Behavioral Genetics and Animal Domestication - Genetics and the Behavior of Domestic Animals - page 55

time point that protein is expressed. In that way, such protein coding changes
may be far more pleiotropic, whereas regulatory mutations will allow
more specific effects to be manifested without relying on potentially large
trade-offs.
Furthermore, most regulatory mutations are co-dominant, whereas
protein-coding changes are recessive (i.e. two copies are required to manifest
an effect). This enables selection to act more efficiently on heterozygotes
in the case of regulatory mutations (as there will be a difference between the
heterozygotes and the two different homozygotes).

Copy Number Variation
Copy number variation (CNV) refers to the situation whereby a region
contains one or more duplications (or indeed deletions) in one individual
relative to other individuals. Technically, these regions are greater than 1 kb
(1 kb 1000 bases) and can be up to several megabases, or even greater, in

length ( Henrichsen et al., 2009 ), though more recently much smaller duplica-
tions are now being detected and classed as CNVs.
Initially, the analysis of such CNVs rose to prominence around 2006/2007
( Feuk et al., 2006 ), though now they are becoming more and more a part of
standard analysis for the detection of the genetic basis of phenotypic diversity.
In standard analysis they are typically detected using a Competitive Genomic
Hybridization Array (CGH) ( Pinkel et al., 1998 ), whereby the intensity of
regions are compared between two different individuals, pools, or populations,
for example, and the intensity gives an indication of the degree of duplication.
More recently Whole Genome Resequencing can also be used for this. In this
case, individuals have their entire transcriptome (all transcribed genes)
sequenced using resequencing technology. The transcriptome is first amplified
and then randomly broken into smaller segments. These segments then have
the first (and in some cases last) parts “read”, with these reads then aligned
against the reference genome. This allows both a very accurate distinction of
which precise allele is being expressed, and the relative number of reads for
each given region can then be compared between multiple individuals or pools
of individuals.
Such CNVs have been found to typically occur in regions of segmented
duplication (SD; regions of DNA with almost identical sequences) and also
in genes affecting immunity, sensory perception and response to stimuli
( Clop et al., 2012; de Smith et al., 2008 ). There can even be large differ-
ences between individuals—for example, even within mouse inbred strains
(thought to be largely isogenic—meaning essentially clones of one another)
differences in CNVs occur. Domestic animals appear no different to the
other species looked at, with SD regions and immune genes harboring
the greatest numbers of CNVs, with such CNVs found in cattle, pigs,

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