Aus dem Institut für Tierzucht und Tierhaltung
der Christian-Albrechts-Universität zu Kiel
Reproduction and health in Holstein Warmblood mares
- Impact of population structure and data recording –
Dissertation
zur Erlangung des Doktorgrades
der Agrar- und Ernährungswissenschaftlichen Fakultät
der Christian-Albrechts-Universität zu Kiel
vorgelegt von
M.Sc. agr. Lukas Philipp Roos
aus Speyer, Rheinland-Pfalz
Dekan: Prof. Dr. E. Hartung 1. Berichterstatter: Prof. Dr. J. Krieter 2. Berichterstatter: Prof. Dr. G. Thaller
Tag der mündlichen Prüfung: 12. November 2014
Die Dissertation wurde mit dankenswerter finanzieller Unterstützung der H. Wilhelm Schaumann Stiftung, Hamburg angefertigt
MEINEN ELTERN
TABLE OF CONTENTS
GENERAL INTRODUCTION ………………………………………………….. 1
CHAPTER ONE
Inbreeding depression in horses: A review ……………………………...….. 5
CHAPTER TWO
Investigations into genetic variability in Holstein horse breed using pedigree data ….………………………………………………………… 27
CHAPTER THREE
Effect of inbreeding on female fertility in Holstein horse breed …..……….. 50
CHAPTER FOUR
Standardisierte Erfassung von Gesundheitsdaten beim
Holsteiner Pferd …….………………………………………………………….. 72
GENERAL DISCUSSION …………………………………………………….. 96
GENERAL SUMMARY …….………………………………………………….. 104
ZUSAMMENFASSUNG …………………………………………………..….. 107
GENERAL INTRODUCTION
Reproductive performance and health are important key factors in equine breeding and business (Dohms, 2002; Zent, 2003; Sairanen et al., 2009). Equine fertility is known as a tangled functional trait with lots of influencing environmental and management factors such as the age of the animal, the individual servicing at farm level or the season. Thus, it is difficult to determine the fundamental factors directly linked to the individuals (Mucha et al., 2012; Sairanen et al., 2009). Compared to other livestock species, horses generally have lower fertility and are characterised by a large generation interval (Mucha et al., 2012). Several risk factors such as various kinds of fertility disorders could further complicate breeding activities.
Not only in horses inbreeding is known as a genetic factor that is capable of affecting fertility, depending on its severity (Charlesworth and Charlesworth,
1987;Charlesworth and Willis, 2009;Falconer and Mackay, 1996). Highly selected and mostly line-bred populations with closed studbooks such as the Holstein horse breed are more likely to produce closely related animals. Increased inbreeding together with decreased effective population size maximise the risk of negative effects on functional traits with low heritability (e.g. health and fertility) (Nomura et al.,
2001; Sierszchulski et al., 2005).
Besides high-quality pedigree information, consistently recorded phenotypes are essential to estimate any kind of genetic and non-genetic effect on functional traits or to establish new breeding strategies such as genomic selection. Standardised and comprehensive data recording with a centrally managed database for health phenotypes is currently not practiced in German horse breeding. A consistent key system to manage, standardise and to analyse veterinary data is missing. Thus, there is a lack of epidemiological knowledge needed to provide reasonable
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emphases for selection with regard to health aspects (Sarnowski, 2013). The implication of equine health into breeding schemes, focused on the estimation of breeding values and the implementation of genomic selection, is currently limited by using indirect traits such as conformation and performance (Koenen et al., 2004).
In Chapter One of this thesis, a review is presented of the current knowledge of the occurrence and the estimation of inbreeding depression in horses. The objective was to represent a general overview of the extent to which different kinds of traits (fertility, morphology, pathological findings and performance) are affected by the population structure of several horse breeds.
Against the background of traditional breeding policies with closed studbooks and restricted licensing of foreign stallions, Chapter Two especially deals with the population structure of Holstein Warmblood horses. The aim was to point out updated levels of inbreeding, the proportions of foreign blood and to specify the genetic contributions of outstanding founders to the current structure of the breeding stock.
Additionally, some alternative concepts regarding the evolution of inbreeding were applied. According to the fact that increased inbreeding is able to affect fitness- associated traits in a negative way, Chapter Three investigated the possible impacts of inbreeding and other relevant factors (age effect) on fertility (foaling rate) and the occurrence of fertility disorders (stillbirth) in Holstein Warmblood horses. Building on this, any kind of research into genetic or non-genetic impacts on functional traits necessarily depends on standardised and consistent phenotypic data. Inconsistent phenotypes potentially skewed statistical analysis. Therefore, the aim of Chapter
Four was the initial development of a standardised monitoring system for centralised equine health and fertility data recording. An attempt was made to acquire clinical data, using a sample of selected breeding facilities in Schleswig–Holstein, together
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with their caring veterinarians. The final aspect of this study was the development of a consistent key system to categorise and standardise veterinary field data.
