In mammals, an individual’s sex is determined by the chromosomes it inherits from its parents. Two X chromosomes lead to a female, whereas one X and one Y lead to a male. Y chromosomes are only passed from fathers to sons, so each Y chromosome represents the male genealogy of the animal in question.
In contrast, mitochondria are passed on by mothers to all their offspring. This means that an analysis of the genetic material or DNA of mitochondria can give information on the female ancestry. For the modern horse, it is well known that mitochondrial DNA is extremely diverse and this has been interpreted to mean that many ancestral female horses have passed their DNA on to modern horse breeds. In the Thoroughbred there are ~17 different mitochondrial haplotypes that make up the commercial breed (there are approximately 33 in the entire breed, but many are non-commercial and small in terms of overall representation).
Until recently, though, essentially no sequence diversity had been detected on the Y chromosome of the domestic horse. Not only does the lack of sequence markers on the Y chromosome make it impossible to trace male lineages with confidence, it also represents a scientific paradox. How can a species with so many female lines (all breeds, not just Thoroughbreds) have so few male lines? This gap has been filled by Barbara Wallner and colleagues at the University of Veterinary Medicine, Vienna, who present information on the genetic variability in the horse Y chromosome and show how various breeds of the modern horse are interrelated. The paper "Identification of genetic variation on the horse Y chromosome and the tracing of male founder lineages in modern breeds" by Barbara Wallner, Claus Vogl, Priyank Shukla, Joerg P Burgstaller, Thomas Druml and Gottfried Brem can be read by clicking here.
The results confirmed what had previously suspected by many: that the Y chromosomes of modern breeds of horse show far less variability (only five positions turned out to be variable) than those of other domestic animals. An examination of over 600 stallions from various equine breeds showed that the horse could be grouped into just six Y Chromosome haplotypes which is an incredibly small number. Reflective of pedigree records and previous studies by Cunningham et al, in turns out that in terms of the modern Thoroughbred, the Y Chromosome is dominated by Eclipse, or more specifically his great grand-son Whalebone, and that Whalebone (across multiple breeds) had a unique Y Chromosome mutation that identified him and his sons as a separate Y haplotype altogether when compared to other descendants of Eclipse (as well as in descendants of the less popular Matchem & Herod sirelines).