Genomic basis for drought resistance in European beech forests threatened by climate change
- Senckenberg Biodiversity and Climate Research Centre, Germany
- Institute for Human Genetics, University Medical Center, Johannes Gutenberg University, Germany
- Senckenberg Research Institute and Natural History Museum, Germany
- Department of Biology, Technische Universität Darmstadt, Germany
- Hochschule Geisenheim University, Germany
- Biodiversity and Climate Research Centre, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Germany
- Senckenberg Gesellschaft für Naturforschung, Germany
Abstract
In the course of global climate change, central Europe is experiencing more frequent and prolonged periods of drought. The drought years 2018 and 2019 affected European beeches (Fagus sylvatica L.) differently: even in the same stand, drought damaged trees neighboured healthy trees, suggesting that the genotype rather than the environment was responsible for this conspicuous pattern. We used this natural experiment to study the genomic basis of drought resistance with Pool-GWAS. Contrasting the extreme phenotypes identified 106 significantly associated SNPs throughout the genome. Most annotated genes with associated SNPs (>70%) were previously implicated in the drought reaction of plants. Non-synonymous substitutions led either to a functional amino acid exchange or premature termination. A SNP-assay with 70 loci allowed predicting drought phenotype in 98.6% of a validation sample of 92 trees. Drought resistance in European beech is a moderately polygenic trait that should respond well to natural selection, selective management, and breeding.
Data availability
Sequencing data have been deposited at ENA under project code PRJEB41889.The genome assembly including the annotation is available under the Access. No. PRJNA450822.
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Genomic basis of drought resistance in Fagus sylvatica by PoolGWASEuropean Nucleotide Archive, PRJEB40079.
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Funding
There was no particular funding for this work; all work was financed by regular budgets
Copyright
© 2021, Pfenninger et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Genomic basis for drought resistance in European beech forests threatened by climate change
eLife 10:e65532.
https://doi.org/10.7554/eLife.65532
Further reading
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- Genetics and Genomics
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Evolution of gene expression frequently drives antibiotic resistance in bacteria. We had previously (Patel and Matange, eLife, 2021) shown that, in Escherichia coli, mutations at the mgrB locus were beneficial under trimethoprim exposure and led to overexpression of dihydrofolate reductase (DHFR), encoded by the folA gene. Here, we show that DHFR levels are further enhanced by spontaneous duplication of a genomic segment encompassing folA and spanning hundreds of kilobases. This duplication was rare in wild-type E. coli. However, its frequency was elevated in a lon-knockout strain, altering the mutational landscape early during trimethoprim adaptation. We then exploit this system to investigate the relationship between trimethoprim pressure and folA copy number. During long-term evolution, folA duplications were frequently reversed. Reversal was slower under antibiotic pressure, first requiring the acquisition of point mutations in DHFR or its promoter. Unexpectedly, despite resistance-conferring point mutations, some populations under high trimethoprim pressure maintained folA duplication to compensate for low abundance DHFR mutants. We find that evolution of gene dosage depends on expression demand, which is generated by antibiotic and exacerbated by proteolysis of drug-resistant mutants of DHFR. We propose a novel role for proteostasis as a determinant of copy number evolution in antibiotic-resistant bacteria.
