Experimental Validation of Genome‐Environment Associations in Arabidopsis

TL;DR

This study experimentally validates genes identified through genotype-environment associations in Arabidopsis, finding some contribute to local adaptation under drought.

Contribution

The paper experimentally validates genome-environment association candidates in Arabidopsis, linking them to adaptive traits and GxE interactions.

Findings

16 out of 42 GEA-identified genes showed significant effects on traits related to local adaptation or environmental response.

wrky38 mutants exhibited GxE effects for fitness and reduced stomatal conductance under drought, suggesting adaptive drought avoidance.

GEA identified natural variants of WRKY38 and LSD1 alleles associated with dry environments and flowering time variation.

Abstract

Identifying the genetic basis of local adaptation is a key goal in evolutionary biology. Allele frequency clines along environmental gradients, known as genotype‐environment associations (GEA), are often used to detect potential loci causing local adaptation but are rarely followed by experimental validation. Here, we tested loci identified in three moisture‐related GEA studies on Arabidopsis. We studied 42 GEA‐identified genes using t‐DNA knockout lines under drought and tested effects on flowering time, an adaptive trait, and genotype‐by‐environment (GxE) interactions for performance and fitness. In total, 16/42 genes had significant effects on traits involved in local adaptation or performance responses to the environment. We found that wrky38 mutants had significant GxE effects for fitness; lsd1 plants had a significant GxE effect for flowering time, and 11 genes showed flowering time effects with no drought interaction. However, most GEA candidates did not exhibit GxE. In the follow‐up experiments, wrky38 caused decreased stomatal conductance and specific leaf area under drought, indicating potentially adaptive drought avoidance. Additionally, GEA identified natural putative LoF variants of WRKY38 associated with dry environments, as well as alleles associated with variation in LSD1 expression. While only a few GEA‐identified genes were validated for GxE interactions for fitness, we likely overlooked some genes because experiments might not well represent natural environments and t‐DNA insertions might not well represent natural alleles. Nevertheless, GEAs apparently identified some genes contributing to local adaptation. GEA and follow‐up experiments are straightforward to implement in model systems and demonstrate prospects for GEA discovery of new local adaptations.

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