Genotype-environment associations to reveal the molecular basis of environmental adaptation

A fundamental goal in plant biology is to identify and understand the variation underlying plants' adaptation to their environment. Climate change has given new urgency to this goal, as society aims to accelerate adaptation of ecologically important plant species, endangered plant species, and crops to hotter, less predictable climates. In the pre-genomic era, identifying adaptive alleles was painstaking work, leveraging genetics, molecular biology, physiology, and ecology. Now, the rise of genomics and new computational approaches may facilitate this research. Genotype-environment associations (GEAs) use statistical associations between allele frequency and environment of origin to test the hypothesis that allelic variation at a given gene is adapted to local environments. Researchers may scan the genome for GEAs to generate hypotheses on adaptive genetic variants (environmental genome-wide association studies). Despite the rapid adoption of these methods, many important questions remain about the interpretation of GEA findings, which arise from fundamental unanswered questions on the genetic architecture of adaptation and limitations inherent to association-based analyses. We outline strategies to ground GEAs in the underlying hypotheses of genetic architecture and better test GEA-generated hypotheses using genetics and ecophysiology. We provide recommendations for new users who seek to learn about the molecular basis of adaptation. When combined with a rigorous hypothesis testing framework, GEAs may facilitate our understanding of the molecular basis of climate adaptation for plant improvement.

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Work Title Genotype-environment associations to reveal the molecular basis of environmental adaptation
Access
Open Access
Creators
  1. Jesse R. Lasky
  2. Emily B. Josephs
  3. Geoffrey P. Morris
License In Copyright (Rights Reserved)
Work Type Article
Publisher
  1. The Plant Cell
Publication Date August 25, 2022
Publisher Identifier (DOI)
  1. https://doi.org/10.1093/plcell/koac267
Deposited May 29, 2023

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Version 1
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  • Created
  • Added Lasky_etal_2022.pdf
  • Added Creator Jesse R. Lasky
  • Added Creator Emily B. Josephs
  • Added Creator Geoffrey P. Morris
  • Published
  • Updated Publisher, Publication Date Show Changes
    Publisher
    • Plant Cell
    • The Plant Cell
    Publication Date
    • 2023-01-02
    • 2022-08-25
  • Updated