Freezing Tolerance in the Triticeae - Translational Genomics for Crop Breeding: Abiotic Stress, Yield and Quality - page 110

detected in the expression of genes related to
vernalization and signaling in barley (Greenup
et al. 2011). Comparison of transcriptomes of
wild type barley and mutants affected in chloro-
plast development revealed the major role of
the chloroplasts in the control of the molecu-
lar adaptation to cold (Svensson et al. 2006).
It is well established that cold acclimation
in the Triticeae involves large transcriptome
reconfiguration through major “regulatory hubs”
(Svensson et al. 2006; Greenup et al. 2011;
Laudencia-Chingcuanco et al. 2011). Evidence
of an additional response mechanism that results
in further modulation of the transcriptome was
obtained in previously cold-acclimated wheat
plants exposed to the “more severe conditions”
(second-phase hardening) of -3 and -12 ◦ C,
by Herman and colleagues (2006) and Skinner
(2009) respectively. This treatment resulted in
additional freezing tolerance, up-regulation of
stress-related genes, and down-regulation of the
ones related to photosynthesis in shoots (Herman
et al. 2006). Although it is still unclear how much
metabolic activity is retained by the plant as it
cools below -10 ◦ C, a quarter of the 423 genes
that were significantly up/down-regulated in the
report by Skinner (2009) were not similar to any
gene of known function.
On the other hand, as certain genes were dif-
ferentially regulated in wheat cultivars with dif-
ferent tolerance during cold treatment, the iden-
tification of particular alleles related to a greater
freezing survival can be determined in this exper-
imental system. The transcriptional profile of
wheat and barley was compared only at optimal
growth temperature (not during cold treatment),
and a high correlation was found between the
two species (Schreiber et al. 2009). It was found
that highly expressed genes are evolutionarily
conserved, both in sequence and transcriptional
activity. Alterations in the transcript levels result-
ing from the evolution of new roles of duplicated
genes, which may derive from changes in the
promoter sequence or in the trans regulation, was
investigated in this study too. Gene activity levels
across tissues after gene duplication positively

correlated in wheat and barley. However, expres-
sion profiles of duplicated wheat genes were less
similar to their barley orthologs than those of the
duplicated barley genes to their wheat orthologs
(Schreiber et al. 2009). This controversy can be
explained by the following possibilities: (1) Dif-
ferent genes were duplicated in wheat and barley;
(2) In the hexaploid wheat a greater functional
divergence of the duplicated genes occurred than
in the diploid barley because of the presence of
the three genomes and the replacement of the
functions by the homoeolog genes on the other
genomes. Based on the observed correlation in
the gene expression between the two species in
the individual tissues, such a relationship can be
also assumed between them if they are exposed
to similar environmental conditions, such as low
temperature.
A special way of exploring the differences
between the barley and wheat transcriptomes
was the characterization of wheat-barley chro-
mosome addition lines (Cho et al. 2006). With
a barley chip containing 22,792 probe sets,
4,014 transcripts could be detected specifically
from barley, and, from these 4,014, 1,787 from
5 wheat-barley disomic chromosome addition
lines. Thus, this system based on sequence and
expression differences can be used for large-
scale physical mapping of genes. Although cold-
induced alterations in the transcript profile were
not compared in barley and wheat, such a com-
parison was made in the case of CBF transcrip-
tion factors (Campoli et al. 2009), which play
a major role in the regulation of cold acclima-
tion due to their effects on a large set of genes
(Galiba et al. 2009). From a comparison of the
expression of several CBF genes in Triticeae
(rye, wheat, barley), it turned out that sample
timing, induction temperature and light-related
factors have significant effects on transcript lev-
els, but there were no clear differences between
the genotypes of a certain species (Campoli
et al. 2009). At the proteome level, no compari-
son was made between barley and wheat. Cold-
induced changes in the proteome were stud-
ied only in bread wheat (Sarhadi et al. 2010;