Plant Molecular Biology 43: 179–188, 2000. M.A. Matzke and A.J.M. Matzke (Eds.), Plant Gene Silencing. © 2000 Kluwer Academic Publishers. Printed in the Netherlands. 179 Epigenetic aspects of somaclonal variation in plants Shawn M. Kaeppler * , Heidi F. Kaeppler and Yong Rhee Department of Agronomy, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI 53706, USA ( * author for correspondence; e-mail: smkaeppl@facstaff.wisc.edu) Key words: DNA methylation, mutagenesis, somaclonal variation, tissue culture Abstract Somaclonal variation is manifested as cytological abnormalities, frequent qualitative and quantitative phenotypic mutation, sequence change, and gene activation and silencing. Activation of quiescent transposable elements and retrotransposons indicate that epigenetic changes occur through the culture process. Epigenetic activation of DNA elements further suggests that epigenetic changes may also be involved in cytogenetic instability through modification of heterochromatin, and as a basis of phenotypic variation through the modulation of gene function. The observation that DNA methylation patterns are highly variable among regenerated plants and their progeny provides evidence that DNA modifications are less stable in culture than in seed-grown plants. Future research will determine the relative importance of epigenetic versus sequence or chromosome variation in conditioning somaclonal variation in plants. Introduction Variation in plant phenotype is determined by genetic and epigenetic factors. Phenotypic and DNA varia- tion among putative plant clones is termed somaclonal variation. The purpose of this review is to describe evidence indicating that epigenetic variation is an im- portant mechanistic basis of somaclonal variation in plants. Somaclonal variation is defined as genetic and phe- notypic variation among clonally propagated plants of a single donor clone (reviewed in Sunderland, 1973; D’Amato, 1977, 1985; Bayliss, 1980; Larkin and Scowcroft, 1981, 1983; Orton, 1984; Ahloowahlia, 1986; Larkin, 1987; Lee and Phillips, 1988; Sun and Zheng, 1990; Peschke and Phillips, 1992; Kaep- pler and Phillips, 1993a; Duncan, 1997; Kaeppler et al., 1998; Veilleux and Johnson, 1998; Olhoft and Phillips, 1999). Somaclonal variation caused by the process of tissue culture is also called tissue culture-induced variation to more specifically define the inducing environment. Somaclonal variation can be manifested as either somatically or meiotically stable events. Somatically stable variation includes phenotypes such as habituation of cultures and physi- ologically induced variation observed among primary regenerants. This type of variation is often not trans- mitted to subsequent generations and is of most impact in situations where the primary regenerant is the end product such as the amplification of ornamental plants or trees for direct use. Meiotically heritable variation also occurs and is important in situations where the end product of the tissue culture is propagated and sold as seed. Mechanisms producing both somatically and meiotically heritable variation also contribute to the decline in vigor and regenerability of cultures over time. The loss of culture health with time is a major detriment to the efficiency of transgenic plant produc- tion and much effort has been devoted to avoiding this problem. Epigenetic control of gene expression can be de- fined as a somatically or meiotically heritable alter- ation in gene expression that is potentially reversible and is not due to sequence modification. Epigenetic as- pects of somaclonal variation would therefore involve mechanisms of gene silencing or gene activation that were not due to chromosomal aberrations or sequence change. These changes might be unstable or reversible somatically or through meiosis, although certain epi- genetic systems outside of tissue culture are quite [ 59 ]