References
Charlesworth, D., and B. Charlesworth. 1987. Inbreeding Depression and its
Evolutionary Consequences. Annu. Rev. Ecol. Syst. 18(1):237–268.
doi:10.1146/annurev.es.18.110187.001321.
Charlesworth, D., and J. H. Willis. 2009. The genetics of inbreeding depression. Nat
Rev Genet 10(11):783–796. doi:10.1038/nrg2664.
Dohms, T. 2002. Einfluss von genetischen und umweltbedingten Faktoren auf die
Fruchtbarkeit von Stuten und Hengsten. Wissenschaftliche Publikation //
Deutsche Reiterliche Vereinigung 25. FN-Verl. der Dt. Reiterlichen Vereinigung,
Warendorf.
Falconer, D. S., and Mackay, Trudy F. C. 1996.Introduction to quantitative
genetics.4th ed. Longman, Essex, England.
Koenen, E., L. Aldridge, and J. Philipsson. 2004. An overview of breeding objectives
for warmblood sport horses. Livestock Production Science 88(1-2):77–84.
doi:10.1016/j.livprodsci.2003.10.011.
Mucha, S., A. Wolc, and T. Szwaczkowski. 2012. Bayesian and REML analysis of
twinning and fertility in Thoroughbred horses. Livestock Science 144(1):82–88.
Nomura, T., T. Honda, and F. Mukai. 2001. Inbreeding and effective population size
of Japanese Black cattle. J. Anim. Sci. 79(2):366–370.
Sairanen, J., K. Nivola, T. Katila, A.-M.Virtala, and M. Ojala. 2009. Effects of
inbreeding and other genetic components on equine fertility. Animal 3(12):1662.
doi:10.1017/S1751731109990553.
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Sarnowski, S., Stock, K. F., Kalm, E.,Reents, R. 2013. Aufbau einer
Gesundheitsdatenbank für Pferde. 7. Pferde-Workshop Uelzen, 17th and 18th of
september 2014:108–117.
Sierszchulski, J., M. Helak, A. Wolc, T. Szwaczkowski, and W. Schlote. 2005.
Inbreeding rate and its effect on three body conformation traits in Arab mares.
Animal Science Papers and Reports 23(1):51–59.
Zent, W. 2003. Foal Heat-Breeding. In: Current Therapy in Equine Medicine.
Elsevier. p. 248–250.
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CHAPTER ONE
Inbreeding depression in horses: A review
L. Roos and J. Krieter
Institute of Animal Breeding and Husbandry, Christian-Albrechts-University, Kiel, Germany
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Abstract
In livestock production, the phenomenon of inbreeding depression is known as the decreasing mean phenotypic performance in related individual’s progeny and is caused by a reduction in homozygosity. This special kind of genetic change is more likely to occur in traits related to fertility and fitness. For other livestock species, it is considered proven that morphological traits are less sensitive to inbreeding depression because of weakly pronounced dominant gene effects. In commercial horse breeding facilities, depressed fitness-related traits or the increased volume of fertility disorders as well as unfavourable morphological development could lead to considerable economic loss. Against this background, the objective of this review article was to give an overview of today’s knowledge of the occurrence and estimation of the extent of inbreeding depression in various horse breeding traits
(fertility, morphology, pathological findings and racing performance). Inconsistent findings indicate that, also in horses, fitness-associated traits such as reproductive performance and fertility disorders as well as morphological traits are affected by inbreeding depression. Depending on the structure, quality and depth of the pedigree information, fluctuations were observed in the extent of inbreeding and its impact on the traits analysed when compared in different studies.
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Introduction
Deleterious effects of inbreeding have long been recognised in domesticated species
(Darwin, 1868). Inbreeding depression is widely known as the reduction of mean phenotypic performance in related individual’s progeny (Charlesworth and
Charlesworth, 1987; Charlesworth and Willis, 2009; Falconer and Mackay, 1996). It is more likely to occur in traits related to reproduction and fitness (Charlesworth and
Charlesworth, 1987; Falconer and Mackay, 1996; Hansson and Westerberg, 2002).
Morphological traits are less sensitive to this kind of genetic change because of weakly pronounced dominant gene effects (Falconer and Mackay, 1996; Fioretti et al., 2002; Van Eldik et al., 2006; Van Wyk et al., 2009). Generally, inbreeding depression is caused by increased homozygosity in individuals (Falconer and
Mackay, 1996; Charlesworth and Willis, 2009). The genetic basis for the loss of heterozygosity is explained by two main hypotheses. First, the partial dominance hypothesis (Davenport, 1908), in which inbreeding depression is caused by the expression of deleterious recessive alleles in the homozygous state. Inbreeding increases the frequency of homozygotes and deleterious recessive alleles become increasingly expressed (Charlesworth and Willis, 2009). The second hypothesis, known as the overdominance hypothesis (East, 1908; Shull, 1908), attributes inbreeding depression to the advantages of heterozygotes over both homozygotes.
