Genomic diversity and historical legacy of Baroque horses: a living cultural heritage.

Overview

• This study investigates the genetic diversity and population history of Baroque horse breeds that originated between the 16th and 18th centuries, using genomic data from multiple breeds to understand their relationships, inbreeding levels, and historical gene flow.

Background and Objective

• Baroque horses are a group of distinctive horse breeds developed primarily for European royalty and their courts.
• Although recognized as separate breeds, they share common ancestry and similar breeding goals influenced by their historical context.
• The study aimed to:
  • Evaluate the genomic diversity within and between these breeds.
  • Understand their population structure and patterns of genetic admixture.
  • Assess historical and contemporary population dynamics.

Breeds and Samples Analyzed

• Genomic data were collected from 1,160 individuals representing eight Baroque horse breeds:
  • Lipizzan (with national subpopulations)
  • Old Kladruby Horse (divided by coat color: black and grey)
  • Pura Raza Española (including the Carthusian strain as a unique subpopulation)
  • Lusitano
  • Friesian
  • Criollo
  • Peruvian Paso
  • Puerto Rican Paso Fino
• The Croatian Arab horse was used as an outgroup to provide comparative genomic context.
• Genotyping involved analysis of 34,026 single-nucleotide polymorphisms (SNPs), a type of genetic marker.

Genetic Diversity Findings

• Diversity was assessed by heterozygosity (a common measure of genetic variation) and haplotype richness (variety of genetic combinations).
• Most breeds had broadly similar levels of genetic diversity, but extremes were noted:
  • Friesian showed the lowest genetic diversity.
  • Lusitano and Criollo exhibited the highest diversity.

Inbreeding Levels

• Inbreeding was estimated through:
  • Runs of Homozygosity (ROH) to measure F (inbreeding coefficient based on homozygous genomic regions).
  • Homozygosity-by-descent (segments shared identically due to common ancestry).
• Inbreeding coefficients ranged:
  • ROH-based F values: approximately 0.06 to 0.29, indicating low to moderate inbreeding across breeds.
  • Homozygosity-by-descent F values: approximately 0.14 to 0.27, reinforcing similar conclusions.
• These relatively high values suggest:
  • Closed breeding practices with limited new genetic inputs.
  • Small effective population sizes.
• Interestingly, individual inbreeding coefficients (F) were often negative, implying active management to avoid mating close relatives.

Effective Population Size and Demographic History

• Contemporary effective population size (Nₑ), a measure of genetic health and breeding potential, ranged approximately from 50 to 240 depending on the breed and estimation method.
• Historical population size trajectories revealed two key periods of demographic decline:
  • One approximately 12 generations ago.
  • Another roughly 22 generations ago.
• These declines may reflect historical events affecting breeding populations, such as wars, changes in breeding practices, or other bottlenecks.

Population Structure and Gene Flow

• Gene flow analysis demonstrated:
  • Recent genetic exchanges among the Iberian breeds (such as Lusitano and Pura Raza Española).
  • Gene flow between the Croatian Arab breed and the Lusitano, indicating cross-breeding or historical admixture.
• Shared genetic ancestry patterns were found across the Baroque breeds, supporting their common historical roots despite breed distinctions.

Implications and Conclusions

• The study provides valuable insight into the genomic diversity and historical genetic relationships among Baroque horses.
• Information about inbreeding and effective population sizes is essential for developing breeding strategies to maintain genetic health.
• Understanding gene flow and population structure aids in conserving the genetic heritage of these culturally important horses.
• The results can guide breeding programs aiming to preserve Baroque horses as a living cultural heritage while maintaining their genetic viability.