Skip to main content Skip to main navigation menu Skip to site footer
Original article
Austral J. Vet. Sci.
Vol 58, e5812 (2026)
DOI: 10.4206/ajvs.58.12

Pedigree-Based Assessment of Inbreeding Effects on Conformation and Performance Traits in the Peruvian Paso Horse: Implications for Sustainable Genetic Improvement

1 Grupo de Investigación en Ciencia Equina y Animales Autóctonos, Facultad de Medicina Veterinaria y Zootecnia, Universidad Científica del Sur, Lima, Perú.
Keywords: Peruvian horse Inbreeding depression Genetic Diversity Breeding Value

Submitted: 2026-04-08

Accepted: 2026-08-11

Published: 2026-10-01

*Corresponding author:
jvilela@cientifica.edu.pe

How to Cite

Vilela-Velarde, J. L., Quintana-Dolores, P. G. M., Velarde-Marcos, M. L., & Dextre-Chacon, J. C. (2026). Pedigree-Based Assessment of Inbreeding Effects on Conformation and Performance Traits in the Peruvian Paso Horse: Implications for Sustainable Genetic Improvement. Austral Journal of Veterinary Sciences, 58, e5812. https://doi.org/10.4206/ajvs.58.12

License

Copyright (c) 2026 Jorge Luis Vilela-Velarde, Paola Giovanna María Quintana-Dolores, María Lourdes Velarde-Marcos, José Carlos Dextre-Chacon

Creative Commons License

This work is licensed under a Creative Commons Attribution 4.0 International License.

Abstract

The Peruvian Paso Horse (PPH) is a breed distinguished by its unique four-beat lateral gait. Nowadays, it faces significant genetic challenges related to declining genetic diversity and inbreeding depression, which may substantially affect conformation and performance traits. This study aimed to analyze inbreeding depression in PPH, focusing on its effects on gluteal temperature and morphometric and functional traits. A total of 35 traits were evaluated in 148 animals using pedigree records from 1945 to 2023 provided by the National Association of Breeders and Owners of PPH. Bayesian animal models were employed to estimate heritability and estimated breeding values (EBVs), accounting for fixed effects, including sex, breeder, gait velocity, and age. The findings provide suggestive evidence that both the inbreeding coefficient (F) and its rate of change (ΔF) could exert measurable effects on several traits, although these findings should be interpreted as exploratory. Pedigree analyses revealed that both parents were recorded for over 94% of the animals, indicating a good pedigree depth. Certain historical periods were identified as having reduced ancestral diversity, highlighting the importance of monitoring genetic diversity to prevent population bottlenecks in the future. Inbreeding was associated with reductions in key traits, such as withers height and scapulo-humeral angle. Furthermore, ΔF suggests a more immediate and pronounced effect on specific traits. Correlations between EBVs calculated with and without inclusion of inbreeding as a covariate were significant for certain traits, suggesting that inbreeding introduces estimation bias. Preliminary analyses suggest a tendency for inbreeding to be associated with variations not only in linear body measurements but also in anatomical angles, potentially reflecting the influence of pleiotropic genes affecting multiple morphological traits. Moreover, functional and physiological traits appear to be particularly sensitive to inbreeding effects, underscoring the need for strategic genetic management of this breed.

Downloads

Download data is not yet available.

