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Natural CMT2 variation is associated with genome-wide methylation changes and temperature seasonality.

Shen X, De Jonge J, Forsberg SK, Pettersson ME, Sheng Z, Hennig L, Carlborg Ö - PLoS Genet. (2014)

Bottom Line: Here, we used public data from two collections of A. thaliana accessions to associate genetic variability at individual loci with differences in climates at the sampling sites.We use a novel method to screen the genome for plastic alleles that tolerate a broader climate range than the major allele.This approach reduces confounding with population structure and increases power compared to standard genome-wide association methods.

View Article: PubMed Central - PubMed

Affiliation: Swedish University of Agricultural Sciences, Department of Clinical Sciences, Division of Computational Genetics, Uppsala, Sweden; Karolinska Institutet, Department of Medical Epidemiology and Biostatistics, Stockholm, Sweden; University of Edinburgh, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit, Edinburgh, United Kingdom.

ABSTRACT
As Arabidopsis thaliana has colonized a wide range of habitats across the world it is an attractive model for studying the genetic mechanisms underlying environmental adaptation. Here, we used public data from two collections of A. thaliana accessions to associate genetic variability at individual loci with differences in climates at the sampling sites. We use a novel method to screen the genome for plastic alleles that tolerate a broader climate range than the major allele. This approach reduces confounding with population structure and increases power compared to standard genome-wide association methods. Sixteen novel loci were found, including an association between Chromomethylase 2 (CMT2) and temperature seasonality where the genome-wide CHH methylation was different for the group of accessions carrying the plastic allele. Cmt2 mutants were shown to be more tolerant to heat-stress, suggesting genetic regulation of epigenetic modifications as a likely mechanism underlying natural adaptation to variable temperatures, potentially through differential allelic plasticity to temperature-stress.

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cmt2 mutant plants display an increased tolerance to heat-stress.A. The survival rate is significantly higher for cmt2-5 mutant than for Col-0 plants under severe heat-stress (24 h at 37.5°C). P-values in A were obtained using a log-linear regression. B. The cmt2-5 mutant was also more tolerant to less severe heat-stress heat-stress (6 h at 37.5°C) than Col-0, here illustrated by its significantly faster growth of the root (P = 0.026; one-sided t-test) during the first 48 h following heat stress.
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pgen-1004842-g005: cmt2 mutant plants display an increased tolerance to heat-stress.A. The survival rate is significantly higher for cmt2-5 mutant than for Col-0 plants under severe heat-stress (24 h at 37.5°C). P-values in A were obtained using a log-linear regression. B. The cmt2-5 mutant was also more tolerant to less severe heat-stress heat-stress (6 h at 37.5°C) than Col-0, here illustrated by its significantly faster growth of the root (P = 0.026; one-sided t-test) during the first 48 h following heat stress.

Mentions: To functionally explore whether CMT2 is a likely contributor to the temperature-stress response, we have subjected cmt2 mutants to two types of heat-stress. First, we tested the reaction of Col-0 and the cmt2-5 mutant (S45 Figure) to severe heat-stress (24 h at 37°C). This treatment was used because it can release transcriptional silencing of some TEs [27] and could thus be a good starting point to evaluate potential stress effects on cmt2. Under these conditions, the cmt2 mutant had significantly higher survival-rate (1.6-fold; P = 9.1×10−3; Fig. 5A) than Col-0. To evaluate whether a similar response could also be observed under less severe, non-lethal stress, we subjected the same genotypes to heat-stress of shorter duration (6 h at 37°C) and measured root growth after stress as a measure of the ability of plants to recover. Also under these conditions, the cmt2 mutant was found to be more tolerant to heat-stress, as its growth was less affected after being stressed (Fig. 5B; 1.9-fold higher in cmt2; P = 0.026, one-sided t-test). This striking improvement in tolerance to heat-stress of cmt2 plants suggests CMT2-dependent CHH methylation as an important alleviator of stress responses in A. thaliana and a candidate mechanism for temperature adaptation.


