAS; Bolting:
 Presence (1) or absence (0) of bolting 2-wk after transplanting to the
 field; log_BbLe_max: Aphid abundance represented by the
 log(x+1)-transformed number of aphids (*Lipaphis erysimi* and *Brevicoryne
 brassicae*) per plant. ### figures This directory includes original
 images, output figures from R, and figures used for the manuscript. *
 original_GelDoc 2022-10-27 10hr 48min.tif\ An original gel image of
 sqRT-PCR experiments. * FigS_gel_annotation.tiff\ Annotated gel image of
 sqRT-PCR experiments. The primer information is available in the
 supplementary tables of the manuscript. * mutantPhoto.png\ A photograph of
 the wild type and mutant plant cultivated in the lab. * AT3G13882.pdf\
 Annotations on the ribosomal gene AT3G13882 made using QIAGEN CLC Main
 Workbench. * database_snapshot.png\ Browsing results of GWA-portal
 phenotypes and 1001 Genome Viewer near Chr3-4579292. ### scripts This
 directory includes R scripts for the analysis of GWAS outputs and
 *Arabidopsis* mutant data. * GWAp_output.R\ R script to prepare the input
 file of GWA-portal, summarize aphid abundance in the field, analyze output
 from GWA-portal, and depict GWAS plots. Run the GWA-portal before
 depicting GWAS plots. * aphid.R\ R script to analyze and visualize the
 results laboratory experiments using aphids and *Arabidopsis* mutants.