Behavioral Genetics and Animal Domestication - Genetics and the Behavior of Domestic Animals - page 53

means is that genes that lie physically close to one another tend to show the
same expression pattern.
Examples come from microarray data (whole-genome expression pro-
files) using inbred lines, or Recombinant Inbred Lines (RILs). What is strik-
ing is that in many of the microarray studies comparing wild and domestic
populations (that show large-scale differential expression), the QTL architec-
ture appears to be relatively simplistic. Litvin found that the total number
of transcriptional differences could be reduced down to a relatively small
number of modules ( Litvin et al., 2009 ), whilst Chesler et al. found that a
small number of QTL modulated large transcriptional gene expression sets
that also correlated with behavior ( Chesler et al., 2005 ). These gene modules
may therefore represent pleiotropy or close linkage, with a single gene poten-
tially leading to numerous changes in gene expression. In effect the large-scale
changes would be downstream effects of the initial causative change. Wild
inbred lines also show this pattern, with differentially expressed genes grouped
together in clusters in the genome ( Ayroles et al., 2009 ). In these examples it
is once again hard to know if these represent multiple linked loci, genuine
pleiotropy, or a combination of the two. Pleiotropic hotspots have also been
discovered in other eQTL studies (see a review in Breitling et al.(2008) ),
though there is some debate as to whether these are genuine or not, and how
common they are ( Breitling et al., 2008 ).

WHAT TYPES OF MUTATIONS CAUSE THE
DOMESTIC PHENOTYPE?
Having seen how gene expression differences can lead to variation in a phe-
notype and their architecture in the genome, it remains to be seen what kind
of mutations actually cause these gene expression differences and hence the
domestication phenotypes. The genome itself is usually made up of between
13 30 k genes, but the actual size of the genome can vary tremendously

between species. Some genomes are rather compact (for example the chicken
is around 1.09 Gb), whilst others are larger (humans have 3 Gb and mice

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3.4 Gb). The genes themselves are made up of exons (which are actively
transcribed and often translated to form proteins) and introns (the regions
between exons which are spliced out of the gene during transcription).
Promoters are regions at the start of a gene which help determine how
the gene is regulated, whilst other enhancers and transcription factor binding
sites can be present around the gene (commonly referred to as a cis effect—
when the mutation is close to the gene it is affecting) or even much further
away (trans effect), and also regulate the degree of expression. Therefore
mutations can either affect the coding regions themselves (resulting in
altered proteins, or even the absence of a particular protein), or the non-
coding regions that regulate expression. Coding DNA is the proportion of
the genomic DNA that is translated into proteins. For each gene (which is

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