The Equine SNP Chip
In the middle of January on PLOS One, the paper that outlined the development of the Equine 50K SNP chip was released. The chip, or genotyping array, was actually developed back in 2008 and since that time they have gone on to add another 11,000 SNP's to another chip tabbed the Equine 70K chip (even though it only has ~65,000 usable SNP's), which was the technology that we used to complete our genome wide study on athletic performance in thoroughbreds and in turn create the genetic component of the Sales Select report. The 50K equine SNP genotyping array was developed and evaluated on a panel of samples representing 14 domestic horse breeds and 18 evolutionarily related species including a thoroughbred named Twilight. This array, and the subsequent 70K SNP chip, now allows researchers to compare groups of horses and look at what makes one group different from another at a genomic level and it is how researchers are currently starting to work their way down to what variations within genes cause diseases like laryngeal paralysis, wobbler syndrome, heaves, etc.
The chip also allowed the authors of the paper to show the level of inbreeding and linkage disequilibrium (LD occurs when genotypes at two loci are not independent of another) that occurred in each of the breeds. Of the 14 breeds studied, the extent of LD and the level of inbreeding were highest in the Thoroughbred and lowest in the Mongolian and Quarter Horse. The authors noted that the high LD and inbreeding in the thoroughbred is reflective of the breed's low diversity, high inbreeding, and closure of the studbook to outside genetic influence for more than 300 years. Previous work has demonstrated that approximately 78% of Thoroughbred alleles are derived from 30 founders, and that a single founder stallion is responsible for approximately 95% of paternal lineages. Now, before anyone starts jumping to any conclusions and starts thinking that we are breeding ourselves to oblivion, two things need to be noted about this:
1) While it was the most inbred of the 14 breeds studied, the Thoroughbred is not, at this present time, in danger of a fitness depression through lack of genetic diversity (like say the Irish Draught has been). There have been two other papers that have used the same 50K SNP chip to discuss the concept as it relates to the thoroughbred itself. The first paper, based on ~450 horses noted that the inbreeding in Thoroughbreds has increased over the past 40 years demonstrating that there is a highly significant, though relatively weak correlation between the year of birth and inbreeding coefficients. The authors noted that the majority of the increase in inbreeding is post-1996 and coincides with the introduction of stallions covering larger numbers of mares. The second paper, completed on ~800 thoroughbreds, noted a similar increase in LD (interestingly this paper did note that because of the high level of LD in the thoroughbred, it was a good model for selection by using genomic techniques). Both papers noted that inbreeding and LD is high, and increasing in the thoroughbred and it should be something that we should monitor to ensure that we are not getting too inbred, but we are not at the point of genetic fitness concerns.
2) The level of inbreeding is not the cause for the apparent lack of soundness in the breed in North America. There are a number of people that believe (some in almost manic fashion that defies belief unless you read/hear what they say!) that inbreeding equals unsoundness and there is just not the evidence to suggest this at this time. The thoroughbred in North America may well be apparently less sound than it was in the past, and certainly less sound (in terms of starts per horse and breakdowns/fatalities per runner), but to pin this on the rising level of inbreeding is a long bow to draw. What is more probable is that as we have selected for speed, we have been selecting for variants within genes that either confer unsoundness or when interacting with environmental considerations (how they are raised, feed, etc) creates genetic expression that results in unsoundness, which makes unravelling the genetic components of unsoundness and athleticism a challenge to come.