DISCUSSION
The level of pedigree information quality affects the average coefficient of inbreeding. The
length of pedigrees has an impact on the parameter indicating the effective number of ancestors
(Boichard et al., 1997). In the previous study on
the populations of eight European Lipizzan breeds,
more than 32 generations of ancestors were indicated (Zechner et al., 2002). In the population of
the Andalusian breed, Valera et al. (2005) found
more than 20 generations of ancestors. Druml et
al. (2009) reported a maximum pedigree length
(31 generations of ancestors) in the Austrian Norik
population. They evaluated 2808 individuals, and
the size of pedigree information was 13 035 individuals based on the book of the Austrian Norik but
only 4649 individuals had to be supplemented from
the original pedigree, which could be the factor
causing our results to be lower. In the population
of the Hanoverian warm-blooded horses, Hamann
and Distl (2008) found more than 23 generations of
ancestors. Our results for the Slovak Sport Pony do
not correspond with the findings of these authors
as within preparing the pedigree file for the fifth
generation of ancestors, our work had to be suspended due to the short history of the breed.
The best criterion for assessing the quality of
pedigree information is the equivalent number of
generations (Maignel et al., 1996). This was used
in the calculation of the individual increase of
inbreeding and, subsequently, in the estimation
of the realized population size. In the Spanish
Arabian population born within the years 1995
to 2004 Cervantes et al. (2008b) found 7.9 equivalent generations of ancestors. In 8 studs of the
Lipizzan horses, including individuals from the
National Stud Farm Topoľčianky (42 individuals),
Zechner et al. (2002) indicated 15.2 equivalent
generations of ancestors, which is by up to five
equivalent generations of ancestors more than was
found in our study. They found that the quality
of the pedigree information varied according to
the study. They proposed to evaluate the pedigree
information for more studs to create a dataset of
pedigrees more complete and interdependent,
which could have a major influence on the higher
average value of this parameter. Curik et al. (2003)
indicated 15.07 equivalent generations of ancestors
for 360 mares of the Lipizzan horses. Álvarez et al.
(2010) investigated the population of the Mallorquí
horses born within the years 2005–2007 and found
2.4 equivalent generations of ancestors. Cervantes
et al. (2008b) found that up to 6 generations were
known for over 90% of ancestors in the population of the Spanish Arabian horses born within
the years 1995–2004. This was consistent with our
results, as we found that 90.56% of ancestors were
known up to 6 generations. Zechner et al. (2002)
reported that in 10 generations of the Lipizzan
population, 90% of the ancestors were known. For
61
Czech J. Anim. Sci., 57, 2012 (2): 54–64 Original Paper
the Lipizzan population in Slovakia, 90% of ancestors were known in the sixth generation and
50% in the twelfth generation. In the Andalusian
horse population, Valera et al. (2005) found 90%
of known ancestors in the fifth generation. From
the seventh to the tenth generations, the value of
this parameter significantly decreased from 80%
to 33% of the known ancestors. After the eleventh
generation of ancestors, less than 10% were known.
A similar trend was also found in our study in the
Hucul, Lipizzan and Shagya Arabian horses.
Generation intervals are also important factors
of population management measures. In the population of the Arabian horses in France, Moureaux
et al. (1996) found an average generation interval
of 10.6 years. In the Andalusian horse population
Valera et al. (2005) reported an average generation
interval of 11.01 years, while for the Carthusian
strain it was 12.43 years. Vostrý et al. (2011) found
a value of 8.53 years for the Silesian Norik breed,
8.88 years for the Norik horses and 8.56 years for
the Czech-Moravian Belgian horses; these findings
correspond to the results of our study.
The average value of inbreeding characterizes a
population in terms of changing its genetic structure in favour of homozygotes, thus resulting in a
loss of genetic diversity,
which may affect the fitness of the population. High levels of the coefficient
of inbreeding, the average relatedness coefficient,
individual increase of inbreeding and low effective
population size values indicate the loss of genetic
variability and possible phenotypic expression of
genetic defects. Our results for the Shagya Arabian
were similar to those found in the French population (Moureaux et al., 1996) and the Polish population of the Arabian horse (Głażewska and Jezierski,
2004), which is related to the similar quality of pedigree information employed. However, Zechner et
al. (2002), Curik et al. (2003), Valera et al. (2005),
and Cervantes et al. (2008b) recorded lower values
in the populations they evaluated, which could be
due to a lower level of pedigree completeness. This
finding was also confirmed in a study by Curik et al.
