Agriculture Reference
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well recognized now that complete (alleles) or partial (orthologues and
paralogs) genome duplication can create more variability through
neofunctionalization or subfunctionalization (Lynch and Force 2000)
at duplicated loci (Chen and Pikaard 1997; Lee and Chen 2001; Wang
et al. 2006a,b,c; Chen 2007; Klironomos et al. 2013). Allele-speci
c
(biased) expression is clearly controlled by epigenetic mechanism(s),
undoubtedly involving chromatin chemistry and structure and DNA
methylation, and could dramatically increase the potential variation
and resilience of information encoded in the genome especially to adapt
to a changing environment (Autran et al. 2011; Feil and Fraga 2012).
Recently, DNA methylation analysis of
Arabidopsis
F1 hybrids and
their relative parental lines,
A. thaliana
Landsberg erecta and C24, has
revealed increasing DNAmethylation in the F1 plants in different regions
compared with the parental lines. It has also been shown that the
newly methylated regions in the hybrids were associated with small
RNAs, indicating that the RNA-directed DNA methylation(RdDM) path-
waymaymediateDNAmethylation inF1 hybrids. This pathway is known
to function in transcriptional regulation, and may thereby contribute
to heterosis through altering the expression of speci
c genes. Numerous
studies have established, throughQTL analysis, that most heterotic events
are polygenic. A model is emerging where the different epigenomes
of imbred lines combine to form a unique epigenotype in the F1 hybrid
that can initiate a vigorous phenotype through speci
c gene expression
patterns.
E. Beyond the Ping
Pong Model
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Of course, the epigenetic mechanisms that underlie the ping
pong-like
transitions in meiosis and fertilization in plants also drive the phenotype
changes that can occur within a single sporophyte generation, as evi-
denced during heterochrony and its extrememanifestation, metamorpho-
sis. Less established, but potentially of great importance, is the idea that
the process of environmental adaptation in general should be considered
in this context of the organism existing in different developmentally
stabilized, or epigenetic states, that is, adapted and unadapted (Bressan
et al. 1985; Amzallag 2000, 2005; Maggio et al. 2006; Feil and Fraga 2012),
as in progressive differentiation. The sensitivity of plants to extreme
environments has long been known to depend dramatically on stage of
development (Foolad 2004). Metastable states with altered tolerance to
stress even can exist in cultured immortalized cells, which exhibit a very
strong dependence of adaptability on developmental stage (Binzel et al.
1985). Plants produced from pluripotent cells and adapted to stress also
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