With an increase in homozygosity, the expression of overdominance is reduced by the minored frequency of heterozygotes (Charlesworth and Willis, 2009). Additionally, a third hypothesis by Templeton and Read (1994) partly explains inbreeding depression as a consequence of a breakdown of epistatic interaction between loci
(Köck et al., 2009). Especially in horse breeding, depressed fitness-related traits such as fertility could lead to considerable economic loss (Sairanen et al., 2009; Mucha et al., 2012).
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Compared to other livestock species, horses have lower fertility, characterised by a large generation interval (Cothran et al., 1984; Mucha et al., 2012).
The aim of this review was to give an overview of today’s knowledge on the occurrence and extent of inbreeding depression in various traits in horse breeding.
After describing methods to estimate inbreeding depression in horses, the results of different studies are presented. The majority of the reviewed research papers investigated inbreeding effects on reproductive performance and fertility disorders in mares. Additionally, the results of scientific projects working on the impact of inbreeding on male reproduction and on morphological traits are scoped in this review article.
Methods to estimate inbreeding depression
Generally, two different ways to estimate inbreeding depression are distinguished
(Charlesworth and Willis, 2009). The direct way uses pedigree information to analyse the relationship between trait values and inbreeding coefficients (e.g. Cothran et al.,
1984; Sierszchulski et al., 2005; Gómez et al., 2009; Sairanen et al., 2009). Another direct approach is the experimental creation of individuals with various inbreeding coefficients, using different kinds of mating schemes (e.g. Ehiobu et al., 1989;
Hinrichs et al., 2007; Moss et al., 2008). An indirect solution to detect inbreeding depression is the use of inbreeding coefficients estimated from frequencies of homozygotes and heterozygotes of genomic markers or SNPs (Curik et al., 2003).
For all of the stated methodologies, the estimated quantity could be described as
“inbreeding load” (Charlesworth and Willis, 2009).
In most of the studies dealing with the effect of inbreeding in horses, direct methods, regressing pedigree-based inbreeding coefficients are used on various fertility, conformation or performance traits (Cothran et al., 1984; Klemetsdal and Johnson,
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1989; Klemetsdal, 1998; Sevinga et al., 2004; Langlois and Blouin, 2004). A minority of research projects on horse breeding worked with SNP-data (e.g. Curik et al., 2003;
Binns et al., 2012).
The most common measures to quantify the inbreeding load of a subset of animals are the inbreeding coefficient F of an individual i (F i, e.g. Cothran et al., 1984; Dolvik and Klemetsdal, 1994; Sevinga et al., 2004; Sairanen et al., 2009) and the rate of inbreeding over time ( ΔF) (Ehiobu et al., 1989; Sevinga et al., 2004; Pedersen et al.,
2005; Boer, 2007). The inbreeding coefficient F is classically defined as the probability of an individual having two genes identical by descent (Wright, 1922). It depends on the quality of the pedigree information and on pedigree completeness and depth (Cothran et al., 1984; Boichard et al., 1997; Curik et al., 2003). Missing pedigree information, even for the most recent generations of ancestors, could lead to biases when estimating the rate of inbreeding (Boichard et al., 1997). Different population sizes over time and an intensive use of preferred males could also cause increasing changes in inbreeding coefficients (Nomura et al., 2001; Sierszchulski et al., 2005). As investigated by Ehiobu et al. (1989) and Pedersen et al. (2005) faster rates of inbreeding ( ΔF) were found to have greater impact on the extent of inbreeding depression than slower ones.
The two most common ways to estimate pedigree-based inbreeding coefficients for large populations are the methods of Meuwissen and Luo (1992) and Van Raden
(1992). The alternative concepts of Ballou (1997) as well as new and ancestral inbreeding coefficients by Kalinowski et al., (2000) were developed to ascertain when inbreeding mostly evolves in a population. The inbreeding concept of Kalinowski et al. (2000) splits the conventional inbreeding coefficient into two parts.
One part covers ancestral inbreeding, whereas the other one embraces new inbreeding. Ancestral inbreeding involves all homozygous alleles which have met in
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the past. On the other hand, new inbreeding allocates all alleles which are homozygous for the first time (Mc Parland et al., 2009).
