47uct derived from the combined contribution of the three genomes of hexaploid
wheat and thus, exists only at the hexaploid level.
On the other hand, increased gene dosage may lead to redundancy or in some
cases may have a deleterious effect. Moreover, allopolyploids contain two or three
diverse genomes in one nucleus and therefore, there is an immediate need to achieve
a harmonious function of the genes of the different genomes. The processes that
bring redundant or unbalanced gene systems in allpolyploids toward a diploid-like
mode of expression is genetic or functional diploidization. Studies with synthetic
allopolyploids as well as genome sequencing data indicate that a broad range of DNA
rearrangements have occurred during, soon or after allopolyploidization leading to
genetic diploidization (International Wheat Genome Sequencing Consortium, 2014 ).
These rearrangements including deletion, pseudogenization, and subfunctionaliza-
tion of genes, and transposons activation or deactivation, are extensive and relatively
rapid. Feldman and Levy ( 2005 ) distinguished between revolutionary changes,
occurring during or immediately after allopolyploidization and evolutionary changes
that take place throughout the life of the allopolyploid. Revolutionary changes
include genetic and epigenetic alterations, that lead to cytological diploidization,
improve the harmonious functioning of the divergent genome s, stabilize the nascent
allopolyploid and facilitate its establishment as a new species in nature—all of which
are species specifi c. Evolutionary changes comprise mostly genetic changes, pro-
mote genetic diversity, fl exibility and adaptability—all of which are biotype or popu-
lation specifi c. Examples of functional diploidization in allopolyploid wheat involves
mainly genes that code for structural or storage proteins, e.g., histones, subunits of
tubulins, subunits of glutenins and gliadins, and ribosomal RNA (and possibly also
tRNA). In such genes, expression of all homoeoalleles might be redundant and even
deleterious, due to over-production and ineffi ciency. In this case, traits controlled by
genes from only or mostly one genome may have a higher adaptive value. It is there-
fore expected that such gene loci would have been targets for genetic diploidization.
In allotetraploid wheat for example, αCENH3 and βCENH3 transcripts are derived
more from the A genome than from the B genome (Yuan et al. 2014 ). The Hardness
(Ha) locus constitutes another example of genetic diploidization, through gene dele-
tion, in polyploid wheat (Chantret et al. 2005 ). In addition, recent analysis of the
sequences of wheat group 1 chromosomes shows signifi cant deviations from synteny
with many of the nonsyntenic genes representing pseudogenes (Wicker et al. 2011 ).
The discovery of premature termination codons in 38 % of expressed genes in 3A
double ditelosomic lines in the genetic background of wheat ( Triticum aestivum
‘Chinese Spring’) was consistent with ongoing pseudogenization of the wheat
genome (Akhunov et al. 2013 ).
Genetic diploidization might be achieved through epigenetic silencing of one of
the homeoalleles via cytosine methylation or activation of silenced genes due to
their demethylation. Such changes in gene expression were observed in newly
formed wheat allopolyploids (Shaked et al. 2001 ; Kashkush et al. 2002 ). Epigenetic
changes can result in chromatin modifi cation s or remodeling as well as alter the
activity of small RNA molecules. Changes in microRNAs, such as miR168 which
targets the Argonaute1 gene, were shown to occur in newly synthesized wheat
2 Origin and Evolution of Wheat and Related Triticeae Species