DOI: 10.5061/dryad.nj29qb8
title: Data from: Genomic evidence of genetic variation with pleiotropic effects on caterpillar fitness and plant traits in a model legume

description: Plant-insect interactions are ubiquitous, and have been studied intensely
 because of their relevance to damage and pollination in agricultural
 plants, and to the ecology and evolution of biodiversity. Variation within
 species can affect the outcome of these interactions. Specific genes and
 chemicals that mediate these interactions have been identified, but
 studies of genome- or metabolome-wide intraspecific variation might be
 necessary to better explain patterns of host-plant use and adaptation in
 the wild. Here, we present such a study. We assess the consequences of
 genome-wide genetic variation in the model plant Medicago truncatula for
 Lycaeides melissa caterpillar growth and survival (larval performance).
 Using a rearing experiment and a whole-genome SNP data set (&gt;5
 million SNPs), we find that polygenic variation in M. truncatula explains
 9-41% of the observed variation in caterpillar growth and survival.
 Genetic correlations among caterpillar performance and other plant traits,
 including structural defenses and some anonymous chemical features,
 suggest that multiple M. truncatula alleles have pleiotropic effects on
 plant traits and caterpillar performance (or that substantial linkage
 disequilibrium exists among distinct loci affecting subsets of these
 traits). A moderate proportion of the genetic effect of M. truncatula
 alleles on L. melissa performance can be explained by the effect of these
 alleles on the plant traits we measured, especially leaf toughness. Taken
 together, our results show that intraspecific genetic variation in M.
 truncatula has a substantial effect on the successful development of L.
 melissa caterpillars (i.e., on a plant-insect interaction), and further
 point toward traits mediating this genetic effect.
description: Leaf size and trichome
 number dataThis csv files contains
 the leaf length and width measurements and trichome counts for each
 replicate and Medicago truncatula line.Trichome-density_leaf-area.csvMedicago truncatula plant height dataThis csv files contains the plant height (in mm) measurements for each replicate and Medicago truncatula line.height.csvMedicago truncatula leaf toughness dataThis csv files contains the leaf toughness data for each replicate and Medicago truncatula line. Toughness measures are for the left, middle and right leaflets of a single leaf and are based on the force required to puncture the leaf with a penetrometer.penetrometer.csvMedicago truncatula leaf weight dataThis csv files contains the dry weight (in g) for the middle leaflet for each replicate and Medicago truncatula line.leaf_weight.csvCaterpillar performance dataThis csv files contains the larval performance data for the Lycaeides melissa caterpillars. Metrics include 8 and 16 day weight, pupal weight, and pupation and eclosion dates (which were used to compute survival to pupation/eclosion). Caterpillar IDs and Medicago truncatula plant lines are given.caterpillars_matrix.csvMedicago truncatula genetic dataThis csv files contains the genotype estimates for the Medicago truncatula lines formatted for analysis with gemma. There is one SNP per row, and each row begins with the SNP ID (chromosome:position). Posterior means for genotypes are given.mod_pntest_mtrunc_pruned_rep.txt.gzIR chemistry dataThis csv file provides IR transmittance values for each Medicago truncatula line and replicate for each of 58 IR chemical features.Gompert_trans_table.csvR scriptsThis compressed directory contains the main R scripts used for data analysis. BayesModAv.R performs the Bayesian model averaging analysis. windowMavEffComps.R examines window-based association of effect sizes among traits. ineEffectsLmer-cat.R and LineEffectsLmer.R perform the linear mixed model estimates of variance components.RScripts.tar.gzGenomic estimated breeding valuesThis compressed directory contains three text files with genomic estimated breeding values (GEBVs) for each line and trait. GEBVs for chemistry, caterpillar and plant traits are in bv_pred_ir.txt, bv_pred_cat.txt and bv_pred_plant.txt, respectively.GEBVs.tar.gz