EQUINE | Equine Disease Quarterly
desired characteristics and thus of the beneficial genes in
the offspring. At the same time, negative consequences
of inbreeding are well known. In small populations such
as captive bred species, the loss of diversity associated
with inbreeding is a major concern, and significant
losses of diversity may lead to extinction. The increased
expression of recessive deleterious genotypes can also
lead to embryonic loss or other defects, some of which
can be fatal. Furthermore, inbreeding can lead to a
phenomenon called inbreeding depression. Inbreeding
depression is commonly manifest in poor performance
of traits that are complex (due to contributions of
many different genes), such as fertility and athleticism.
Mindful of the dangers inherent with inbreeding,
breeders traditionally balance the benefits and dangers
of inbreeding by monitoring their breeding stock,
culling poor performers and avoiding matings of closely
related individuals.
Recently, genetic tools have become available that
provide an alternative approach to unambiguously
quantify and manage inbreeding relative to the
traditional use of pedigrees. Today, a genomic survey of
a horse’s DNA may cost $70 to $180. A comprehensive
whole genome sequence, including analyses, may cost
$1,000 to $2,500. So far, over 1,000 horses have had
their entire DNA sequenced in connection with research
projects. Those genome sequences have been used to
identify the genetic bases of diseases, coat colors and
even some performance traits. Nevertheless, the overall
performance of horses is complex, involving over
20,000 genes and probably millions of other functional
elements. Studying genes one at a time is unlikely to be
effective to significantly improve performance. Genomic
tools, however, make it possible to identify associations
between the genome and traits that contribute to
success or which may cause problems.
One of the areas in which genomics excels is in
determining levels of inbreeding. An animal’s
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inbreeding coefficient is the likelihood that both parents
transmitted the same piece of DNA to their offspring
that they each inherited from a common ancestor.
Traditionally, we measured inbreeding by identifying all
common ancestors – those that appear in the paternal
and maternal sides of an individual’s pedigree. After
common ancestors are identified, the relationship
between the parents of the individual in question can
be calculated. Using this method, on average, pedigree-
based inbreeding coefficients for Thoroughbred horses
are reported to be between 12.5%-13.5%, however
individual horses may have values that range from less
than 5% to over 20%. When genomic measures have
been made in other species, geneticists discovered
that inbreeding levels calculated from pedigrees are
poorly correlated (50%-80%) with genomic measures
of inbreeding. This is not surprising since pedigrees
inaccurately assume a random and equal transmission
of genes each generation. Which variant of each gene is
inherited, however, is not predictable. For example, full-
siblings share, on average, 50% of their genes; however,
at any particular part of the genome they may share 0,
50, or 100%. Further, genes are not randomly distributed
in a breed since selection practices are applied in
mating horses. If we are good breeders, the genetic
constitution of our current generation is not a random
representation of the ancestors, but rather, a selection
of the genes contributing to their success.
There are other ways to apply genomics to horse
breeding. As noted above, both the genome and the
traits we value are complex. Our genomic tools are.
powerful, and we can begin to seek genetic patterns
correlated with measures valued by horse owners. The
limitation for such studies is the quality and availability
of data for traits related to fertility, conformation,
durability and athleticism. Collecting these data and
using genomics to identify genes associated with
these complex traits would be a more sensible way to
improve performance rather than simply seeking to
• Equine Health Update •