Walking On Volume 7, Issue 1, January 2020 | Page 8

For the Health of It
Inbreeding and Genomics
Reprinted with permission from Equine Disease Quarterly, Volume 29, Number 1
Inbreeding has played a key role in the improvement
of livestock breeds, resulting in more uniform popula-
tions with highly specialized performance traits. Selec-
tion for desirable traits entails identifying individuals
with superior performance and often mating them to
relatives (inbreeding) who possess the same superior
traits. The goal of this practice is to increase the frequen-
cy of the desired characteristics and thus of the beneficial
genes in the offspring. At the same time, negative con-
sequences of inbreeding are well known. In small popu-
lations 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 tradi-
tionally 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 pro-
vide 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 mil-
lions 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 de-
termining levels of inbreeding. An animal’s inbreeding
coefficient is the likelihood that both parents transmitted
8 • Walking On
the same piece of DNA to their offspring that they each
inherited from a common ancestor. Traditionally, we
measured inbreeding by identifying all common ances-
tors – 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 coeffi-
cients for Thoroughbred horses are reported to be be-
tween 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 limit inbreeding.
CONTACT:
Ernest Bailey, ebailey@uky .edu
Ted Kalbfleisch, ted.kalbfleisch@uky .edu
Maxwell H . Gluck Equine Research Center
University of Kentucky, Lexington, Kentucky
Jessica Petersen Jessica.petersen@unl .edu
University of Nebraska-Lincoln, Lincoln, Nebraska