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

Abstract

The aim of this work was to analyze genetic parameters such as the inbreeding coefficient (F), relatedness coefficient (AR) and partial inbreeding coefficient (Fij) 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 Fij was estimated for the whole PRE population, resulting in a database of 58,772,533 records containing one record for each Fij that each animal receives from a certain common ancestor (CA). A total of 10,244 CAs contributed to the Fij 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 Fij 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.

Genetic inbreeding depression load for fertility traits in Pura Raza Española mares

“…Numerous studies have shown, in practically all species, that reproductive characteristics are among those most affected by inbreeding depression ( Charlesworth and Willis, 2009 ). In comparison with other livestock species, horses have higher inbreeding coefficients, due mainly to the use of breeding schemes focused on morphological traits ( Perdomo-González et al, 2020 ) or sport performance ( Todd et al, 2018 ; Azcona et al, 2020 ), the lack of genetic control of mating ( Gómez et al, 2009 ), the search of a certain type of animal, or the use of breeds with very small effective population sizes. The historical change of average inbreeding coefficients for F3 and F found here is similar to the latest studies carried out with the total PRE population ( Perdomo-González et al, 2020 ; Poyato-Bonilla et al, 2020 ).…”

“…As a result, inbreeding levels are extremely high ( Valera et al, 2005 ; Poyato-Bonilla et al, 2018 ). In fact, the average PRE inbreeding is 7.25%, with over 46% of the current population having an inbreeding coefficient equal or higher than 6.25% ( Perdomo-González et al, 2020 ).…”

Discriminant Canonical Analysis of the Contribution of Spanish and Arabian Purebred Horses to the Genetic Diversity and Population Structure of Hispano-Arabian Horses

“…The determination of Mendelian sampling of the non-founders of a population has recently been reported to be of help when determining partial inbreeding in equine populations [ 92 ]. Inbreeding can be broken down into the sources of the coancestry between the parents of each individual, which becomes even more relevant in the case of composite breeds whose ancestors may belong to differentiated breeds.…”

“…In line with these results, we may determine that relative founder contributions may tend to stabilize after a short number of generations, which has been described in Thoroughbred horses [ 94 ]. Either the population is closed or remains open, as is the case of the Há horse breed [ 17 , 92 ].…”

Impaired Reproductive Function in Equines: From Genetics to Genomics

“…By this reason, it has also been pointed out as one of the most important causes of reduced fertility in wildlife [ 64 ], as well as livestock populations [ 65 , 66 ]. In horses, inbreeding rates are normally higher in comparison with other livestock species for several reasons, such as the existence of breeds with very small effective population sizes [ 67 , 68 ] or the development of breeding schemes focused mainly on morphological traits [ 69 ] or athletic performance [ 70 , 71 ], or the lack of genetic control of mating [ 72 ].…”