Genetic inbreeding depression load for morphological traits and defects in the Pura Raza Española horse

Abstract

Background Inbreeding is caused by mating between related individuals and is associated with reduced fitness and performance (inbreeding depression). Several studies have detected heterogeneity in inbreeding depression among founder individuals. Recently, a procedure was developed to predict hidden inbreeding depression load that is associated with founders using the Mendelian sampling of non-founders. The objectives of this study were to: (1) analyse the population structure and general inbreeding, and (2) test this recent approach for predicting hidden inbreeding depression load for four morphological traits and two morphology defects in the Pura Raza Española (PRE) horse breed. Results The regression coefficients that were calculated between trait performances and inbreeding coefficients demonstrated the existence of inbreeding depression. In total, 58,772,533 partial inbreeding coefficients (Fij) were estimated for the whole PRE population (328,706 horses). We selected the descendants of horses with a Fij ≥ 6.25% that contributed to at least four offspring and for which morphological traits were measured for the subsequent analysis of inbreeding depression load (639 horses). A pedigree was generated with the last five generations (5026 animals) used as the reference population (average inbreeding coefficient of 8.39% and average relatedness coefficient of 10.76%). Heritability estimates ranged from 0.08 (cresty neck) to 0.80 (height at withers), whereas inbreeding depression load ratios ranged from 0.01 (knock knee) to 0.40 (length of shoulder), for an inbreeding coefficient of 10%. Most of the correlations between additive and inbreeding depression load genetic values and correlations between inbreeding depression load genetic values for the different traits were positive or near 0. Conclusions Although the average inbreeding depression loads presented negative values, a certain percentage of the animals showed neutral or even positive values. Thus, high levels of inbreeding do not always lead to a decrease in mean phenotypic value or an increase in morphological defects. Hence, individual inbreeding depression loads could be used as a tool to select the most appropriate breeding animals. The possibility of selecting horses that have a high genetic value and are more resistant to the deleterious effects of inbreeding should help improve selection outcomes.

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

“…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 ). The ongoing change of the average inbreeding values reflects the greater frequency of homozygous loci and loss of genetic variability.…”

“…However, over the last few decades, more research has been carried out into the genetic nature of this phenomenon and how unfavorable alleles are transmitted from the common ancestors. This has revealed a heterogeneity in inbreeding depression among founder and non-founder individuals for different traits in several species ( Miglior et al, 1994 ; Carolino and Gama, 2008 ; Casellas et al, 2009 ; Todd et al, 2018 ; Varona et al, 2019 ; Poyato-Bonilla et al, 2020 ). The results show that inbreeding depression sometimes has neutral or positive impact to phenotypes ( Varona et al, 2019 ; Poyato-Bonilla et al, 2020 ; Martinez-Castillero et al, 2021 ).…”

“…This has revealed a heterogeneity in inbreeding depression among founder and non-founder individuals for different traits in several species ( Miglior et al, 1994 ; Carolino and Gama, 2008 ; Casellas et al, 2009 ; Todd et al, 2018 ; Varona et al, 2019 ; Poyato-Bonilla et al, 2020 ). The results show that inbreeding depression sometimes has neutral or positive impact to phenotypes ( Varona et al, 2019 ; Poyato-Bonilla et al, 2020 ; Martinez-Castillero et al, 2021 ). This evidence leads us to conclude that inbreeding depression is not homogeneous among individuals with the same level of homozygosity but depends on the proportion of inbreeding by descendant (IBD) alleles received from each ancestor.…”

“…The MCMC model was implemented using ad hoc software written in FORTRAN90 ( Varona et al, 2019 ) and one single chain of 5,500,000 samples and a burning period of 500,000 were used for each trait. This analysis will also allow us to calculate the inbreeding depression load ratios, which should be interpreted as the proportion of the variation of each phenotypic unit value in the population that is attributable to the variation in the inbreeding depression effects in a theoretical population where each of the individuals has a partial inbreeding coefficient generated by a single, specific ancestor ( Varona et al, 2019 ; Poyato-Bonilla et al, 2020 ; Martinez-Castillero et al, 2021 ). Simple linear regression coefficients between the inbreeding coefficients (F3, F, and Fk) and the phenotypic values of analyzed traits were performed to assess the effect of inbreeding depression.…”

“…In the last few decades, the variability of inbreeding depression has been confirmed in different breeds, mainly for growth or milk traits ( Miglior et al 1994 ; Carolino and Gama, 2008 ; Casellas et al, 2009 ; Varona et al, 2019 ). To date, however, only a few articles have analyzed inbreeding depression in horses, and these have focused on racing performance ( Todd et al, 2018 ) and morphology ( Gómez et al, 2009 ; Poyato-Bonilla et al, 2020 ). Although these studies have revealed deleterious effects due to inbreeding depression, inbreeding actually shows an extensive range of negative, neutral, and positive effects in livestock.…”