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OPINION

The potential of genomics for restoring ecosystems and biodiversity

Abstract

Billions of hectares of natural ecosystems have been degraded through human actions. The global community has agreed on targets to halt and reverse these declines, and the restoration sector faces the important but arduous task of implementing programmes to meet these objectives. Existing and emerging genomics tools offer the potential to improve the odds of achieving these targets. These tools include population genomics that can improve seed sourcing, meta-omics that can improve assessment and monitoring of restoration outcomes, and genome editing that can generate novel genotypes for restoring challenging environments. We identify barriers to adopting these tools in a restoration context and emphasize that regulatory and ethical frameworks are required to guide their use.

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Fig. 1: Potential applications of genomics in restoration.
Fig. 2: Potential applications of population genomics to ecological restoration.
Fig. 3: Integrating predictive climate modelling with population genomics to guide provenance decision-making.
Fig. 4: Schematic overview of how meta-omics can be used to improve restoration assessment and monitoring.
Fig. 5: Gene drives for modifying the genomes of wild populations.

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Acknowledgements

We thank J. Robinson for help preparing figure 1 and P. Cassey and B. Potts for comments on earlier versions of this manuscript. M.F.B. is funded by Australian Research Council (ARC) grants DP180100668, DE150100542 and DP150103414. P.A.H is supported by ARC grant IC150100004. V.G. is supported by a Postdoctoral Research Project awarded by Water Research Australia (1110–17).

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M.F.B., P.A.H., R.H. and D.A.S. researched data for the article. M.F.B., P.A.H., C.B., M.B., V.G., S.V.C.G., R.H., J.G.M., T.A.A.P., D.A.S. and J.J.M. made substantial contributions to discussions of the content of the manuscript. M.F.B., P.A.H., C.B., V.G., N.J.C.G., S.V.C.G., J.G.M., T.A.A.P., D.A.S. and J.J.M. wrote the article. All authors reviewed and/or edited the manuscript before submission.

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Correspondence to Martin F. Breed.

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Related links

AFR100: https://afr100.org/

Earth Microbiome Project: http://www.earthmicrobiome.org/

Initiative 20×20: https://www.wri.org/our-work/project/initiative-20x20

REDD+: https://redd.unfccc.int/

The Bonn Challenge: http://www.bonnchallenge.org/

UNFCCC Paris Agreement: https://unfccc.int/process-and-meetings/the-paris-agreement/the-paris-agreement

Supplementary information

Glossary

Adaptive variation

Genetic variation that increases the fitness of an organism.

Alpha diversity

The species diversity within a given sample or site.

Beta diversity

The turnover of species diversity across a landscape.

CRISPR–Cas9 system

A targeted genome-editing tool comprising two components: the programmable Cas9 endonuclease, which introduces double-strand breaks into the DNA; and a guide RNA, which targets the Cas9 nuclease to a specific DNA sequence.

Effective population sizes

The size of ideal breeding populations, which meet Hardy–Weinberg equilibrium assumptions, that would maintain the same allele frequencies as a census population.

Environmental DNA or RNA

DNA or RNA present in an environmental sample, such as water, soil and air.

Gene flow

The exchange of genetic material within or between populations as a result of the movement of gametes or individuals.

Genetic drift

The change in allele frequencies through generations of a population due to random sampling.

Genotype-by-environment

Differential trait responses (such as growth or survival) of genotypes grown in contrasting environments, resulting in a statistical genotype and environment interaction for traits.

Guide RNA

(gRNA). A small sequence of synthetic RNA (about 20 bases long) located within a longer RNA scaffold, which binds to DNA and directs the Cas9 endonuclease to the targeted genomic location.

Metabarcoding

A meta-omics approach that combines DNA identification and DNA sequencing, in which universal primers are used to amplify DNA barcodes from bulk samples, such as soil environmental DNA.

Metabolomic turnover

The change in metabolic molecules within cells, biofluids, tissues or organisms.

Metagenomics

A meta-omics approach similar to metabarcoding, but instead of using DNA barcodes it involves random sequencing of DNA from bulk samples.

Metatranscriptomic

Pertaining to a meta-omics approach similar to metagenomics, but instead of randomly sequencing DNA it randomly sequences transcriptomes or expressed genes.

Meta-omics

A collection of methods (including metabarcoding, metagenomics and metatranscriptomics) that use next-generation sequencing to characterize whole communities of organisms.

Neutral variation

Genetic variation that is not shaped by natural selection and does not directly impact the fitness of an organism.

Population genomics

The application of high-density, genome-wide molecular markers to the study of neutral and adaptive evolutionary processes occurring within species.

Provenance

The geographical location of a plant population or seed source.

Seed transfer zones

The geographical regions over which seeds can be transferred with minimal maladaptive responses.

Transfer functions

The relationships between the performance of multiple plant populations within a test site and the environmental dissimilarity between the populations’ home site and test site.

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Breed, M.F., Harrison, P.A., Blyth, C. et al. The potential of genomics for restoring ecosystems and biodiversity. Nat Rev Genet 20, 615–628 (2019). https://doi.org/10.1038/s41576-019-0152-0

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