A decade ago Emmeline Hill, Dr Patrick Cunningham and others from the Trinity College in Dublin published a seminal paper on thoroughbred mitochondrial DNA. The paper, which caused some controversy at the time showed that the maternally inherited mitochondrial DNA (mtDNA) did not correspond with pedigree records, that is, as good a job that Bruce Lowe, Bobinski and Shirai had done, the pedigree records were inaccurate at some point in time. Hill found that almost half of the female families, which are each considered from pedigrees to have matrilines converging to one of >30 historically recognized female ancestors, contained sequences which were inconsistent with common descent. A great outline of what Hill's Study found can be found on the Thoroughbred Heritage web site here.
Following Hill's study, Dr's Harrison and Turrion-Gomez released another interesting paper in 2006 that outlined the performance aspect of mitochondrial DNA. Mitochondria provide energy for muscle contraction. Greater quantity of mitochondria per unit of muscle weight the greater the oxidative capacity of the muscle. As the thoroughbred is an athletic beast, and a lot of its performance relies on muscle (which dominates over 60% of its total mass), it is apparent that mtDNA variation cannot only limit elite performance, but that ancient mtDNA adaptive polymorphisms may be directly affecting maximum performance capacity. This is why actually getting the 'mtDNA families' corrected is important.
Harrison expanded on the 'errors' that Hill had found (some as late as the 1980's), but as he looked outside the d-loop (a select part of the mitochondrial DNA), he found that there were other areas in the mtDNA that not only suggested different female families, but differing performance levels also. Since Harrison's study (from which he patented some key findings), there has only been a few mtDNA studies in thoroughbreds. One of the more interesting ones was completed by Dr Mim Bower, et al, where they found that the horse known as Bend Or was in fact most likely to be another horse in Tadcaster (solving a long argued point by turf historians) and that the statue of Eclipse in the Royal Veterinary College was indeed his. Another interesting paper was completed by Bower, et al that showed that the thoroughbred owes its maternal lineage more to native Irish and British mares than it does to Arabians and other breeds.
This brings us to the latest paper, published today in Animal Genetics, that is the third paper to be published by Bower, et al in regards to mtDNA in Thoroughbreds. This paper looked at the mtDNA of 296 Thoroughbreds (the largest Thoroughbred mtDNA study yet), specifically the d-loop, to ascertain the matrilineal paternity of each of the horses. The study found 25 unique mitochondrial sequences which is considerably more than was found by Hill and Harrison, expanding the number of mtDNA families in the thoroughbred. The key findings were that only 6 in 10 Thoroughbreds in their sample shared the same mitochondrial haplotype as their pedigree suggested. That is, if you took 10 horses that should trace to the #1 family (Tregonwells' Natural Barb) only 6 of them actually do, the other 4 are from other haplotypes/families.
However, Thoroughbred sub-lineages are considerably more accurate than the actual families themselves. 9 in 10 of the thoroughbreds traced to the same sub-lineage family, that is, they had identical mtDNA to the sub-lineage founding mare. The breaking up of the families into sub-lineages (1,1a,1b,1c, etc) was rather arbitrary (indeed the sub lineage 1-x for La Troienne was proposed by Janeen Oliver in the 1990's and some, but not all databases have picked up this change) and there was no scientific reason behind doing this by Bruce Lowe and others. While this may have been done in a haphazard fashion, it turns out that it is a much more accurate way of identifying female families.
While this study is the most comprehensive done to date, it does not cover all of the female families in the stud book so there are some branches that have not been tested. However there are some interesting finds within the data provided by Bower, et al pointing to shared haplotypes in the breed and rather larger true mtDNA families.
It has been hypothesized that the #4 family is the same as the #2 family by turf historians, the mtDNA data does not support this claim.
Family #1 (Tregonwell's Natural Barb) is a bit of a mess. Firstly sub-branches that share the same haplotype to suggest that they are all from the same #1 family are 1-e, 1-k, 1-l, 1-n (part of the n branch), 1-s (part of the s branch), 1-t, the 16 branch of the 16 family and American family #1.
