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  • Review Article
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Forest tree genomics: growing resources and applications

Key Points

  • Long-lived woody perennial plants, such as forest trees, offer the possibility of understanding fundamental aspects of plant biology, such as the genetic basis of longevity and adaptation to the environment. These properties cannot be learned from standard plant model systems, which are herbaceous and have an annual life cycle.

  • Forest trees are found in both a domesticated and undomesticated state, and they are among the most genetically diverse plants.

  • Genome sizes of forest trees vary enormously from 485 Mb in the poplar to more than 20 Gb in the pine.

  • The first genome to be sequenced was Populus trichocarpa, using Sanger sequencing technology. The large-genome conifer species will be sequenced using next-generation technology. Populus has served as the model taxa for forest trees but, because of the large evolutionary distance between angiosperms and gymnosperms (conifer species), Populus is a less-than-ideal model for the conifers.

  • Traits of interest, such as growth, properties of wood and biotic and abiotic adaptation to environmental stresses are quantitatively inherited. QTL mapping and association genetics are used to dissect these and other complex traits.

  • Marker-based breeding strategies and programmes are developing rapidly and stand to greatly accelerate breeding activities.

  • The genomics of adaptation to changing environments is a priority research area aimed at mitigating the effects of climate change.

Abstract

Over the past two decades, research in forest tree genomics has lagged behind that of model and agricultural systems. However, genomic research in forest trees is poised to enter into an important and productive phase owing to the advent of next-generation sequencing technologies, the enormous genetic diversity in forest trees and the need to mitigate the effects of climate change. Research on long-lived woody perennials is extending our molecular knowledge of complex life histories and adaptations to the environment — enriching a field that has traditionally drawn biological inference from a few short-lived herbaceous species.

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Figure 1: A schematic representation of the breeding and production cycles used for the genetic improvement of many forest tree species.
Figure 2: Landscape genomics in forest trees.

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Glossary

Common garden

A siteat which organisms are reared under identical conditions.

Angiosperms

A taxonomic group that includes plants with seeds that are surrounded by the wall of the ovary, which forms the fruit.

Gymnosperms

A taxonomic group that includes plants with seeds that are not enclosed in the ovary that goes on to form the fruit (for example, a pine cone). Conifer trees are examples of gymnosperms.

Whole-genome shotgun approach

A DNA sequencing method in which genomic DNA is broken up randomly into numerous small segments (reads), which are sequenced. Multiple overlapping reads are computationally assembled into a continuous sequence.

Coverage

The average number of reads representing a given nucleotide in the reconstructed sequence obtained using the whole-genome shotgun approach.

UniGene set

The cluster of several ESTs that represents a unique gene, without taking into account the assembly of the ESTs.

Restriction fragment length polymorphism marker

A molecular marker based on the differential hybridization of cloned DNA to DNA fragments in a sample of restriction enzyme-digested DNA.

Random amplified polymorphic DNA marker

A molecular marker based on the differential PCR amplification of a sample of DNA using short, random oligonucleotide sequences.

Amplified fragment length polymorphism marker

A molecular marker generated by a combination of restriction digestion and PCR amplification.

Single sequence repeat marker

A molecular marker corresponding to the repeated sequences of DNA. The repeated sequence corresponds often to stretches of 1–6 nucleotides.

Landscape genomics

The study of genomic variation among trees or populations that takes into account their spatial, geographical and ecological distribution at the landscape scale.

Abiotic stress

A stress caused by physical or chemical environmental constraints, in contrast to biotic stress, which is caused by interactions with other living organisms.

Heritability

The proportion of phenotypic variation in a population that is attributable to genetic variation among individuals.

Phenology

In trees, the study of seasonal life cycle events (bud flushing, flowering, fruiting) and of the timing of these events along the growing season.

Synthetic (population)

A population assembled by taking individuals from distinct and unrelated populations.

Marker-assisted breeding

A method of selection in which genetic information of a given molecular marker is used to predict and select for a trait of interest (that is,biomass production, height, wood quality or disease resistance).

Flower-stimulation techniques

Artificial techniques (involving girdling of the stem, injection of flowering hormones or use of fertilizers) that are used to induce flowers at a young stage in trees before the time natural fruiting would occur.

Breeding value

The breeding value of a tree for a given trait (that is, biomass production or height) accounts for the sum of gene effects that contribute to that trait. It is estimated by the performance of its progeny

Stand

A forest stand is a population of trees (covering usually several hectares) in a given forest; trees of a stand may or may not be of the same age, and stands can be composed of different tree species.

Common garden experiment

A plantation in which tree populations corresponding to different geographical origins (provenances) are compared using statistical designs.

Positive selection

The selective process by which new advantageous alleles increase continuously in frequency in a population, leading to the decay of genetic diversity.

Balancing selection

The selective process by which multiple alleles are favoured in a natural population, allowing genetic diversity to be maintained.

Clinal variation

The continuous pattern of variation of allelic frequencies along environmental or geographical gradients.

Bayesian (approach)

A statistical approach that assesses the probability of a hypothesis being correct by incorporating the prior probability of the hypothesis and the experimental data supporting the hypothesis.

Principal component analysis

A statistical method used to simplify data sets by transforming a series of correlated variables into a smaller number of uncorrelated factors.

Minor allele frequency

The frequency of the less common allele of a polymorphism. It has a value between 0 and 0.5, and can vary between populations.

Bayes factor

The ratio of the prior probabilities of the null versus the alternative hypotheses over the ratio of the posterior probabilities. This can be interpreted as the relative odds that the hypothesis is true before and after examining the data.

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Neale, D., Kremer, A. Forest tree genomics: growing resources and applications. Nat Rev Genet 12, 111–122 (2011). https://doi.org/10.1038/nrg2931

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