Freezing Tolerance in the Triticeae - Translational Genomics for Crop Breeding: Abiotic Stress, Yield and Quality - page 114

known functional allelic diversity at the locus,
FIGS selected landraces that were rich in new
functional diversity demonstrating the success of
the strategy (Bhullar et al. 2009). This strategy
could be implemented for abiotic stress toler-
ance as well, for example, for identifying more
allelic diversity for genes involved in winter har-
diness. Most reports deal with allelic diversity
of VRN genes in cultivated wheat and barley;
however, wild progenitor accessions were also
investigated in barley. For example, a large-scale
survey of haplotype diversity at VRN-H1 and
VRN-H2 loci in 429 spring, winter and fac-
ultative barley commercial European varieties
enabled identification of three novel VRN-H1
alleles present at low frequencies within EU
germplasm (Cockram et al. 2007). Analysis of
VRN-H1 intron 1 In/Del variation showed that,
while 98% of accessions carried winter alle-
les, three wild barley accessions (all originat-
ing in Israel) harbored spring alleles, one of
which was not previously described in cultivated
materials (Cockram et al. 2011). The develop-
ment in less than ten years of the NGS (next-
generation sequencing) platforms has led to a
significant improvement in the throughput and
cost of sequencing. This has made feasible the
resequencing of candidate genes, transcriptomes
and entire genomes, as well as comparisons
with a reference genome sequence (Kumar et al.
2010). The availability of sequence information
should assist in the management of germplasm
resources, for example, to reduce redundancy
of “core collections” (Glaszmann et al. 2010),
assure homogeneity, and enable correct taxo-
nomic classification. Once generated, sequence
data will have to be followed by the devel-
opment of appropriate bioinformatics tools; in
addition, common standards and biobank infor-
mation management systems (BIMs) will need
to be adopted to manage such complex sets of
data (Kilian and Graner 2012). Finally, high-
throughput genotyping should be coupled with
an effective and accurate phenotyping that com-
bines conventional with novel technologies such
as noninvasive imaging, spectroscopy, robotics,

and high-performance computing, giving birth to
phenomics, which could be described as “high-
throughput plant physiology” (Furbank and

Tester 2011).

From Sequence to Varieties:
Advances inAssisted Selection
of Large Genome CerealCrops

Until now, a prerequisite for any application
of DNA-based technologies in plant breeding
has been the knowledge of the genetic basis
of the trait, that is, the inheritance of the
trait, number and position of loci, contribution
of each locus, and locus interactions. Addi-
tional prerequisites should be markers associ-
ated with (in linkage disequilibrium with) the
loci, together with a knowledge of their infor-
mation content, alleles, and distance from the
locus. A recent improvement in these applica-
tions has been brought about by gene and QTL
cloning, including cloning for abiotic stresses.
In many cases cloning has allowed moving from
associated, linked, markers, to “perfect” candi-
date gene-derived markers (Salvi and Tuberosa
2005; Varshney et al. 2005). Vinocur and Alt-
man (2005) reviewed how plants could be engi-
neered for tolerance to abiotic stresses, using the
increasing number of available cloned genes,
with expected achievements and limitations;
however this could be a practical option only for
those countries having a permissive regulatory
system.
A second step that should improve the
precision of the DNA-based interventions in
plant breeding is the implementation of high-
throughput whole genome surveys, such as high-
throughput SNP platforms and genotyping by
sequencing using NGS techniques (Varshney
et al. 2009). However, such advanced tools
will be used routinely in plant breeding only
when costs per sample can be lowered suffi-
ciently. As detailed in the previous paragraphs,
there have been significant gains in understand-
ing the genetic bases for freezing tolerance
in the Triticeae, which has turned out to be