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Natural allelic variation defines a role for ATMYC1: trichome cell fate determination.

Symonds VV, Hatlestad G, Lloyd AM - PLoS Genet. (2011)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America. v.v.symonds@massey.ac.nz

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.

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Median joining network of 28 ATMYC1 inferred cDNA haplotypes representing alleles sampled from 72 A. thaliana accessions.Each circle represents a unique coding haplotype and the area of each circle indicates the relative frequency at which each haplotype was sampled. Unsampled haplotypes required to complete the network are drawn as filled-in circles. Branch lengths reflect nucleotide change between any two haplotypes. The large block of variation within exon six falls along the long branch that connects the Type I to the Type II haplotype clusters. The accessions discussed in the text are indicated adjacent to the haplotype they possess.
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pgen-1002069-g003: Median joining network of 28 ATMYC1 inferred cDNA haplotypes representing alleles sampled from 72 A. thaliana accessions.Each circle represents a unique coding haplotype and the area of each circle indicates the relative frequency at which each haplotype was sampled. Unsampled haplotypes required to complete the network are drawn as filled-in circles. Branch lengths reflect nucleotide change between any two haplotypes. The large block of variation within exon six falls along the long branch that connects the Type I to the Type II haplotype clusters. The accessions discussed in the text are indicated adjacent to the haplotype they possess.

Mentions: In a screen of 72 A. thaliana accessions, considerable sequence variation was discovered among natural alleles of ATMYC1 with a total of 28 (inferred) cDNA haplotypes discovered (GenBank accession #s: JF801957-JF802028). Median-joining analyses yielded a network that is split into two diverged clusters (Figure 3); these have been labeled as Type I and Type II, with 16 and 12 haplotypes, respectively. Alleles of these two Types consistently differ by 25 substitutions, which translate to 17 amino acid replacements. Interestingly, nearly all of this variation (24 of 25 substitutions and all 17 replacements) is in exon six (Figure S2).


Natural allelic variation defines a role for ATMYC1: trichome cell fate determination.

Symonds VV, Hatlestad G, Lloyd AM - PLoS Genet. (2011)

Median joining network of 28 ATMYC1 inferred cDNA haplotypes representing alleles sampled from 72 A. thaliana accessions.Each circle represents a unique coding haplotype and the area of each circle indicates the relative frequency at which each haplotype was sampled. Unsampled haplotypes required to complete the network are drawn as filled-in circles. Branch lengths reflect nucleotide change between any two haplotypes. The large block of variation within exon six falls along the long branch that connects the Type I to the Type II haplotype clusters. The accessions discussed in the text are indicated adjacent to the haplotype they possess.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3111535&req=5

pgen-1002069-g003: Median joining network of 28 ATMYC1 inferred cDNA haplotypes representing alleles sampled from 72 A. thaliana accessions.Each circle represents a unique coding haplotype and the area of each circle indicates the relative frequency at which each haplotype was sampled. Unsampled haplotypes required to complete the network are drawn as filled-in circles. Branch lengths reflect nucleotide change between any two haplotypes. The large block of variation within exon six falls along the long branch that connects the Type I to the Type II haplotype clusters. The accessions discussed in the text are indicated adjacent to the haplotype they possess.
Mentions: In a screen of 72 A. thaliana accessions, considerable sequence variation was discovered among natural alleles of ATMYC1 with a total of 28 (inferred) cDNA haplotypes discovered (GenBank accession #s: JF801957-JF802028). Median-joining analyses yielded a network that is split into two diverged clusters (Figure 3); these have been labeled as Type I and Type II, with 16 and 12 haplotypes, respectively. Alleles of these two Types consistently differ by 25 substitutions, which translate to 17 amino acid replacements. Interestingly, nearly all of this variation (24 of 25 substitutions and all 17 replacements) is in exon six (Figure S2).

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America. v.v.symonds@massey.ac.nz

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.

Show MeSH