Abstract
The loss of genetic variability in livestock populations bred under strict selection processes is a growing concern, as it may lead to increased inbreeding values and lower fertility, as a consequence of the “inbreeding depression” effect. This is particularly important in horses, where inbreeding levels tend to rise as individuals become more and more closely related. In this study, we evaluated the effect of increased inbreeding levels on mare fertility by combining an SNP-based genomic approach using runs of homozygosity and the estimation of genetic breeding values for reproductive traits in a large population of Pura Raza Española mares. Our results showed a negative correlation between whole-genome homozygosity and fertility estimated breeding values (EBVs) at the genome level (ρ = −0.144). However, the analysis at chromosome level revealed a wide variability, with some chromosomes showing higher correlations than others. Interestingly, the correlation was stronger (−0.241) when we repeated the analysis in a reduced dataset including the 10% most and least fertile individuals, where the latter showed an increase in average inbreeding values (FROH) of around 30%. We also found 41 genomic regions (ROHi, runs of homozygosity islands) where homozygosity increased 100-fold, 13 of which were significantly associated with fertility after cross-validation. These regions encompassed 17 candidate genes previously related to oocyte and embryo development in several species. Overall, we demonstrated the relationship between increased homozygosis at the genomic level and fertility in mares. Our findings may help to deal with the occurrence of inbreeding depression, as well as further our understanding of the mechanisms underlying fertility in mares.
Highlights
The increase in average inbreeding rates has become a serious concern in wild and livestock populations over the past two decades [1, 2]
We measured the potential effect of increased homozygosity on fertility in mares using a combined approach of high-throughput genomic analysis and genetic estimations of fertility
The analysis of the reduced dataset (RD) showed a ≈ 40% decrease in homozygosity rates in High-Fert mares, suggesting that the relationship between fertility and inbreeding depression in mares may be based on a threshold model [42], which could explain why the effect is more noticeable when inbreeding values rise above certain values
Summary
The increase in average inbreeding rates has become a serious concern in wild and livestock populations over the past two decades [1, 2]. This phenomenon leads to a decrease in phenotypic values in fitness and fertility traits [3] known as inbreeding depression. Inbreeding and Fertility in Mares with the genetic architecture of the traits For this reason, two individuals with the same inbreeding value (estimated from pedigree and/or molecular methodologies) may show increased homozygosity in different regions of the genome, affecting its phenotype to a different extent [4]. Breeds with open studbooks, such as Polo ponies, have been affected, probably by increased selection intensity in mares, driven by the use of large-scale embryo transfer programs and cloning [7, 8]
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