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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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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- 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.
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.
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.
A meta-omics approach similar to metabarcoding, but instead of using DNA barcodes it involves random sequencing of DNA from bulk samples.
Pertaining to a meta-omics approach similar to metagenomics, but instead of randomly sequencing DNA it randomly sequences transcriptomes or expressed genes.
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.
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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