Genetic diversity of the Italian thoroughbred horse population

Population structure and genetic diversity of Polish Arabian horses based on pedigree data

With a history tracing back to at least the 18th century and a substantial global influence on various breeds, Polish Arabian horse population is of paramount importance for both breeders and conservationists. However, its genetic makeup and the population dynamics are still not well understood. This study presents an analysis of the modern Polish Arabian horse population using pedigree data, focusing on the breed's genetic diversity and population structure. Our analysis encompassed 1 498 individuals defined as the reference population (RP) and their 11 065 ancestors, which resulted in the dataset of 12 254 individuals (total population). We traced their genealogy to assess inbreeding coefficients (F), founder effects, and genetic variability measures such as the effective number of founders (fe), ancestors (fa), or founder genome equivalents (fge). The results indicated a good pedigree quality with an average of 28.1 maximum traced generations, revealing high pedigree completeness for initial generations with a decline beyond the seventh generation. The genetic diversity parameters showed a considerable bottleneck effect, with an effective number of founders at 73, which reflects a substantial loss of genetic diversity over time. Despite the vast total number of founders (852), only a few have had a lasting impact on the current population, signaling the need for revised breeding strategies to maintain diversity. The study identified a slight but consistent rise in inbreeding over the last century, with a marginal recent decline, and a significant difference in the contribution of various founders. The average F was 5.8%, with 99.6% of the reference population being inbred. The analysis of effective population size (Ne) highlighted potential risks for genetic diversity, urging for revision of breeding goals to consider a wider array of founder lineages. The study indicated that stallions belonging to RP can be attributed to 15 distinct sirelines, whereas mares to 45 unique damlines, more than considered in the current breeding program (8 and 15, respectively). Conclusively, the study underlines the need for ongoing monitoring and strategic breeding to maintain and enhance the genetic diversity of Polish Arabians, considering the breed's historical significance and contemporary genetic challenges.

Unlocking Horse Y Chromosome Diversity

The present equine genetic variation mirrors the deep influence of intensive breeding programs during the last 200 years. Here, we provide a comprehensive current state of knowledge on the trends and prospects on the variation in the equine male-specific region of the Y chromosome (MSY), which was assembled for the first time in 2018. In comparison with the other 12 mammalian species, horses are now the most represented, with 56 documented MSY genes. However, in contrast to the high variability in mitochondrial DNA observed in many horse breeds from different geographic areas, modern horse populations demonstrate extremely low genetic Y-chromosome diversity. The selective pressures employed by breeders using pedigree data (which are not always error-free) as a predictive tool represent the main cause of this lack of variation in the Y-chromosome. Nevertheless, the detailed phylogenies obtained by recent fine-scaled Y-chromosomal genotyping in many horse breeds worldwide have contributed to addressing the genealogical, forensic, and population questions leading to the reappraisal of the Y-chromosome as a powerful genetic marker to avoid the loss of biodiversity as a result of selective breeding practices, and to better understand the historical development of horse breeds.

Genetic Diversity and Structure of the Main Danubian Horse Paternal Genealogical Lineages Based on Microsatellite Genotyping

Simple Summary

The Danubian horse was created on the former Klementina stud farm near Pleven to satisfy the demands of the Bulgarian Army for light draft horses and to improve the working capacity of the local horse population. The privatization of the Klementina stud farm in the late 1990s and the lack of economic activity have led to a sharp reduction in the number of mares and stallions and their sale to private owners. At present, only six of the main paternal lines which participated in the creation of the Danubian horse breed are preserved: Zdravko, NONIUS XVII-30, Torpedo, Lider, Kalifa, and Hrabar. This is the first study on the genetic and population diversity of the Danubian horse paternal lines based on microsatellite markers (STRs). The results showed that the studied Danubian horse population was characterized by a high level of genetic diversity with a medium value of 0.84. The fixation index (F_ST) was 0.08 for all studied markers, which is indicative of the low genetic differentiation of the Danubian horse population. Our analysis also confirmed the low level of inbreeding and heterozygous deficiency among the animals selected from the six paternal lineages of the Danubian horse. The present research could be helpful for the development of breeding and conservation programs for the Danubian horse, as well as for making informed decisions on the management of paternal lines.

Abstract

The Danubian horse, together with the Pleven and the Eastern Bulgarian horse breeds, is one of the modern breeds in Bulgaria. The objective of this study was to compare the genetic structure and genetic diversity of six paternal genealogical lineages of the Danubian horse breed (Zdravko, NONIUS XVII-30, Torpedo, Lider, Kalifa, and Hrabar). In total, 166 individuals from the six genealogical lines were investigated, based on 15 STR markers (short tandem repeats, also known as microsatellites). In total, 184 alleles were found in the six populations, using 15 microsatellite loci. The mean number of alleles, the effective number of alleles, and the polymorphic information content (PIC) values per locus were 12.28, 9.48, and 0.73, respectively. In a comparison of the allelic diversity among sire lineages, the highest genetic diversity (Na) was observed in Lider and Kalifa (14.60 ± 0.21), while the lowest value of this parameter was observed in the Zdravko lineage 4.20 ± 0.35. The largest genetic diversity was found in loci HMS3 and HMS7, with 13 alleles, and the smallest polymorphism was noted for the locus ASB17, with 10 alleles. The level of observed heterozygosity was in the range of 0.65 ± 0.069 for the Zdravko lineage to 0.93 ± 0.01 for the Torpedo lineage. The expected heterozygosity level range was from 0.57 ± 0.048 to 0.91 ± 0.01 for all horse lineages. Structure analysis revealed three main gene pools in the study population. The first pool included the Zdravko lineage; the second had the NONIUS XVII-30, Torpedo, Lider, and Kalifa lineages; and the third defined the Hrabar lineage, which was significantly differentiated from the other genealogical lineages.

