500 years of breeding in the Carthusian Strain of Pura Raza Español horse: An evolutional analysis using genealogical and genomic data.

The research explores the population structure and variability of the Carthusian strain of Pura Raza Español (PRE) horse using genealogical and genomic data. It uncovers the unique genetic footprint, variability, and introgression of the strain over its 500-year breeding history, revealing a recent genetic bottleneck and a shift in breeding trends.

Methodology

• The researchers used both genealogical and genomic data to analyse the strain’s population structure and variability.
• Data was collected from 348,429 pedigree records, which included 56,105 horses from the Carthusian strain.
• High-density genotypes, consisting of 670,804 Single Nucleotide Polymorphisms (SNPs), were used to conduct genomic analysis on 287 of these horses.

Accuracy of Pedigree Data

• The accuracy of the pedigree data was confirmed by the completeness of the records.
• There was a good correlation between the inbreeding coefficient calculated from genealogical analysis (GEL-F) and that from genomic analysis (GEN-F). This correlation was notably lower in fully Carthusian horses due to the significant impact of founders not detected by GEL analysis.

Population Differentiation and Introgression

• Using both genomic (PCA, AMOVA, and Admixture) and genealogical analysis, researchers identified clear differentiation between subpopulations.
• At the same time, they observed a high level of introgression (the transfer of genetic information from one species to another) of the Carthusian strain into the breed over past decades.

Recent Genetic Changes

• Interestingly, a recent shift in breeding trends has caused a significant reduction in Carthusian strain variability and a genetic bottleneck (a sharp reduction in the size of a population due to environmental events or human activities).
• In the last generation, effective population sizes of 31.57 and 30.20 respectively were observed in genealogical and genomic analysis.

Pura Raza Español Breed Variability

• In spite of these changes, the PRE horse breed has maintained its variability.
• The researchers observed a significant difference in the estimated N (a measure of the effective population size) calculated from genealogical (60.77) and genomic (188.0) data.
• This implies a notable genetic diversity within the breed which has survived over the centuries.

Unique Genetic Landmark

• The study ultimately uncovered the existence of an ancient strain of PRE horses with a distinct genetic signature, mostly free from the influence of other equine populations.
• This makes the Carthusian strain a unique and valuable genetic resource from an evolutionary and breeding perspective.