48
(Kenan-Eichler et al. 2011 ). A high proportion of microRNAs showed nonadditive
expression upon polyploidization, potentially leading to differential expression of
important target genes (Li et al. 2014a , b ). Their data may provide insights into
small RNA–mediated dynamic homoeolog regulation mechanisms that may con-
tribute to heterosis in nascent hexaploid wheat.
New interactions between regulatory factors of the parents, i.e., between the
trans factor from one species and the cis or trans factors of the other parental species
may account for the observed case of inter-genomic suppression (Galili and Feldman
1984 ; Tirosh et al. 2009 ). Genetic suppression or reduction of gene activity can be
also caused by DNA elimination (Liu et al. 1998a ; Kashkush et al. 2002 ). Methylation
and demethylation of retrotransposons were also observed in wheat allopolyploids
(Yaakov and Kashkush 2011a , b ) affecting their state of activity (Sabot et al. 2005 ).
Active retrotransposons, that constitute most of the DNA of the allopolyploids of
this group but they are normally transcriptionally silent, may silence or activate
neighboring genes (Kashkush et al. 2003 ). Retrotransposon promoters retain activ-
ity under normal conditions and initiate either read-in transcripts of the transposon
itself, or read- out transcripts into fl anking host sequences (Kashkush et al. 2002 ;
Kashkush et al. 2003 ; Kashkush and Khasdan 2007 ). Following allopolyploidization
events in wheat, the steady-state level of expression of LTR retrotransposons was
massively elevated (Kashkush et al. 2002 , 2003 ). In many cases, these read-out tran-
scripts were associated with the expression of adjacent genes, depending on their
orientation: knocking-down or knocking-out the gene product if the read-out tran-
script was in the antisense orientation relative to the orientation of the gene tran-
script (such as the iojap-like gene); or over-expressing the gene if the read-out
transcript was in the sense orientation (such as the puroindoline-b gene) (Kashkush
et al. 2003 ). Recent studies on tracking methylation changes around a LTR ret-
rotransposon in the fi rst four generations of a newly formed wheat allopolyploid
(Kraitshtein et al. 2010 ), indicate that this read-out activity is restricted to the fi rst
generations of the nascent polyploid species.
Functional diversifi cation of duplicated genes, i.e., differential or partitioning of
expression of homoeoalleles in different tissues and in different developmental
stages, is also a form of genetic diploidization. Bottley et al. ( 2006 ) reported that
differential expression of homoeoalleles in different plant tissues is common in
hexaploid wheat. The activity of silenced genes could be restored in aneuploid lines,
suggesting that no mutation was involved but rather new cis-trans interactions took
place or reversible epigenetic alterations. Mochida et al. ( 2006 ) also presented evi-
dence for differential expression of homoeoalleles in wheat and suggested that inac-
tivation of homoeoalleles is a nonrandom effect. Similarly, subfunctionalization of
all the homoeologues of the Q- locus in hexaploid wheat was recently described
(Zhang et al. 2011 ).
Many studies on gene expression compare the expression level in the allopoly-
ploid to those of its parents and ⁄or to the average of its parents, expressed as the
mid-parental value. In hexaploid wheat, Pumphrey et al. ( 2009 ) found that approxi-
mately 16 % of the 825 analyzed genes displayed nonadditive expression in the fi rst
generation of synthetic hexaploid wheat. Chague et al. ( 2010 ) analyzed 55,052
M. Feldman and A.A. Levy