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Heritable variation in gene expression is common within and among species and contributes to phenotypic diversity. Mutations affecting eithercis- ortrans-regulatory sequences controlling gene expression give rise to variation in gene expression, and natural selection acting on this variation causes some regulatory variants to persist in a population for longer than others. To understand how mutation and selection interact to produce the patterns of regulatory variation we see within and among species, my colleagues and I have been systematically determining the effects of new mutations on expression of theTDH3gene inSaccharomyces cerevisiaeand comparing them to the effects of polymorphisms segregating within this species. We have also investigated the molecular mechanisms by which regulatory variants act. Over the past decade, this work has revealed properties ofcis- andtrans-regulatory mutations including their relative frequency, effects, dominance, pleiotropy and fitness consequences. Comparing these mutational effects to the effects of polymorphisms in natural populations, we have inferred selection acting on expression level, expression noise and phenotypic plasticity. Here, I summarize this body of work and synthesize its findings to make inferences not readily discernible from the individual studies alone. This article is part of the theme issue ‘Interdisciplinary approaches to predicting evolutionary biology’.
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Trans -regulatory loci shape natural variation of gene expression plasticity in Arabidopsis
Abstract Organisms regulate gene expression in response to environmental cues, a process known as plasticity, to adjust to changing environments. Research into natural variation and the evolution of plasticity frequently studies cis-regulatory elements with theory suggesting they are more important evolutionarily than trans-regulatory elements. Genome-wide association (GWA) studies have supported this idea, observing a predominance of cis-loci affecting plasticity. However, studies in structured populations provide a contrasting image, raising questions about the genetic architecture of natural variation in plasticity. To circumvent potential statistical difficulties present in GWA studies, we mapped loci underlying transcriptomic plasticity in response to salicylic acid (SA) using recombinant inbred lines generated from 2 random Arabidopsis thaliana accessions. We detected extensive transgressive segregation in the SA response, suggesting that plasticity to salicylate in Arabidopsis is polygenic. Most loci (>75%) underlying this variation act in trans, especially for loci influencing plasticity. Trans-acting loci were enriched in genome hotspots, with predominantly small-effect sizes distributed across many genes. This could potentially explain their under-discovery in GWA studies. This work reveals a potentially important role for trans-acting loci in plastic expression responses, with implications for understanding plant adaptation to different environments.
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- PAR ID:
- 10612332
- Publisher / Repository:
- Oxford University Press
- Date Published:
- Journal Name:
- GENETICS
- ISSN:
- 1943-2631
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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