Another measure to derive the exposure of a population to inbreeding depression is the effective population size (N e) (Teegen et al., 2009). It is defined as the number of individuals in an ideal population that would give rise to the same variance of gene frequencies or the same rate of inbreeding as observed in the breeding population studied (Falconer and Mackay, 1996). If pedigree data is available, effective population size could be estimated from the increase in inbreeding over time (ΔF) as suggested by (Wright, 1931): . Studies by Meuwissen and Woolliams (1994) revealed fundamental relationships between the effective population size, inbreeding depression and the genetic variances of fitness traits, respectively. They concluded that the critical size for N e, i.e. the size below which the fitness of the population steadily decreases, lies between 50 and 100 animals. In closed populations (e.g. the Trakehner or Holstein horse breeds), the effective population size depends on the number of animals selected to be parents in each year, the variance of the family size and the average generation interval (Meuwissen and
Woolliams, 1994).
Gómez et al. (2009) included the individual increase in inbreeding over time ( ΔFi) as a measure of inbreeding load into one of their models as a linear covariate to quantify inbreeding depression for body measurements in Spanish Arab horses. ΔFi was computed as ΔFi = , where t is the number of generations. It was suggested by González-Recio et al. (2007) and Gutiérrez et al. (2008) as an alternative measure of inbreeding adjusted for the pedigree depth of an individual, making it possible to distinguish between two animals with the same inbreeding coefficient but differences in the number of generations in which this level of
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inbreeding has appeared (Gómez et al., 2009). The ΔFi coefficients share the properties of ΔF (Falconer and Mackay, 1996) and, contrary to the F i values, the individual increase in inbreeding coefficients are expected to have a linear behaviour over generations (Gómez et al., 2009). In the same work, Gómez et al. (2009) applied the parameter δ (also described by Fox et al., 2007 and Charlesworth and
Willis, 2009) as δ = , where and
are the phenotypic values for each analysed trait for F = 0, F = 0.25 and for ΔFi = 0 and ΔFi = 0.25, respectively (Gómez et al., 2009). They defined the parameter δ as the proportional decrease in the trait values in inbred individuals compared to outbreds, which is expected to be 0 when there is no inbreeding depression.
Negative or positive values indicate that inbred individuals have lower or higher performance than outbreds (Gómez et al., 2009).
Impact of inbreeding on studied traits
The majority of research projects dealing with the effect of inbreeding in various horse breeds have focused on reduced female reproductive performance and the occurrence of fertility disorders such as twinning, stillbirth, early abortion or retained placenta (Mahon and Cunningham, 1982; Cothran et al., 1984; Klemetsdal and
Johnson, 1989; Langlois and Blouin, 2004; Sevinga et al., 2004; Wolc et al., 2006;
Van Eldik P. et al., 2006; Sairanen et al., 2009; Wolc et al., 2009) (Table 1). Female fertility has mostly been evaluated using binary traits such as foaling rate (analysed as the individual outcome of a mating) with a value of 0 if no foal was born and value of 1 if a foal was born (Langlois and Blouin, 2004; Sairanen et al., 2009; Wolc et al.,
2009) or the conception rate, assessed as the conception rate per cycle and per year
(Cothran et al., 1984).
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Table 1 Studies investigating the impact of inbreeding on various traits in different horse breeds
Study/ Scope Breed n Trait Average inbreeding coefficient F(%)
Female reproduction and fertility disorders Klemetsdal and Johnson (1989) Norwegian Trotter 41,816 foaling rate 3.90, 4.30, 5.70 d) Mahon and Cunningham (1982) Thoroughbred 6,550 lifetime reproductive 1.00 performance a) Cothran et al. (1984) Standardbred horse 318 conception rate, foaling rate 10.3 (trotters), 7.40 (pacers) Langlois and Blouin (2004) French Warmblood, 535,746 b) numeric productivity 1.01 French Coldblood (declared foalings) 1.02 Sevinga et al. (2004) Frisian horse 52,392 retained Placenta 15.6 – 15.7 c) (mean ΔF= 1.90) Wolc et al. (2006) Thoroughbred 2,033 twinning n.s. Sairanen et al. (2009) Finnhorse, 32,731 foaling rate 3.60 Standardbred Trotter 33,679 foaling rate 9.90 Wolc et al., (2009) Warmblood 3,965 foaling rate n.s.
