DISCUSSION The level of pedigree information quality affects for slovak horses

  DISCUSSION The level of pedigree information quality affects the average coefficient of inbreeding. The length of pedigrees has an impact ...

 

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.,

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