Plants do use epigenetics to adapt to diverse environments

16 Mar
If you’ve ever grown plants that come from a distant land, you may be familiar with the fact that you may need an adaptive process of one or more generations to get the best of them. Oddly enough this time is often too short for genetic adaption to happen and sweep over, especially as most of the ill-adapted plants don’t really die nor fail to reproduce (i.e. they are not too aggressively selected against). How does it happen then? Epigenetics may have the answer.
Robert J. Schmidt et al., Patterns of population epigenomic diversity. Nature 2013. Open accessLINK [doi:10.1038/nature11968]


Natural epigenetic variation provides a source for the generation of phenotypic diversity, but to understand its contribution to such diversity, its interaction with genetic variation requires further investigation. Here we report population-wide DNA sequencing of genomes, transcriptomes and methylomes of wild Arabidopsis thaliana accessions. Single cytosine methylation polymorphisms are not linked to genotype. However, the rate of linkage disequilibrium decay amongst differentially methylated regions targeted by RNA-directed DNA methylation is similar to the rate for single nucleotide polymorphisms. Association analyses of these RNA-directed DNA methylation regions with genetic variants identified thousands of methylation quantitative trait loci, which revealed the population estimate of genetically dependent methylation variation. Analysis of invariably methylated transposons and genes across this population indicates that loci targeted by RNA-directed DNA methylation are epigenetically activated in pollen and seeds, which facilitates proper development of these structures.

From the body of the article:

Epiallele formation in the absence of genetic variation can result in
phenotypic variation, which is most evident in the plant kingdom, as
exemplified by the peloric and colorless non-ripening variants from Linaria vulgaris and Solanum lycopersicum, respectively6, 7. Although rates of spontaneous variation in DNA methylation and mutation can be decoupled in the laboratory8, 9, 10, 11,
in natural settings, these two features of genomes co-evolve to create
phenotypic diversity on which natural selection can act.

Similarly to the limited examples of pure epialleles (methylation
variants that form independent of genetic variation), few examples of
DNA methylation variants linked to genetic variants are known15, 16, 17.

And the ‘Conclusion remarks’ (emphasis is mine):

Natural epigenomic variation is widespread within A. thaliana,
and the population-based epigenomics presented here has uncovered
features of the DNA methylome that are not linked to underlying genetic
variation, such as all forms of SMPs and CG-DMRs. However, C-DMRs have
positional association decay patterns similar to linkage disequilibrium
decay patterns for SNPs and in some cases are associated with genetic
variants, but the majority of C-DMRs were not tested by association
mapping due to low allele frequencies and could result from rare
sequence variants. Our combined analyses of genetic and methylation
variation did not uncover a correlation between major effect mutations
and genes silenced by RdDM, suggesting that this pathway may target
these genes for another purpose. This purpose could be to restrict
expression from vegetative tissues similarly to transposons. Another
possible purpose of being targeted by RdDM could be to coordinate
expression specifically in pollen and in seed to ensure proper
gametophytic and embryonic development. Animals also use small
RNA-directed DNA methylation and heterochromatin formation mechanisms to
maintain the epigenome of the germ line through the use of
Piwi-interacting RNAs36.

In both plants and animals these small RNAs are derived from the genome
of companion cells, which are terminal in nature and can afford
widespread reactivation of transposon and repeat sequences as they are
not passed on to the next generation. Our study provides evidence that
RdDM-targeted genes may have co-opted this transposon silencing
mechanism to maintain their silenced state in vegetative tissues and
transgenerationally, as well as to ensure proper expression important
for pollen, seed and germ line development.

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Posted by on March 16, 2013 in epigenetics, evolution, Genetics, plant genetics


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