Fine-Scale Analysis of Runs of Homozygosity Islands Affecting Fertility in Mares

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.

Analysis of the genomic landscape of inbreeding in two divergent groups of Spanish Florida goats

“…In the last few years, ROHi analysis has been used to examine regions that might be under positive selection across several domesticated species, such as cattle (Peripolli et al, 2018), pigs (Schiavo et al, 2020), sheep (Mastrangelo et al, 2017), horses (Laseca et al, 2022) and even goats (Cardoso et al, 2018; Signer‐Hasler et al, 2022). Using the same approach, we detected 13 regions located in six different chromosomes in which ROH blocks were significantly overrepresented in the whole population, as well as five additional regions (in five different chromosomes) which were only associated with recent inbreeding increases ( F ROH >8 Mb).…”

“…In this sense, Casellas et al (2019) and Poyato-Bonilla et al ( 2020) demonstrated, using quantitative data, that individuals with the same F PED can show differences in the onset of inbreeding depression, but also in their capacity to induce inbreeding depression in their offspring (inbreeding depression load). Similarly, studies performed on beef (Pilon et al, 2021), dairy cattle (Martikainen et al, 2018) and mares (Laseca et al, 2022) demonstrated that individuals showing increased homozygosity in specific regions of the genome were more prone to show a decrease in their phenotypic values. In our case, the high levels of variability in the genetic regions with increased inbreeding across the genome fit in with the idea that in some regions increased homozygosity is better tolerated in terms of phenotypic effect.…”

Designing an early selection morphological traits index for reproductive efficiency in Pura Raza Española mares

“…On the other hand, reproductive traits are also influenced by interactions between multiple genes and genetic pathways ( Li et al., 2020 ; Laseca et al., 2022 ), which can make it difficult to identify specific genes or genetic markers associated with globally assessed traits. As a result, the heritability values of reproductive traits are typically lower than those for morphology, conformation, or sport traits.…”

Estimation of the Genetic Components of (Co)variance and Preliminary Genome-Wide Association Study for Reproductive Efficiency in Retinta Beef Cattle

“…During the last few years, the use of an indirect fertility criterion, including precocity and the calving interval, which can be estimated indirectly based on reproductive records, has been demonstrated as an interesting option for selecting more fertile females in extensively-bred livestock species [13,14]. This parameter, called reproductive efficiency (Re), is estimated as the percentage deviation of the number of calvings that a cow has at each age, from the number of calvings that this cow could have had in optimal conditions.…”