DOI: 10.5061/dryad.7wm37pvxm
title: Biomass data to accompany Inter-chromosomal linkage disequilibrium and linked fitness cost loci associated with selection for herbicide resistance

description: The adaptation of weeds to herbicide is both a significant problem in
 agriculture and a model of rapid adaptation. However, significant gaps
 remain in our knowledge of resistance controlled by many loci and the
 evolutionary factors that influence the maintenance of resistance. Here,
 using herbicide-resistant populations of the common morning glory (Ipomoea
 purpurea), we perform a multi-level analysis of the genome and
 transcriptome to uncover putative loci involved in nontarget-site
 herbicide resistance (NTSR) and to examine evolutionary forces underlying
 the maintenance of resistance in natural populations. We found loci
 involved in herbicide detoxification and stress sensing to be under
 selection and confirmed that detoxification is responsible for glyphosate
 resistance using a functional assay. We identified interchromosomal
 linkage disequilibrium (ILD) among loci under selection reflecting either
 historical processes or additive effects leading to the resistance
 phenotype. We further identified potential fitness cost loci that were
 strongly linked to resistance alleles, indicating the role of genetic
 hitchhiking in maintaining the cost. Overall, our work suggests that NTSR
 glyphosate resistance in I. purpurea is conferred by multiple genes which
 are potentially maintained through generations via ILD and that the
 fitness cost associated with resistance in this species is likely a
 by-product of genetic-hitchhiking.
description: On Jan 10, 2022, we planted 215 replicate seeds from multiple
 resistant and susceptible lineages per population (Table S10) in
 Cone-Tainers (Stewe and Sons) in a controlled growth room. After 30 days
 we subjected plants to four treatments: malathion (1 kg ai/ha OrthoMAX,
 Scotts Co.), glyphosate (3.4 kg ai/ha RoundUp PowerMax, Bayer), glyphosate
 and malathion, or a control. Prior to this experiment, we exposed 20
 plants to five rates of malathion (N = 100) and identified 1 kg ai/ha as a
 rate that did not influence <em>I. purpurea </em>biomass or
 cause damage on its own. Malathion was applied using a handheld CO2
 sprayer, and glyphosate was applied 1 hour later, again using a hand-held
 CO2 sprayer (Spraying Systems Co., Wheaton, IL) calibrated to deliver 187
 L/ha. Twenty-four days post-treatment, we recorded death, harvested and
 dried plants for 3 days at 70C, and weighed each sample for an estimate of
 biomass. To compare death and biomass between resistant
 and susceptible plants, we used log-likelihood tests and generalized
 linear models. Biomass was log-transformed (transformTukey function;
 Rcompanion v.2.0.0; Mangiafico, 2015) and used as the dependent variable
 with population type (R/S) and treatment as independent variables (biomass
 ~ population type + treatment). We assessed significance using the Anova
 function of the car package v.3.0.10 (Fox & Weisberg, 2018), and
 performed a pairwise comparison between groups using the lsmeans function
 from package lsmeans v2.30.0 (Lenth, 2016), adjusted for multiple tests
 using Tukey correction. Using the same general model, we also compared
 biomass between treatments for each population type (R vs S). To control
 for inherent differences in plant size across lineages, we standardized
 the biomass of each individual grown in the treatment environment by
 dividing biomass by the average of plants from the same maternal line
 grown in the control environment.