Epigenetics Connects the Genome to Its Environment - Plant Breeding Reviews - page 119

screens that have been the historical platform for dissecting the
genotype

phenotype relationship. Thus, a list of the participating
components of quantitative or even emergent traits can be compiled,
but only by a combinatorial suf

-

ciency approach can these phenomena

be produced.
The essence of the relationship of epigenetics to evolution resides in
the concept of modi

ed quantitative or even emergent phenomena. One
altered component (a key allele) that is insuf cient to produce alone

complex or emergent characters may still be able to modify or shift such
traits when they already exist, and be subject to natural selection. This is
because evolution can function by altering ontogeny (complex but
modular processes) without de novo reconstruction of the many com-
ponents of a module. Excellent illustrations for the existence of modules
are homeotic mutations, where a developmental module is changed to
another module such as antennae to leg or anther to petal. Critical alleles
that affect complex trait modules clearly exist. Besides homeotic mod-
ules, another good example that is clearly critical to adaptation is
transition to flowering, a complex ontogenic molecular trait (module),

which in Arabidopsis is dramatically affected by several single speci c

loci (Maggio et al. 2006). To our dismay, however, other complex traits,
for example, tolerance to many stresses, are still not easily modi ed by

just increasing or decreasing the availability of one component of a
module. The reason for this is certainly the lack of suf

cient allele
variation at key loci in both Arabidopsis and our important crops. This is
the result of the very narrow germplasm pool for these traits among both
the commonly utilized Arabidopsis ecotypes and commonly used culti-
vars of crop species (Maggio et al. 2006). Therefore, in the future we
should seek mutants unable to make or alter the manner in which they
make speci c types of epigenetic phenotype transitions, through the

epigenetic/genetic control loop process using marker systems of loci
already known to participate in the development of complex phenotypes
such as stress tolerance. We could then examine much more precisely
how such genetic changes control molecular epigenetic shifts in levels
of stress adaptation that occur in naturally tolerant species such as
extremophilic Arabidopsis relative model systems (ARMS) (Orsini
et al. 2010). ARMS species undoubtedly possesses the key genetic alleles
missing from the Arabidopsis ecotype genomes that control shifts in epi
states.
This concept that epigenetics is actually controlled by genetic factors
(genes or DNA sequences) that are critically important to the control loop
between the two worlds of information that is encoded in both the
DNA sequence and in the epigenetic template has enormous importance.