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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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Genetic complementation test results.To test for genetic complementation of the atmyc1 mutant, a series of test-crosses were made between Col-0, Ler-0, and the atmyc1 mutant (in the Col-0 background). Two phenotypes were scored for each genotype: trichome number on first true leaves and trichome density on fifth true leaves; means (+SE) are shown for each ATMYC1 genotype and genotypes with different letters within each bar chart are significantly different from each other (p<0.01, except B vs. C (p<0.05). Both first and fifth leaf phenotypes were used in previous QTL mapping studies. Note that the trends for the two phenotypes are nearly identical, simply shifted up or down, depending on the leaf scored. By comparing the Col (CC), Col x atmyc1 (C-) and atmyc1 (--) genotypes (- denotes a nonfunctional mutant allele), all of which are in an otherwise Col-0 background, it is clear that a single copy of the Col allele of ATMYC1 recovers the mutant phenotype to near wildtype levels. In contrast, comparisons between the Col x Ler (CL) and atmyc1 x Ler (L-) genotypes, each of which is in an otherwise Col/Ler background show that the Ler allele of ATMYC1 does not recover the mutant phenotype.
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pgen-1002069-g002: Genetic complementation test results.To test for genetic complementation of the atmyc1 mutant, a series of test-crosses were made between Col-0, Ler-0, and the atmyc1 mutant (in the Col-0 background). Two phenotypes were scored for each genotype: trichome number on first true leaves and trichome density on fifth true leaves; means (+SE) are shown for each ATMYC1 genotype and genotypes with different letters within each bar chart are significantly different from each other (p<0.01, except B vs. C (p<0.05). Both first and fifth leaf phenotypes were used in previous QTL mapping studies. Note that the trends for the two phenotypes are nearly identical, simply shifted up or down, depending on the leaf scored. By comparing the Col (CC), Col x atmyc1 (C-) and atmyc1 (--) genotypes (- denotes a nonfunctional mutant allele), all of which are in an otherwise Col-0 background, it is clear that a single copy of the Col allele of ATMYC1 recovers the mutant phenotype to near wildtype levels. In contrast, comparisons between the Col x Ler (CL) and atmyc1 x Ler (L-) genotypes, each of which is in an otherwise Col/Ler background show that the Ler allele of ATMYC1 does not recover the mutant phenotype.

Mentions: Previous QTL mapping results for trichome density in A. thaliana localized a QTL to the top of chromosome four in four independent mapping populations [40]. Although no known trichome regulator was apparent in this region, ATMYC1, a paralog of three genes with known roles in trichome initiation was discovered. To determine if ATMYC1 has a role in trichome initiation, we examined TDNA insertion (knock-out) lines. A homozygous TDNA insertion line for ATMYC1 (SALK_057388) in a Col-0 background was determined to have a significantly different number of trichomes/first true leaf and trichome density phenotype on fifth true leaves relative to the wildtype Col-0 accession (Figure 2). The atmyc1 mutant produced fewer trichomes than wildtype on first true leaves and had a lower trichome density on fifth leaves. The trichome phenotype of atmyc1 has since been verified in two additional independent TDNA insertion lines of the gene (Figure S1).


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

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

Genetic complementation test results.To test for genetic complementation of the atmyc1 mutant, a series of test-crosses were made between Col-0, Ler-0, and the atmyc1 mutant (in the Col-0 background). Two phenotypes were scored for each genotype: trichome number on first true leaves and trichome density on fifth true leaves; means (+SE) are shown for each ATMYC1 genotype and genotypes with different letters within each bar chart are significantly different from each other (p<0.01, except B vs. C (p<0.05). Both first and fifth leaf phenotypes were used in previous QTL mapping studies. Note that the trends for the two phenotypes are nearly identical, simply shifted up or down, depending on the leaf scored. By comparing the Col (CC), Col x atmyc1 (C-) and atmyc1 (--) genotypes (- denotes a nonfunctional mutant allele), all of which are in an otherwise Col-0 background, it is clear that a single copy of the Col allele of ATMYC1 recovers the mutant phenotype to near wildtype levels. In contrast, comparisons between the Col x Ler (CL) and atmyc1 x Ler (L-) genotypes, each of which is in an otherwise Col/Ler background show that the Ler allele of ATMYC1 does not recover the mutant phenotype.
© Copyright Policy
Related In: Results  -  Collection

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

pgen-1002069-g002: Genetic complementation test results.To test for genetic complementation of the atmyc1 mutant, a series of test-crosses were made between Col-0, Ler-0, and the atmyc1 mutant (in the Col-0 background). Two phenotypes were scored for each genotype: trichome number on first true leaves and trichome density on fifth true leaves; means (+SE) are shown for each ATMYC1 genotype and genotypes with different letters within each bar chart are significantly different from each other (p<0.01, except B vs. C (p<0.05). Both first and fifth leaf phenotypes were used in previous QTL mapping studies. Note that the trends for the two phenotypes are nearly identical, simply shifted up or down, depending on the leaf scored. By comparing the Col (CC), Col x atmyc1 (C-) and atmyc1 (--) genotypes (- denotes a nonfunctional mutant allele), all of which are in an otherwise Col-0 background, it is clear that a single copy of the Col allele of ATMYC1 recovers the mutant phenotype to near wildtype levels. In contrast, comparisons between the Col x Ler (CL) and atmyc1 x Ler (L-) genotypes, each of which is in an otherwise Col/Ler background show that the Ler allele of ATMYC1 does not recover the mutant phenotype.
Mentions: Previous QTL mapping results for trichome density in A. thaliana localized a QTL to the top of chromosome four in four independent mapping populations [40]. Although no known trichome regulator was apparent in this region, ATMYC1, a paralog of three genes with known roles in trichome initiation was discovered. To determine if ATMYC1 has a role in trichome initiation, we examined TDNA insertion (knock-out) lines. A homozygous TDNA insertion line for ATMYC1 (SALK_057388) in a Col-0 background was determined to have a significantly different number of trichomes/first true leaf and trichome density phenotype on fifth true leaves relative to the wildtype Col-0 accession (Figure 2). The atmyc1 mutant produced fewer trichomes than wildtype on first true leaves and had a lower trichome density on fifth leaves. The trichome phenotype of atmyc1 has since been verified in two additional independent TDNA insertion lines of the gene (Figure S1).

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