Abstract
Natural variation is defined as the phenotypic variation caused by spontaneous mutations. In general, mutations are associated with changes of nucleotide sequence, and many mutations in genes that can cause changes in plant development have been identified. Epigenetic change, which does not involve alteration to the nucleotide sequence, can also cause changes in gene activity by changing the structure of chromatin through DNA methylation or histone modifications. Now there is evidence based on induced or spontaneous mutants that epigenetic changes can cause altering plant phenotypes. Epigenetic changes have occurred frequently in plants, and some are heritable or metastable causing variation in epigenetic status within or between species. Therefore, heritable epigenetic variation as well as genetic variation has the potential to drive natural variation.
Highlights
Variation in DNA sequence can cause variation in gene expression, which influences quantitative phenotypic variation in organisms and is an important factor in natural variation
Increasing numbers of epialleles are being reported in various species, and it is clear that epi-mutations can affect plant phenotypes
Metastable inheritance may be more useful in adaptation than genetic mutations because metastable epigenetic changes are more flexible and may contribute to phenotypic plasticity under environmental stress conditions [111,112]
Summary
Variation in DNA sequence can cause variation in gene expression, which influences quantitative phenotypic variation in organisms and is an important factor in natural variation. The promoter region of FWA is DNA methylated and FWA is not expressed in vegetative tissues, this DNA methylation is removed in the ddm mutant and FWA is expressed in vegetative tissues (Figure 1) and causes late flowering [43] This late flowering phenotype is observed in the met mutant [44,45], but not in the drm drm cmt triple mutant [46], suggesting that silencing of FWA is mainly dependent on CG methylation. DNA methylation spreads into the BNS gene from the LINE sequence in a CMT3-KYP dependent manner, and stochastically induces silencing of the BNS gene Another mutant phenotype seen in the ddm background, change of plant structure (short and compact inflorescence with reduced plant height), is bns (BONSAI), which is unstably inherited in the presence of the DDM1 gene. Cmt triple mutant are due to SDC misexpression caused by the elimination of DNA methylation in its promoter region [56]
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