References

  1. Bartolomé, E., Perdomo-González, D. I., Sánchez-Guerrero, M. J. & Valera, M. (2021). Genetic Parameters of Effort and Recovery in Sport Horses Assessed with Infrared Thermography. Animals, 11, 832. https://doi.org/10.3390/ani11030832
  2. Becker, P. J. J., Hegelbach, J., Keller, L. F. & Postma, E. (2016). Phenotype-associated inbreeding biases estimates of inbreeding depression in a wild bird population. Journal of Evolutionary Biology, 29(1), 35–46. https://doi.org/10.1111/jeb.12759
  3. Bjelland, D. W., Weigel, K. A., Vukasinovic, N., & Nkrumah, J. D. (2013). Evaluation of inbreeding depression in Holstein cattle using whole-genome SNP markers and alternative measures of genomic inbreeding. Journal of Dairy Science, 96(7), 4697–4706. https://doi.org/10.3168/jds.2012-6435
  4. Benjamini, Y., & Hochberg, Y. (1995). Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society: Series B (Methodological) 57(1), 289–300. https://doi.org/10.1111/j.2517-6161.1995.tb02031.x
  5. Boichard, D., Maignel, L., & Verrier, E. (1997). The value of using probabilities of gene origin to measure genetic variability in a population. Genetics Selection Evolution, 29(1), 5–23. https://doi.org/10.1186/1297-9686-29-1-5
  6. Bussiman, F. O., Perez, B. C., Ventura, R. V., Peixoto, M. G. C., Curi, R. A. & Balieiro, J. C. (2018). Pedigree analysis and inbreeding effects over morphological traits in Campolina horse population. Animal, 12(11), 2246–2255. https://doi.org/10.1017/S175173111800023X
  7. Caballero, A., Villanueva, B. & Druet, T. (2021). On the estimation of inbreeding depression using different measures of inbreeding from molecular markers. Evolutionary Applications, 14(2), 416–428. https://doi.org/10.1111/eva.13126
  8. Cervantes, I., Molina, A., Goyache, F., Gutiérrez, J. P. & Valera, M. (2008). Population history and genetic variability in the Spanish Arab Horse assessed via pedigree analysis. Livestock Science, 113(1), 24–33. https://doi.org/10.1016/j.livsci.2007.02.011
  9. Chaves, L. J., Vencovsky, R., Silva, R. S. M., de Campos, Telles, M. P., Zucchi, M. I., & Coelho, A. S. G. (2011). Estimating inbreeding depression in natural plant populations using quantitative and molecular data. Conservation Genetics, 12(2), 569–576. https://doi.org/10.1007/s10592-010-0164-y
  10. Cortes, O., Cañon, J., Andrino, S., Fernanadez, M. & Carleos, C. (2024). Inbreeding depression and runs of homozygosity islands in Asturiana de los Valles cattle breed after 30 years of selection. Journal of Animal Breeding and Genetics, 141(4), 440–452. https://doi.org/10.1111/jbg.12853
  11. Curik, I., Ferenčaković, M. & Sölkner, J. (2014). Inbreeding and runs of homozygosity: A possible solution to an old problem. Livestock Science, 166, 26–34. https://doi.org/10.1016/j.livsci.2014.05.034
  12. Diedenhofen, B. & Musch, J. (2015) cocor: A Comprehensive Solution for the Statistical Comparison of Correlations. PLOS ONE, 10(4), e0121945. https://doi.org/10.1371/journal.pone.0121945
  13. Dos Santos, W. B., Schettini, G. P., Maiorano, A. M., De Albuquerque, L. G., & Peripolli, E. (2021). Fine-scale estimation of inbreeding rates, runs of homozygosity and genome-wide heterozygosity levels in the Mangalarga Marchador horse breed. Journal of Animal Breeding and Genetics, 138(2), 161–173. https://doi.org/10.1111/jbg.12508
  14. Food and Agriculture Organization of the United Nations (FAO). (2011). Molecular genetic characterization of animal genetic resources. FAO Animal Production and Health Guidelines No. 9. http://www.fao.org/3/i2413e/i2413e.pdf
  15. Frigo, M. J., Mangolin, C. A., Oliveira Jr, R. S. & Machado, M. D. F. (2009). Esterase polymorphism for analysis of genetic diversity and structure of wild poinsettia (Euphorbia heterophylla) populations. Weed Science, 57(1), 54–60. https://doi.org/10.1614/WS-08-096.1
  16. Gómez, M. D., Valera, M., Molina, A., Gutiérrez, J. P. & Goyache, F. (2009). Assessment of inbreeding depression for body measurements in Spanish Purebred (Andalusian) horses. Livestock Science, 122(2–3), 149–155. https://doi.org/10.1016/j.livsci.2008.08.007
  17. Gómez-Raya, L., Rodríguez, C., Barragán, C. & Silió, L. (2015). Genomic inbreeding coefficients based on the distribution of the length of runs of homozygosity in a closed line of Iberian pigs. Genetics Selection Evolution, 47(1), 81. https://doi.org/10.1186/s12711-015-0153-1
  18. Gonçalves, R. W., Costa, M. D., Rezende, A. S. C., Rocha Júnior, V. R. & Leite, J. R. A. (2012). Effect of inbreeding on morphometric traits in Mangalarga Marchador horses. Arquivo Brasileiro de Medicina Veterinaria e Zootecnia, 64(2), 419–426. https://doi.org/10.1590/S0102-09352012000200023
  19. Goyache, F., Gutiérrez, J. P., Fernández, I., Alvarez, I., & 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(2), 95–105. https://doi.org/10.1046/j.1439-0388.2003.00378.x
  20. 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(4), 359–378. https://doi.org/10.1186/1297-9686-40-4-359
  21. Gutiérrez, J. P. & Goyache, F. (2005). A note on ENDOG: a computer program for analyzing pedigree information. Journal of Animal Breeding and Genetics, 122, 172–176. https://doi.org/10.1111/j.1439-0388.2005.00512.x
  22. Hadfield, J. D. (2010). MCMC methods for multi-response generalized linear mixed models: The MCMCglmm R package. Journal of Statistical Software, 33(2), 1–22. https://doi.org/10.18637/jss.v033.i02
  23. Ivanković, A., Ramljak, J., Dovč, P., Kelava, N. & Konjačić, M. (2009). Genetic structure of three Croatian horse breeds: Implications for their conservation strategy. Italian Journal of Animal Science, 8(4), 677–689. https://doi.org/10.4081/ijas.2009.677
  24. Jensen, P., Overgaard, J., Loeschcke, V., Schou, M. F., Malte, H. & Kristensen, T. N. (2014). Inbreeding effects on standard metabolic rate investigated at cold, benign and hot temperatures in Drosophila melanogaster. Journal of Insect Physiology, 62(1), 11–20. https://doi.org/10.1016/j.jinsphys.2014.01.003
  25. Karlau, A., Azcona, F., Molina, A., Trigo, P., Sánchez-Serrano, J. P., & Demyda-Peyrás, S. (2025). Exploring the genetic link between coat colour and morphological traits: The case of Peruano de Paso horse. Animals, 15(18), 2720. https://doi.org/10.3390/ani15182720
  26. Keller, L. F. & Waller, D. M. (2002). Inbreeding effects in wild populations. Trends in Ecology and Evolution, 17(5), 230–241. https://doi.org/10.1016/S0169-5347(02)02489-8
  27. Larrea Izurieta, C. O. L., Carpio, M. G., Landi, V., Hurtado, E. A., Andrade, J. I. M, Loor, L. E. V., Rivadeneira, E. L. & Macas, L. F. C. (2022). Evaluation of inbreeding and genetic variability of the Peruvian Paso Horse registered in Ecuador. Revista de Investigaciones Veterinarias Del Peru, 33(5), e21672. https://doi.org/10.15381/rivep.v33i5.21672
  28. Leroy, G., Mary-Huard, T., Verrier, E., Danvy, S., Charvolin, E. & Danchin-Burge, C. (2013). Methods to estimate effective population size using pedigree data: Examples in dog, sheep, cattle and horse. Genetics Selection Evolution, 45(1), 1–12. https://doi.org/10.1186/1297-9686-45-1
  29. Leroy, G. (2014). Inbreeding depression in livestock species: Review and meta-analysis. Animal Genetics, 45(5), 618–628. https://doi.org/10.1111/age.12178
  30. Li, Z., Ran, Z., Zhang, Y., Xiao, X. & An, M. (2023). Genetic Diversity and Structure of Geodorum eulophioides, a Plant Species with Extremely Small Populations in China. Diversity, 15(9), 990. https://doi.org/10.3390/d15090990
  31. Lin, L. I. (1989). A concordance correlation coefficient to evaluate reproducibility. Biometrics, 45(1), 255–268. https://doi.org/10.2307/2532051
  32. Lowman, B. (2004). Estimated breeding values for beef cattle. In Practice, 26(4), 206–211. https://doi.org/10.1136/inpract.26.4.206
  33. Makanjuola, B.O., Maltecca, C., Miglior, F., Schenkel, F.S. & Baes, C.F. (2020). Effect of recent and ancient inbreeding on production and fertility traits in Canadian Holsteins. BMC Genomics, 21, 605. https://doi.org/10.1186/s12864-020-07031-w
  34. 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(2), 322–331. https://doi.org/10.2527/jas.2006-367
  35. Montenegro, V., Vilela, J. L. & Wurzinger, M. (2018). Assessment of generation interval and inbreeding in Peruvian Paso Horse. Proc XI World Congress on Genetics Applied to Livestock Production. Auckland, New Zealand. https://www.researchgate.net/publication/340875981_Assessment_of_Generation_Interval_and_Inbreeding_in_Peruvian_Paso_Horse
