Effects of Selection on Breed Contribution in the Caballo de Deporte Español

Citation: Bartolomé, E.; Valera, M.; Fernández, J.; Rodríguez-Ramilo, S.T. Effects of Selection on Breed Contribution in the Caballo de Deporte Español. Animals 2022,12, 1635. https://doi.org/10.3390/ ani12131635 Academic Editor: Cristina Sartori Received: 16 April 2022 Accepted: 21 June 2022 Published: 25 June 2022 Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations. Copyright: © 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/). animals Article Effects of Selection on Breed Contribution in the Caballo de Deporte Español Ester Bartolomé1,* , Mercedes Valera 1, Jesús Fernández 2and Silvia Teresa Rodríguez-Ramilo 3 1Departamento de Agronomía, ETSIA, Universidad de Sevilla, 41013 Sevilla, Spain; [email protected] 2Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-Centro Superior de Investigaciones Científicas, 28040 Madrid, Spain; [email protected] 3GenPhySE, Universitéde Toulouse, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Ecole Nationale Vétérinaire de Toulouse, 31326 Castanet-Tolosan, France; [email protected] *Correspondence: [email protected] Simple Summary: The Caballo de Deporte Español (CDE) is a sport horse breed, which originated from crosses between different sport horse breeds in the search for a good sport aptitude for Dressage, Eventing and Show Jumping disciplines. The main aim of this study was to determine the effects of 15 years of selection on this breed and find out whether it has been effective and adequate regarding the CDE main breeding objectives. The whole known pedigree was used, comprising 47,884 animals (18,799 males and 29,085 females). Pedigree analyses were performed in order to check the population structure, origins and evolution over the years. For the analyses, animals were divided into fourteen breed groups. Performance data used in the analyses were the estimated breeding values (EBV) of the Show Jumping, Dressage and Eventing sport disciplines from the routine genetic evaluations of the CDE breeding programme. Results showed some degree of subdivision within the population and, therefore, inbred matings. Regarding the evolution of breeding values, we found that EBVs of offspring were higher than the EBVs of parents showing that genetic gain has actually occurred. Moreover, selection decisions seem to be taken by breeders based, to certain extent, on the genetic evaluations. Abstract: The equine breeding industry for sport’s performance has evolved into a fairly profitable economic activity. In particular, the Caballo de Deporte Español (CDE) is bred for different disciplines with a special focus on Show Jumping. The main aim of this study was to determine the effects of 15 years of selection and to find out whether it has been effective and adequate regarding the CDE main breeding objectives. The whole pedigree of 19,045 horses registered as CDE was used, comprising 47,884 animals (18,799 males and 29,085 females). An analysis performed to check for the pedigree completeness level yielded a number of equivalent complete generations (t) equal to 1.95, an average generation interval (GI) of 10.87 years, mean inbreeding coefficient (F) of 0.32%, an average relatedness coefficient (AR) of 0.09% and an effective population size (Ne) of 204. For the analyses, animals were divided into fourteen breed groups. Additionally, in order to study the evolution of these breeds over time and their influence on CDE pedigree, five different periods were considered according to the year of birth of the animals. