biostudies-literatureGalanti DDeutsche ForschungsgemeinschaftHorizon 2020 Framework ProgrammeRP95510https://www.ebi.ac.uk/biostudies/studies/S-EPMC11658765biostudies-literatureUnknown13Understanding the genomic basis of natural variation in plant pest resistance is an important goal in plant science, but it usually requires large and labor-intensive phenotyping experiments. Here, we explored the possibility that non-target reads from plant DNA sequencing can serve as phenotyping proxies for addressing such questions. We used data from a whole-genome and -epigenome sequencing study of 207 natural lines of field pennycress (<i>Thlaspi arvense</i>) that were grown in a common environment and spontaneously colonized by aphids, mildew, and other microbes. We found that the numbers of non-target reads assigned to the pest species differed between populations, had significant SNP-based heritability, and were associated with climate of origin and baseline glucosinolate contents.eLifeDiscarded sequencing reads uncover natural variation in pest resistance in <i>Thlaspi arvense</i>.PMC11658765764965401829393Galanti DMuller CJung JHBossdorf OfalseDiscarded sequencing reads uncover natural variation in pest resistance in <i>Thlaspi arvense</i>.Understanding the genomic basis of natural variation in plant pest resistance is an important goal in plant science, but it usually requires large and labor-intensive phenotyping experiments. Here, we explored the possibility that non-target reads from plant DNA sequencing can serve as phenotyping proxies for addressing such questions. We used data from a whole-genome and -epigenome sequencing study of 207 natural lines of field pennycress (<i>Thlaspi arvense</i>) that were grown in a common environment and spontaneously colonized by aphids, mildew, and other microbes. We found that the numbers of non-target reads assigned to the pest species differed between populations, had significant SNP-based heritability, and were associated with climate of origin and baseline glucosinolate contents.2024-01-01T00:00:00Z2024 Dec2026-06-01T15:12:27.448Z2025-04-04T21:11:41.671ZS-EPMC116587653969958310.7554/eLife.95510