Abstract
The molecular nature of biological variation is not well understood. Indeed, many questions persist regarding the types of molecular changes and the classes of genes that underlie morphological variation within and among species. Here we have taken a candidate gene approach based on previous mapping results to identify the gene and ultimately a polymorphism that underlies a trichome density QTL in Arabidopsis thaliana. Our results show that natural allelic variation in the transcription factor ATMYC1 alters trichome density in A. thaliana; this is the first reported function for ATMYC1. Using site-directed mutagenesis and yeast two-hybrid experiments, we demonstrate that a single amino acid replacement in ATMYC1, discovered in four ecotypes, eliminates known protein–protein interactions in the trichome initiation pathway. Additionally, in a broad screen for molecular variation at ATMYC1, including 72 A. thaliana ecotypes, a high-frequency block of variation was detected that results in >10% amino acid replacement within one of the eight exons of the gene. This sequence variation harbors a strong signal of divergent selection but has no measurable effect on trichome density. Homologs of ATMYC1 are pleiotropic, however, so this block of variation may be the result of natural selection having acted on another trait, while maintaining the trichome density role of the gene. These results show that ATMYC1 is an important source of variation for epidermal traits in A. thaliana and indicate that the transcription factors that make up the TTG1 genetic pathway generally may be important sources of epidermal variation in plants.
Highlights
Understanding the origins, maintenance, and loss of natural variation remain important goals of evolutionary biology; ideally, we should like to know what types of molecular genetic changes generate the variation that natural selection acts on
We show that plants carrying a knockout of the bHLH transcription factor ATMYC1 have a reduced trichome density phenotype; this is the first reported function for ATMYC1
We have shown here that a low frequency polymorphism that results in a simple amino acid replacement in ATMYC1 reduces trichome density in natural ecotypes of A. thaliana, thereby ascribing the first function to ATMYC1
Summary
Understanding the origins, maintenance, and loss of natural variation remain important goals of evolutionary biology; ideally, we should like to know what types of molecular genetic changes generate the variation that natural selection acts on. Common first approaches to characterizing the genetic bases of natural variation include quantitative trait locus (QTL) mapping (see reviews [3,4,5]) and, more recently, genome-wide association mapping (e.g., [6,7,8]). While these methods provide many genetic insights, mapping results largely remain hypotheses regarding the molecular nature of biological diversity. Information about the molecular changes that underlie natural variation within and among species provides important insights into the mechanisms that drive local adaptation, morphological evolution, and speciation. King and Wilson [19]
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