Bovenhuis, H.

Ducro, B.J.

Hellinga, I.

Windig, J.J.

Name not available

Genetic diversity and measures to reduce inbreeding in Friesian Horses

NARCIS 

Wageningen Yield 

Proceedings, 10th World Congress of Genetics Applied to Livestock Production 
 
Genetic diversity and measures to reduce inbreeding in Friesian Horses 
 
B.J. Ducro1, J. Windig2, I. Hellinga3, and H. Bovenhuis1  
1Animal Breeding and Genomics Centre, Wageningen University, Wageningen, the Netherlands, 2Animal Breeding 
and Genomics Centre, Wageningen UR Livestock Research, Wageningen, the Netherlands, 3Koninklijke Vereniging 
“Het Friesch Paarden-Stamboek”, Drachten, the Netherlands,  
ABSTRACT: The pedigree structure of the Friesian horse 
breed was analysed with the purpose to characterise 
inbreeding with special emphasis on the recent period in 
which measures to reduce inbreeding were taken. Measures 
taken consisted of implementing a mating quota and 
publishing individual kinship coefficients for breeding 
stallions. For many generations the average inbreeding was 
0.015 per generation. Since 2000 the inbreeding rate is 
steadily decreasing from 0.018 to about 0.0065 during the 
years 2010-2012 and is preceded by a reduction in average 
additive genetic relationship from 0.012 in 2000 to 
approximately 0.006 during the years 2010-2012. This 
reduction coincide with the period in which the taken 
measures to reduce inbreeding became effective. 
Additionally, the method of individual kinship coefficients 
of the breeding stallions have been compared to the 
estimated genetic contributions under application of optimal 
contribution theory. A substantial negative relationship was 
found between individual kinship coefficients and genetic 
contributions. It was concluded that individual kinship 
coefficients are a reasonable approximation to genetic 
contributions to determine the impact of breeding animals 
on maintaining genetic diversity.  
Keywords: horse, inbreeding, kinship, genetic contribution 
 
 
Introduction 
 
The Friesian horse is an old horse breed 
originating from the Netherlands with daughter studbooks 
in more than 30 countries. The Royal Friesian Horse 
Studbook has been registering horses since its foundation in 
1879. The current size of the active breeding population is 
with about 100 stallions and 8,000 mares quite large. 
However, the history of the population shows several 
periods in which the active breeding population was much 
smaller (Osinga, 2000). The breed has been closed over a 
long period of time and this has inevitable led to 
accumulation of inbreeding and decrease of genetic 
diversity. Besides the small population size during certain 
time periods and the closed status of the population, 
selection has contributed to a substantial increase of 
inbreeding (Ducro et al., 2006). As a result the Friesian 
horse might be sensitive to inbreeding depression as well as 
high incidences for particular genetic defects such as 
dwarfism (Orr et al., 2010; Schurink et al., 2014). 
To prevent the further loss of genetic diversity, 
emergence of new genetic disorders and to reduce the 
negative effects of inbreeding depression the studbook has 
implemented measures. From a theoretical perspective 
optimal contribution selection is an effective method to 
conserve genetic diversity in the next generation. Practical 
implementation of optimal contribution selection, however, 
appears to be difficult. Further, optimal contribution 
selection requires the herdbook to be in control of imposing 
individual mating quota to breeding stallions as well as 
setting the matings. Both aspects are not applicable to horse 
breeding as studbooks are not the owners of the breeding 
animals. The role of optimal genetic contribution would 
therefore be restricted to attach a figure to each breeding 
animal by which their value for maintaining genetic 
diversity is expressed. An alternative strategy has been 
developed for the Friesian Studbook by calculating the 
individual kinship value of each breeding animal. For this 
purpose the additive genetic relation of a breeding animal to 
all animals of the last 3 generations has been calculated and 
averaged. This method has been implemented since 2003.  
Now the measures have been implemented for a couple of 
years its effectiveness needs to be evaluated. Further, 
optimal contribution might outperform the implemented 
method and consequently there might be a need to further 
investigate possibilities to overcome the practical 
difficulties in implementing optimal contribution selection.  
The aim of this study is to characterise inbreeding 
in the Friesian Horse breed with special emphasis on the 
recent period in which measures to reduce inbreeding rate 
were taken. Additionally, possibilities to implement optimal 
contribution selection will be investigated and compared to 
the method of individual kinship.    
 
Materials and Methods 
 
Data. The pedigree used in this study included the 
registrations from the foundation of the studbook in 1879 
until the end of 2012. In total 122,644 horses were 
registered in the Friesian horse studbook. Each registration 
comprised parents, birth date and sex. Horses for which 
information on their parents was missing were excluded 
from the analysis when they had less than 3 progeny and 
those progeny were not parents themselves. Missing birth 
dates of parents were arbitrarily set to 10 years before the 
average birth year of their progeny. The time interval of 10 
years is approximately the generation interval in horses. An 
arbitrary birth year was set for 18 females. After editing the 
pedigree data consisted of 117,322 horses, descending from 
29,388 dams and 1047 sires. 18,000 dams had less than 4 
progeny, and 159 dams had more than 15 progeny. 
Methods. Individual inbreeding coefficients were 
calculated using the method of Meuwissen and Luo (1992) 
and averaged by year of birth. Average additive genetic 
relationship among horses within a birth year were 
calculated based on the Pedig software and implemented in 
the website application Poprep (Groeneveld et al., 2009)  
Rate of inbreeding in a birth year was calculated as the 
difference of the average inbreeding of that birth year and 
the average of the birth year of parents (in which the 
parents birth year is the current birth year minus the 
generation interval). The difference is then scaled by 1 – F 
with F being the inbreeding in the birth year of the parents. 
Rate of additive genetic relationship was calculated along 
the same line of reasoning. 
Influential ancestors of the current generation  
were identified based on their marginal genetic contribution 
to the current generation, using the software package Pedig 
(Boichard et al., 2002). 
Active breeding population was considered to 
comprise of the sires with more than 10 progeny in 2012 
and the dams they were mated to. Individual kinship values 
of these sires were calculated based on their relationship to 
the reference population, in which the reference population 
consist of the foals born in 2010-2012. Calculations were 
performed using the software package Pedig (Boichard et 
al., 2002). 
Optimal genetic contribution was calculated for 
the sires and dams of the active breeding population using 
the software Gencont (Meuwissen, 2002) for overlapping 
generations. The software finds the optimal contribution, in 
terms of % of progeny, of each selection candidate which 
maximizes genetic gain while restricting the rate of 
inbreeding to the desired level.  In this study maximising 
genetic gain was not considered and thus the rate of 
inbreeding was minimalized. The contribution of dams was 
restricted to 1/#dams, which implies that each dam should 
be covered and should produce one foal in the next round.    
 
Results and Discussion 
 
Pedigree Size and Completeness. During the first 
years after foundation of the breed the number of foals 
registered each year remained small and came above 50 
foals for the first time in 1930. Until 1986 the number of 
foals yearly registered did not exceed 1,000 (Fig. 1). Since 
then there has been a considerable increase in population 
size and the number of yearly registered foals increased to a 
maximum of 6,719 in 2004 and remained approximately at 
6,000 thereafter. The increase in population size was 
accompanied by an increase in the number of breeding 
stallions and by an increase in the average number of 
progeny per sire. In 1986, 47 stallions were listed for 
breeding while in 2004 more than 140 stallions were listed 
for breeding. The average number of progeny per sire was 
22 in 1986 and 45 in 2004. The completeness of the 
pedigree, in terms of percent of ancestors known per 
parental generation, was over 90% for the first 7 
generations, which can be considered as relative complete.  
Inbreeding and kinship More than 90% of the 
horses in the population showed some degree of inbreeding 
and 20 horses had inbreeding coefficients between 0.35 and 
0.38. These horses were all born in the last 30 years of the 
study. Mean inbreeding coefficient per birth year increased 
from 0.02 in 1908 to 0.162 in 2010 with considerable 
fluctuations in the early years (Fig. 1). The value of 0.162 is 
higher than the level of inbreeding resulting from half-sib 
mating of unrelated parents (0.125). The rate of inbreeding 
increased up to 0.015 per generation but was even higher 
than 0.20 in the years 1997-1999. The average additive 
genetic relationship has been correspondingly higher during 
these years. Since 2000 the inbreeding rate is steadily 
decreasing from 0.018 to about 0.0065 during the years 
2010-2012. This reduction has been preceded by a 
reduction in average additive genetic relationship from 
0.0118 in 2000 to approximately 0.006 during the years 
2010-2012. The reduction in inbreeding rate already begun 
a few years before the measures were introduced. 
Introduction of the measures started after a public 
discussion with the members of the herdbook. It is likely 
that these discussions resulted in an increasing awareness 
among the members of the herdbook on the problem of 
inbreeding. Therefore it is not surprising that the decrease 
in the rate of inbreeding started before the formal 
implementation of the measures. 
Influential ancestors. The 4 ancestors with 
highest marginal contribution are responsible for more than 
50% of the genetic diversity in the current generation. 
Largest marginal contribution was 23.04% and came from a 
male born in 1924, that had 297 progeny. Three of those top 
4 ancestors were born in the 1920’s indicating that the 
population went through a genetic bottleneck in that period. 
The youngest influential ancestors was born in 1956 and 
ranked 9. There were three females among the 10 most 
influential ancestors.  
Individual kinship values. Kinship to the 
reference population was calculated for 74 stallions, which 
were identified as active breeding stallions in 2012. The 
average individual kinship was 0.175, which can be 
considered as an estimate of the inbreeding level in the next 
generation, when these stallions would contribute equally to 
the next generation. The kinship of individual stallions 
ranged between 0.156 and 0.193. 
Genetic contributions. Optimal genetic 
contributions were calculated for the breeding stallions 
available for the year 2012. Under the restriction that all 
females available should be covered optimal contribution to 
the next round of selection  was calculated using Gencont. 
There were 27 out of 74 stallions that should not be used 
any longer for mating. The contributions of the remaining 
breeding sires varied between 0.06% and 8.43%. As a 
reference, if all 74 breeding stallions would equally 
contribute then each stallion would produce 2.1% of the 
progeny crop and if all 27 selected breeding stallions would 
contribute equally, then each sire would produce 7.7% of 
the progeny crop. Selection according the Gencont analysis 
would reduce the average inbreeding from 17.2% in the 
parental generation to 4.2% in the progeny generation. This 
value can be considered a lower bound of what can be 
achieved when all selection capacity is devoted to 
inbreeding reduction.   
The relation between optimal contributions and the 
individual kinship is negative indicating that stallions with 
high kinship estimate should contribute less to the next crop 
of foals (Figure 2). Deviations from a straight line are due 
to the zero-boundary of %progeny in case of optimal 
contribution. A few stallions with low individual kinship 
have a genetic contribution of (close to) zero, probably 
because they have a close relative among the sires. 
Individual kinships do not account for relationships among 
the stallions, whereas optimal contribution does not account 
for progeny of the stallions already included in the 
population. The latter is an option for further fine-tuning in 
applying the Gencont program.  
 
