The American Quarter Horse: population structure and relationship to the thoroughbred.

The study explores how selective breeding has affected the genetic diversity and structure of the American Quarter Horse (QH) breed across six performance groups. The study also observes the impact of Thoroughbred ancestry on QH diversity. It finds significant population structure differences among all QH performance groups, and highlights potential issues with inbreeding within performance groups, owing to the increased relatedness linked to the influence of popular sires.

Methodology

• The research employed pedigree analysis and genome-wide SNP (single nucleotide polymorphisms) data from horses in six performance groups: halter, western pleasure, reining, working cow, cutting, and racing.
• Genotype data (36,037 SNP) derived from 36 Thoroughbreds was analyzed in comparison with the data accumulated from 132 performing QHs. This approach was designed to evaluate the impact of Thoroughbred ancestry on QH genetic diversity.

Findings

• The study discovered significant population structure variations among all the QH performance groups studied. The only exception was the similarity between the cutting and working cow horses.
• The study observed the greatest divergence between the cutting and racing QHs, wherein the latter had a considerable influence of Thoroughbred ancestry.
• There are notable coancestry levels and potential for inbreeding within performance groups, particularly among the elite performers. This is a result of increased relatedness within groups following the input of popular sires contributing disproportionate levels of variation to each discipline.
• The QH breed can, in general, be broadly categorized into three groups: stock, racing, and pleasure/halter, per the expected heterozygosity, inbreeding, F ST, cluster, and haplotype analyses.

Implications of the Research

• While the QH breed overall contains significant genetic diversity, current breeding practices have caused this diversity to be divided into subpopulations.
• Understanding the effect of selective breeding on QH genetic diversity can influence future breeding practices to maintain and enhance genetic diversity within the breed.