Genetic structure and connectivity analysis in a large domestic livestock meta‐population: The case of the Pura Raza Español horses

Abstract

The Pura Raza Español (PRE) is an autochthonous Spanish horse population distributed in 65 countries and managed by a single association. Since 1960s, breeding animals have been steadily exported to other countries to establish local subpopulations. We analysed the genetic structure of a PRE horse meta-population (MP) of 215,500 animals from countries with at least 80 active animals (27 countries comprising 77% of the total animals in the complete pedigree). Genotypes from active animals (59% of the total animals in the complete pedigree) were also studied. Genetic analysis of the MP was performed using classical parameters such as inbreeding (F), coancestry, founder contribution, effective number of founders/ancestors (fe/fa) and gene flow between countries. Results showed that the MPF coefficient decreased in the last two decades (1990-2013), indicating an explicit management against F. Founder contribution to genetic variability across countries mainly came from females (73.6%). In general, unbalanced contributions of founders reflected the high loss of genetic diversity along generations (fe/fa as low as 32/19 for the whole MP). Despite this differential contribution, the proportional contribution to the global diversity of each country was similar. The highest within-country coancestry value corresponded to Cuba (0.1509), being the only country with highly inbred individuals (over 12%), and the lowest value corresponded to Spain (0.0574). These results should help to avoid further declines in genetic variability and increases in F levels, especially in small countries like Cuba. In parallel, only nine countries presented descendants in a single population, suggesting a common origin for all countries and/or a substantial exchange of genetic material between populations. Spain and the US showed the highest gene flow rates. These results support the need of a coordinated management strategy, especially promoting the exchange of genetic material to increase the effective population size and maintain the levels of genetic diversity in the PRE horse population.

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

“…The PRE breeding program is managed by ANCCE, and includes functional conformation, dressage and riding abilities, in addition to morphology, as the main selection criteria [41,42]. The fact the average F ij that a common ancestor transmits to its descendants has decreased is mainly due to the increasing awareness among horse breeders about the inbreeding depression [2] and the better information available about the animals' breeding values, which enables them to choose the best stallions and mares (also with the lowest AR) to obtain foals with the desired characteristics and less F, thus reducing the average founder's contribution to the population [34].…”

“…A single association, the National Association of Pure Spanish Horse Breeders (ANCCE), manages all of them, despite the fact that 23.3% of PRE horses are distributed abroad, in over sixty countries [1]. PRE is a breed with ancestors dating back thousands of years in the Iberian Peninsula, and was recognized as an official breed in the 15th century [2]. This breed has exceptional temperamental and functional qualities, making it highly suitable for different equine competitions, above all, classic dressage [3].…”

“…Pedigree-based relationship coefficients are often used to manage the inbreeding in a population when effects of the inbreeding depression begin to be manifested. Although, in recent decades, attempts have been made to maintain genetic variability in the PRE population, in general, unbalanced contributions of founders reflect the great loss of genetic diversity over the generations [2].…”

Survey of Risk Factors and Genetic Characterization of Ewe Neck in a World Population of Pura Raza Español Horses

“…For example, a slight Ewe Neck could be positively influenced by the development of the dorsal neck muscles due to training; it is a hypothesis which would positively affect to trained horses. It is also possible that moderate differences in the genetic pool of subpopulations of PRE horses in different parts of the world (since they could originate from the founders which carried this defect) [ 5 ] may have contributed to the differences observed in the prevalence of Ewe Neck. This also happened in the case of Cresty Neck, vitiligo, and melanoma, where, curiously, the same geographical regions (American region) show higher prevalence of PRE affected [ 27 , 37 ].…”

“…The breed census currently stands at 252,852 animals (125,824 stallions and 127,010 mares) [ 4 ]. Since the 1960s, breeding animals have been regularly exported to other countries to establish local subpopulations, which are now distributed in more than 66 countries, with 23.29% of registered horses bred in foreign countries [ 5 ]. The popularity of this breed lies in its inherent ethological and morphological attributes and its excellent sports skills in certain disciplines, such as dressage [ 6 , 7 ].…”