Male reproduction Van Eldik et al. (2006) Shetland pony 285 sperm quantity and quality 3.00 Boer, (2007) Frisian horse 1,146 sperm quantity and quality 15.2 Morphology and conformation Gandini et al. (1992) Italian Haflinger 4,736 morphological traits 1.21 (1925-33) – 6.59 (1979-87) Dolvik and Klemetsdal (1994) Norwegian Trotter 508 arthritis in carpal joints 3.90, 4.30, 5.70 d) Curik et al. (2003) Lipizzan horse 360 morphological traits 10.3 Sierszchulski et al. (2005) Arabian 706 morphological traits 0.88 Gómez et al. (2009) Andalusian horse 16,472 morphological traits 8.20 (mean ΔF= 1.00) Performance Klemetsdal, (1998) Norwegian Trotter 7,866 racing performance 5.50 a) Proportion of mare’s successful years at stud, adjusted for the decline in fertility with age, scaled to have an average of 1.0, and transformed to stabilise variance b) Declarations of mating c) Mean inbreeding coefficients of the foals born in 1999 and 2000, respectively d) Mean level of inbreeding for the potential offspring, mares and stallions, respectively
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The findings for the impact of inbreeding on female fertility in different horse breeds are inconsistent. Most of the studies investigating genetic effects on foaling or conception rates have not been able to clearly emphasise the negative genetic impact on female reproductive efficiency (Mahon and Cunningham, 1982; Langlois and Blouin, 2004; Wolc et al., 2006; Wolc et al., 2009).
In the study by Mahon and Cunningham (1982) on inbreeding and the inheritance of fertility in the thoroughbred mare, the lifetime reproductive history of a mare was used to calculate the average adjusted number of live foals per year at stud and was summarised in a fertility score. The measure was computed as the proportion of successes for each mare, but with the outcome of each year at stud weighted by the reciprocal of the proportion of successes for mares of that age in the population of mares. The inbreeding coefficient was treated as an independent covariate on which the fertility score was regressed. As a result, recent inbreeding was not seen as an important source of variation in fertility since the mating of close relatives was rare.
Although lower fertility was associated with inbreeding, the effect was not statistically significant. Discussing their results, the authors stated that selection, both natural and artificial, counteracted any effect of inbreeding on fertility (Mahon and Cunningham,
1982).
Cothran et al. (1984) detected a statistically significant trend for conception and foaling rate to decrease with increased inbreeding. However, this relationship accounted for less than two percent of the variation. In addition, the relationship between reproductive performance and inbreeding was not consistent between the
Standardbred populations of pacers and trotters. Pacers showed the usual negative relationship between inbreeding and reproductive performance. The trend for the trotters indicated an increased reproductive potential with greater inbreeding
(Cothran et al., 1984).
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Similarly to Mahon and Cunningham (1982), they also discussed that, in the presence of selection, the magnitude of inbreeding depression is dependent on the rate of inbreeding as well as on the overall inbreeding level. They generally concluded that inbreeding does not appear to be a significant factor influencing reproductive performance in Standardbred horses (Cothran et al., 1984).
Sairanen et al. (2009) investigated the effects of inbreeding and other genetic components on equine fertility for Standardbred trotters (SB) and Finnhorses (FH).
The average level of inbreeding was 9.9% in the SB and 3.6% in the FH population.
Average foaling rates were better in the SB (72.6%) than in the FH (66.3%), but intense inbreeding had a statistically significant negative effect on foaling rate within each breed (Sairanen et al., 2009). Instead of using inbreeding coefficients as linear covariates, as had been done in earlier studies on horses, their attempt was to study the effects of different levels of inbreeding within a breed. Corresponding to results in cattle and as previously discussed by Mahon and Cunningham (1982) and Cothran et al. (1984), Sairanen et al. (2009) were also able to show that the effect on fertility became more distinct after reaching a certain level of inbreeding. It was stated that the avoidance of matings with very high inbreeding coefficients would improve foaling rates (Sairanen et al., 2009).
A nearly significant effect of inbreeding on foaling rate (p = 0.08) was found in
Norwegian trotters by Klemetsdal and Johnson (1989). The foaling rate declined by
0.43% per 1% increase in the inbreeding coefficient of potential offspring.
Additionally, a total of 32 out of 354 mares showed early abortion. The occurrence of early abortion was significantly affected by the inbreeding coefficient and the age of the mare (Klemetsdal and Johnson, 1989). A one percent increase in the mares inbreeding coefficient increased the frequency of early abortion by 1.27%
(Klemetsdal and Johnson, 1989).
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Besides the potential of moderate selection for fertility in mares to compensate or counteract for inbreeding depression (see also: Mahon and Cunningham, 1982), they discussed the accuracy of fertility measurement. They hypothesised that if fertility is recorded precisely, horses would show inbreeding depression, as would most other livestock species (Klemetsdal and Johnson, 1989). The problem of accuracy and consistency in data recording was also addressed by Mucha et al. (2012) investigating fertility and twinning in Thoroughbred horses. It was suggested that data quality is one of the most important problems in the analysis of fertility and fertility disorders in horses.
