Had there have been a formal debate among equine geneticists on the Jockey Club’s proposal to limit the book size of Thoroughbred stallions, geneticists would likely have formed “selective breeding” and “mutational load” camps.  Selective breeding occurs when a stallion is chosen for a mare with the goal of producing a foal with an advantageous combination of genes.

But equine geneticists agree that mutational load has the potential to counter the positive effects of selective breeding.  Mutational load refers to the accumulation of gene mutations in populations over time, increasing the risk that succeeding generations show decreased vigor.  The negative effects of mutational load are more likely to occur when horses are inbred, as serious negative traits can appear when two mutations pair up, which occurs more frequently in inbred foals. The Jockey Club’s public statement that it was “…concerned with the narrowing of the diversity of the Thoroughbred gene pool….” implies that they are especially sympathetic to this “mutational load” argument. 

The Jockey Club proposal motivated the authors of this note (1) to research the Jockey Club’s contention that genetic diversity had decreased, and (2) to review recent scholarly analyses regarding the merits of the Jockey Club’s concerns. We analyzed degrees of incremental inbreeding for mid- and upper-tier stallions by comparing pedigrees from the 2000 and 2020 BloodHorse Stallion Registers.  Based on analyses of five-cross pedigrees, the average stallion in our 2020 sample was more inbred.  The average stallion in 2020 was slightly less inbred than Maclean’s Music, whose only inbreeding arises from the appearance of Mr. Prospector in his third, fourth, and fifth generations (a 3 by 4 by 5 cross). 

We doubt that a veterinarian would view this degree of inbreeding with trepidation, though we expect that many observers would be somewhat concerned about the smaller group of stallions that exhibited significantly higher degrees of incremental inbreeding.  But increased incremental inbreeding does not necessarily mean that modern Thoroughbreds are at increased risk genetically.  To shed light on this question, we reviewed recent scholarly publications regarding the genetics of selective breeding and mutational load.

One of the earliest genomic analyses of inbreeding in Thoroughbreds was Binns et al’sInbreeding in the Thoroughbred Horse” (2011).  These researchers focused on the “big book” era beginning in 1996.  Their results regarding incremental inbreeding mirror our own findings.  The authors label the inbreeding trend as “…not excessive, (but) worrisome.”  They temper this concern by pointing out that the Thoroughbred breed has been highly inbred from its founding.

Evelyn Todd et al’sFounder Specific Inbreeding Depression…”  analyzed a large sample of Australian Thoroughbred runners using pedigree analysis and was among the earliest research to analyze (a much smaller sample) using genomic analysis.  They contributed useful discussions pertaining to “gene purging” (using selective breeding to rid a population of unwanted genes), but their findings did not definitively support either the selective breeding or mutational load camps.

More recent analyses of geneticists provide the most cogent discussions of trends in inbreeding in Thoroughbreds.  In February of 2020, a genome-based study authored by McGivney et al reported results on trends in inbreeding complementary to our and Binns’ analyses.  The McGivney paper is more reliable than either our paper or the Binns’ analysis for three reasons.

  • It uses a much larger sample.
  • It is based solely on genomic analysis. Because gene transmission is somewhat random and pedigree-based analysis cannot adequately assess random transmission, genome-based analysis of inbreeding better measures degrees of inbreeding.
  • Genome-based analysis considers the cumulative effects of inbreeding rather than focusing only on recent incremental inbreeding.

The McGivney study was especially interesting because most of its authors had connections to PlusVital, the equine genetics firm commissioned in 2019 to provide “expert genomics advice” to the Jockey Cub.  The McGivney paper definitively confirmed the consensus of industry observers that inbreeding has been increasing in the Thoroughbred breed and expressed concern about that trend.  However, the Jockey Club’s decision to impose a 140-mare limit on stallions was almost certainly viewed by PlusVital as a “blunt instrument” solution not at the top of PlusVital’s recommendations.

While the McGivney paper can perhaps be characterized as viewing selective breeding uninformed by genomic analysis and as a “blunt instrument” in trying to guide breeding decisions, the contributions of Dr. Ernest Bailey and his co-authors are more optimistic that selective breeding can lead to good breeding decisions.  Bailey says that “…inbreeding is actually the process of selective breeding…for good genes…and against bad genes, and so the process results in a steady increase in inbreeding and a steady decrease in genetic diversity.  That’s how you end up with an improved population.”

For a detailed discussion of this topic, access

Robert L. Losey can be contacted at

Horse Racing Business 2020


  1. It may be a “blunt instrument,” but it’s worked for quite some time. Still, it’s always good to see that genomic analysis is improving the genetics of thoroughbreds.