Does inbreeding contribute to pregnancy loss in Thoroughbred horses?

Warmblood fragile foal syndrome: Pregnancy loss in Warmblood mares

BACKGROUND

Fragile foal syndrome (FFS) or warmblood FFS Type 1 (WFFS) is a recessive, autosomal, hereditary, genetic defect causing late abortions, stillbirths and non-viable foals. Whether early pregnancy losses occur is unknown.

OBJECTIVES

To investigate how WFFS affects pregnancies and whether early pregnancy losses occur in WFFS matings and if there is a difference in pregnancy success between matings where both parents were allele carriers and those where only mare or stallion were WFFS carriers.

STUDY DESIGN

Retrospective cohort study.

METHODS

Breeding records from a Warmblood stud farm were evaluated (2016-2019) and 2682 cycles of 177 mares analysed. Matings were assigned to four study groups, depending on the WFFS carrier status of the mare and stallion: N/WFFS × N/WFFS (n = 46), N/WFFS (mares) × N/N (n = 511), N/N × N/WFFS (stallions) (n = 191) and N/N × N/N (n = 2149).

RESULTS

There were no differences in pregnancy rates between matings with only one WFFS carrier and those with non-carriers. When comparing N/WFFS × N/WFFS matings to those with only one or no WFFS-carrier, there were no increased pregnancy losses in the embryonic phase (day <42). By contrast, the N/WFFS × N/WFFS group had significantly more abortions (53.8%) than the other three study groups (7.9-9.2%; adjusted p < 0.0001). The higher losses were evenly distributed between the early (D42-150: 22.7% losses, n = 5) and late (D150-300: 29.4% losses, n = 5) foetal phase. The live foal rate per pregnancy for N/WFFS × N/WFFS matings was lowest (34.5%) and differed significantly (other groups 81%-84%; adjusted p < 0.0001); the peri- and postnatal mortality was higher (25%) compared with the other study groups (2.6%-3%).

MAIN LIMITATIONS

Low sample size in N/WWFS × N/WFFS matings, unbalanced study design, outcomes are descriptive, all mares from one stud farm.

CONCLUSIONS

The mating of two WFFS carriers may lead to increased risks of pregnancy and foal loss.

Analyses of whole-genome sequences from 185 North American Thoroughbred horses, spanning 5 generations

Whole genome sequences (WGS) of 185 North American Thoroughbred horses were compared to quantify the number and frequency of variants, diversity of mitotypes, and autosomal runs of homozygosity (ROH). Of the samples, 82 horses were born between 1965 and 1986 (Group 1); the remaining 103, selected to maximize pedigree diversity, were born between 2000 and 2020 (Group 2). Over 14.3 million autosomal variants were identified with 4.5-5.0 million found per horse. Mitochondrial sequences associated the North American Thoroughbreds with 9 of 17 clades previously identified among diverse breeds. Individual coefficients of inbreeding, estimated from ROH, averaged 0.266 (Group 1) and 0.283 (Group 2). When SNP arrays were simulated using subsets of WGS markers, the arrays over-estimated lengths of ROH. WGS-based estimates of inbreeding were highly correlated (r > 0.98) with SNP array-based estimates, but only moderately correlated (r = 0.40) with inbreeding based on 5-generation pedigrees. On average, Group 1 horses had more heterozygous variants (P < 0.001), more total variants (P < 0.001), and lower individual inbreeding (FROH; P < 0.001) than horses in Group 2. However, the distribution of numbers of variants, allele frequency, and extent of ROH overlapped among all horses such that it was not possible to identify the group of origin of any single horse using these measures. Consequently, the Thoroughbred population would be better monitored by investigating changes in specific variants, rather than relying on broad measures of diversity. The WGS for these 185 horses is publicly available for comparison to other populations and as a foundation for modeling changes in population structure, breeding practices, or the appearance of deleterious variants.

Unveiling the population genetic structure of Iranian horses breeds by whole-genome resequencing analysis

Preserving genetic diversity is pivotal for enhancing genetic improvement and facilitating adaptive responses to selection. This study focuses on identifying key genetic variants, including single nucleotide polymorphisms (SNPs), insertion/deletion polymorphisms (INDELs), and copy number variants (CNVs), while exploring the genomic evolutionary connectedness among seven Iranian horses representing five indigenous breeds: Caspian, Turkemen, DareShuri, Kurdish, and Asil. Using whole-genome resequencing, we generated 2.7 Gb of sequence data, with raw reads ranging from 1.2 Gb for Caspian horses to 0.38 Gb for Turkoman horses. Post-filtering, approximately 1.9 Gb of reads remained, with ~ 1.5 Gb successfully mapped to the horse reference genome (EquCab3.0), achieving mapping rates between 76.4% (Caspian) and 98.35% (Turkoman). We identified 2,909,816 SNPs in Caspian horses, constituting around 0.1% of the genome. Notably, 71% of these SNPs were situated in intergenic regions, while 8.5 and 6.8% were located upstream and downstream, respectively. A comparative analysis of SNPs between Iranian and non-Iranian horse breeds showed that Caspian horses had the lowest number of shared SNPs with Turkoman horses. Instead, they showed a closer genetic relationship with DareShuri, Quarter, Arabian, Standardbred, and Asil breeds. Hierarchical clustering highlighted Caspian horses as a distinct cluster, underscoring their distinctive genomic signature. Caspian horses exhibit a unique genetic profile marked by an enrichment of private mutations in neurological genes, influencing sensory perception and awareness. This distinct genetic makeup shapes mating preferences and signifies a separate evolutionary trajectory. Additionally, significant non-synonymous single nucleotide polymorphisms (nsSNPs) in reproductive genes offer intervention opportunities for managing Caspian horses. These findings reveal the population genetic structure of Iranian horse breeds, contributing to the advancement of knowledge in areas such as conservation, performance traits, climate adaptation, reproduction, and resistance to diseases in equine science.