Genetic variability in Hanoverian warmblood horses using pedigree analysis H. Hamann and O. Distl J ANIM SCI 2008, 86:1503-1513. doi: 10.2527/jas.2007-0382 originally published online February 29, 2008 The online version of this article, along with updated information and services, is located on the World Wide Web at: http://www.journalofanimalscience.org/content/86/7/1503 www.asas.org Downloaded from www.journalofanimalscience.org by guest on October 27, 2014 Genetic variability in Hanoverian warmblood horses using pedigree analysis1 H. Hamann and O. Distl2 Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Bu¨ nteweg 17p, 30559 Hannover, Germany ABSTRACT: A data set constituting a total of number of founders and the effective number of ances- 310,109 Hanoverian warmblood horses was analyzed tors was 3.15 for the reference population, 3.25 for the to ascertain the genetic variability, coefficients of in- stallions, and 3.06 for the breeding mares. The effective breeding, and gene contributions of foreign populations. population size in the Hanoverian warmblood reference The reference population contained all Hanoverian population was 372.34. English Thoroughbreds contrib- horses born from 1980 to 2000. In addition, Hanoverian uted nearly 35% of the genes to the Hanoverian refer- stallions born from 1980 to 1995 and Hanoverian breed- ence population and even slightly greater contributions (39%) to the stallions. Trakehner and Arab horses con- ing mares from the birth years 1980 to 1995 with regis- tributed approximately 8 and 2.7%, respectively, to the tered foals were analyzed for the same genetic parame- Hanoverian gene pool. The most important male ances- ters. The average complete generation equivalent was tors were Aldermann I from the A/E line, Fling from approximately 8.43 for the reference population. The the F/W line, and Absatz from the Trakehner line, mean coefficient of inbreeding was 1.33, 1.19, and 1.29% whereas the breeding mare Costane had the greatest for the reference population, stallions, and breeding contribution to the reference population, stallions, and mares, respectively. The effective number of founders breeding mares. From 1996 onward, the stallions Welt- was largest in stallions (364.3) and smallest in the refer- meyer and Donnerhall had the largest genetic impact ence population (244.9). The ratio between the effective on the Hanoverian horse population. Key words: effective population size, genetic diversity, Hanoverian, horse, inbreeding ©2008 American Society of Animal Science. All rights reserved. J. Anim. Sci. 2008. 86:1503–1513 doi:10.2527/jas.2007-0382 INTRODUCTION Andalusian, Napolitan, Holsteiner, Preußen, Mecklen- burger, and English Thoroughbred stallions, and the in- The present Hanoverian breed is composed of approxi- troduction of a central registration of coverings and foal- mately 19,000 registered breeding mares and 420 regis- ings marked the beginning of the breeding of the Han- tered stallions; it is therefore the largest breed of warm- overian horse (Lo¨we, 1988). blood horses worldwide and currently supplies Germany A lack of knowledge exists concerning the present con- with the largest proportion of riding and sport horses of dition of the Hanoverian gene pool. Breeding programs any breed. Moreover, the Hanoverian breed has greatly based on prediction of breeding values using animal mod- influenced other warmblood horse breeds through the els and the intensive use of reproductive technologies exchange of breeding animals. The 7 breeding districts such as artificial insemination in Hanoverian horses aim of the Hanoverian breed extend over the state of Lower at the use of fewer superior animals, particularly of stal- Saxony and its neighboring regions. The original core lions. By using these advancements in horse breeding breeding area of the “Hanoverian Marschzucht” was sit- and the traditional strong emphasis on sire lines, there uated within the low-lying areas of the rivers Elbe, can be an increase in the genetic contributions of fewer Weser, and Ems. The foundation of the royal stallion ancestors and in the long-term rate of inbreeding. There- fore, the objective of this study was to monitor current station (Landgestu¨t) Celle as early as 1735, the use of levels and trends of inbreeding and the proportion of foreign blood in the Hanoverian population, and to deter- mine the genetic contributions of important founders and ancestors to the current genetic structure. 1The authors are grateful to VIT (Verden/Aller, Germany), which provided the Hanoverian warmblood data set and the Association of Hanoverian Warmblood Breeders (Verden/Aller, Germany) for sup- MATERIALS AND METHODS port of this analysis. 