Symonds VV, Hatlestad G, Lloyd AM. Natural allelic variation defines a role for ATMYC1: trichome cell fate determination.
PLoS Genet 2011;
7:e1002069. [PMID:
21695236 PMCID:
PMC3111535 DOI:
10.1371/journal.pgen.1002069]
[Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Accepted: 03/24/2011] [Indexed: 11/19/2022] Open
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.
Among the goals of modern evolutionary biology is to identify the molecular genetic sources of natural variation. Although genetic mapping has led to an increased understanding of the genetic architecture of natural variation, there are surprisingly few cases where the molecular source of the variation has been identified. Here, we utilize previous mapping results to identify the gene and ultimately a polymorphism that underlies natural variation for a dynamic trait in Arabidopsis thaliana: trichome density. We show that plants carrying a knock-out of the bHLH transcription factor ATMYC1 have a reduced trichome density phenotype; this is the first reported function for ATMYC1. Using traditional and molecular genetic approaches, we identify a single base change in natural alleles of ATMYC1, which leads to an amino acid replacement that qualitatively alters protein–protein interactions with known partners, presumably altering the trichome cell fate pathway. In a broad screen for molecular variation in ATMYC1, we identify a dense block of amino acid replacements that differentiates two high-frequency allele types. Although this block of variation does not appear to affect trichome density, based on paralogs of ATMYC1, we propose that this variation has arisen due to directional selection on another epidermal trait.
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