  36. Nogueira, M. B., McManus, C., de Faria, D. A., Santos, S. A. O., Ianella, P., & Paiva, S. R. (2021). Fine-scale genetic diversity of the Brazilian Pantaneiro horse breed adapted to flooded regions. Tropical Animal Health and Production, 53, 525. https://doi.org/10.1007/s11250-021-02971-1
  37. Oh, S. H. (2012). Evaluation of optimum genetic contribution theory to control inbreeding while maximizing genetic response. Asian-Australasian Journal of Animal Sciences, 25(3), 299–303. https://doi.org/10.5713/ajas.2011.11315
  38. Pekkala, N., Knott, K. E., Kotiaho, J. S., Nissinen, K., & Puurtinen, M. (2014). The effect of inbreeding rate on fitness, inbreeding depression and heterosis over a range of inbreeding coefficients. Evolutionary applications, 7(9), 1107–1119. https://doi.org/10.1111/eva.12145
  39. Perdomo-González, D. I., Laseca, A., Molina, A., Valera, M. (2022). Fine-tuning genomic and pedigree inbreeding rates in equine population with a deep and reliable stud book: The case of the Pura Raza Española horse. Journal of Animal Science and Biotechnology, 13, 127. https://doi.org/10.1186/s40104-022-00781-5
  40. Poyato-Bonilla, J., Perdomo-González, D. I., Sánchez-Guerrero, M. J., Varona, L., Molina, A., Casellas, J. & Valera, M. (2020). Genetic inbreeding depression load for morphological traits and defects in the Pura Raza Española horse. Genetics Selection Evolution, 52, 62. https://doi.org/10.1186/s12711-020-00582-2
  41. R Core Team. (2024). R: A language and environment for statistical computing. R Foundation for Statistical Computing. https://www.R-project.org/
  42. Silió, L., Rodríguez, M. C., Fernández, A., Barragán, C., Benítez, R., Óvilo, C., & Fernández, A. I. (2013). Measuring inbreeding and inbreeding depression on pig growth from pedigree or SNP-derived metrics. Journal of Animal Breeding and Genetics, 130(5), 349–360. https://doi.org/10.1111/jbg.12031
  43. Sørensen, A. C., Sørensen, M. K. & Berg, P. (2005). Inbreeding in Danish dairy cattle breeds. Journal of Dairy Science, 89(5), 1865–1872. https://doi.org/10.3168/jds.S0022-0302(05)72861-7
  44. Steiger, J. H. (1980). Tests for comparing elements of a correlation matrix. Psychological Bulletin, 87(2), 245–251. https://doi.org/10.1037/0033-2909.87.2.245
  45. Townsend, S. M. & Jamieson, I. G. (2013). Molecular and pedigree measures of relatedness provide similar estimates of inbreeding depression in a bottlenecked population. Journal of Evolutionary Biology, 26(4), 889–899. https://doi.org/10.1111/jeb.12109
  46. Valera, M., Molina, A., Gutiérrez, J. P., Gómez, J. & Goyache, F. (2005). Pedigree analysis in the Andalusian horse: population structure, genetic variability and influence of the Carthusian strain. Livestock Production Science, 95(1–2), 57–66. https://doi.org/10.1016/j.livprodsci.2004.12.004
  47. Vilela, J. L., Quintana, P. G., Velarde, M. L., Vargas, T., Gonzales, R. G., Dextre, J. (2025). Preliminary analysis of the development of a breeding program of the Peruvian Paso horse in field conditions. Revista Mexicana De Ciencias Pecuarias, 16(1), 194–207. https://doi.org/10.22319/rmcp.v16i1.6669
  48. Vilela Velarde, J. L., Quintana Dolores, P. G. M., Velarde Marcos, M. L., & Dextre Chacon, J. C. (2025). Correlations among morphometric traits, functional performance, and gluteal temperature in the Peruvian Paso horse. Austral Journal of Veterinary Sciences, 57(1), e570116. https://doi.org/10.4206/ajvs.57.16
  49. Vostry, L., Vostra-Vydrova, H., Citek, J., Gorjanc, G. & Curik, I. (2021). Association of inbreeding and regional equine leucocyte antigen homozygosity with the prevalence of insect bite hypersensitivity in Old Kladruber horse. Animal Genetics, 52(4), 422–430. https://doi.org/10.1111/age.13075

Make a Submission

Make a Submission

Journal Metrics (2025) & Ranking

JOURNAL METRICS & RANKING (2025)

Impact Factor (2025) 0.5
5 years Impact Factor 1.0
JCR Quartile Q4
JIF Rank 146/170 (Veterinary Sciences)
SJR (2025) 0.208

Indexed in

Publisher


This journal is published by the Facultad de Ciencias Veterinarias, Universidad Austral de Chile

Keywords