PEDIGREE ANALYSIS OF FOUR DECADES OF QUARTER HORSE BREEDING

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1 PEDIGREE ANALYSIS OF FOUR DECADES OF QUARTER HORSE BREEDING J. A. Tunnell, J. O. Sanders, J. D. Williams 1 and G. D. Potter Texas Agricultural Experiment Station 2, Texas A&M University, College Station Summary Pedigrees of randomly selected Quarter Horses born in each of the years 1946, 1956, 1966 and 1976 and of winning halter, cutting and race horses born in the same years were evaluated and compared. Average inbreeding and inter se relationship levels and relationships of influential ancestors to the sample were calculated for each sample. The amount of Thoroughbred influence and the average generation interval were also determined for each random sample. The levels of inbreeding found in the random samples were low, ranging from 1,3% in 1956 to 2.6% in 1966; however, these levels were higher than would be expected if mating were random. Show and race winners born in 1976 appeared to be less inbred than random horses of the breed. The estimated average inter se relationship within the random samples increased from % in 1946 to 3% in 1966, decreasing again to % in 1976, Horses in the elite samples appeared to be more closely related to each other than those in the random samples. Fifteen ancestors of horses in the random samples were identified as influential to the Quarter Horse breed. Many of these same ancestors were influential in the halter and cutring samples, but only one was influential in the race samples. The percentage of pedigree lines in the random samples that contained a Thoroughbred ancestor were as follows: 1946, 27.5%; 1956, 19.2%; 1966, 23.2% and 1976, 31.4%. The average generation interval fluctuated from approximately 8 yr to approximately 1 yr for the random samples. adept, of Vet. Microbiol. and Parasitol. and of Statist. 2 Dept. of Anim. Sci. Received June 28"; Accepted February 11, (Key Words: Quarter Horse, Pedigrees, Inbreeding, Relationship, Thoroughbred, Generation Interval.) I ntroduction The breed most responsible for the rapid growth in horse numbers in the United States is the American Quarter Horse. This breed has increased in numbers faster than any other, and the American Quarter Horse Association is now the largest horse registry in the world. Relatively few studies, and no recent studies, have been conducted on how the Quarter Horse has actually been bred since its beginning. Fletcher (1945) analyzed the breed structure of the American Quarter Horse at the time of its official formation, and Rhoad (1961) later conducted a similar study. The purpose of this study was to evaluate Quarter Horse pedigrees at four regular intervals of the breed's existence in order to update information concerning the genetic history and breed structure of the American Quarter Horse. Materials and Methods Four random samples of approximately 1 horses each, representing horses born in the years 1946, 1956, 1966 and 1976, were drawn from the Stud Book of the American Quarter Horse Association. Two-line pedigrees were used to extend random lines of ancestry beyond the sire and dam of each animal in the samples. The sire and dam of each animal were recorded, and a random sequence of male and female ancestors was listed beneath each parent. These random sequences were extended sufficiently to allow the pedigrees to be traced as far as possible. When a Thoroughbred ancestor occurred, no attempt was made to trace the line of ancestry beyond that Thoroughbred animal. Pedigree information was obtained from the Stud Book and also from various sources of 585 JOURNAL OF ANIMAL SCIENCE, Vol. 57, No. 3, 1983

