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Genetic Diversity Within and Gene Flow Between Three Draught Horse Breeds Using Genealogical Information

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Genetic Diversity Within and Gene Flow Between Three Draught Horse Breeds Using Genealogical Information Original Paper Czech J. Anim. Sci., 61, 2016 (10): 462–472 doi: 10.17221/91/2015-CJAS Genetic diversity within and gene flow between three draught horse breeds using genealogical information H. Vostrá-Vydrová2, L. Vostrý1,2, B. Hofmanová1, E. Krupa2, Z. Veselá2, J. Schmidová1,2 1Czech University of Life Sciences Prague, Prague, Czech Republic 2Institute of Animal Science, Prague-Uhříněves, Czech Republic ABSTRACT: Three draught horse breeds are maintained in the Czech Republic: the Silesian Noriker (SN), the Noriker (N), and the Czech-Moravian Belgian (CMB). Because the SN and CMB populations are currently closed to outside breeding and are endangered (Genetic Resources), the loss of the genetic variation these horses represent is concerning. Genetic diversity within and between these three breeds and their population structures was analyzed based on pedigree information. Our goal was to identify and quantify factors that affected their genetic variability. The effective population size was analyzed in each breed. The numbers of generations were 22, 32, and 32 for the SN, N, and CMB breeds, respectively, with average equivalent known generations of 9.81, 8.45, and 8.91, respectively. The effective numbers of founders and ancestors contributing to the current genetic pool were, respectively, 69.42 and 22.32 for the SN breed, 98.48 and 42.20 for the N breed, and 43.33 and 23.32 for the CMB breed. The average inbreeding coefficients were 4.6%, 2%, and 4% for the SN, N, and CMB breeds, respectively, and the average inbreeding rate was 0.5% for the SN and CMB breeds and 0.2% for the N breed. The corresponding estimates of effective population size were 95, 195, and 101 for the SN, N, and CMB breeds, respectively. These statistics suggest that the genetic variability has decreased, and without changes in breeding strategy the genetic variability might continue to decline. Using genealogical F-statistics, small genetic differences were identified between the analyzed populations (FST = 0.02). Keywords: genetic drift; inbreeding; Silesian Noriker; Noriker; Czech-Moravian Belgian horse INTRODUCTION Old Kladruber and Hutsul horse, belong to a group of endangered horse breeds recognized as Genetic The preservation of endangered species is one Resources in the Czech Republic (CR). Over the of the most important goals in current biological last 120 years, the CMB breed was developed on science. Conservation programmes are needed to the CR territory primarily using imported Belgian preserve breeds with significant genetic diversity. stallions and, to a lesser extent, Walloons. CMB The genetic structure of a population is shaped by horses have a medium square frame and mature different mechanisms, including gene flow, selec- earlier than other typical draught breeds. The SN tion pressure, mutation, and genetic drift, all of breed was developed over the last 100 years from which might vary in magnitude over time and be imported Noriker stallions and Bavarian draught influenced by factors intrinsic or extrinsic to the stallions. SN horses have a longer than average population. These factors are the most relevant frame and are a late maturing breed. Another for structuring within-breed diversity. draught breed maintained on a large scale on the The Silesian Noriker (SN), Czech-Moravian Bel- CR territory is the Noriker (N), which contributed gian (CMB) draught horse breeds, along with the to the generation of the SN breed and has been Supported by the Ministry of Agriculture of the Czech Republic (Project No. QJ1510141). 462 Czech J. Anim. Sci., 61, 2016 (10): 462–472 Original Paper doi: 10.17221/91/2015-CJAS continuously maintained on the CR territory for Secondly, we analyzed the genetic relationships 150 years. To a large extent, the SN and CMB between the breeds and between individual horses breeds have been geographically separated. within these breeds. World War II negatively impacted breeding pro- grammes because there was a steep decrease in MATERIAL AND METHODS the number of horses. The post-war expansion of farm mechanization caused a further decrease in Data. A total of 27 022 pedigree records of regis- the numbers. The SN, N, and CMB breeds were tered individuals in studbooks dating from 1900 to registered as separate breeds until the 1960s, but June 31, 2013 were provided from the Association because of their decreasing numbers, all animals of Horse Breeders’ Unions of the Czech Republic. were merged into a single studbook – “synthetic Pedigree analyses were performed using one ref- breed” called the Czech Draught Horse (CDH). erence population containing animals potentially At this