Motivated by the hypothesis that the incidence of retained placenta (RP) in Friesian horses is associated with inbreeding, the objectives of Sevinga et al. (2004) were to calculate the inbreeding rate in the total registered Friesian horse population and to study the association between the inbreeding coefficients of foal and mare and the incidence of retained placenta. Additionally, heritability of RP in Frisian mares after normal foaling was studied. Inbreeding rate ( ΔF) of the total base population
(1979 to 2000) was estimated at 1.9%. The effective population size (N e) was estimated at 27 individuals. The regression coefficients for the incidence of RP on inbreeding coefficients of the foal and the mare were found to be 0.12 ± 0.052 and
-0.016 ± 0.019 respectively. Mean heritability estimates of RP as a foal trait and as a mare trait were 0.046 ± 0.088 and 0.105 ± 0.123, respectively. It was concluded that in order to avoid further increase in the incidence of RP in Frisian mares, a decrease in the inbreeding rate is required by increasing the effective breeding population. The findings indicate that the high incidence of RP in Frisian horses is at least partly a result of inbreeding (Sevinga et al., 2004).
A small number of research papers have discussed the context of reduced stallion fertility and inbreeding (Van Eldik et al., 2006;Boer, 2007). These research projects
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have provide indications for the impacts of inbreeding (Van Eldik et al., 2006;Boer,
2007). A study of inbreeding effects on semen quality in 1,146 Frisian stallions was carried out by Boer (2007). The degree of inbreeding and the ancestral decomposition of inbreeding was calculated for each stallion analysed. 26 ancestors were observed to investigate whether inbreeding on these specific ancestors can influence semen quality. Mean inbreeding, estimated over the entire pedigree, was found to be 15.2 ± 1.75 % and ejaculate volume increased at higher inbreeding levels. Specific inbreeding in 12 out of 26 ancestors analysed had a significant effect
(either positively or negatively) on the total number of motile sperms, the ejaculate volume, the sperm cell concentration, motility class, morphologically normal sperms (%) and abnormal acrosomes (%) (Boer, 2007).
Van Eldik et al., (2006) focused on the effects of inbreeding on semen quality in
Shetland pony stallions. The authors examined 285 immature Shetland pony stallions e.g. for percentage of motile and morphologically normal sperm. The coefficients of inbreeding ranged from 0 to 25% (av. F = 3.0 ± 4.6%). As mentioned earlier in studies on female fertility (e.g. Sairanen et al., 2009), a certain level of inbreeding also affects many aspects of sperm production and quality. In particular, coefficients of inbreeding above 2% were associated with lower percentages of motile (p ≤ 0.01) and morphologically normal sperm (p ≤ 0.001) (Van Eldik et al., 2006). Their findings support the hypothesis that inbreeding has a detrimental effect on semen quality in
Shetland pony stallions. Estimating high values of heritability for semen characteristics such as progressive motility (0.46) and concentration (0.24), the authors summarised that these traits could be improved by phenotypic selection (Van
Eldik et al., 2006).
The effect of inbreeding on body conformation traits was investigated by Gandini et al. (1992), Curik et al. (2003), Sierszchulski et al. (2005) and Gómez et al. (2009).
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Gandini et al. (1992) analysed inbreeding and co-ancestry effects on body conformation traits in Italian Haflinger horses. They stated a significantly decreasing height at withers and girth of respectively 1.1 and 2.9 cm with a 10% increase in inbreeding coefficient.
Sierszchulski et al. (2005) estimated the effect of inbreeding on height at withers, chest circumference and circumference of the cannon as biometrical measures in
Arab mares (n = 706). Inbreeding coefficients were obtained from the additive genetic relationship matrix. The effects of inbreeding rate were described using regression coefficients in a linear animal model. The mean inbreeding level of mares was 0.88% and no considerable effect of inbreeding was found. The obtained regression coefficients were close to zero (Sierszchulski et al., 2005).
Investigating conformation traits for a much broader sample (n = 16,427), Gómez et al. (2009) assessed inbreeding depression for body measurements in Spanish
Purebred (Andalusian) horses. The following eight measurements were recorded: height at withers and chest, leg and body length, width of chest, heart girth circumference, knee perimeter and cannon bone circumference. The biometric values were directly obtained from the left side of the individual, using a Lydthin stick and tape measure. To estimate genetic parameters and regression coefficients for the individual inbreeding coefficient (F i) and the individual rate of inbreeding ( ΔFi), multivariate animal models were used. The average Fi value for the whole population was 8.2%. The average individual increase in inbreeding ( ΔFi) was similar in males and females for the total population and the animals measured (1% and 0.9%, respectively) (Gómez et al., 2009). Their findings show significant inbreeding effects on body measurements in Spanish Purebred (Andalusian) horses.
