Mapping the Thoroughbred in the Equine Mitochondrial Tree

Pedigree Matters

Deep-Rooted Anomalies
In Female Families

Equine Genetic Genealogy

The radial tree below visualizes the incremental differentiation due to spontaneous mutations that has occurred over the course of the last 100 to 300 thousand years* in the mtDNA type ancestral to all modern horses ("Modern MRCA", below) . The Thoroughbred encompasses no fewer than nine of the eighteen equine mitochondrial DNA haplogroups (A through R) that have evolved from that ancestral type. The tree is further populated by an array of modern breeds/types that's diverse, albeit incompletely so, native British and Iberians being under-represented among the available full sequences necessary for proper reconstruction of the tree.  The scarcity of Iberians, among others, in which group L is known from partial sequences to predominate, masks the fact that L accounts for 30-40% of the modern domestic horse population overall, commensurate with its share of the Thoroughbred population.  Only groups I and N account for a disproportionately greater share of the Thoroughbred than of the overall population.
*  The more recent limit of the date range was calculated using 2M ybp as divergence time between caballine and non-caballine equids, the more distant limit using 4M ybp  [1,8,12].

The Pot8os sequence was included with the gracious permission of the National Horseracing Museum at Newmarket and Alison Schwabe.

GanBank accession numbers for full mt TB sequences used: AP013101, KC202957, KC202968, KC203024,.KJ917256 through KJ917308, KT757764 ("Twilight"), KT221842. Placement of some of the historic TBs depicted above was validated by partial d-loop GenBank sequences HM581890, HM591893, HM581895, HM581897, HM581898, HM581900, HM581902, HM581903, and HM581904.  As no full mt sequences are available for TB haplotypes N1 and N1a, they were imputed from reported partial coding region and d-loop sequences[10, 11], as well as partial d-loop GenBank TB sequences AB329605, AB329607, AB329608, AB329610, AB329621, AF481305, AF481309, AF481323, EU580148, EU580156, EU580159, EU580168, EU580170.  Mitochondrial nomenclature follows Achilli et al. 2012 as expanded by Peng et al.2015 except where the classifications are defined solely by mutational 'hotspot(s)'. 

Phylogenetic analysis was conducted using MEGA version 6 (Tamura, Stecher, Peterson, Filipski, and Kumar 2013).

Published sources consulted additional to the relevant stud books:

1. Achilli A, Olivieri A, Soares P, Lancioni H, Kashani BH, Perego UA, Nergadze SG, Carossa V, Santagostino M, Capomaccio S, Felicetti M, Al-Achkar W, Penedo M C, Verini-Supplize A, Houshmand M, Woodward S R, Semino, O, Silvestrelli M, Giuliotto E, Pereira L, Bandelt H J, Torroni A: Mitochondrial genomes from modern horses reveal the major haplogroups that underwent domestication. PNAS USA. 2012 Feb 14;109(7):2449-54

2. Bower M A, Campana M G, Nisbet R E R, Weller R, Whitten M, Edwards C J, Stock F, Barrett E, O’Connell T C, Hill E W, Wilson A M, Howe C J, Barker G, Binns M. Truth in the bones: Resolving the identity of the founding elite thoroughbred racehorses. Archaeometry. 2012[A]. doi:10.1111/j.1475-2012.00666.x

3. Bower M A, Whitten M, Nisbet R E R, Spencer M, Dominy K M, Murphy A M, Cassidy R, Barrett E, Hill E W, Binns M. Thoroughbred racehorse mitochondrial DNA demonstrates closer than expected links between maternal genetic history and pedigree records. J Anim Breed. Genet. 2012[B]. doi:10.1111/j.1439.0388.2012.01018

4. Galtier N, Enard D, Radondy Y, Bazin E, Belkhir K. Mutation hot spots in mammalian mitochondrial DNA. Genome Res. 2006 Feb;16(2):215-22.

5. Hill E W, Bradley D G, Al-Barody M, Ertugrul O, Splan R K, Zakharov I, Cunningham E P. History and integrity of thoroughbred dam lines revealed in equine mtDNA variation. Anim Genet. 2002 Aug;33(4):287-94.

6. Kong Q-P, Salas A, Sun C, Fuku N, Tanaka M, Zhong L, Wang C-Y, Yao Y-g, Bandelt H-J. (2008) Distilling Artificial Recombinants from Large Sets of Complete mtDNA Genomes. PLoS ONE 3(8):e3016. doi:10.1371/journal.pone.00030

7. Lin, Xiang, Hong-Xiang Zheng, Allan Davie, Shi Zhou, Li Wen, Jun Meng, Yong Zhang, Qimude Aladaer, Bin Liu, Wu-Jun Liu & Xin-Kui Yao (2017): Association of low race performance with mtDNA haplogroup L3b of Australian thoroughbred horses, Mitochondrial DNA Part A, DOI: 10.1080/24701394.2016.1278535
(Ed. note: in the nomenclature of Peng et al. haplogroup[sic] L3b = L4a above)

8. Lippold S, Matzke NJ, Reissmann M, Hofreiter M. Whole mitochondrial genome sequencing of domestic horses reveals incorporation of extensive wild horse diversity during domestication. BMC Evol Biol. 2011, Nov 14, 11:328.

9. Peng MS, Fan L, Shi NN, Ning T, Yao Y-G, Murphy RW, Wang WZ, Zhang YP. DomeTree: a Canonical Toolkit for Mitochondrial DNA Analyses in Domesticated Animals. Mol Ecol Resour. (2015)DOI: 10.1111/1755-0998.12386

10. Rogers, B. Finding Tregonwell’s Natural Barb Mare. Bluebloods. Oct., 2014:30-35.

11. Rogers, Byron. CEO, Performance Genetics. Personal communications. 2017.

12. Vilstrup JT, Seguin-Orlando A, Stiller M, Ginolhac A, Raghavan M, et al. (2013) Mitochondrial Phylogenomics of Modern and Ancient Equids. PLoS ONE 8(2): e55950. doi:10.1371/journal.pone.0055950

2018 Judy Baugh