The genetic landscape of horse breeds has been profoundly shaped by human-directed breeding programs aimed at enhancing specific traits. This study delves into the genomic signatures of selection within four distinct German warmblood horse breeds – Trakehner, Holsteiner, Hanoverian, and Oldenburger – to understand how historical and contemporary breeding objectives have influenced their genomes. By analyzing genetic data from 942 stallions, researchers employed multiple methods, including Integrated Haplotype Score (iHS), cross-population Extended Haplotype Homozygosity (xpEHH), and Runs of Homozygosity (ROH), to pinpoint genomic regions subjected to selective pressure. The findings reveal both shared and breed-specific selection signatures, shedding light on the genetic underpinnings of traits crucial for athletic performance, such as muscle function, energy metabolism, embryonic development, and fertility. This research not only deepens our understanding of equine evolution through artificial selection but also provides valuable insights for future breeding strategies in sport horses.
Exploring Genetic Diversity and Selection Signatures
The domestication and subsequent breeding of horses have led to a remarkable diversity of breeds, each sculpted by human needs and preferences. Warmblood horses, particularly those bred for competitive equestrian disciplines like show-jumping, dressage, and eventing, represent a pinnacle of this artificial selection. This study focuses on four prominent German warmblood breeds, examining their genetic makeup to identify regions of the genome that have been under intense selective pressure.
Breed Histories and Breeding Goals
The four breeds investigated – Trakehner, Holsteiner, Hanoverian, and Oldenburger – share a common goal of producing high-performance sport horses but possess distinct historical trajectories and breeding policies.
- Trakehner: Known for its historical role in cavalry and a strong emphasis on riding horses, the Trakehner breed experienced a significant population bottleneck after World War II. This breed has largely maintained its purity over centuries, with limited introduction of foreign bloodlines, primarily English Thoroughbreds and Arabians for refinement. Their breeding objective is a versatile leisure and sport horse, with a tradition in eventing.
- Hanoverian: Originally bred for agricultural and military purposes, the Hanoverian breed transitioned towards a lighter riding horse after World War II, incorporating Thoroughbred and Trakehner bloodlines. The studbook now focuses on aptitude for show-jumping, dressage, eventing, or carriage driving.
- Oldenburger: Historically favored for carriage driving, the Oldenburger breed initially focused on heavier warmbloods. Since the 1950s, the studbook has shifted towards breeding lighter riding horses, with a contemporary goal of producing powerful, high-performance sport horses suited for various disciplines. The Oldenburger International studbook, founded in 2001, specifically targets show-jumping.
- Holsteiner: Primarily used as draught horses, Holsteiners later shifted their breeding focus to sports, with a pronounced emphasis on show-jumping today. They accept sires from various warmblood breeds, as well as English Thoroughbreds and Arabians, for refinement, particularly for jumping aptitude.
These differing historical contexts and selection pressures are hypothesized to be reflected in unique genomic signatures across the breeds.
Methodologies for Identifying Selection Signatures
To uncover the genetic footprints of selective breeding, this study employed a multi-pronged approach:
Runs of Homozygosity (ROH)
ROH are contiguous stretches of homozygous genotypes within an individual’s genome. Their presence and distribution can indicate historical population bottlenecks and the extent of inbreeding or recent selective sweeps. By analyzing ROH shared among individuals within and across breeds, researchers can identify genomic regions that have been under strong selection, leading to a reduction in genetic variation.
Integrated Haplotype Score (iHS)
The iHS method detects positive selection by comparing the haplotype homozygosity around an ancestral allele versus a derived allele. A significant positive iHS score suggests that an ancestral allele is increasing in frequency due to selection, while a negative score indicates selection favoring a derived allele. This method is particularly effective at identifying incomplete selective sweeps within a population.
Cross-population Extended Haplotype Homozygosity (xpEHH)
xpEHH is designed to detect complete selective sweeps by comparing haplotype homozygosity between two distinct populations. It is powerful in identifying genomic regions that have become fixed for a particular allele in one breed but remain polymorphic in another. This comparative approach helps to highlight breed-specific selection events.
Candidate Gene Identification
Following the detection of selection signatures, the study scanned these genomic regions for annotated genes. Candidate genes were identified based on their overlap with known Quantitative Trait Loci (QTL), their potential functional relevance to breeding goals (e.g., athleticism, fertility), enrichment in specific biological pathways, and previous findings in scientific literature.
Key Findings and Genomic Insights
The analysis revealed significant patterns of selection across the four German warmblood breeds. A Principal Component Analysis (PCA) based on genotype data showed a tentative separation of the breeds, with Trakehner forming a distinct cluster, while Holsteiner clustered more separately from Hanoverian and Oldenburger, which largely overlapped.
Shared and Breed-Specific Selection Signatures
Across-breed analyses identified shared selection signatures on chromosomes 1, 4, and 7. Notably, Oldenburger and Hanoverian exhibited very similar iHS signatures, suggesting common breeding influences. However, breed-specific signals were also detected using xpEHH, highlighting unique selection pressures within each breed. Trakehner horses displayed the highest number of breed-specific ROHs, likely reflecting their historical population bottleneck and potentially more intense selection.
Candidate Genes and Biological Pathways
The study identified several candidate genes and biological pathways that appear to have been targeted by selection:
- Muscle Functionality and Metabolism: Genes such as TPM1, TMOD2-3, MYO5A, and MYO5C were implicated in muscle function and motor activity. Furthermore, genes related to energy metabolism and growth, including AEBP1, RALGAPA2, and IGFBP1, 3-4, were highlighted, suggesting selection for enhanced athletic performance and efficient energy utilization.
- Development and Growth: The HOXB gene complex, crucial for embryonic development and patterning, was identified, indicating selection pressure related to skeletal development and overall growth.
- Fertility: Genes associated with reproductive processes, such as THEGL, ZPBP1-2, TEX14, ZP1, SUN3, and CFAP61, were found within selection signatures, suggesting that fertility has also been a target of selection, likely influenced by both natural and artificial selection pressures.
- Pigmentation: The KITLG gene, known to influence pigmentation, showed evidence of selection pressure, underscoring the continued importance of coat color traits in horse breeding.
The enrichment analysis of genes within selection signatures revealed significant associations with pathways involved in embryonic development, growth factor signaling, cell proliferation, and metabolic processes.
Conclusion and Future Directions
This comprehensive genomic study has successfully identified selection signatures within four German warmblood horse breeds, revealing both shared evolutionary pressures and breed-specific genetic adaptations. The findings underscore the significant impact of selective breeding on the equine genome, particularly concerning traits vital for athletic performance, development, and reproduction. The candidate genes and pathways identified provide a foundation for further research aimed at validating these associations and understanding their functional roles. Future studies integrating detailed phenotypic data with genomic information from comprehensively phenotyped sport horses will be crucial for confirming these candidate genes and regions and for optimizing breeding strategies to further enhance athletic capabilities and overall well-being in warmblood horses.
References
- Nolte W, Thaller G, Kuehn C (2019) Selection signatures in four German warmblood horse breeds: Tracing breeding history in the modern sport horse. PLoS ONE 14(4): e0215913. https://doi.org/10.1371/journal.pone.0215913
