Proceedings of the World Congress on Genetics Applied to Livestock Production, 11.749 Assessment of Generation Interval and Inbreeding in Peruvian Paso Horse V. Montenegro 1,J. Vilela, 2 &M. Wurzinger 3 1 ALLPA Association, FORMAGRO Program 2 Universidad Peruana Cayetano Heredia, Facultad de Veterinaria y Zootecnia, Lima, Perú jorge.vilela.v@upch.pe 3 University of Natural Resources and Life Sciences, BOKU Summary Peruvian Paso Horse it s a local breed from Perú, which has contributed to the development of the economic activities of the Peruvian people. Few studies have been done, so far, on the genetic characterization and breeding plans of this breed. Therefore, the objectives of this study were to estimate the generation interval and the inbreeding coefficients using records available from ANCPCPP, as a first step to implement monitoring programs of genetic improvement and diversity. This study was carried out within formation from Peruvian Paso Horse Genealogical Registry, from its creation in August 1960 to November 2013. Data was processed using the EndoG 4.8 program (Gutierrez and Goyache, 20005). Individual inbreeding coefficients and Generation intervals were computed. For calculations, 29105 animals were processed for this study. The generational interval for females was 8.72 ± 4.49 years and the generational interval of males was 8.88 ± 4.63 years, with an average of 8.76 ± 4.53 years for the total population. Inbreeding coefficient was 5.44 ± 6.29. Also, 12.66% (n = 3687) of the animals had very high inbreeding, higher than 12.5%, and 5.52% of males could be considered as highly inbreed (0.16% between full siblings (n = 47), 3.88% between half siblings) and 1.48% between parents and children (n = 430). In conclusion, use of male for a long period of years and their permanency in the farm as stallion, could explain longer generation interval in comparison to females. The inbreeding level is low but the rate of inbred animals is major than 1%, which must be considerer a new strategy of selection like optimal contribution to avoid an increased inbreeding in the population and maintain diversity genetic to levels below 1%. Keywords: Inbreeding coefficients, horse, pedigree Introduction The Peruvian Paso Horse (PPH) is a breed native to Perú, and since its formation in 1531, from the horses that arrived at South America during the Spanish invasion, has contributed to the development of the economic activities of the Peruvian people, thus becoming a sociocultural element important for our society (ANCPCPP, 1994). The entity responsible for promoting the breeding, selection, evaluation and registration of the PPH in the National Association of Breeders and Owners of Peruvian Paso Horses (ANCPCPP) and currently has more than 29 000 registered horses. Few studies have been conducted, on the genetic characterization and breeding plans of this breed. The constant use of few males as stallions has resulted in an increase in the inbreeding rate over several years. Between 2002 and 2005 the inbreeding and kinship of the PPH were calculated from samples of some of the generations recorded in the registry. In these studies, an increase in inbreeding was estimated from 1.54% to 3.86%, from 1970 to 1986, and a slight decrease later, with
the coefficient reaching 3.61% in 2002 (Cañote, 2005). To date no study has been conducted including all the information of the animals of all the generations registered. Such a study would permit documentation of the evolution of the genetic diversity of the population and its current state. Prospectively, periodic evaluations could be executed to design a program of sustainable management that minimizes losses of genetic diversity, which may be associated with a decrease in the reproductive and productive parameters of this breed or to increase the presence of genetic defects, due to inbreeding. The generation interval defined as the average age of the parents at the birth of the offspring or the offspring used for reproduction, is important in a breeding program because it is correlated with the annual rate of genetic change. At present, there is no information about generation interval in Peruvian paso horse. Inbreeding coefficients and generation interval are essential for monitoring populations for mating programs and for management of genetic variability and conservation strategies (Falconer and Mackay, 1996; FAO, 1998).Therefore, the objectives of this study were to estimate the generation interval and the inbreeding coefficients using records available from ANCPCPP, as a first step to implement monitoring programs of genetic improvement and diversity. Materials and methods Pedigree information. This study was carried out using records from the establishment of the Peruvian Paso Horse Genealogical Registry, (August 1960 to November 2013). This data contained 29,105 animals, 10,652 males and 18,453 females. The registry was in charge of the Universidad Nacional Agraria La Molina from August 1960 to 1976, and later, in charge of the National Association of Breeders and Owners of Peruvian Paso Horse. Data edits were applied to eliminate wrong information at population and individual level. Determination of genetic parameters. Data was processed using the EndoG 4.8 program (Gutierrez and Goyache, 2005). Individual inbreeding coefficients (F), defined as the probability that an individual has two alleles identical by descent, were calculated by means of the algorithm of Meuwissen and Luo (1992) included in the program. Generation intervals were computed for the 4 paths of selection (fathers-sons, fathers-daughters, mothers-sons and mothers-daughters). Both parameters were computed for the whole population, males, and females. Significant statistical differences were determined with SAS program (SAS/STAT, 1999) when needed. Results and discussion Genealogy 29,105 animals were processed for this study, similar to studies by Hreidarsdottir et al., (2014) for the Icelandic horse (n = 30,203); but more than that used by Zechner et al (2002) in the Lipizzana breed, as well as Poncet et al., (2006) for the Freiberger breed and in Cervantes et al., (2008) for each of the races of Spanish Arabian horses. Table 1 shows a summary of the proportion of known parents. There were few animals that had both progenitors unknown, which favors the calculation of parameters of consanguinity and relationship.
Table 1. Number and percent of animals and parents of the genealogy of PPH Females Males Total population Total no. of Animals 18,453 10,652 29,105 Animals with both parents known 1,723 (9.34%) 1,288 (12.09%) 1,818 (6.25%) Animals with just one parent known 514 (2.79%) 313 (2.94%) 633 (2.17%) Table 2 shows the number of maximum, complete and equivalent generations with their respective standard deviation across the population by sex. Table 2. Average of Maximum generations, completes and equivalents (Average ± Dev. Std.) Maximum number of generations Maximum number of complete generations Equivalent completes generations Total Population 9.73 ± 4.62 3.10 ± 1.51 4.91 ± 2.12 Foals 10.31 ± 4.40 3.28 ± 1.43 5.19 ± 1.98 Mares 9.39 ± 4.71 3.00 ± 1.55 4.75 ± 2.19 The importance of considering the total number of animals in the population in each generation is because the amount of inbreeding depression that a species is able to support depends on population size. In addition, the lower number of animals in previous generations, the greater the number of related ancestors and therefore, the higher the inbreeding coefficient (Falconer and Mackay 1996). On the other hand, although it is necessary to take into account the number of animals for the interpretation of certain parameters such as average relationship coefficient or effective population size, most important are the indicators of depth of the genealogy as the number of complete equivalent generations Generation Interval The generational interval for females was 8.72 ± 4.49 years and the generational interval of males was 8.88 ± 4.63 years, with an average of 8.76 ± 4.53 years for the total population (Table 3)
Table 3. Generation Interval in the population Generation Interval Route Generation interval N Years ± Dev. Std. Father - son 2,595 9.02 ± 4.89 a Father - daughter 7,533 8.71± 4.63 b Mother - son 2,475 8.74 ± 4.35 b Mother - daughter 7,247 8.72 ± 4.34 b Average 19850 8.76 ± 4.53 Different letters in the same column show significant difference, p<0.01 These results are similar to those of the Dutch Harness Horse (8.6 years Schurink et al., 2012) but were lower than most values reported for other breeds such as the Lusitano horse (10.28 years, 11.33 ± 5.33 for males and 9.71 ± 4.48 for females (10.1 years, Cervantes et al., 2009) and the Spanish Andalusian breed (10.11 years, Valera et al., 2005). The differences in the IG between breeds are due to the use of these horses. Sport horses have longer IG's, because their participation in sporting events delays reproduction. Draft horses tend to have shorter IG s because they do not constantly compete and training is not incompatible with breeding. In other hand, the Peruvian Paso Horse is a saddle