2 586 TUNNELL ET AL. information on earlier horses that were not registered. The approximate method of evaluating random lines of ancestry developed by Wright and McPhee (1925) was used to calculate average coefficients of inbreeding and inter se relationship for each of the samples. To calculate inbreeding, it was noted which of the two-line pedigrees contained a tie, i.e., a common ancestor appearing in both lines of the pedigree. Because the pair of lines in which a tie is found is only one out of a total of 2 n+n' pairs of lines going from the horse of concern to the nth generation of the sire's pedigree and the n 'th generation of the dam's pedigree, the contribution of the tie to this horse's inbreeding coefficient [i.e., (l/2)n+n'+l(1 + Fa)] is multiplied by this total number of pairs of lines to give the contribution of this pedigree to the average inbreeding coefficient of the sample. Therefore, a pedigree containing a tie is assigned the value of 1/2(1 + Fa), and a pedigree that does not contain a tie is assigned the value of zero for inbreeding. The values for each pedigree were then averaged to obtain the estimate of the average coefficient of inbreeding for the sample. The standard error of this estimate (SE F) was calculated using the formula (Wright and McPhee, 1925): where Fx SE F = X --~-, N = number of pairs of lines compared, p = observed chance of occurrence of a tie (i.e., the fraction of the paired lines that contained a tie), q = 1 - p (the chance of nonoccurrence) and Fx = the average coefficient of inbreeding. To determine the average inter se relationship, each line of a two-line pedigree was randomly matched with a line from a different pedigree in the sample. Those pairs of lines not containing a tie were assigned the value of zero for relationship, and those containing a tie were assigned the value where F a was again the inbreeding coefficient of the common ancestor, and Fx and Fy were the inbreeding coefficients of the paired animals as used in estimating the average inbreeding coefficient of the sample. Inter se relationship was also estimated by substituting the average coefficient of inbreeding found for the entire sample for Fx and Fy. After rounding off, the results were the same for both methods. The values f9 r each pair of lines were averaged to give the average inter se relationship of the sample. The standard error of the average inter se relationship coefficient was calculated by using the formula (Wright and McPhee, 1925) Rx_._._y_y SE I = X P, with p, q and N being the same as previously defined and Rxy equal to the calculated average coefficient of relationship. The level of inbreeding that would be expected if mating was random was calculated by the formula F = R/(2 - R), where F is the expected inbreeding coefficient and R the calculated inter se relationship (McPhee and Wright, 1925). Influential ancestors to the Quarter Horse breed were identified as those animals that had a total relationship of 5% or more to one or more of the samples. The direct relationship of an animal to the breed was estimated by dividing the number of lines in which the animal appeared by the total number of lines in the sample. If an animal had a direct relationship to the breed of 2% or more, then its collateral relationship to the breed was also measured. Collateral relationship was estimated by dividing the number of lines in which that animal's parents or grandparents appeared, excluding those lines in which the animal itself appeared, by the total number of lines in the sample. Total relationship of an animal to the breed was then estimated by summing the estimates for direct and collateral relationship. The standard error of the relationship coefficient of an ancestor to the breed was calculated by using the formula 1+~ X/(1 + Fx)(1 + Fy) ' SE R = P~-~,

$PEDIGREE ANALYSIS OF QUARTER HORSE BREEDING 587 where p = fraction of lines in the sample that contained the animal or its parents or grandparents, q = 1 - p and N = number of lines in the sample.$

3 PEDIGREE ANALYSIS OF QUARTER HORSE BREEDING 587 where p = fraction of lines in the sample that contained the animal or its parents or grandparents, q = 1 - p and N = number of lines in the sample. Thoroughbred influence on the Quarter Horse breed was estimated by calculating the percentage of lines in each sample that ended with a Thoroughbred ancestor. The formula for the standard error of this measure was the same as that for the relationship coefficient of ancestors to the breed, with the exception that p equaled the fraction of the lines that contained a Thoroughbred ancestor. To obtain the average generation interval, the birthdates, if known, of the parents of each animal in the sample were recorded. The ages of the parents at the time the animals in the sample were born were then averaged to give the generation interval. In addition to the random sample, 12 samples of elite (winning) halter, cutting and race horses of the Quarter Horse breed were used to compare the breeding of show and race winners with that of randomly selected American Quarter Horses. These samples each consisted of approximately 1 horses and represented approximately the same birth years represented by the random samples. These horses were chosen from various sources: World Championship Quarter Horse Show, Southwestern Exposition and Fat Stock Show, National Cutting Horse Association (NCHA) Futurity, NCHA Top Ten Cutting Horse Award, Leading Money Earning Horses and Champion Quarter Running Horse Award. Details of the sampling procedure were discussed by Tunnell (1981). Complete pedigrees were traced for each animal in the elite samples, again tracing the pedigrees as far as possible and stopping at Thoroughbred ancestors. Average coefficients of inbreeding and inter se relationship within the samples and relationship of influential ancestors to the samples were calculated by standard procedures using the complete pedigrees. Results and Discussion Inbreeding. The average coefficients of inbreeding found in each of the random samples were low (table 1), ranging from 1.3% in 1956 to 2.6% in These coefficients, however, were slightly larger than the amount of in- breeding expected if mating had been random. This expected inbreeding would be due to expected relationships between randomly chosen animals in the population and would be approximately one-half of the inter se relationship. Because the generation intervals were found to be approximately 1 yr, the expected inbreeding levels for particular sample years were calculated from the previous sample year's inter se relationship level. The differences between calculated levels of inbreeding and expected levels with random mating were not large enough to indicate more than a small amount of planned inbreeding. A possible explanation for low levels of inbreeding during the formation of the breed is that the early Quarter Horses were required to be of a particular type, but not of a particular pedigree, to be eligible for registration; and there was a large number of horses of that type from which to start the breed. The largest increase in inbreeding was found in the 1966 sample. A large number of influential ancestors with a high relationship to the breed was also found in the 1966 sample (table 4). The appearance of famous sires will often lead to incidental increases in inbreeding (Lush, 193). The largest amount of Thoroughbred influence on the Quarter Horse breed was found in the 1976 samples, indicating more outcrossing to the Thoroughbred at this time. This outcrossing probably led to the slight drop observed in the TABLE 1. AVERAGE COEFFICIENTS OF INBREEDING AND INTER SE RELATIONSHIP OF THE BREED AND EXPECTED INBREEDING DUE TO RANDOM MATING Year Ob- Exserved Inter se pected Fxa relationship Fxa o b _ af x refers to average inbreeding coefficient of horses in the sample. bdue to the formula for calculating the standard error of the relationship coefficient obtained by the approximate method, realistic standard errors for coefficients of zero could not be calculated. %

588 TUNNELL ET AL. average inbreeding coefficient from 1966 to 1976.

4 588 TUNNELL ET AL. average inbreeding coefficient from 1966 to The elite samples of winning halter, cutting and race horses born in 1976 all had slightly lower average coefficients of inbreeding than the random sample of 1976 (table 2). Horses in the 1946, 1956 and 1966 halter samples had higher average coefficients of inbreeding than the random samples of those years, and lower coefficients of inbreeding were found in all of the race samples as compared with the random samples. Inter Se Relationship. Although the coefficients of relationship obtained from the random samples did not differ significantly, there did appear to be a rise in inter se relationship from 1946 to 1966 (table 1). This rise was probably due to an increase in the number and degree of relationship to the breed of influential ancestors from 1946 to 1966 (table 4). The direction of the breed appeared to change after 1966, as indicated by an inter se relationship of zero in the 1976 sample. Again, the heavy Thoroughbred influence found in the 1976 sample probably led to the decrease in inter se relationship. The horses within the elite halter, cutting and race samples appeared to have a higher relationship among themselves than did random horses of the breed in all years (table 3). The low levels of inter se relationship observed in the random samples and the coefficients of inbreeding observed, which were low but slightly greater than the amount expected with random mating, indicate only a slight tendency for separation of the breed into family lines. Influential Ancestors. Fifteen ancestors of animals in the random samples were identified as influential to the Quarter Horse breed (table 4). No horse had a total relationship to the breed of 5% or greater in the 1946 sample, and only one horse, Peter McCue, had a direct relationship of 2% or greater. There were three horses that had a relationship of 5% or greater to all of the remaining three samples. These horses were King, Zantanon and Old Sorrel. Peter McCue's calculated relationship to the breed was due strictly to direct relationship, and his direct relationship was noticeably higher than that of any other horse in any of the samples except the 1976 sample. Also, eight of the influential ancestors were direct descendants of Peter McCue (figure 1). The horse King became influential at a younger age than any other horse. King first appeared on the list of influential ancestors in the 1956 sample, at the age of 24; and in the 1976 sample King had the highest relationship to the breed. King was a son of Zantanon and grandson of Little Joe, who also were influential sires. Only three of the influential ancestors, King, Old Sorrel and Wimpy, were registered Quarter Horses. The only influential Thoroughbred ancestor as identified from the random samples, and also the only mare, was Nora M, the dam of Peter McCue. The remaining influential ancestors were unregistered horses. Peter McCue was 1/2 Thoroughbred, Flying Bob was 3/4 Thoroughbred (figure 1), and Old Sorrel was out of a Thoroughbred type mare. Many of the influential ancestors in the random samples also had a relationship of 5% or greater to the halter or cutting samples or both (tables 5 and 6). In the race samples, however, Little Joe was the only influential ancestor that was also influential in the raj~dom samples (table 7). Little Joe and Three Bars, a Thoroughbred, were the only horses determined to be influential in all three of the categories of halter, cutting and racing. Relationships among the influential ancestors of the elite samples are shown in figure 2. Tborougbbred Influence. The percentage of TABLE 2. AVERAGE COEFFICIENTS OF INBREEDING (PERCENTAGE) FOUND IN ELITE SAMPLES Year Halter Cutting Racing TABLE 3. INTER SE RELATIONSHIP (PERCENTAGE) AMONG HORSES IN ELITE SAMPLES Year Halter Cutting Racing

5 PEDIGREE ANALYSIS OF QUARTER HORSE BREEDING 589 +t l +1,.-~ it-.., ~ i>. r~ O~ t,,d ~ ~,,4,4 m e. o o d >, t~ Z l t l o 5. ~a Z Z~ Ox~e..l~ e,l@,.~ t~o,o,.4.,-;e,i,.4 ~,i e4,.4,.4 e.lei,..; l 'as 9 "~ [- Z 4d44o "d "~d4 "ddd Z e [.., e~ 4 M.=.~ ~ 5 ~ = ~ z ~ z ~ S s

6 59 TUNNELL ET AL. ~ Little Rondo ~.... [.~.~1~ ~ ~..~Jaba ina q[ Strait Horseq( Yellov Jacket ~- ~ R a r e ~ O C k ' s Rondol.... Sab, ~.th~ ~'~f " ~ $ o l i s ~ ~ Dan ~ -., S.g,r~/ "~ hllie lrulel~ Ace P Tucker Old O J (TB) Figure 1. Relationship of influential ancestors in random samples. The names of influential ancestors are enclosed in boxes. lines in the random samples that ended with a Thoroughbred ancestor ranged from 19.2% in 1956 to 31.4% in 1976 (table 8). More than one-fourth of the lines in the 1946 sample traced to Thoroughbred ancestors, indicating that the Thoroughbred was fairly influential in founding the Quarter Horse breed. The amount of Thoroughbred influence decreased in the 1956 sample, but by 1976 the Thoroughbred influence had increased to nearly one-third of TABLE 5. RELATIONSHIP (PERCENTAGE) OF INFLUENTIAL ANCESTORS TO ELITE HALTER SAMPLES Ancestor Three Bars (TB) Leo 1335 Old Sorrel Hired Hand 2495 Hickory Bill Peter Mc Cue King Soils Peppy Little Joe 6.1 Harmon Baker 5.1 Midnight 5.8 Old Joe Bailey

7 PEDIGREE ANALYSIS OF QUARTER HORSE BREEDING 591 the lines, surpassing the amount of influence that the Thoroughbred had at the time of the Quarter Horse breed's official formation. Generation Interval. The average generation intervals found in the four random samples fluctuated from approximately 8 yr to approximately 1 yr (table 9), with the generation intervals of the 1946 and 1966 samples shorter (P.5) than those of the 1956 and 1976 sampies. The generation interval of the 1946 sample may actually be longer than that calculated due to a large number of unregistered parents of unknown birthdates in that sample. Those unregistered animals were probably older animals in many cases. The horse King appeared to have contributed to the longer generation interval found in the 1956 sample. At 24 yr of age, King sired three of the horses in the sample. The Quarter Horse breed expanded greatly during the 196's. As a breed expands, more and more younger animals become available for breeding. This expansion would result in a shorter generation interval, as found in the 1966 sample. No single horse appeared to contribute to the increase in generatiem interval found in the 1976 sample; however, more emphasis in recent years on the use of progeny tested sires and dams probably contributed to this increase. General Discussion Results of this study generally corresponded with those of Fletcher (1945) and Rhoad (1961). Fletcher's study showed an average inbreeding coefficient of 1.7% and an average inter se relationship of.98% in Quarter Horses born in 194 and 1941, and Rhoad reported an average inbreeding coefficient of 1.2% for Quarter Horses born in Rhoad also reported, however, a decreasing inter se relationship in the breed from 1941 to 1958, which is not consistent with the findings of this study. Rhoad's study utilized five generation pedigrees, TABLE 6. RELATIONSHIP (PERCENTAGE) OF INFLUENTIAL ANCESTORS TO ELITE CUTTING SAMPLES Ancestor Doe Bar 76, Poco Tivio 17, Poco Bueno Three Bars (TB) Old Sorrel King Wimpy Hickory Bill Zantanon 5.3 Solis 5.2 Peter McCue Joe Reed Little Joe 5.2 TABLE 7. RELATIONSHIP (PERCENTAGE) OF INFLUENTIAL ANCESTORS TO ELITE RACE SAMPLES Ancestor Three Bars (TB) Top Deck (TB) 6.2 Leo Joe Reed Clabber Little Joe 8.3 Old D J (TB) 6.9

8 592 TUNNELL ET AL. ~ \ \ L i t t ~./M'Sl S Taylor ~,~L ~ ~ ~ ~Yar e.dr""- // -... "qf ~ p... S...,q~ ~ lol~j,, s,il,, I Lightning Bar~ "~" Dandy Doll4t aar Raid F-4I- ~ -- Nelly Bly 91 Red Joe of Arizona.qF~ ~ ~ Little Fanny b" Figure 2. Relationship of influential ancestors in elite samples. The names of influential ancestors are enclosed in boxes. whereas in this study, pedigrees were traced as far as possible. Many of the influential ancestors found in this study were old enough that they might not have appeared in many of the five generation pedigrees of horses born in the later years of Rhoad's study, possibly resulting in the smaller inter se relationship that Rhoad found. The Quarter Horse appears to be similar to other light breeds of horses in levels of inbreeding (Fletcher, 1946; Gazder, 1954; Steele, 1944). The low levels of inbreeding and inter se relationship indicate that the Quarter Horse breed has not increased greatly in genetic homogeneity since its official formation. Fletcher (1945) identified the horse Peter McCue as having the highest relationship of any ancestor to the Quarter Horse breed. Peter McCue was also found to have a high relationship to the breed in this study. Fletcher reported a generation interval of slightly less than Year TABLE 8. LINES IN RANDOM SAMPLE PEDIGREES THAT ENDED WITH A THOROUGHBRED (TB) ANCESTOR Total Lines no. of ending lines with TB, % TABLE 9. GENERATION INTERVAL MEANS (GI) AND STANDARD DEVIATIONS AS FOUND IN THE RANDOM SAMPLES Year G1, yr SD, yr b a b a 4.8 a'bmeans with different superscripts differ (P.5) as determined by Duncan's new multiple range test.

PEDIGREE ANALYSIS OF QUARTER HORSE BREEDING 593 9 yr in the Quarter Horse breed, which is similar to the generation intervals found in this study, Li

9 PEDIGREE ANALYSIS OF QUARTER HORSE BREEDING yr in the Quarter Horse breed, which is similar to the generation intervals found in this study, Literature Cited Fletcher, J. L. 1945, A genetic analysis of the American Quarter Horse. 3. Hered. 36:346. Fletcher, J. L, 1946, A study of the first fifty years of Tennessee Walking Horse breeding. J. Hered. 37: 369. Gazder, P. J The genetic history of the Arabian Horse. J. Hered. 45:95. Lush, J. U 193. Inbreeding and the foundation of breeds. The Cattleman 16(1):16. McPhee, H. C. and S. Wright Mendelian analysis of the pure breeds of livestock. III. The Shorthorns. J. Hered. 16:25. Rboad, A. O The American Quarter Horse. Quarter Horse J. 13(6):33. Steele, D. G A genetic analysis of recent Thoroughbreds, Standardbreds, and American Saddle Horses. Kentucky Agr. Exp. Sta. Bull Tunnell, J. A Pedigree evaluation of four decades of Quarter Horse breeding. M.S. Thesis. Texas A&M Univ:, College Station. Wright, S. and H. C. McPhee An approximate method of calculating coefficients of inbreeding and relationship from livestock pedigrees. J. Agr. Res. 31:377.

GENETICS OF RACING PERFORMANCE IN THE AMERICAN QUARTER HORSE: II. ADJUSTMENT FACTORS AND CONTEMPORARY GROUPS 1'2

GENETICS OF RACING PERFORMANCE IN THE AMERICAN QUARTER HORSE: II. ADJUSTMENT FACTORS AND CONTEMPORARY GROUPS 1'2 S. T. Buttram 3, R. L. Willham 4 and D. E. Wilson 4 Iowa State University, Ames 50011 ABSTRACT