Inbreeding in Livestock Populations
Kelly L. Murray
April 22, 2004
As the livestock industry continues to strive to provide food to the global market,
many owners are utilizing various breeding schemes to increase genetic gain in their
herds. Due to these strategies, many populations have undergone an increase in
inbreeding levels in recent decades.
In order to preserve the highest quality traits as well as alleviate aggression among
male stock, many owners castrate the vast majority of males in a population. While this
practice may contribute to increased levels of inbreeding, the major factors have been the
global ranking of sires, artificial insemination, and embryo transfer (Miglior & Burnside,
1995). Since the widespread introduction of artificial insemination in the 1930’s, the
practice has become extremely common among purebred stock. According to local beef
herd owners Don and Kathy Murray, artificial insemination not only provides owners
with previous performance records, but also gives them the luxury of being able to
synchronize their herd. In addition, artificial insemination removes the need to have an
aggressive and sometimes dangerous male on the premises (Murray, 2004). In recent
years, embryo transfer has also gained popularity for similar reasons. Regardless of the
origins, the rise of inbreeding level is having a major impact on the livestock industry.
A common practice in breed development and propagation, inbreeding is simply the
mating of two related individuals. In general, animals are not considered to be inbred if
there is no common ancestor in the previous 5 generations. Inbreeding can be in the form
of parent-offspring crosses as well as the mating of full or half siblings. According to
Vogt et al, an animal is considered to be 50% inbred if it is the result of a parent-
offspring or full sibling mating. Offspring from half-sib matings are only 25% inbred as
there is additional genetic variation from the dams at the grandparent generation(Vogt,
While many livestock breeding schemes incorporate inbreeding, many schemes utilize
linebreeding. Even though it is actually a milder form of inbreeding, linebreeding
typically has lower inbreeding levels. Linebreeding is specifically designed to produce
distinct breed lines which have a link to a common, desirable ancestor (Cassell, 1999).
III. Effects on heterozygosity
One of the major effects of inbreeding is the decrease in heterozygosity. Since the
mating of related animals increases the chance that the offspring will acquire alleles
which are identical by descent, continued inbreeding increases the number of
homozygotes in a population. This loss of genetic diversity is the primary factor which
leads to inbreeding depression. According to Holloway, such homozygosity will result
in a “concentration of undesirable genes” and may result in “a greater susceptibility to
disease” (Holloway, 1951). Meuwissen continues this idea by warning breeders to
avoid breeding schemes which cause deleterious alleles to drift to high frequencies. He states
that by breeding for certain production traits, “reproductive traits will suffer from
substantial inbreeding depression, which will eventually increase their weight in the
breeding goal, but by then a lot of positive reproduction genes might have been lost due
to inbreeding” (Meuwissen, 1997). As a result of such loss, livestock consultant Maurice
Bichard fears a lower resistance to disease and parasites could occur in populations
Increased homozygosity can also lead to such an extreme decrease in genetic variation
that a population is actually in danger of extinction. For example, the Japanese Black
Cattle have such high levels of homozygosity due to the exclusive use of 5 nationally
ranked sires that the calves are experiencing severe inbreeding depression. As a result,
the species may not survive. (Nomura, Honda, and Mukai, 2001) As a result of problems
such as this, D.R. Notter suggests that inbreeding levels must be controlled via genetic
resource conservation, evaluation, and crossbreeding in order to create fit animals in the
future (Notter, 1999).
IV. Current Levels
In order to understand the impact which inbreeding is having on populations, several
studies have focused on the current levels of inbreeding in various populations. Based
on the analysis of national registries as well as herd records, it has been found that
several populations of sheep, cattle, and swine have relatively high levels of inbreeding.
For instance, Miglior and Burnside found that the Canadian Holstein population was
91% inbred before the introduction of cross bred and grade cattle (Miglior and Burnside,
1995). Roughsedge et al found a similar pattern in the British Holstein population before
the introduction of imported sires (Roughsedge et al,1999).
While cattle, particularly dairy cattle, were found to have high levels of inbreeding,
the swine industry reported even higher levels. According to research conducted in 1990
by Hubbard et al, all of the registered herds of swine were at least 35% inbred.
Hampshire herds, which have undergone relatively high levels of crossbreeding, were
35% while Landrace and Duroc were both at 50%. Most alarming was that the popular
Yorkshire breed had 80% inbred stock(Hubbard et al, 1990).
IV. Advantages of Inbreeding
With increasing competition in the global livestock market, owners are continuously
trying to increase the genetic quality of their herds. By incorporating inbreeding into
breeding schemes, several advantages are available. The primary benefit of inbreeding in
a population is the uniformity among progeny. Since inbred animals have an increased
level of similar genes, the animal is more likely to produce progeny with similar traits. In
particular, animals with an abundance of dominant alleles will “stamp” their
characteristics on their offspring (Vogt et al, 1999). As the primary market for feeder
calves is large feedlots which prefer uniform features among calves, this aspect of
inbreeding can be extremely profitable (Murray, 2004).
Another advantage of inbreeding in livestock is the elimination of deleterious alleles.
While it is true that inbreeding can result in the exposure of deleterious alleles in a
homozygous recessive form, research shows that this can actually increase the overall
fitness of the herd. By exposing such traits in a homozygous form, the animals will either
die naturally or be culled from the herd; therefore, the deleterious alleles will not be
passed to future generations. In a naturally occurring population, on the other hand, these
traits may continue to be passed by carriers in a recessive form (Vogt et al, 1999).
