The genomic basis of adaptation in plants

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Highlights

  • The genomics of adaptation in plants is entering a period of accelerated discovery.

  • The sessile nature of plants makes them powerful models for studying adaptation.

  • Modes of adaptation are diverse, including hard and soft sweeps and adaptive introgression.

  • Combining population genomics and quantitative genetics is a worthwhile approach.

Plants are powerful models for the study of adaptive evolution. Since they are rooted in place, they must directly face environmental insults, making adaptation to local conditions vital. In addition to adaptation to natural conditions, some plant species have held a central role in human subsistence over the past several thousand years. In these species, humans exerted strong selective pressures on traits of agricultural importance. Recently, an increasing number of studies have aimed to identify the genomic basis of adaptation. These studies have provided insights into the mechanisms through which the raw materials of adaptation were introduced as well as the modes of adaptation in wild and domesticated species.

Introduction

“Plants stand still and wait to be counted.” JL Harper [1]

Due to their sessile nature, plants represent an excellent system to study adaptation. The ease of sampling (and resampling) populations, the ability to systematically sample across environmental gradients, and the possibility to conduct transplant experiments provide outstanding opportunities to study temporally and spatially varying selection. In addition to adaptation to the natural environment, many plant species co-evolved with humans, either as commensals or because humans actively selected for traits that they valued. Comparing and contrasting the genomic consequences of selection from natural and human-driven forces can provide insights into adaptive processes and the constraints on these processes. Here, we review and discuss recent developments from genome-scale studies that illuminate the basis of adaptive evolution in plant species. Due to space limitations, we provide only a brief overview of models and methods and focus on studies that use population genomic approaches to interrogate the genome using dense genome-wide datasets. We refer to previous reviews for readers interested in learning more about models and methods used to detect adaptive evolution [2, 3].

Section snippets

Approaches for detecting adaptive evolution

Broadly speaking there are two approaches to detecting adaptive evolution. One works from the phenotype down and the other from the genotype up [4]. With the top down approach an adaptive phenotype is identified and then forward genetics approaches are taken to elucidate the underlying genetic factors. In the bottom up approach specific patterns of polymorphism in the genome are used to identify genomic regions that are likely to be experiencing positive selection. The advantage of the bottom

Adaptation in the wild

Natural populations are exposed to a variety of selection pressures, including climate, soil components and human-associated factors. Depending on the selection pressure and the extent of a species’ range, these factors may underlie species-wide adaptation or adaptation on a more local level.

The possibilities of obtaining genomic data across diverse species are increasing rapidly as sequencing technologies improve and costs fall. Below we highlight several such exciting studies. However, there

Adaptation during domestication

Crop species were subject to strong selective forces during the breeding process, making them prime targets for studies of adaptation. However, the genome-wide effects of domestication bottlenecks followed by massive population expansions are a major challenge for identifying adaptive loci because they mimic the patterns that result from strong selective sweeps. Explicit modeling of demographic histories provides one method to differentiate sweep signatures from patterns of reduced variation

Conclusions and future directions

Studies over the past few years have shown that there are diverse paths to adaptation both in the sources of adaptive variants (i.e., novel, pre-existing and introgressed variants) and in the scale of adaptation. These findings illustrate how important it is to study adaptive phenomena in diverse populations and species. Emerging model systems [86], many of which have the benefit of years of ecological and/or genetic study are poised to yield exciting new results.

In addition to more thorough

References and recommended reading

Papers of particular interest, published within the period of review, have been highlighted as:

  • • of special interest

  • •• of outstanding interest

Acknowledgements

This work was supported by the Max Planck Gesellschaft and ERC Grant CVI_ADAPT to AMH.

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