All of the regression coefficients estimated were negative and significant. Those for F i were around 10 times higher than those for ΔFi. The parameter δ was also negative
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and significant (p ≤ 0.05), characterising inbreeding depression. They discussed that inbreeding depression clearly appeared even though inbreeding levels and the individual increase in inbreeding coefficients tended to decrease and to remain stable for the breed studied in the last few decades of the 20 th century (Gómez et al., 2009).
The ranking order of the individuals according to their EBVs was affected by the inclusion of inbreeding measures into the evaluation models. They stated that the likelihood of the models fitted including inbreeding measured to estimate genetic parameters for body measurements is significantly higher than that of the simpler model (Gómez et al., 2009). It was concluded that the inclusion of inbreeding measures into the models to estimate variance components and EBVs for body measurements could be advantageous in terms of more precise estimations (Gómez et al., 2009).
In addition to pedigree information, Curik et al. (2003) applied molecular markers from 17 dinucleotide repeat microsatellite loci dispersed over 14 different chromosomes to analyse the impact of inbreeding on morphological traits in Lipizzan horses (n = 360). Additionally, they examined association between individual heterozygosity as well as mean squared distance (mean ) between microsatellite alleles and morphological traits (Curik et al., 2003). Individual heterozygosity was calculated as the number of loci at which a mare was heterozygous, divided by the total number of loci at which a mare was scored (Curik et al., 2003). All mares were measured for 27 morphological traits. Multivariate analysis of variance (MANOVA) was used to assess the effects of inbreeding, heterozygosity and mean on the recorded conformation measures (Curik et al., 2003).
Significant associations were obtained between the length of the pastern-hind limbs and the inbreeding coefficient (p ≤ 0.01), the length of the cannons-hind limb and mean (p ≤ 0.01) and the length of the neck and mean (p ≤ 0.001). Thus, no
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overall large effects of inbreeding, microsatellite heterozygosity and mean on morphological traits were observed in the Lipizzan horse (Curik et al., 2003).
Dolvik and Klemetsdal (1994) diagnosed arthritis in the carpal joints (carpitis) of
508 four-year-old Norwegian trotters and estimated their heritabilities. Individual inbreeding coefficients were those calculated by Klemetsdal and Johnson, (1989).
Initially, the effect of inbreeding on bilateral and overall carpitis was inspected by calculating the prevalence for groups of animals with similar inbreeding coefficients.
They performed a simultaneous estimation of the effect of inbreeding and sire. A prevalence of 10 and 27% was reported for bilateral and overall carpitis, respectively.
Heritability estimates, based on data of 407 horses sired by 34 stallions, were 0.67 and 0.25. Significant effects of inbreeding on bilateral carpitis were estimated. The probability of diseases was respectively, 6.7% and 12.3% among horses with lower or higher inbreeding coefficient than average (Dolvik and Klemetsdal, 1994).
Further evidence for the presence of inbreeding depression of traits not directly related to fitness is the study done by Klemetsdal (1998). He estimated the effect of inbreeding on racing performance in Norwegian cold-blooded trotters, as measured by accumulated, transformed and standardised earnings (ATSE). The estimated regression coefficients were negative showing that the trait studied was depressed by inbreeding. Klemetsdal (1998) also stated, focusing on racing performance, that inbreeding depression depends on the overall level of inbreeding.
Conclusion
Although negative impacts of increased inbreeding in various livestock species are known, the findings in horses are inconsistent. The negative effects of an increased inbreeding coefficient (F) or of the rate of inbreeding ( ΔF) could not been clearly
19
detected in the reviewed studies, independent of the trait studied. Some of the authors refer to the fact that the magnitude of inbreeding depression is dependent on the rate of inbreeding as well as on the overall inbreeding level. Additionally, it was stated that the amount of F is dependent on the quality and depth of the pedigree and that selection, both natural and artificial, has the potential to compensate for or to counteract inbreeding depression. Incomplete and Inconsistent recording of phenotypes was mentioned as one of the most important sources of error in the detection of inbreeding depression, not only in fitness-related fertility traits.
Depending on the structure and depth of the pedigree as well as on sample size and the quality of the phenotypes, fluctuations were observed in the extent of inbreeding and its impact on the traits analysed when comparing the different studies. Non- genetic and environmental effects such as the age of the animal were confirmed as the main factors influencing the traits investigated. Also in horses, the avoidance of matings of closely related individuals could generally prevent the long-term negative effects of inbreeding on reproductive performance as well as on pathological findings and morphological traits.
