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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- Chromosomes and Gene Expression
- Genetics and Genomics
Among the major classes of RNAs in the cell, tRNAs remain the most difficult to characterize via deep sequencing approaches, as tRNA structure and nucleotide modifications can each interfere with cDNA synthesis by commonly-used reverse transcriptases (RTs). Here, we benchmark a recently-developed RNA cloning protocol, termed Ordered Two-Template Relay (OTTR), to characterize intact tRNAs and tRNA fragments in budding yeast and in mouse tissues. We show that OTTR successfully captures both full-length tRNAs and tRNA fragments in budding yeast and in mouse reproductive tissues without any prior enzymatic treatment, and that tRNA cloning efficiency can be further enhanced via AlkB-mediated demethylation of modified nucleotides. As with other recent tRNA cloning protocols, we find that a subset of nucleotide modifications leave misincorporation signatures in OTTR datasets, enabling their detection without any additional protocol steps. Focusing on tRNA cleavage products, we compare OTTR with several standard small RNA-Seq protocols, finding that OTTR provides the most accurate picture of tRNA fragment levels by comparison to "ground truth" Northern blots. Applying this protocol to mature mouse spermatozoa, our data dramatically alter our understanding of the small RNA cargo of mature mammalian sperm, revealing a far more complex population of tRNA fragments - including both 5′ and 3′ tRNA halves derived from the majority of tRNAs – than previously appreciated. Taken together, our data confirm the superior performance of OTTR to commercial protocols in analysis of tRNA fragments, and force a reappraisal of potential epigenetic functions of the sperm small RNA payload.