(2003), who found an average value of inbreeding of
10.13%, with 15.07 known equivalent generations
of ancestors in Lipizzan mares. As only 10.57 of
equivalent generations of ancestors were found, the
average value of inbreeding was only 5.78%. These
investigators found a highly significant correlation between high inbreeding, as calculated from
all available pedigree information, and five generations of pedigrees. In our study, the equivalent
number of generations of ancestors in the Lipizzan
population was 10.25. The average value of the
coefficient of inbreeding was 4.02% based on the
pedigree information. The lower value of the average coefficient of inbreeding may be due to the fact
that for the most important ancestors explaining
the genetic diversity, their marginal contributions
are not homogeneous. In the next generation, the
average value of inbreeding is expected to grow
mainly in the Hucul and Slovak Sport Pony due
to higher values of average coancestry coefficient.
Parland et al. (2007) explained the lower average
value of inbreeding found in populations of Irish
dairy and meat cattle by the import of genetic material into Ireland. Migration can be a significant
factor lowering the level of inbreeding coefficient,
especially in the populations of the Shagya Arabian
and the Lipizzan. A different situation was found
in Mallorquí horses, where the average value of
inbreeding was found to be 4.7%, and in the equivalent generations it was 2.4%. In Czech populations of the cold-blooded Norik, Silesian Norik
and Czech-Moravian Belgian horses, Vostrý et al.
(2011) found average values of inbreeding of 1.51,
3.23 and 3.53%, respectively.
The parameter of the effective population size is
one of the most sensitive parameters, depending on
the quality of pedigree information (Boichard et al.,
1997; Zechner et al., 2002; Goyache et al., 2003).
The Slovak Sport Pony presented a larger realized
size than the actual population size. According to
the definition of effective population size, it is evident that this size can never exceed the real size
because it represents the conversion of a number of
unrelated individuals in a randomly mating population, which it is in reality. The calculation of the
realized effective size is limited by the number of
complete generations. Gutiérrez et al. (2009) recommend a minimum of two full generations before
giving the individuals the opportunity to be inbred.
There are three main factors that may be obtained
by calculating the effective population size and
that may have caused unexpected results in the
present study. The first factor is a small number
of generations of ancestors that was available for
calculating the intensity of inbreeding. A missing
parent was considered a founder. Additionally,
foreign imported individuals may have been present in
the population, therefore interdependency would
arise only after many generations. The effective
population size calculated through the increase
of inbreeding is dependent on the individual in-
62
Original Paper Czech J. Anim. Sci., 57, 2012 (2): 54–64
breeding coefficient. For the Austrian Norik horses,
Druml et al. (2009) indicated an effective population size of 157.4. The actual population size was
2808 individuals. The average value of inbreeding
was 5%. However, when the effective population
size was computed by studs, it made from 137 to
194.5 individuals. The average value of inbreeding
ranged from 4.5% to 5%. For example, the effective
population size of 130.4 individuals was calculated
in Vorarlberg studs. Negative values of the effective population size were discussed by Boichard
et al. (1997), Zechner et al. (2002), and Cervantes
et al. (2008b). Vostrý et al. (2011) indicated the
effective population size of 86.3 for the Silesian
Norik, 162.3 for the Norik and 104.4 for the CzechMoravian Belgian horses; the average inbreeding
increase was 1.22, 0.35 and 1.01%, respectively.
Cervantes et al. (2010) presented a method for estimating the effective population size through the
increase of coancestry.
The method employed the
calculation of the equivalent number of generations of parents and their ancestry, as well as the
calculation of all possible mating combinations of
individuals in the reference population. Parameters
related to the probability of a gene origin detected
recent significant changes in breeding strategies
before the sequence of increasing inbreeding can
be uncovered. Only a small number of ancestors
were needed to explain half of the genetic variability in the studied populations. Thus, it is likely
that these groups will produce half sibs, which will
mate, and subsequent generations of descendants
will increase the average value of inbreeding. The
use of these parameters is important when the
breeding strategy encourages the population gene
pool (genetic program management) and where a
small population exists when reviewing the selection of animals. The decrease of genetic variability
assessed through parameters related to the probability of the gene origin is reflected in lower values
as concerns effective number of founders and effective number of ancestors. An offspring population
with unequal representation of the fundamental
founders will exhibit less genetic variation due to
the reduction of heterozygosity and allelic variation than a population with the same founders in
which the founders made equal contributions to
future generations. Moureaux et al. (1996) evaluated 860 Arabian thoroughbreds born in 1992 in
France, and their results indicated 962 founders and
the effective number of founders of 135. The loss
of genetic diversity due to unequal contributions
of founders was 86% in relative terms.