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CHAPTER TWO
Investigations into genetic variability in Holstein
Horse breed using pedigree data
L. Roos 1, D. Hinrichs 1, T. Nissen 2 and J. Krieter 1
1Institute of Animal Breeding and Husbandry, Christian-Albrechts-University, Kiel, Germany
2Verband der Züchter des Holsteiner Pferdes e.V., Abteilung Zucht, Kiel, Germany
Accepted for publication in Livestock Science
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Abstract
A pedigree data set including 129,923 Holstein Warmblood horses was analyzed to determine genetic variability, coefficients of inbreeding, the age of inbreeding and the genetic contributions of founder animals and foreign breeds. The reference population contained all horses which had been born between 1990 and 2010. The average Pedigree Completeness Index (PEC) for the reference population was determined as 0.88 and the average complete generation equivalent (GE) was computed at 5.62. The mean coefficient of inbreeding for the reference population
(inbred and non-inbred horses) was 2.27%. Most of the inbreeding was defined as
“new” inbreeding, which had evolved during recent generations. The effective population size and the effective number of founders were calculated to be 55.31 and
50.2 effective individuals respectively. The most influential foreign breed was the
English Thoroughbred with a contribution of 25.98%, followed by Anglo Normans
(16.38%) and Anglo Arabians (3.27%). At 2.75%, Hanoverian Warmblood horses were determined to be the most important German horse breed. The stallions Cor de la bryere, Ladykiller xx and Cottage son xx were found to be the most important male ancestors. The mare Warthburg was defined as the most affecting female. It was possible to detect the occurrence of the loss of genetic diversity within the Holstein horse breed, related to unequal founder contributions caused by the intensive use of particular sire lines. However, a slight increase in the effective population size and a stagnation of inbreeding during the last generation might show the impact of more open access given to foreign stallions in the recent past.
Keywords: effective population size, foreign breeds, genetic diversity, horse, inbreeding
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Introduction
Based on its success in international riding competitions, the Holstein horse breed has become one of the most popular breeds, especially in show jumping.
The official breeding association was founded in 1935 and today’s complete breeding population includes 7,693 registered mares and 225 licensed stallions within twelve breeding districts. In the 19 th century, the Holstein horse breed was influenced by the
Yorkshire Coach horse and by Thoroughbreds (Löwe, 1988).
Due to rising mechanization, the breeding goal has shifted from medium- weight draft or riding horse for agricultural and cavalry use (before 1950) to a large framed, athletic and expressive sport horse with a preferential aptitude for show jumping.
This process of refinement has been driven by an increased use of English
Thoroughbred and Anglo- Norman stallions.
Together with the Trakehner Horse breed, the Holstein horse is the unique German sport horse breed working with closed studbooks.
Accordingly, the studbook for mares is strictly closed and the use of stallions from foreign breeds in terms of breeding trails is minimized. Due to the increased use of artificial insemination and against the background of the intensive use of certain sires, an increase in terms of the rate of inbreeding and the contributions of fewer ancestors is probable. A refreshment of previous knowledge is needed concerning the composition of the Holstein gene pool.
There has not been any investigation concerning genetic composition of Holstein horse breed. However, Hamann and Distl (2008) and Teegen et al. (2009) did some research on the population structure of the Hanoverian and Trakehner breed respectively.
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Therefore, the aim of this study was to point out the updated levels of inbreeding, the proportion of foreign blood and to specify the genetic contributions of outstanding founders to the current structure of breeding stock. Additionally, the study applied some alternative concepts regarding the evolvement of inbreeding.
Material and methods
Pedigree data
Pedigree data used for this study was provided by the Association of Holstein Horse
Breeders (Kiel/Germany) with support of the “Landeskontrollverband Schleswig-
Holstein” which is assigned to administer the pedigree data base. In 2010 the whole pedigree data set contained 131,272 animals.
After revision and verification, a data-set of 129,923 animals with 55,796 males and
74,127 females was included in the analysis. Approximately 1% of undetermined data was excluded.
The reference population applied in this study included all horses born between 1990 and 2010 (n = 78,677, with known parents). The first recorded ancestor was born in the year 1869. Choosing a reference population consisting of all animals born in a period of two generation intervals, the intension was to depict inbreeding situation for the actual breeding stock completely as possible. Even if some of the animals died or probably not used anymore, evaluating a shorter period of time would exclude reproductive individuals and their progeny from the analysis (e.g. competing mares, resuming their breeding use after several years).
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Data analysis
The following parameters of population structure were exploited in the analysis for all horses within the reference population, based on the whole pedigree data-set: The average coefficient of inbreeding, the effective number of founders, the effective number of ancestors and the effective number of founder genomes. Additionally, the generation intervals were determined for the four pathways sire to sire, sire to dam, dam to sire and dam to dam. Therefore, the average age of the parents at the time of birth of their first reproductive offspring was used.
To identify the amount of pedigree completeness and to quantify the possibility to ascertain inbreeding, the pedigree completeness index ( PEC ) (Mac Cluer et al.,
1983) was computed as follows: