US Arabian Horse Registry has marked in the On Line Stud Book all known horses registered as Purebred Arabian but proven by testing to carry Thoroughbred DNA as INELIGIBLE for registration and their progeny as well as all progeny of the excluded stallions named by HARC.
Ralph Clark at age 29 was hired on at the Registry as the new field secretary. Later years when asked if the Arabian Horse Registry of America (AHRA) would use DNA testing for parentage verification or as a way to determine “breed purity,” Registrar Ralph Clark responds, “Our only focus is on parentage verification. By multiple generations of parentage verification you don’t have a breed purity issue. The ISAG [International Society of Animal Genetics] agrees this is the only effective way to do this.” copyright 1995 by Robert J. Cadranell from Arabian Visions Mar/Apr 1995
EXCERPT: Samantha Brooks: “What we found in these samples was not that much Arabian ancestry was part of the Thoroughbred line, but the opposite: that Thoroughbred DNA exists in most of the modern racing Arabian lines, indicating a more recent interbreeding within this group,” Brooks said. “I can’t speculate on the how or why, but this is clearly the story the DNA is telling us.” Another implication of this study, Brooks said, is the potential to identify the genetic regions that determine some of the Arabian’s unique traits, like their facial profile. This could be expanded to identify the marker for other horse breeds’ head shapes, for example. Some critics argue that the lines bearing Thoroughbred influence should be made public—something Brooks said her team refuses to do—and removed from the registry. “Deregistering these horses all at once would not have good outcomes for the welfare of these beautiful animals,” she said. “And anyway, the issue is widespread enough that there wouldn’t be much of the racing population left. These data document a Thoroughbred breed influence much more expansive than most people realized. It’s just everywhere, really.”
AMER – Amer was recently discovered to not, in fact, be a Purebred Arabian.
A genetic mutation specific to a single Thoroughbred stallion, Whalebone, was discovered to have been passed on by Amer. This means he had a TB sireline, NOT an Arabian. He was bred in Saudi Arabia, and exported to Qatar before he was registered. He was also registered in the French Stud Book, SBFAR. He sired hundreds of foals, and has hundreds of “purebred” sons who are now airing more foals, and these are all still being registered as purebred; the problem is being swept under the rug.
Amer, the best “Purebred” Arabian stallion in the world, died at the age of 33 (IN 2017). Born in 1984, he was a very good racehorse, especially over the mile. But it is as a sire he became famous. In the history of racing, he is the stallion that produced the biggest number of Group race winners, just like Galileo did in the Thoroughbred studbook. A huge breeding impact. The offspring of Amer has won more that 130 Group races, including 80 Group I’s. He is the first sire to achieve that number. Around the world, hundreds of his sons are used as stallions in studs. Seven Qatar Arabian World Cup Winners are sons or grandsons of Amer. In France, for the 2016 racing season, he was the leading sire. His sons Dahess, Af Albahar and Majd Al Arab, were second, fifth and eighth in the same stallion ranking. In 2017, he was available at a record stud fee for a Purebred Arabian sire (€ 40.000).”
This link carries a photo of Amer and the following blurb: The Saudi-bred, Qatari-raced, UK-owned ‘Arabian’ stallion Amer (1984, Wafi x Bushra) has apparently been confirmed to carry a Thoroughbred sireline, tracing back to the TB group Tb-dW1, which according to this study links back to the Darley Arabian through his sireline descendant, Whalebone. This mutation is unique to Whalebone himself, and therefore it cannot be said that the presence of Tb-dW1 comes from the Darley Arabian and is therefore natural to the Arabian gene pool. The Genetic Diversity Study removed the word “apparent” making it IS in reference to Amer carrying the TB DNA of Whalebone.
In the US, Amer blood: his sons, ASSY, KASIH, AF ALBAHAR, AMARETTO, DARWEESH, AND HIS SON, VALIANT BOY SBFAR, GAZWAN, SIR BANI YAS, MU’AZZAZ, MAJD AL ARAB with his imported son, RB EPIC (AHR 683018), GENERAL, RATHOWAN, DAHESS and his son AL MOURTAJEZ, as well as Dahess daughters to name a few, TU SHAA, TOP THESS, THESS IS IT, TAYLORS TOUCHOF CLASS, ALL N ALL, and many more from these stallions and the daughters of Amer with their foals in the US: SHEHAADA, MA’MA’AH, ALWIYA and FARAB SBFAR.
This Amer blood is being crossed on the Burning Sand daughters and daughters of the sons of Burning Sand. Several times Burning Sand has been bred to his own daughters making the blood 75% Burning Sand. Burning Sand is the only American bred Race Arabian Sire excluded from the HARC accepted bloodlines for Purebred, Authentic, Arabians.
FRENCH RACE ARABIAN SBFAR STUD BOOK
The US has long had many horses registered as Purebred Arabian which carry the DNA genetic blood of stallions excluded from HARC. USAHR has included the requirements for any of these excluded stallions and their progeny to be recognized as Purebred Arabian. This is discussed at length on the webpage Thoroughbred DNA and USAHR.
MORE GENETIC INFORMATION AND THOROUGHBRED DNA TESTING RESULTS – MORE OF SAMANTHA BROOKS DIVERSITY PAPER
The results confirmed what had previously suspected by many: 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 Whalebone (across multiple breeds) had a unique Y Chromosome mutation 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).
Whalebone: The “Adam” of the modern Thoroughbred AND THE STALLION WHO CREATED AMER , THE RACING ARABIAN SIRE – see more on Whalebone under Haploid DNA testing. DNA tests show Whalebone to not be of the Godolphin Arabian sire line but that of the Byerley Turk sire line. Whalebone’s sire, the bay 1793 Derby winner Waxy, grandson of Eclipse and from a Herod mare, was a successful sire of sires and broodmares.
The immortal sire & broodmare sire of the founding family 3m. Whalebone – 19 x’s via Jigg, Basto, mares family 1 and 3, or family 27? Whalebone, winner of the Newmarket Stakes & the Derby on his first 2 appearances later became a formidable campaigner in four mile events with weights up to 12 stone. He stood no higher than 15 hands & 1/2. The Petworth groom states: the lowest & longest & most double-jointed horse, with the best legs and worst feet that I have ever seen. Small, insignificant he becomes an enormous influence. ⇒ Sire of Camel, Sir Hercules and Defence. Sir Peter Teazle – deep body, powerful shoulders & quarters, a short neck and a large head. His coat, dark brown to a prominent white star to his forehead. His stock mostly the richness of brown. Great constitution and they required very strong work. Full sister to Brown Bess dam line to Sister One True Blue, family 3. https://thethoroughbredlink.com/2020/11/28/byerly-turk-selective-history/
During the past 300 years HG Tb was extensively spread by the English Thoroughbred. The Thoroughbred sire lines trace back to three founder stallions that were imported to England at the end of the 17thcentury. Here, we fully resolved the heritage of the Thoroughbred sire lines with MSY haplotyping. The haplotype structure of 65 males was highly consistent with their paternal genealogy inferred from the pedigree. We now clearly discriminate discrete sublines of Darley Arabian, born in 1700 (Tb-d) and Godolphin Arabian, born in 1724 (formerly Tb-g, now Tb-oB3b). The third founder, Byerley Turk, born in 1680, was newly characterised by an allelic variation of the tetranucleotide microsatellite fBVB (GATA14/GATA15; Supplementary Table S8) that defines the Tb-oB1 clade. According to pedigree information only few of the tested males trace back paternally to Byerley Turk. We thus screened a representative dataset of 109 purebred males by genotyping fBVB and detected allelic variation of fBVB only in Tb clade horses (Supplementary Table S9). All 30 patrilineal descendants that coalesce in Herod, born in 1758, whose ancestry in turn traces back to Byerley Turk, carried the Tb-oB1 specific allele 208 (Supplementary Table S9). We also confirmed Tb-oB1 in eleven horses tracing back to St. Simon, born in 1881. According to stud records, St. Simon was the son of Galopin, born in 1872, who was sired by Vedette, born in 1854. The line should trace back to Eclipse, born in 1764 (Fig. 3) according to stud books. All descendants of St. Simon carry Tb-oB1, undoubtedly the HT of Herod (Fig. 3), and not that of Eclipse (Tb-dW*). Thus, an incorrect paternity assignment must have occurred in this lineage. http://www.tbheritage.com/Portraits/Whalebone.html and https://www.performancegenetics.com/single-post/2013/04/10/Whalebone-The-Adam-of-the-modern-Thoroughbred
MUCH OF THE FOLLOWING IS VERY TECHNICAL AND CARRIES THE RESULTS OF SCIENTIFIC PAPERS IN 2019, 2020
Genetic Study Challenges Common Beliefs By Mark Andrews
Here we studied 378 Arabian horses from 12 countries using equine single nucleotide polymorphism (SNP) arrays and whole-genome re-sequencing to examine hypotheses about genomic diversity, population structure, and the relationship of the Arabian to other horse breeds. We identified a high degree of genetic variation and complex ancestry in Arabian horses from the Middle East region. Also, contrary to popular belief, we could detect no significant genomic contribution of the Arabian breed to the Thoroughbred racehorse, including Y chromosome ancestry. However, we found strong evidence for recent interbreeding of Thoroughbreds with Arabians used for flat-racing competitions.
RFMix analysis of outcrossing to the Thoroughbred.
We used RFMix26 to explore the genetic relationship among Arabian horses used for flat racing competitions and the Thoroughbred breed (analysis data set: 293,293 SNP genotypes from 335 samples). We detected genomic segments of Thoroughbred origin totaling from 2% to 62% of the genome in racing Arabians. In some registered flat-course racing Arabian horses, near full length chromosomes appear to originate from Thoroughbreds.
We included data from Icelandic horses as a negative control, as any contact between Icelandic and Arabian horses in the last 1000 years would be extremely unlikely given the recorded history of these two breeds. As predicted, we found negligible evidence for shared ancestry between the Icelandic horse and Arabians (1% overall).
We also included samples of Turkemen horses from Iran (including individuals of the Akhal-Teke breed, a descendant of the extinct Turkoman horse) as a reference group, given previous studies that have suggested that the Arabian is closely related to these populations, and the possibility of admixture, given the overlapping historical geographic ranges of these two populations. However, we observed minimal local ancestry assignment to the Turkemen reference group (2% overall). The autosomal admixture patterns illustrated by the RFMix analysis strongly indicate that some modern flat-course racing Arabians have recent Thoroughbred ancestry in their heritage.
A study involving Arabian horses from 12 countries has found that some populations maintained more genetic diversity and that the breed did not contribute genetically to the modern-day Thoroughbred, contrary to popular thought. An international team of scientists was led by the University of Florida’s Samantha Brooks, and Doug Antczak and Andy Clark at Cornell University in New York. The group collected and examined DNA samples from 378 Arabian horses from Qatar, Iran, United Arab Emirates, Poland, United States, Egypt, Jordan, Kuwait, United Kingdom, Australia, Denmark, and Canada. The research is published in the journal Scientific Reports.
Other than the horse’s location and whether it was used for endurance, racing, or showing, the samples were anonymized for data analysis purposes. The researchers also incorporated information gained in previous studies, which included breeds such as Thoroughbred, Persian Arabian, Turkmen, and Straight Egyptian. “The Arabian horse has a special mystique due to the long-recorded history of the breed,” Brooks said. “Arabian horse breeders in particular know their horse’s bloodlines many generations back. What we found was that in the area where this breed originates — likely the near East region, but we don’t know exactly — there’s a healthy level of diversity. This is particularly evident in populations from Bahrain and Syria, which suggests these are some pretty old populations.”
The Arabian is prized for characteristics such as heat tolerance and endurance, as well as its unique appearance, with a dish-shaped facial profile, wide-set eyes, an arched neck, and a high tail carriage. It has been exported from its ancestral homeland for centuries, with some modern lineages drawn strictly from these smaller genetic pools, giving the breed a reputation for inbred disorders. While this was true for some groups they tested, Brooks noted, they also found remarkable diversity when considering the breed as a whole. Brooks contrasted the discovery of more diverse populations with the samples they received from racing Arabians. Another longstanding myth says that the Arabian contributed genetically to the modern Thoroughbred, but the racing Arabians’ DNA told a different story. The research team found little influence of the Arabian in the modern Thoroughbred’s DNA.
The study has a long list of co-authors, with contributors from the University of Tehran, Iran; Weill Cornell Medical College in Qatar; the University of Kentucky; the University of Agriculture in Kraków, Poland; the Hong Kong Jockey Club; the Equine Veterinary Medical Center in Doha, Qatar; and the University of Veterinary Medicine Vienna, Austria. Elissa Cosgrove from the Clark lab and Raheleh Sadeghi, a visiting scientist from Iran in the Antczak lab, shared first co-authorship of the study. “An exceptional aspect of this project was the wonderful level of open collaboration and sharing of resources by veterinary geneticists, equine scientists, and horsemen from around the world,” Antczak said. “It was a great pleasure to conduct this global study for the benefit of the horse.” For more details, see Genome Diversity and the Origin of the Arabian Horse.
Published with the kind permission of Mark Andrews, Equine Science Update.
The research, published June 16 in the journal “Scientific Reports,” was conducted over an 8-year period, beginning in 2014 before Brooks made the move from Cornell to UF. The process was a lot of effort, she said, in part due to traveling to collect the Arabians’ blood and hair samples, as well as natural delays in working with international colleagues to collect and ship other samples. The research was funded by a grant from the Qatar National Research Fund with additional support from the Harry M. Zweig Memorial Fund for Equine Research, Arabian Horse Foundation, Animal Health Foundation, associated with Humane Society of US, Dorothy Russell Havemeyer Foundation, Inc., and a Meinig Family Investigator award.
Y chromosome haplotyping.
Given that RFMix analysis identified recent admixture of Thoroughbred genomic regions into present-day Arabian horse genomes, we explored the sire-dam direction of interbreeding by examining the Y chromosome haplotypes of selected male Arabian horses used for show or racing competitions, using recently published methods. The 29 non-racing Arabian horses all carried one of three Y haplogroups previously associated with Arabian horses.
The two most common haplogroups, Ao-1 and Ao-2, were previously documented as ancestral to modern Arabian horses. The Ta haplogroup is genetically more similar to haplogroups of modern Thoroughbreds, but is only observed in Arabians. Notably, only two of the 10 male race-use Arabian horses examined carried any of these three Arabian Y haplogroups (Ao-1, Ao-2 and Ta).
Five of the race-use horses carried the Tb-oB1* haplogroup attributed to the “Byerley Turk” foundation sire of the Thoroughbred breed. Tb-oB1* is found within a variety of breeds and lineages, including the Turkomen. Therefore, these five horses may carry Y chromosomes derived from ancestors common to both racing Arabians and the Thoroughbred breed.
However, the remaining three racing Arabian horses carried the Tb-dW1 haplogroup, also known as the Whalebone haplotype. The mutation leading to Tb-dW1 occurred around 1829, after the establishment of the Thoroughbred studbook, and is linked to the “Whalebone” sire line within the modern Thoroughbred breed. Tb-dW1 in Thoroughbred horses has not been reported previously in modern Arabians.
The presence of Thoroughbred-specific Y chromosome haplogroups among Arabian racehorses indicates that the large chromosomal blocks of Thoroughbred origin detected in flat racing Arabian horses are likely derived, at least in part, from crosses with Thoroughbred stallions that occurred after the emergence of the “Whalebone” haplotype in the 1800’s.
” the y chromosome in Amer’s offspring displaying the same unique genetic mutation that characterizes the offspring of the English Thoroughbred stallion Whalebone. This mutation is not present in the y chromosome of other English TB male descendants of the Darley Arabian. The Darley Arabian is the sireline for Whalebone, and the main foundation sireline of the English TB breed overall.” Edouard Aldahdah daughterofthewind.org/genetic-study-on-english-tb-ancestry-of-amer/
Y-chromosome haplotypes were determined by genotyping 14 key Y-chromosomal variants using LGC KASP® technology. Because the Y-haplotyping procedure requires both higher quality and a larger quantity of DNA, we were only able to perform Y-haplotype analysis for five of the 12 male racing Arabian samples included in the RFMix analysis and 11 of the male non-racing Arabian samples. In order to strengthen the analysis, we conducted the Y-haplotyping analysis for new samples from five male racing Arabians and 18 male non-racing Arabians.
For more than 100 years the influence of Arabian horses in “improving” other horse breeds has been generally accepted among horsemen, the study team said. “The best-documented example of such influence is in the pedigree of the Thoroughbred breed, which has been maintained as a Stud Book since 1791.
In a pedigree-based analysis of founder lines of the Thoroughbred, three stallions imported to England from the Middle East around the turn of the 18th century remain major contributors to the modern-day Thoroughbred gene pool: the Godolphin Arabian, estimated to contribute 13.53% of the modern gene pool by pedigree analysis, as well as the Darley Arabian, and the Byerley Turk.
Recently however, Y chromosome analysis has indicated that the Y haplotype of the Darley Arabian actually originated from the Turkoman horse, an ancient breed from the Middle East and Central Asia that is like the Arabian Horse — also an “Oriental” type breed.
They found significant differences between all Arabian subgroups examined in the study. Three subgroups of Arabian horses segregate uniquely, they said: the Straight Egyptian, the Polish Arabians, and the horses from Saudi Arabia. “This finding agrees with the written histories of these groups, characterized by closely controlled breeding of these lineages over the past 200 years.”
Previous study which would be PEER Relavent
The identity of the probed animals will remain anonymous
Partbred Arabians show an even mix of several HTs, mostly “Arabian” HTs (Ao*, Ao-aA*, Ta*) but also others like Tb-oB* and Tb-dW. Per definition, Partbred Arabians need an Original Arabian, Shagya-Arabian or Anglo-Arabians ancestor in the second generation of their pedigree, no matter which breed they were mated with. However, the pedigree of the tested horses claimed that their paternal ancestors were all Arabians. If the pedigrees are correct, even those Partbred Arabians should not have HT Tb-dW1 or Tb-oB*, as these HTs indicate a Thoroughbred or Akhal-Teke ancestry (Wallner et al. 2017).
This work aimed at revealing the genetic background and diversity of Omani Arabian horses by comparing them with Arabian horses from a diverse genetic background. To that end, we genotyped 63 randomly sampled Arabian horses from Oman using the Illumina Equine SNP70. For comparison, SNP genotypes of 12 Saudi Arabian horses, 27 French, 77 Egyptian, 11 Polish and 36 US Arabians were included in the study. We additionally included 17 Thoroughbred horses and 21 horses representing large and small breeds as an outgroup. Our MDS analysis and phylogenetic analysis showed that the Arabian horses in Oman cluster primarily with French Arabian horses, with a few horses clustering within the Polish/US Arabians. The French Arabian horse cluster was the closest to the Thoroughbred horses.
Part of the study above: https://www.squ.edu.om/research/Research-Output/Latest-Research-Highlights/ArticleID/598/Madyanm-SQU-host-traqining-to-manage-industrial-waste-water
“In line with our expectations, no pure Omani Arabian bloodlines exist today in Oman. This was confirmed both by the horse owners as well as the MDS analysis. The average genomic inbreeding levels in the French and Omani Arabian horses (-0.009 and -0.05) were the lowest compared to the Egyptian (0.156), Polish (0.05) and US Arabians (0.043).
Analysis of Arabian stallion lines with Y chromosomal markers paper 2019 by Eva Michaelis. This scientific paper deals with Poland, Germany, Austria and Babolna (Hungary) https://www.vetmeduni.ac.at/hochschulschriften/diplomarbeiten/AC15615171.pdf
All the sires in this paper are from either the 1800’s or early 1900’s with the exception of Amer, who is named and the Shagyas. She goes into detail on the importance of the Y Chromosome. Haplotype is covered extensively. Of the 63 samples, 19 samples were assigned to Ao* and 44 to Ao-aA. Horses from seven stallion lines show HT Ao, namely those founded by Hadban, Kidwan al Harzan, Krzyżyk, Kuhailan Kharas, Mirage, Shuwayman Sabbah and Telmese. Lines founded by A Saglawi DB, Felhaan Alshawaf, Hadban (Ibn Galal), Ibrahim, Ilderim, Koheilan Adjuze, Mahmoud Mirza and Saglawi I mainly carried Ao-aA. However, in the Saglawi I line there were also three samples with HT Ao and one with Tu. In the A Saglawi DB line one sample was assigned to HT Ta and one from the Ilderim line to Ta-a*. Table 16 provides an overview of the number of samples that were examined for each stallion line and their respective HTs.
3.2.2 Haplogroup Ta
HG Ta was found in 30 samples, representing nine stallion lines. If both, the sPZ and the sPY assay, showed the derived allele (sPZ_1 and sPY_1), which was observed in seven samples, they were summarized as Ta-a. 23 samples had the derived allele at sPZ but the ancestral allele at sPY, they therefore cluster at Ta. The stallion lines which showed the Ta* HT were founded by Dahman-Amir, Hamdani Semri (except for one sample with HT Ta-a), O Bajan, Shagya, Souakim and one sample from A Saglawi DB line, a line mainly showing Ao-aA. The seven samples showing Ta-a* represented the lines Bairactar, Hamdani Semri, Mersuch and one sample assigned to Ilderim (Sample Y_PR_02_009), a line mainly showing Ao-aA*.
3.2.3 Other Haplotypes
A few samples showed HTs previously not assigned to Arabians. One sample clustered as Tu, two as Tb-oB and four had Tb-dW1. P090273 from the Saklawi I line was assigned the Tu* HT (rA_1, sPZ_0 and rT_1). The two samples clustering at Tb-oB* were one from the Hamdani el Samra line (P112348) and one from the Kuhailan-Abu-Urkub line (Y_PR_05_116). Both samples showed the derived alleles at the rA and rB locus, yet all other possible assays of this part of the phylogenetic tree yielded the ancestral alleles. Four samples clustered at HT Tb-dW1. They carried the derived alleles at rA, rB, rC and rD. Two were descendants of the stallion Amer (Y_PR_05_137 and Y_PR_05_138) and the only two samples of this line. Sample Y_PR_05_039 descended from Kuhailan-Abu-Urkub (the other sample of this line showed the Tb-oB* HT, as mentioned above).
HG Ta was split into two subgroups: Ta* and Ta-a*. Felkel et al. (2018) found HG Ta in a single Arabian sample and identified three markers that determine this HT. Two of these markers (sPY and sPZ) were tested for and all samples that were found clustering in HG Ta carried the derived allele of sPZ (sPZ_1), but only some of them had the derived allele at sPY (sPY_1). Deep pedigree reconstruction suggests that the enormous impact of Nazeer (born in 1934; a descendant of Saklawi I) is responsible for the high frequency of HT Ao-aA* amongst Original Arabians bred in Europe.
. . . the pedigree of the tested horses claimed that their paternal ancestors were all Arabians. If the pedigrees are correct, even those Partbred Arabians should not have HT Tb-dW1 or Tb-oB*, as these HTs indicate a Thoroughbred or Akhal-Teke ancestry (Wallner et al. 2017). As long as no Thoroughbred stallion is introduced to the line, the male offspring will have an ‘Arabian’ HT. In the paper from 2017, Wallner et al. described the HT Tb-dW1 as specific for a widely distributed English Thoroughbred line tracing back to the stallion Whalebone (1897), while TboB* (in their paper referred to as basal HT Tb) was also found in horses tracing back paternally to the English Thoroughbred founder Byerly Turk (1680) as well as other breeds, especially the Akhal-Teke. The Akhal-Teke is the remnant of the influential and now extinct Turkoman horse.
This study has been approved by the Ethics Committee of the University of Veterinary Medicine in Vienna regarding the Guidelines of Good Scientific Practise and the national law. The identity of the probed animals will remain anonymous.