# 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.

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.