Genetic Structure Analysis of the Pura Raza Español Horse Population through Partial Inbreeding Coefficient Estimation

SIMPLE SUMMARY: The Pura Raza Español horse (PRE) is an autochthonous Spanish horse recognized as an official breed since the 15th century. In 1912, with the creation of its studbook, it became a closed population (only animals belonging to the breed acts as breeders: 23,530 stallions and 75,870 mares), in which relatedness between individuals and inbreeding has tended to increase. Inbreeding estimation measures the probability in an individual of possessing, in one gene, two identical alleles derived from a common ancestor. Each common ancestor provides part of the descendant’s total inbreeding (partial inbreeding coefficient, F(ij)). This work analyzes the F(ij), calculated using a recently developed approach (based on founders and Mendelian sampling of the non-founders) in the whole PRE population. The identification of 10,244 common ancestors and their relationship with the seven most influential individuals of the breed allowed us to determine that a genetic bottleneck due to an unequal contribution over the generations occurred. Computing F(ij) has being an important tool to determine which are the breeding animals, with more or less massive use, whose are determining a loss of genetic variability in the population at each moment and has enabled us to expand our knowledge about PRE genetic demographic evolution. ABSTRACT: The aim of this work was to analyze genetic parameters such as the inbreeding coefficient (F), relatedness coefficient (AR) and partial inbreeding coefficient (F(ij)) of the whole PRE population, and the ancestors which account for 50% of the total genetic variability of the current population, from genealogical information. The average F of the whole PRE population (328,706 animals) has decreased from 8.45% to 7.51% in the least 20 years. The F(ij) was estimated for the whole PRE population, resulting in a database of 58,772,533 records containing one record for each F(ij) that each animal receives from a certain common ancestor (CA). A total of 10,244 CAs contributed to the F(ij) with an average of 5370 descendants, with each descendant having an average of 170 CAs. Over the generations, the number of CAs has increased, while the proportion of F(ij) by each one has decreased. In addition, the contributions of the more influential ancestors have changed. The increased census, the limited use of artificial insemination and our increased knowledge about inbreeding depression and the animals’ breeding values allow breeders to select horses more for their functionality and conformation than for their pedigree reputation, which is the cause of all these changes.