Conclusion 
 
Breeding history of the Friesian horse shows an 
inbreeding rate over many years which is much higher than 
the limit set by FAO (1998). The studbook has 
implemented measures to reduce the inbreeding rate, 
namely mating quota and publishing future kinship 
estimates of the selected stallions. Future kinships are a 
reasonable proxy for the optimal contribution values, and 
might give the same source of information to the studbook 
members. Measures taken by the studbook coincide with a 
reduction in inbreeding rate down to 0.006 which is 
accompanied by a reduction of the additive genetic 
relationship down to 0.056. From the latter it is expected 
that the reduction in inbreeding rate will be continuing in 
the coming years. 
 
Literature Cited  
 
Boichard, D., (2002). Proc. 7th WCGALP, Montpellier, 
France CD-ROM 28-13. 
Ducro B.J., Bovenhuis, H., Neuteboom, M., et al. (2006). 
Proc. 8th WCGALP, Belo Horizonte, Brasil,  
Ducro, B. J. (2011). PhD thesis, ISBN 978-90-8585-855-3. 
Falconer, D. S., and Mackay, F. C. T. (1996). Introduction 
to quantitative genetics . 4th ed. Longman Group Ltd., 
Harlow, Essex, England. 
Meuwissen, T.H.E., Luo Z. (1992). Genet. Sel. Evol. 
24:305-313. 
Meuwissen, T.H.E. (2002). Proc. 7th WCGALP, 
Montpellier, France 33:769-770. 
Orr, N., Back, W., Gu, J., et al. (2010). Anim. Genet. 
41(Suppl. 2):2-7. 
Osinga, A. (2000). Het fokken van het Friese Paard (in 
Dutch). Schaafsma & Brouwer, Bv. Dokkum.  
Schurink, A., Hellinga, I., Leegwater, P.A.J., et al. (2014). 
Proc.10th WCGALP, Vancouver, Canada 
 
  
  
Figure 1. Average additive genetic relationship (broken 
line) and inbreeding coefficient (solid line) by year of 
birth. 
 
 
 
 
 
 
 
 
 
 
 
 
 
Figure 2. Relation between individual kinship 
coefficients (x-axis) and genetic contribution (y-axis; as 
%_progeny) of breeding stallions. 
 
0
0.05
0.1
0.15
1912 1932 1952 1972 1992 2012
0
1
2
3
4
5
6
7
8
9
0.155 0.165 0.175 0.185 0.195


Genetic diversity and measures to reduce inbreeding in Friesian Horses

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