Głażewska
and Jezierski (2004) reported that the thoroughbred Arabian population of horses in Poland born
within the years 1993 to 1997 was derived from 203
founders. Kwiecińska and Purzyc (2009) indicated
that the population of the Hucul in Poland with
individuals born in the years 1999–2003 originated
from 112 founders, which is similar to the results
of our stock assessment, indicating the origin from
134 founders. For 6240 individuals, Cervantes et
al. (2008b) listed 860 founders and the effective
number of founders of 39.5, explaining the present
total genetic diversity based on 13 effective ancestors. Zechner et al. (2002) reported from 39.3 to
55.2 founders in the eight Lipizzan studs. For the
population of the Lipizzan horses, our results indicated 428 founders. Compared with the results of
Zechner et al. (2002), our values were much higher,
which may be due to the lower level of pedigree
information available for creating the pedigree file.
This is also reflected in lower values of inbreeding
and a larger realized effective size. In accord with
Zechner et al. (2002), reduction in genetic diversity was caused by an unbalanced contribution of
founders. To explain all the genetic diversity of the
eight Lipizzan populations,
the effective number of
ancestors of 26.2 was required. In the population of
the Lipizzan bred in Slovakia, 32 effective ancestors explained 100% of the genetic variability. The
Norik population in Austria was derived from 1991
founders. Unequal contributions of founders to the
population study indicated an effective number of
founders of 157.4. For explanation of 100% of the
genetic diversity, the effective number of ancestors
of 29.3 was required (Druml et al., 2009).
CONCLUSION
The pedigree information on the endangered
Hucul, Lipizzan, Shagya Arabian and Slovak Sport
Pony breeds was analysed to estimate genetic diversity using parameters on probability of identity by
descent and gene origin. Higher concentration of
gene origin was found in the Lipizzan and Shagya
Arabian populations. Higher values of relatedness
coefficients in the Hucul and Small Sport Pony will
reflect improvement of inbreeding coefficient in
the next generation. In spite of breeders’ efforts to
manage breeds to minimize inbreeding, improvement of the monitoring system would be useful. To
maintain the genetic diversity, use of stallions with
63
Czech J. Anim. Sci., 57, 2012 (2): 54–64 Original Paper
optimal contributions for mating will be proposed
for the genetic management of breeds.
Acknowledgement
We gratefully acknowledge the helpful comments
of anonymous reviewers.
REFERENCES
Álvarez J., Royo L.J., Pérrez-Pardal L., Fernández I., Payeras L., Goyache F. (2010): Assessing losses of genetic
variability in the endangered Mallorquí horse. Czech
Journal of Animal Science, 55, 456–462.
Boichard D., Maignel L., Verrier É. (1997): The value of
using probabilities of gene origin to measure genetic
variability in a population. Genetics Selection Evolution, 29, 5–23.
Cervantes I.,
Goyache F., Molina A., Valera M., Gutiérrez J.P. (2008a): Application of individual increase in
inbreeding to estimate realized effective sizes from
real pedigrees. Journal of Animal Breeding and Genetics, 125, 301–310.
Cervantes I., Molina A., Goyache F., Gutiérrez J.P., Valera
M. (2008b): Population history and genetic variability
in the Spanish Arab Horse assessed via pedigree analysis. Livestock Science, 113, 24–33.
Cervantes I., Goyache F., Molina A., Valera M., Gutiérrez J.P. (2011): Estimation of effective population size
from the rate of coancestry in pedigreed populations.
Journal of Animal Breeding and Genetics, 128, 56–63.
Curik I., Zechner P., Sölkner J., Achmann R., Bodo I., Dovc
P., Kavar T., Marti E., Brem G. (2003):
Inbreeding, microsatellite, heterozygosity, and morpological traits in
Lipizzan horses. Journal of Heredity, 94, 125–132.
De Rochambeau H., Hanocq F.F., Vu Tien Khang J.
(2000): Measuring and managing genetic variability
in small populations. Annales de Zootechnie, 49,
77–93.
Druml T., Baumung R., Sölkner J. (2009): Pedigree analysis in the Austrian Noriker draught horse: genetic
diversity and the impact of breeding for coat colour
on population structure. Journal of Animal Breeding
and Genetics, 126, 348–356.
Dunner S., Checa M.L., Gutiérrez J.P., Martín J.P., Cañon
J. (1998): Genetic analysis and management in small
populations; the Asturcon pony as an example. Genetics Selection Evolution, 30, 397–405.
Folch P., Jordana J. (1998): Demographic characterization, inbreeding and maintenance of genetic diversity
in the endangered Catalonian donkey breed. Genetics
Selection Evolution, 30, 195–201.
Frankham R., Ballou J.D., Briscoe D.A. (2002): Introduction to conservation genetics. Cambridge University
Press, Cambridge, UK, 617 pp.
Głażewska I., Jezierski T. (2004): Pedigree analysis of
Polish Arabian horses based on founder contributions.