Genetic Variability Trend of Lusitano Horse Breed Reared in Italy

The Lusitano Horse (LH) originates from Portugal, but is reared worldwide. Since 1994, the University of Milan has routinely tested the LHs bred in Italy for parentage control. This study aims to assess the genetic variability of the LH reared in Italy using 16 microsatellites markers. Moreover, the genetic variability changes over the years in the total population (n.384) and in unrelated horses (n.47) were evaluated. Horses were grouped according to their date of birth (1975–1990, 1991–2000, 2001–2010, 2010–2019). Standard genetic diversity parameters, including observed (Ho) and expected (He) heterozygosity, Hardy-Weinberg equilibrium (HWE; P-Val), allelic richness, and inbreeding coefficient (Fis) were estimated. In the whole period, the total population showed Ho as high as 0.69, low Fis (0.057), and imbalance for HWE. When considering the unrelated horses, Ho was seen to increase over time (from 0.594 in 1975–1990 to 0.68 in 2010–2019) and frequencies were in HWE, again having low and decreasing values of Fis (from 0.208 in 1975–1990 to 0.019 in 2010–2019). Bottleneck analysis excluded a recent population decline. Principal Coordinate Analysis at the individual level defined two clusters, the major cluster including all the most recent horses. An increasing number of dams (156% more from 2001–2010 to 2011–2019) supports the good variability recorded in the population so far. However, the high number of foals (77.2%) sired by only four stallions in recent years suggests caution in the choice of the sires for the future.

Thoroughbred stallion fertility is significantly associated with FKBP6 genotype but not with inbreeding or the contribution of a leading sire

This is a follow-up study to validate the previously detected association of the FKBP6 gene with stallion subfertility. Using a select cohort of 150 Thoroughbred stallions with detailed breeding records, we confirm significant association (P < 0.0001) between low per-cycle pregnancy rates (≤50%) and a combined A/A-A/A genotype of SNPs chr13:11 353 372G>A and chr13:11 353 436A>C in FKBP6 exon 5. We also show that stallion subfertility and the combined genotype A/A-A/A are not associated with the level of genetic diversity based on 12 autosomal microsatellite markers, or with pedigree-based inbreeding rate, or the extent of contribution of a leading Thoroughbred sire, Northern Dancer, in a stallion's pedigree. We develop a TaqMan allelic discrimination assay for the two SNPs to facilitate accurate and high-throughput genotyping. We determine allele, genotype and combined genotype frequencies of FKBP6 exon 5 SNPs in a global cohort of 518 Thoroughbreds (76% stallions or geldings and 24% mares) and show that the frequency of the A/A-A/A genotype is 4%. Because there is no similar association between the FKBP6 exon 5 genotype and stallion subfertility in Hanoverians, we suggest that the two SNPs are not causative but rather tagging a breed-specific haplotype with genetic variants unique to Thoroughbreds. Further WGS-based research is needed to identify the molecular causes underlying the observed genotype-phenotype association in Thoroughbred stallions.

Dynamics of the Inbreeding Coefficient and Homozygosity in Thoroughbred Horses in Russia

The Thoroughbred (TB) horse has hugely impacted the development of horse breeding around the world. This breed has unique genetic qualities due to having had a closed studbook for approximately 300 years. In Russia, TBs have been bred since the second half of the 18th century. Here, we analyzed the genetic diversity and the inbreeding level in TB horses (n = 9680) for the period from 1990 to 2018 using polymorphisms of 17 microsatellite loci. We found that the genetic structure of the TB breed in Russia is represented by 100 alleles of panel STR (short tandem repeat) loci and has been stable for the past three decades. The conducted monitoring revealed a slight increase in the Wright's inbreeding coefficient in all age and sex groups of TB horses (stallions, broodmares, and foals) from 0.68% to 0.90%, which was followed by a decrease in the degree of heterozygosity, Ho, from 68.5% to 67.6%. The Spearman's rank correlation coefficient between the level of inbreeding and the degree of homozygosity was estimated (r = 0.022; p > 0.05). The obtained data on the DNA genotypes of horses of different breeds provide a unique base for the evaluation of genetic variability and the control of genetic variability of horses in selection programs.

Major inconsistencies of inferred population genetic structure estimated in a large set of domestic horse breeds using microsatellites

STRUCTURE remains the most applied software aimed at recovering the true, but unknown, population structure from microsatellite or other genetic markers. About 30% of structure-based studies could not be reproduced (Molecular Ecology, 21, 2012, 4925). Here we use a large set of data from 2,323 horses from 93 domestic breeds plus the Przewalski horse, typed at 15 microsatellites, to evaluate how program settings impact the estimation of the optimal number of population clusters K opt that best describe the observed data. Domestic horses are suited as a test case as there is extensive background knowledge on the history of many breeds and extensive phylogenetic analyses. Different methods based on different genetic assumptions and statistical procedures (dapc, flock, PCoA, and structure with different run scenarios) all revealed general, broad-scale breed relationships that largely reflect known breed histories but diverged how they characterized small-scale patterns. structure failed to consistently identify K opt using the most widespread approach, the ΔK method, despite very large numbers of MCMC iterations (3,000,000) and replicates (100). The interpretation of breed structure over increasing numbers of K, without assuming a K opt, was consistent with known breed histories. The over-reliance on K opt should be replaced by a qualitative description of clustering over increasing K, which is scientifically more honest and has the advantage of being much faster and less computer intensive as lower numbers of MCMC iterations and repetitions suffice for stable results. Very large data sets are highly challenging for cluster analyses, especially when populations with complex genetic histories are investigated.