Determining the evolutionary forces shaping <i>G</i> × <i>E</i>

Josephs, Emily B.

doi:10.1111/nph.15103

Cited by 61 publications

(55 citation statements)

References 70 publications

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“…Local adaptation is commonly invoked to explain the maintenance of plasticity between populations (Josephs, 2018). In our system, based on the relatively high number of genes showing GEI, it is likely that foothill and alpine habitats differ in their fitness optima.…”

Section: Discussionmentioning

confidence: 99%

Parallelism in gene expression between foothill and alpine ecotypes inArabidopsis arenosa

Wos

Bohutínská

Nosková

et al. 2020

Preprint

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27Parallel adaptation results from independent evolution of similar traits between closely related 28 lineages and allows testing to which extent evolution is repeatable. Parallel adaptation often 29 involves similar gene expression changes but the identity of genes shaped by parallel selection 30 and the causes of expression parallelism remains largely unknown. By comparing genomes 31 and transcriptomes of four independent foothill-alpine population pairs across four 32 treatments, we addressed genetic basis, plasticity and functional consequences of gene 33 expression parallelism in alpine adaptation. Seeds of four population pairs of Arabidopsis 34 arenosa from distinct mountain regions were raised under four treatments that differed in 35 temperature and irradiance, factors varying strongly with elevation. Parallelism in gene 36 expression was quantified by RNA-seq in leaves of young plants. By manipulating 37temperature and irradiance, we also tested for parallelism in plasticity (gene-by-environment 38 interaction [GEI]). We found significant parallelism in differential gene expression across 39 four independently recruited alpine ecotypes with an overrepresentation of genes involved in 40 biotic stress response. In addition, we demonstrated significant parallelism in GEI indicating 41 shared response to environmental variation in our foothill and alpine populations. Fraction of 42 genes showing expression parallelism also encompassed genomic variants showing outlying 43 differentiation, with greater enrichment of such variants in cis-regulatory elements. In 44 summary, our results suggest frequent evolutionary repeatability in shaping expression 45 difference associated with colonization of an alpine environment and support the hypothesis 46 of an important role of genetic variation in cis-regulatory elements in gene expression 47 parallelism.48 49

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Section: Discussionmentioning

confidence: 99%

Parallelism in gene expression between foothill and alpine ecotypes inArabidopsis arenosa

Wos

Bohutínská

Nosková

et al. 2020

Preprint

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“…A reaction norm describes the shape or specific form of the phenotypic response to the environment of an individual or genotype (Scheiner, 1993;Via et al, 1995). Genotypeby-environment interactions (G 9 E) occur when genotypes differ in the slope of their reaction norms (Nussey et al, 2007;Josephs, 2018). The term G 9 E is sometimes used synonymously with plasticity, where differences among genotypes rather than plasticity are of specific interest (e.g.…”

Section: Box 1 Glossarymentioning

confidence: 99%

How to analyse plant phenotypic plasticity in response to a changing climate

2019

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Summary Plant biology is experiencing a renewed interest in the mechanistic underpinnings and evolution of phenotypic plasticity that calls for a re‐evaluation of how we analyse phenotypic responses to a rapidly changing climate. We suggest that dissecting plant plasticity in response to increasing temperature needs an approach that can represent plasticity over multiple environments, and considers both population‐level responses and the variation between genotypes in their response. Here, we outline how a random regression mixed model framework can be applied to plastic traits that show linear or nonlinear responses to temperature. Random regressions provide a powerful and efficient means of characterising plasticity and its variation. Although they have been used widely in other fields, they have only recently been implemented in plant evolutionary ecology. We outline their structure and provide an example tutorial of their implementation.

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“…Particularly, multiple environmental conditions along a gradient of variation are necessary to unravel the quantitative attributes of phenotypic responses. When describing the interaction between genome and environment, understanding phenotypic plasticity helps interpret the evolutionary and environmental forces modifying genetic architectures (Josephs, ). Therefore, investigating phenotypic plasticity will also contribute to crop improvement, when integrated with breeding programs that are facing climate change and instability.…”

Section: Phenotypic Plasticity: a Power To Nurture The Naturementioning

confidence: 99%

Crop genome‐wide association study: a harvest of biological relevance

2018

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Summary With the advent of rapid genotyping and next‐generation sequencing technologies, genome‐wide association study (GWAS) has become a routine strategy for decoding genotype–phenotype associations in many species. More than 1000 such studies over the last decade have revealed substantial genotype–phenotype associations in crops and provided unparalleled opportunities to probe functional genomics. Beyond the many ‘hits’ obtained, this review summarizes recent efforts to increase our understanding of the genetic architecture of complex traits by focusing on non‐main effects including epistasis, pleiotropy, and phenotypic plasticity. We also discuss how these achievements and the remaining gaps in our knowledge will guide future studies. Synthetic association is highlighted as leading to false causality, which is prevalent but largely underestimated. Furthermore, validation evidence is appealing for future GWAS, especially in the context of emerging genome‐editing technologies.

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Determining the evolutionary forces shaping G × E

Cited by 61 publications

References 70 publications

Parallelism in gene expression between foothill and alpine ecotypes inArabidopsis arenosa

Parallelism in gene expression between foothill and alpine ecotypes inArabidopsis arenosa

How to analyse plant phenotypic plasticity in response to a changing climate

Crop genome‐wide association study: a harvest of biological relevance

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