Inbreeding in Livestock Populations

Kelly L. Murray

April 22, 2004

I.                        Introduction    

     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.

II.                     Inbreeding

     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

(Bichard, 2002).

     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

al, 1994).  

     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). 

VIII.  Conclusion

     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.

IX.  Works Cited

Agricultural Research Council-Animal Improvement Institute.  2004.  [Online.] 

Bichard, Maurice.  2002.  Genetic improvement in dairy cattle B an outsider=s perspective.  Livestock Production Science 75, 1-10. 

Bijma, P., J. M. Van Arendonk, and J. A. Wolliams.  2001.  Predicting Rates of inbreeding for livestock improvement schemes.  Journal of Animal Science 79, 840-853. 

Burrow, H. M.  1998.  The effects of inbreeding on productive and adaptive traits and temperament of tropical beef cattle.  Livestock Production Science 55,227-243. 

Cassell, Bennett G.  1999.  Inbreeding.  Virginia Tech Cooperative Extension.  [Online]. 

Christensen, K., P. Jensen, and J. N. Jorgensen.  1994.  A note on effect of inbreeding on production traits in pigs.  Animal Production 58, 298-300 

Ceres Farms, Ltd.  2004.  [Online.] 

Fioretti, M., Rossti, A., Pieramati, C., and D. Van Vleck Lloyd.  2002.  Effect of inbreeding coefficients for animal and dam on estimates of genetic parameters and prediction of breeding values for reproductive and growth traits of Piedmontese cattle.  Livestock Production Science 74, 137-145 

 Gama, L. T.  and C. Smith.  1993.  The role of inbreeding depression in livestock production systems.  Livestock Production Science 36, 203-211. 

Hayes, B., R. K. Shepherd, and S. Newman.  2002.  Look Ahead Mating Schemes for multi-breed beef populations.  Animal Science 74, 13-23. 

Hays, Frank.  1919.  Inbreeding Animals.  Delaware Agricultural Experiment Station Bulletin No. 123. 

Holloway, Robert F.  1951.  Inbreeding and Crossbreeding Swine.  WVU Thesis Collection. 

Hubbard, D. J., O. I. Southwood, and B. W. Kennedy.  1990.  Rates of Inbreeding in Yorkshire, Landacre, Duroc, and Hampshire Performance Tested Pigs in Ontario.  Canadian Journal of Animal Science 70, 401-407. 

Leitch, H. W., Smith, C., Burnside, E. B., and M. Quinton.  1994.  Genetic Response and Inbreeding with Different Selection Methods and Mating Designs for Nucleus Breeding Programs in Dairy Cattle.  Journal of Dairy Science 77, 1702-1718. 

McPhee, H., O. Eaton, N. Russell, and John Zeller.  1931.  An Inbreeding Experiment with Poland China Swine.  Journal of Heredity (22), 393-403.

Meuwissen, T. H. E.  1997.  Maximizing the Response of Selection with a Predefined Rate of Inbreeding.  Journal of Animal Science 75, 934-940 

Miglior, Filippo and Edward Burnside.  1995.  Genetics and Breeding.  Journal of Dairy Science 78,1163-1167. 

Murray, Donald and Kathy Murray.  Personal communication. April 10, 2004. 

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Notter, D. R.  1999.  The Importance of Genetic Diversity in Livestock Populations of the Future.  Journal of Animal Science 77, 61-69. 

Roughsedge, T., T. Brotherstone., and P. M. Bisscher.1999.  Quantifying genetic contributions to a dairy cattle population using pedigree analysis.  Livestock Production Science 60, 359-369. 

Pariacote, F., L.D. Van Vleck, and M. D. MacNeil.  1998.  Effects of Inbreeding and Heterozygosity on Preweaning Traits in a Closed Population of Herefords Under Selection.  Journal of Animal Science 76, 1303-1310. 

Smith, Charles and Margaret Quinton.  1993.  The Effect of Selection in Sublines and Crossing on Genetic Response and Inbreeding.  Journal of Animal Science 71, 2631-2638. 

Snelling, W. M. and M. D. MacNeil.  1996.  Factors influencing Genetic Evaluation of Linebred Hereford Cattle in Diverse Environments.  Journal of Animal Science 74 (7), 1499-1511.

Toro, M. A., et al.  1988.  Inbreeding and Family Index Selection for Prolificacy in Pigs.  Animal Production 46, 79-85. 

Vogt, Dale, Helen Swartz, and John Massey.  1999.  Inbreeding.  University of Missouri Extension.  [Online].

Wiener, G.J, and J. A. Wooliams.1994.  Effects of breed, rapid inbreeding, crossbreeding, and environmental factors on fleece weight and fleece shedding in sheep.  Animal Production 59, 61-70. 

Willham, Oliver S.  1944.  Hybrid Vigor within a Population.  Oklahoma Agricultural Experimental Station Himeographed Circular No. 113.