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copy-number between the reference and the test
sample will produce different signal intensi-
ties, which when expressed as ratios provide
estimates of copy-number differences (Alkan
et al. 2011). Newer sequence-based methods
are expected to overtake CGH in facilitating
both detection of copy-number variable regions
and genotyping other individuals once copy-
number variable regions are defined (Alkan
et al. 2011). Estimates suggest about 12% of
the human genome may be subject to vari-
able copy-numbers (Redon et al. 2006). Struc-
tural variation across the genome is so preva-
lent that the National Center for Biotechnology
Information (NCBI) now maintains a database
solely devoted to genomic structural variation
A number of studies in plants have shown
that these genomes also have variable num-
bers of segments. Hybridizing total genomic
DNA of maize lines B73 and Mo17 to high-
density oligonucleotide microarrays based on the
B73 genome revealed several hundred sequences
that differed in copy-number between the two
genomes. About 180 gene sequences referred to
as presence/absence variation (PAV) were also
detected in one maize line but not in the other
maize line (Springer et al. 2009). Resequenc-
ing of maize lines, including Mo17 and five
additional elite lines, indicated that this phe-
nomenon is widespread (Lai et al. 2010). Inter-
estingly most of the CNV and PAV features in
the maize genome are also variable in teosinte,
the wild ancestor of maize (Swanson-Wagner
et al. 2010). Copy-number variable regions have
also been detected in soybean, and CGH analy-
ses of introgression lines have indicated that this
copy-number variation is stably inherited (Haun
et al. 2011). In a different study it was asked
whether structural variation arose de novo in
response to selection pressure. The
Arabidopsis
thaliana
Columbia ecotype was passed through
five generations at three different temperatures
(16
o
C, 22
o
C, and 28
◦
C), and at each gen-
eration the lines producing the highest seed
yield were selected for the next generation CGH
experiments. This revealed numerous structural
changes occurring at the upper and lower temper-
ature relative to the 22
o
C reference temperature.
Detection of CBFGene Copy-Number
Variation in Triticeae Cereals
Copy-number variable regions have been found
at wheat and barley loci for freezing tolerance
and winter hardiness. These discoveries involved
expression analyses of
CBF
genes and sequenc-
ing of bacteriophage lambda genomic clones
encompassing the
CBF
genes. More than 20
CBF
genes were identified in the genome of
a single barley genotype, 13 of which mapped
to
FR-H2
(Skinner et al. 2005; 2006; Fran-
cia et al. 2007). Two
CBF
genes,
CBF2
and
CBF4
, exhibited much higher transcript levels
in 'Nure' than in 'Tremois' (Stockinger et al.
2007). Expression analyses were then carried
out using pools of doubled haploid (DH) recom-
binants from the 'Nure' x 'Tremois' popula-
tion (NT) in which individuals carried either
the 'Nure'
Fr-H2
allele or the 'Tremois'
fr-H2
allele. DH individuals having the 'Nure' allele
also expressed
CBF2
and
CBF4
to significantly
higher levels than those having the 'Tremois'
allele (Stockinger et al. 2007). Thus rather than
a qualitative difference, there was a quantitative
difference in
CBF
expression levels. Sequencing
genomic clones in bacteriophage lambda vec-
tors encompassing
CBF2
and
CBF4
from both
'Nure' and 'Tremois' and from 'Dicktoo' and
'Morex,' parents of another mapping population
segregating for freezing tolerance (Skinner et al.
2006), indicated that the two frost-hardy bar-
leys 'Nure' and 'Dicktoo,' which have a winter
vrn-H1
allele at
VRN-H1
, harbor two
CBF2
par-
alogs and multiple copies of the
CBF2A
-
CBF4B
genome segment, whereas the two non-frost-
hardy spring barleys 'Tremois' and 'Morex,'
which have a
Vrn-H1
spring allele at
VRN-H1
,
harbor only single paralogs of
CBF2
and
CBF4
(Figure 7.2). It is important to point out that the
transcribed regions are identical and would not
have been revealed as being different through
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