time, stallions and mares were used across contributing to the next generations. The refer- the original breeds and all offspring including the ence population was defined as the entire active crossbreeds were considered as “purebred indi- population of individuals (stallions and mares) viduals” of this new synthetic population. These born in the years 1996–2010 (n = 2202). genetically crossbred animals were also included Pedigree completeness measures. The pedi- in the breeding. However, in 1989, draught horses gree completeness and the number of ancestral in the Czech Republic were reassigned into the generations influence the estimated inbreeding original three populations (SN, N, and CMB) based coefficients and the relationship coefficients be- on morphological analysis. During this period, al- tween animals. The pedigree completeness level though the analyzed breeds were separated, these was assessed as the proportion of ancestors known animals were maintained as open populations and per generation for each offspring (MacCluer et al. “crossbreeding” was conducted between them. 1983). The number of equivalent complete genera- After 1996 and 1999, the populations of SN and tions in the pedigree (t) was computed according CMB horses were certified as rare and endangered to Maignel et al. (1996) as follows: breeds (Genetic Resources), and their studbooks n were closed. Although SN stallions were still used t = Σ(1/2) for breeding with N mares, their offspring, with where: more than 50% of the SN breed’s genes, were in- n = number of generations between an animal and its cluded in the studbook, and these animals were ancestor regularly included in the SN breed (until 2013). Probability of gene origin. Several measures Based on the above-mentioned historical de- of genetic variability were calculated from the velopment, these three analyzed draft breeds can pedigree data. The total number of founders (f) genetically be considered as a single breed with for each breed was determined as the total number three subpopulations. of ancestors with unknown parents. The effective A primary molecular genetic analysis utiliz- number of founders (f ) is defined as the number ing 13 microsatellite markers (Hofmanova et al. e of founders explaining the same level of genetic 2014) suggested high genetic similarity between the diversity as that observed in the reference popula- above-mentioned draught breeds. However, Toro tion (Lacy 1989). This parameter is the reciprocal et al. (2009) suggested that these markers were not of the probability that two randomly drawn genes necessarily good predictors of genomic coancestry in the population under study originated from the because there are problems in estimating genomic same founder (James 1972). The effective number heterozygosity based on only a few molecular mark- of founders (f ) was estimated using the formula: ers. Until recently, no analysis of the gene flow e between these three breeds has been conducted. The objective of the present study was to describe � 1 � � � � the level of genetic variability between and within where:∑��� �� Czech draught horse breeds and to estimate the f = total number of founders -th degree of gene flow and genetic differences among qi = genetic contribution of the i founder to the refer- these animals based on genealogical information. ence population 463 4 Original Paper Czech J. Anim. Sci., 61, 2016 (10): 462–472 doi: 10.17221/91/2015-CJAS The effective number of ancestors (fa) is defined Inbreeding coefficient and relatedness coef- as the minimum number of ancestors, not necessar- ficient. The inbreeding coefficient of each indi- ily of founders, explaining the same genetic diver- vidual (Fi) was estimated using a tabular method sity as that in the reference population (Boichard (Falconer and Mackay 1996) based on the method et al. 1997). The effective number of ancestors was of VanRaden (1992): obtained after determining the marginal genetic Fi = aii – 1 contribution of each ancestor. The parameter fa accounts for losses of genetic variability resulting where: from bottlenecks caused by unequal contributions Fi = inbreeding coefficient of individual i among reproductive individuals to future genera- aii = additive genetic relationship of individual i to itself tions. The effective number of ancestors (fa) was The average relatedness coefficient of each in- estimated using the formula: dividual (AR) was computed as the average coef- ficient integrating the row from the individual in 1 the numerator relationship matrix . This coef- �� � � � A where:∑��� �� ficient indicates the probability that a randomly pi = marginal genetic contribution of ancestor i selected allele in the population occurs in a se- a = total number of ancestors lected individual or among a group of individuals The founder genome equivalent (fge) is defined (Goyache et al. 2003). as the effective number of
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