2Corresponding author: [email protected] Animal Care and Use Committee approval was not Received June 28, 2007. obtained for this study because the data were obtained Accepted February 14, 2008. from an existing database. 1503 Downloaded from www.journalofanimalscience.org by guest on October 27, 2014 1504 Hamann and Distl Table 1. Number of animals in the entire pedigree and the reference population, pedigree depth and completeness, and number and birth years of founders for Hanoverian horses Item All horses Stallions Breeding mares Total horses born 1920–2000, n 310,109 9,241 90,639 Reference population, n 167,063 1,925 33,119 Maximum generations traced, n 23 23 23 Pedigree completeness index 0.98 0.96 0.98 Complete generation equivalent 8.43 7.66 8.17 Founders, n 13,881 5,742 10,991 Average birth year of founders 1939 1920 1930 Range of birth year of founders 1861–2000 1861–1988 1879–1992 The data used in this study were provided by the Asso- of founders (f) contains limited information about the ciation of Hanoverian Warmblood Breeders (Verden/ genetic diversity of the population, because some found- Aller, Germany). Horses born between 1980 and 2000 ers have been used more intensely and therefore make were defined as the reference population (n = 167,063), a greater contribution toward the reference population in which the pedigrees of the animals were traced back than other founders. The effective number of founders to the earliest recorded ancestors. This resulted in a data (fe) is defined as the number of equally contributing set constituting a total of 310,109 animals. The first founders expected to produce the same genetic diversity ancestor recorded was traced to the year 1861 (Table 1). as in the population under study (Lacy, 1989) and is In addition to all registered horses, we distinguished computed as breeding mares and stallions in the reference population. N ⎡ f ⎤ Breeding mares included in the reference population −1 were dams with registered Hanoverian foals and born f = ⎢∑ q2⎥ , e ⎣ i ⎦ between 1980 and 1995 (n = 33,119). The stallion refer- i=1 ence population includes sires with registered Han- overian foals and born between 1980 and 1995 (n = where qi is the genetic contribution of the ith founder 1,925). to the reference population. When founders contribute The average coefficient of inbreeding, effective to the reference population more equally, the effective founder number, effective ancestor number, and effec- number of founders is greater. If all founders contribute tive number of founder genomes were estimated for all equally to the reference population, the effective and Hanoverian horses over a 20-yr period (1980 to 2000) actual numbers of founders are the same. and for breeding mares and stallions over a 15-yr period A further measure of genetic diversity for popula- (1980 to 1995). Generation intervals were computed for tions, which accounts for the loss of allelic diversity the pathways sire to sire, sire to dam, dam to sire, and since the foundation population, was proposed by Boich- dam to dam by using the average age of the parents at ard et al. (1997). This parameter, the effective number the birth of their offspring that were kept for breeding. of ancestors (fa), also accounts for large contributions The pedigree completeness index (PEC) proposed by of all ancestors, not just founders, and is defined as the MacCluer et al. (1983) describes the degree of complete- minimum number of ancestors explaining the complete ness of pedigrees and quantifies the chances for de- genetic diversity of the current population. In contrast tecting inbreeding in the pedigree: to the effective number of ancestors, the effective num- ber of founders would overestimate genetic diversity in such situations. 2CsireCdam PECanimal = , Based on the marginal contribution of the 1,000 most CsireCdam influential ancestors, the effective number of ancestors is computed as where Csire and Cdam are contributions from the paternal and maternal lines. ⎡1000 ⎤ −1 The number of complete generation equivalents (GE) ⎢ 2⎥ was computed for each individual j as fa = ∑ pi , ⎣ i=1 ⎦ G = n /2g, j ∑ i with pi being the marginal genetic contribution of an- cestor i and serving as a measure of genetic diversity. where ni is the number of known ancestors in genera- The marginal contributions of the ancestors are com- tion i and g is the number of known generations for puted in a recursive procedure. The ancestor with the individual j. greatest contribution to the reference population is cho- Ancestors with both parents unknown were consid- sen, and then the contributions of all others are com- ered as nonrelated founder animals. The total number puted, conditional on the contribution of the ancestor Downloaded from www.journalofanimalscience.org