However, parts of 1-n (Chelandry), all of 1-p (Hilarity) and 1-u (Maid of the Glen) do not share the #1 haplotype, rather than shared by the mtDNA haplotype conglomerate #2/#8/#16. Therefore 1-n, 1-p and 1-u were founded from Family #2 or vice versa. This has considerable implications for pedigree analysis as 1-n, 1-p and 1-u all trace back to Web (1808) and the authors suggest that the error may have occurred there. If that is the case then the branch of La Troienne (1-s or 1-x depending on what chart you read) may not be from the #1 family, but from the conglomerate of #2/#8/#16. More testing would clarify this.
The conglomerate of #2/#8/#16 includes the sub-lineages of 1-p, 1-n, 1-u, 2-d, 2-e, -2-f, 2-i, 2-n, 2-o, 2-s, 6-e, 8-a, 8-c, 8-d, 8-h, 16-a, 16-c, 16-g, 16-h, 20 and 52. It is with noting that this is a rather large group of horses that includes some interesting branches including 6-e (Fenella) which is the same family as Selene ( dam of Hyperion).
Family 3 is sort of split. Branch 3-c has an alternate foundation mare that is shared with #18 and includes 3-c (Whisker mare), 18 (Old Woodcock Mare), 18-a and American family 48.
The other parts of Family #3 share commonality with some of #15 and #19 and includes 3-b, 3-d, 3-e, 3-g, 3-l, 3-o, 15-a (Venus) and 19-c (The Twinkle)
Families #4,#11 and #13 share a common founder. This is the same as what was found in Hill's study in 2002. The sub-lineages with this common founder are 4-c, 4-d, 4-j, 4-k, 4-l, 4-r, 11, 11-a, 11-d, 11-f, 11-g, 13-a, 13-b, 13-c.
Family 5 (The Massey mare) stands alone as a well conserved female family excepting branch 5-e (Belvoirina) which stands alone with a separate mtDNA haplotype.
Family #6-a is its own mtDNA haplotype, but 6-b,6-d and 6-f form share the same mtDNA as family #20 (Daffodil's Dam), 23 (Piping Peg's dam) and sub branches 23-a and 23-b. However, there are errors within the subbranches 23-a and 23-b with some of 23-b having its own haplotype and some of 23-a sharing the same haplotype as 21-a. 23-b is the family of 2012 KY Derby winner I'll Have Another although it is unclear if his branch is in the larger 6/20/23 group or in the smaller standalone 23-b group.
Families #7, #17 and #22 share the same mtDNA, specifically 7,7-a, 7-f, 17-b, 22,22-a, 22-b and 22-d. Interestingly in Hill's original study she suggested that 7,17 and 22 were also part of the 2/8/16 conglomerate but further analysis proved this not to be the case.
Family 8-c, that of the great sire Storm Cat, Royal Academy, Last Tycoon and Be My Guest, stands as a separate mtDNA family from the #8 family (in the 2/8/16 conglomerate).
Family #9 is rather split. One mtDNA family comprises of 9,9-a, 9-e and 9-f. The other parts including 9-c (Mumtaz Mahal) find themselves in another haplotype #2/#9/#12 which includes 2-f (Gone West's family), 9-b (part of it), 9-c, 12-c, 12-d, 12-f and American family #29.
Family #10, 14 and 42 share the same haplotype as does part of 9-b. The family is 9-b (part of), 10-a, 10-c, 11-g (Mandane), 14-a, 14-b, 14-c, 14-f and 42.
11-f, that of Sweet Solera and Honest Pleasure has its own haplotype separate to the 11 family.
12-b, that of the Champion Commando and Stimulus, has its own haplotype separate to the 12 family
Excepting part of 19-c which jumps in to the #3/#15 family and also part of family #20, Family #19 is quite well conserved.
Family #20 has some interesting branches to it. Firstly, branch 2-a (Ringbone) is part of it, as is part of 19-c falls into it also as does 20, 20-a, 20-c and 20-d indicating that this is quite a well conserved family.
British Family #4 is its own haplotype
British Family #3 is its own haplotype
Family #26 is its own haplotype
Family #25 is its own haplotype
The American families A1 and A4 actually trace themselves back to the #1 family (Tregonwell's Natural Barb). However the A4 branch has a mutation that actually makes it a branch unto itself in terms of identification.