horse, which is used in competitions and exhibitions, which could influence the reproductive use of them. In addition, similar to others other breeds, the father-to-offspring interval is longer than the others (Hamann and Distl, 2008). Although, the GI of father-to-offspring was not much longer in the PPH the greater length; could be due to the late mating of males after performance tests and the longest reproductive period. The short IG of PPH compared to other breeds would be a factor that could contribute to the increase inbreeding of this breed compared to others. Large IG s contribute to keeping inbreeding levels low so it is recommended in populations with low numbers of breeding animals (Hamann and Distl, 2008, Zechner et al., 2002). Inbreeding coefficients Regarding differences between males and females, most values tend to be higher in foals, except for the rate of increase in annual inbreeding that is slightly higher for females. Thus, the average inbreeding coefficient and the rate of increase of inbreeding per equivalent generation are higher in the mares, and the average relationship and the proportion of inbred animals are higher in foals. To this, it should be added that the average annual inbreeding rate was significant for both sexes of the total population
Table 4. Inbreeding Parameters and Relationship among animals (Ave ± Dev. Std.) Mares Foals Total Inbreeding coefficient average (%) 5.23 ± 6.30 5.23 ± 6.24 5.44 ± 6.29 Realtionship coefficient average (%) 5.59 ± 3.54 6.41 ± 3.3 5.89 ± 3.47 Inbreeding rate by equivalent generation (%) 1 1.26 ± 2.13 1.34 ± 1.98 1.29 ± 2.08 Average of annual individual inbreeding rate (%) 0.15 ± 0.0027* 0.14 ± 0.0037* 0.14 ± 0.0022* Inbreed animals (%) 72.75 80.22 75.49 1 Average of inbreeding coefficient rate *significant regression Figure 1 shows the evolution of the inbreeding rate by equivalent generations for each group by date of birth. The inbreeding rate has increased during this period, reaching 1.54 ± 1.55% for the animals born between 1996 and 2004. However, the rate has decreased for animals born between 2005 and 2013. However, 12.66% (n = 3687) of the animals had very high inbreeding, higher than 12.5%, and 5.52% of males could be considered as highly consanguineous (0.16% between full siblings (n = 47), 3.88% between half siblings ) and 1.48% between parents and children (n = 430) As shown in figure 2, consanguinity has been increasing, so that in the animals born in 2011, 2012 and 2013 are calculated consanguinities of 7.37 ± 7.16, 8.47 ± 5.31 and 9.06 ± 5.05. However, in 1997, this reached 7.15% and has remained relatively stable for 16 years.
The average inbreeding levels found in this study are similar to the results found by Cañote (2005), however they differ from those reported by Tupac-Yupanqui et al. (2004). This difference may be due to Cañote (2005) using an analysis of covariance, with all the animals in the database having levels of 1.43% and 4.10% for the years 1970 and 1986, respectively. The difference is found in the average level of inbreeding found for 2002 in which Cañote (2005) found a value of 3.61% and in the present study was 7.12%. In the study of Tupac-Yupanqui et al., (2004), microsatellite markers were used, resultating in a calculated inbreeding coefficient of 12%. In both cases, the differences were due to the methodologies used and the number of animals involved. In the second case, the differences could also be due to the depth of the genealogy and would support the idea that the inbreeding found here is underestimated, but, on the other hand, microsatellites are not informative markers in and the results obtained by Tupac-Yupanqui et al. (2004), may not be accurate (Reed and Frankham, 2001; Woolliams and Toro, 2007). Inbreeding has been increasing in Peruvian Paso Horse over time (Figure 1) however, although this may be influenced by population structure, mating strategies or population size, inbreeding is directly affected by the depth of the genealogy, and the rate of inbreeding allows us to more specifically monitor the decline of genetic diversity (MacCluer et al., 1983). In this way, the rate of inbreeding per equivalent generation exceeds the rate recommended by FAO (1998) to maintain diversity, which amounts to 1% (Meuwissen and Woolliams, 1994). Conclusion Results indicated that generation interval is 8.76 +/- 4.53 years, but in the route father-son, show significant difference. The use of male for a long period of years and their permanency in the farm
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