Natural CMT2 variation is associated with genome-wide methylation changes and temperature seasonality.

Shen X, De Jonge J, Forsberg SK, Pettersson ME, Sheng Z, Hennig L, Carlborg Ö - PLoS Genet. (2014)

cmt2 mutant plants display an increased tolerance to heat-stress.A. The survival rate is significantly higher for cmt2-5 mutant than for Col-0 plants under severe heat-stress (24 h at 37.5°C). P-values in A were obtained using a log-linear regression. B. The cmt2-5 mutant was also more tolerant to less severe heat-stress heat-stress (6 h at 37.5°C) than Col-0, here illustrated by its significantly faster growth of the root (P = 0.026; one-sided t-test) during the first 48 h following heat stress.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4263395&req=5

pgen-1004842-g005: cmt2 mutant plants display an increased tolerance to heat-stress.A. The survival rate is significantly higher for cmt2-5 mutant than for Col-0 plants under severe heat-stress (24 h at 37.5°C). P-values in A were obtained using a log-linear regression. B. The cmt2-5 mutant was also more tolerant to less severe heat-stress heat-stress (6 h at 37.5°C) than Col-0, here illustrated by its significantly faster growth of the root (P = 0.026; one-sided t-test) during the first 48 h following heat stress.
Mentions: To functionally explore whether CMT2 is a likely contributor to the temperature-stress response, we have subjected cmt2 mutants to two types of heat-stress. First, we tested the reaction of Col-0 and the cmt2-5 mutant (S45 Figure) to severe heat-stress (24 h at 37°C). This treatment was used because it can release transcriptional silencing of some TEs [27] and could thus be a good starting point to evaluate potential stress effects on cmt2. Under these conditions, the cmt2 mutant had significantly higher survival-rate (1.6-fold; P = 9.1×10−3; Fig. 5A) than Col-0. To evaluate whether a similar response could also be observed under less severe, non-lethal stress, we subjected the same genotypes to heat-stress of shorter duration (6 h at 37°C) and measured root growth after stress as a measure of the ability of plants to recover. Also under these conditions, the cmt2 mutant was found to be more tolerant to heat-stress, as its growth was less affected after being stressed (Fig. 5B; 1.9-fold higher in cmt2; P = 0.026, one-sided t-test). This striking improvement in tolerance to heat-stress of cmt2 plants suggests CMT2-dependent CHH methylation as an important alleviator of stress responses in A. thaliana and a candidate mechanism for temperature adaptation.

Bottom Line: Here, we used public data from two collections of A. thaliana accessions to associate genetic variability at individual loci with differences in climates at the sampling sites.We use a novel method to screen the genome for plastic alleles that tolerate a broader climate range than the major allele.This approach reduces confounding with population structure and increases power compared to standard genome-wide association methods.

View Article: PubMed Central - PubMed

Affiliation: Swedish University of Agricultural Sciences, Department of Clinical Sciences, Division of Computational Genetics, Uppsala, Sweden; Karolinska Institutet, Department of Medical Epidemiology and Biostatistics, Stockholm, Sweden; University of Edinburgh, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit, Edinburgh, United Kingdom.

ABSTRACT
As Arabidopsis thaliana has colonized a wide range of habitats across the world it is an attractive model for studying the genetic mechanisms underlying environmental adaptation. Here, we used public data from two collections of A. thaliana accessions to associate genetic variability at individual loci with differences in climates at the sampling sites. We use a novel method to screen the genome for plastic alleles that tolerate a broader climate range than the major allele. This approach reduces confounding with population structure and increases power compared to standard genome-wide association methods. Sixteen novel loci were found, including an association between Chromomethylase 2 (CMT2) and temperature seasonality where the genome-wide CHH methylation was different for the group of accessions carrying the plastic allele. Cmt2 mutants were shown to be more tolerant to heat-stress, suggesting genetic regulation of epigenetic modifications as a likely mechanism underlying natural adaptation to variable temperatures, potentially through differential allelic plasticity to temperature-stress.

Show MeSH
Related in: MedlinePlus