Genetic gain & Inbreeding

Effective Population Size and Inbreeding Dynamics in the Peruvian Paso Horse: A Long-Term Pedigree Analysis

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Abstract

This study aims to genetically evaluate the Peruvian Paso horse (PPH) population by analyzing inbreeding coefficients and effective population size (Ne = 1/(2x∆F**) as critical indicators for the design of sustainable genetic conservation strategies. The analysis is based on a comprehensive pedigree dataset comprising 40,993 animals, processed using the PopReport software suite (FLI, Germany), which integrates pedigree completeness, temporal trends in inbreeding, and multiple methodologies for Ne estimation. Pedigree completeness exceeded 96% for six generations in animals born after 2013, ensuring reliable estimation of genetic parameters. The average inbreeding coefficient (F) has increased steadily since the 1950s, reaching an average of 0.1065 in 2022 and 0.0989 in 2023. However, the annual increase in inbreeding (∆F) accelerated to 0.70% in 2023, indicating a recent intensification of genetic drift. While F provides a cumulative measure of relatedness, ∆F proved more sensitive to recent breeding practices and serves as an early-warning indicator of genetic erosion.The effective population size was estimated using four complementary approaches. The most robust estimate, derived from logarithmic regression of inbreeding over time Ne-Ln where ∆Fln = -1bL, being b = slope from the logarithmic regression of ln (1 - F) on year of birth and L = generation interval, produced Ne = 26, assuming a generation interval of 9 years. Other methods corroborated these findings, reporting similarly low values: Ne-∆Fg = 33, where ∆Fg = (Ft - F(t-1))/(1- Ft-1) , being Ft = inbreeding coefficient and Ft-1 = inbreeding coefficient of direct parents. Ne-Coan = 28, where Δfg = (ft - ft-1)/(1- ft-1) , being ft = additive genetic relationship (AGR) and ft-1 = AGR of parents. Ne-Ecg = 35, where ∆Fi = 1- ecg-1 √1- Fi , being ecg = sum of all known ancestors with (1/2)n and Fi = individual inbreeding coefficient. These estimates fall far below the FAO-recommended threshold of Ne ≥ 50 to minimize inbreeding accumulation and below Ne ≥ 100 for long-term evolutionary potential.A pronounced demographic bottleneck was observed in the breeding pool. Although 5208 dams contributed to the 2022 cohort, only 494 elite females were selected as parents of the next generation, drastically narrowing the genetic base. This intense selection, combined with historical overuse of influential sires, evidenced by one sire producing 573 offspring in 2008, has markedly accelerated genetic drift and eroded genetic diversity. The strong concordance between rising inbreeding levels and critically low Ne estimates indicates that the PPH population is under severe genetic pressure. In conclusion, the PPH breed exhibits high levels of inbreeding and a critically low effective population size, signaling an urgent need for coordinated genetic management. We recommend the implementation of structured mating schemes, genomic-informed selection to minimize kinship, potential introduction of genetically distant individuals

Keywords: 2026

How to Cite:

Dextre, J., Quintana, P., Rivadeneyra, C., Velarde, M. & vilela, j., (2026) “Effective Population Size and Inbreeding Dynamics in the Peruvian Paso Horse: A Long-Term Pedigree Analysis”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2269861. doi: https://doi.org/10.31274/wcgalp.23404

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