Livestock Production Science, 90, 293–298.
Goyache F., Gutiérrez J.P., Fernández I.,
Gomez E., Alvarez I., Díez J., Royo L.J. (2003): Using pedigree information to monitor genetic variability of endangered
populations: the Xalda sheep breed of Asturias as an
example. Journal of Animal Breeding and Genetics,
120, 95–105.
Groeneveld L.F., Lenstra J.A., Eding H., Toro M.A.,
Scherf B., Pilling D., Negrini R., Finlay E.K., Jianlin H.,
Groeneveld E., Weigend S., the GLOBALDIV Consortium (2010): Genetic diversity in farm animals – a
review. Animal Genetics, 41, 6–31.
Gutiérrez J.P., Goyache F. (2005): A note on ENDOG: a
computer program for analysing pedigree information.
Journal of Animal Breeding and Genetics, 122, 172–176.
Gutiérrez J.P., Marmi J., Goyache F., Jordana J. (2005):
Pedigree information reveals moderate to high levels
of inbreeding and a week population structure in the
endangered Catalonian donkey breed. Journal of Animal Breeding and Genetics, 122, 378–386.
Gutiérrez J.P., Cervantes I., Molina A., Valera M., Goyache F. (2008): Individual increase in inbreeding allows
estimating effective sizes from pedigrees. Genetics
Selection Evolution, 40, 359–378.
Gutiérrez J.P., Cervantes I., Goyache F. (2009): Improving the estimation of realized effective population sizes
in farm animals. Journal of Animal Breeding and Genetics, 126, 327–332.
Hamann H., Distl O. (2008): Genetic variability in Hanoverian warm blood horses using pedigree analysis.
Journal of Animal Science, 86, 1503–1513.
Kwiecińska K.M., Purzyc H. (2009): Contribution founders genes in population of Hucul horses born in years
1951–1955 and 1999–2003 [online]. EJPAU, 12, 2.
Available from www.ejpau.media.pl
Lacy R.C. (1989): Analysis of founder representation in
pedigrees: Founder equivalents and founder genome
equivalents. Zoo Biology, 8, 111–123.
MacCluer J.W., Boyce A.J., Dyke B., Wietkamp L.R.,
Pfening D.W., Parsons C.J. (1983): Inbreeding and
pedigree structure in Standardbred horses. Journal of
Heredity, 74, 394–399.
Maignel L., Boichard D., Verrier E. (1996): Genetic variability of French dairy breeds estimated from pedigree
information. Interbull Bulletin, 14, 49–54.
64
Original Paper Czech J. Anim. Sci., 57, 2012 (2): 54–64
Mäki-Tanila A., Fernandez J., Toro M., Meuwissen T.
(2010): Assessment and management of genetic variation. In: Local Cattle Breeds in Europe. Wageningen
Academic Publisher, Wageningen, the Netherlands,
100–119.
McParland S., Kearney J.F., Rath M., Berry D.P. (2007):
Inbreeding trends and pedigree analysis of Irish dairy
and beef cattle populations. Journal of Animal Science,
85, 322–331.
Meuwissen T.H.E. (1998): Maximizing the response of
selection with a predefined rate of inbreeding. Journal
of Animal Science, 76, 2575–2583.
Meuwissen T.H.E., Luo Z. (1992):
Computing inbreeding
coefficients in large populations. Genetics Selection
Evolution, 24, 305–313.
Moureaux S., Verrier E., Ricard A., Mériaux J.C. (1996):
Genetic variability within French race and riding horse
breeds from genealogical data and blood marker polymorphisms. Genetics Selection Evolution, 28, 83–102.
Valera M., Molina A., Gutiérrez J.P., Goméz J., Goyache
F. (2005): Pedigree analysis in the Andalusian horse:
population structure, genetic variability and influence
of the Carthusian strain. Livestock Production Science,
95, 57–66.
Vostrý L., Čapková Z., Andrejsová L., Mach K., Majzlík I. (2009): Linear type trait analysis in Coldblood
breeds: Czech-Moravian Belgian horse and Silesian
Noriker. Slovak Journal of Animal Science, 42, 99–106.
Vostrý L., Čapková Z., Přibyl J., Hofmanová B., VostráVydrová H., Mach K. (2011):
Population structure of
Czech cold-blooded breeds of horses. Archiv für Tierzucht, 54, 1–9.
Wright S. (1922): Coefficients of inbreeding and relationship. The American Naturalist, 56, 330–338.
Zechner P., Sölkner J., Bodo I., Druml T., Baumung R.,
Achmann R., Marti E., Habe F., Brem G. (2002): Analysis of diversity and population structure in the Lipizzan
horse breed based on pedigree information. Livestock
Production Science, 77, 137–146
