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MtDNA and Stud Book Errors - an interesting find.

Over the last few months, along with our performance panel and some other new SNPs we are testing, we have been sequencing mitochondrial SNPs to examine just how correct the General Stud Book really is.

It will come as no surprise that there are errors. Quite a few of them in fact, but many of them are deep rooted and a lot of the more popular families, like say the 1-x Bruce Lowe branch, that of La Troienne (pictured above) is extraordinarily well conserved and a testament to everyone who breeds thoroughbreds and the stud books around the world.

The errors however are quite interesting.

One of the horses we have sequenced is Bachelor Pad (2012 c, Bachelor Duke x Flying Firebird). According to Stud Book records, his third dam Ardee One (NZ) was a non-stud book mare bred in 1979 who gained entry into the New Zealand Stud book after she won the Railway Handicap (gr.I) and her granddam Stradella threw three stakes winners including the Perth Cup (gr.I) winner Ullyatt.

When Ardee One achieved Stud Book status her matriline was assigned the Lowe/Bobinski/Shirai number of Colonial Family 76. While Equineline and Arion terminate her tail female line at Pleasure Craze, a mare bred in 1926, her official tail female pedigree by General Stud Book records terminates at the 6th dam, identified only as a mare by Freedom (NZ 1887).

This is however where the lines get murky and where mitochondrial DNA shines a light on pedigree research that some may not like. a well used resource for many in the Thoroughbred industry had assigned Ardee One (up until the information we had came to light) as the 12-c family by naming the "mare by Freedom" as Hinerewa (NZ 1907 by Freedom out of Black Watch).

When we sequence the mitochondrial DNA we use the nomenclature proposed by Achilli, et al. If Bachelor Pad (NZ) was indeed from the 12-c family he would have the same haplotype as many of the other samples of the 12-c family that we have, that of the "L1" haplotype. The sample from Bachelor Pad (NZ) however comes from the "L4" haplotype so he isn't from the same haplotype as the rest of the 12-c family indicating that his female line descends from a different mare.

So we can establish that the Ardee One female family isn't from the 12-c family but that is only half of the story.

Hinerewa (NZ), who was supposed to be the ancestress of Ardee One was out of the mare Black Watch (NZ 1898 Tasman) and was owned by Auckland Veterinary Surgeon W. C. Ring and his father at their Hinuera Stud along with the stallions Freedom and Valkyrian. Again according to all three sources - PedigreeQuery, Arion and the official Jockey Club Equineline site, the pedigree of Black Watch (NZ) traces back to Maynell (or her granddaughter the Blank Mare (GB) of 1759) who was assigned by Lowe as the source of the 12-c branch of the #12 family.

Obviously if that was the case we would see that any descendant of Black Watch (NZ) through her female family with the same "L1" haplotype shared by most of the other 12-c samples that we have. We also have a sample sequenced from the 2014 Bullbars x Snadame colt who by Stud Book records traces to Black Watch via Hinerewa's half-sister Keep Watch (NZ 1913 Flagfall x Black Watch). That sample doesn't match up with 12-c (L1) or with Bachelor Pad (L4) with this one having the "I" haplotype.

So what does this all mean? Well, there are a few errors in stud book records that render deep pedigree analysis pretty meaningless (so when someone starts going on about something in the 12th generation of a pedigree, its time to tune out as that far back there are errors everywhere!).

Historical corrections aside, there is some significance in accurately knowing what mitochondrial haplotype a mare is actually from as it will help in terms of breeding outcomes. If you take a look at last weekend's Pellegrini (gr.I) winner, Sixties Song (ARG), he's by Sixties Icon - grandson of Sadler's Wells, and the dam of Sixties Song has a half-sister that's produced three stakes winners by Kitten's Joy - grandson of Sadler's Wells, who hadn't run when the Sixties Song mating was done (thus there was no "lead" for the breeder of Sixties Song to go off when planning that mating).

The 6th dam of Sixties Song is Pange. If we look at her pedigree and the descendants from her we have- G1 Sixties Song - by a Sadler's Wells line stallion Bobby's Kitten - by a Sadler's Wells line stallion Theatrical - by Nureyev, a 3/4 brother to Sadler's Wells Startac - by Theatrical G2 Camelot Kitten - by a Sadler's Wells line stallion G3 Charming Kitten - by a Sadler's Wells line stallion Fort Prado - by a Sadler's Wells line stallion SW Major Magic - by a Sadler's Wells line stallion Queen'splatekitten - by a Sadler's Wells line stallion Megantic - by Theatrical Approximately 23% of the graded/group winners and 28% of G1 winners are sired by the Sadler's Wells/Nureyev male line from this direct female family.

That is why knowing the mitochondrial haplotype that your mare comes from is relevant as there are immediate ancestors (within 3-4 generations) that appear in higher frequency in stakes winners from one haplotype than they should and thus look to be positive contributors to stakes performance for horses from that particular haplotype.

Food for thought for broodmare owners and stud book authorities alike.

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