V. Disadvantages of Inbreeding
While there are several genetic advantages with occur with inbreeding, there are also
deleterious effects which occur due to inbreeding depression. Several studies have been
conducted to determine the inbreeding depression which occurs in various livestock
Although there has been research with several livestock and domesticated species, an
abundance of the research has focused on cattle. Several traits were found to be impacted
by inbreeding in several different bovine species. In particular, reproductive traits were
affected by inbreeding. For example, Burrow found that inbreeding in a population of
tropical beef cattle led to a decrease in live weight, daily weight gain, calving rate, and
scrotal circumference. He also found that the meat from inbred animals was tougher
due to a higher pH (Burrow, 1998). In another study with beef cattle, Fioretti et al also
found a decrease in live weight as well as age at first calving and yearling weight
(Fioretti et al, 2002). In a study of Hereford beef cattle, Pariacote et al found similar
patterns. Preweaning traits such as birth weight, daily rate of gain, and weaning weight
were all decreased due to inbreeding (Pariacote et al, 1998.). Furthermore, a study by
Virginia Tech Extension agents found that the life of a dairy cow was actually decreased
on average by 13 days in addition to a loss of 790 pounds of milk during the lifetime of
the animal (Cassell, 1999).
In addition to cattle, the effects of inbreeding on swine have also been found to be
detrimental in some cases. In a 1919 study, Hays found that inbreeding increased
mortality (Hays, 1919). Another early study by McPhee et al found an
abundance of male offspring in addition to abnormalities such as sepia color, hernia, and
cleft palate (McPhee et al, 1931). Despite flaws in experimental design, Christensen et
al found that inbreeding levels were inversely related to daily carcass gain, male
fertility, and litter size (Christensen et al, 1994). Another study by Gama and Smith
found that swine lose .24 pigs per litter with each 1% increase in inbreeding (Gama and
Smith, 1993). Early studies by Willham reported even higher rates of loss in litter
size (Willham, 1944). Daily rate of gain was found to decrease by .4 while back fat
decreased by .2% with each percent increase in inbreeding according to Hubbard et al
found a decrease in birth weight and daily rate of gain in a population of Duroc pigs
(Hubbard et al, 1990). Finally, Toro et al found that .2 pigs were lost for each 10%
increase in inbreeding level (Toro et al, 1988).
In addition to cattle and swine, Gama and Smith found high rates of inbreeding
among registered sheep populations (Gama and Smith, 1993). Wiener and Wooliams
found an inverse relationship between the level of inbreeding and fleece weight in both
purebred and crossbred sheep. In addition, they found that the quality of the fleece was
diminished due to shedding prior to shearing (Wiener and Wooliams, 1994).
VII. Breeding Schemes
It is clear that while inbreeding can in fact have several desirable benefits within
livestock populations, there are also negative impacts which can occur at varying rates of
inbreeding. As a result, several methods have been developed and proposed to optimize
genetic gain without increasing deleterious traits. Through application and computer
simulations, several of these methods have been analyzed by researchers.
Among the most popular breeding schemes is the utilization of BLUP, the best linear
unbiased prediction (Agricultural Research Council, 2004). BLUP provides a statistical
analysis of livestock based on an average score of 100 in order to determine whether an
animal will contribute to its offspring in a negative or positive way (Ceres Farm, 2004).
The data for most of the world's top sires is available online. While this selection tool
has been found to produce higher genetic gain than selection of phenotypes (Smith and
Quinton, 1993). This increased genetic gain, however, was lost in several studies
(Bijma et al, 2001). In particular, studies based with relatively small populations were
adversely affected by the extreme inbreeding rates often associated with BLUP selection
(Smith and Quinton, 1993).
Another method for optimal gain through breeding is phenotype selection. In this
scheme, the genetic and environmental effects on a trait are analyzed and compared
within the herd to determine which animals to breed. While this method is less effective
than BLUP in large populations, it is beneficial in smaller herds due to the lower
inbreeding levels (Smith and Quinton, 1993).
A third scheme, developed by T.H.E. Meuwissen, utilizes a set of dynamic selection
rules in order to maximize response without detrimental effects from inbreeding. In this
scheme, Meuwissen has created a curve which prescribes the optimal rate of inbreeding
in order to maximize selection. According to Meuwissen, this scheme can increase
performance from 21-60% in any population. (Meuwissen, 1997)
A more recent approach is the Look Ahead Mating Scheme (LAMS). LAMS
predicts both the progeny merit and grandprogeny merit in a mate selection index. In a
study conducted by Hayes et al, it was found that LAMS provided
greater genetic gain than selection for progeny only or random mating after analysis of
estimated breeding values due to the decreased level of inbreeding (Hayes et al, 2002)
One final scheme which has gained popularity is the nucleus herd concept. This
scheme uses family information extensively in order to select individuals within
families. While it can be reduced by increasing the herd size or number or dams and
sires, this approach does lead to higher levels of inbreeding than other schemes. As it is
expensive to maintain a larger herd, this study suggests the restriction of mating full sibs
in order to decrease inbreeding without increasing cost to the herd owner. (Leitch et
While each of these methods has negative attributes, each scheme is beneficial in
certain situations. Because of this variation, it has been suggested that the
National Cattle Evaluations include herd specific characteristics in order to aid breeders
in choosing proper selection schemes (Snelling and MacNeil, 1996.) Quinton and Smith
also agree that the breeding scheme should be selected based on the population
characteristics and desired outcomes (Quinton and Smith, 1993).
As the livestock industry continues to expand and explore new techniques, it is
apparent that inbreeding will continue to be a major factor. While breeding schemes
which incorporate inbreeding can create more uniform and desirable offspring,
inbreeding can also be detrimental to reproductive characteristics. In order to acquire the
most desirable offspring while preserving genetic variation for future generations,
researchers and livestock owners need to carefully explore and implement various
breeding schemes which are most beneficial to the herd.
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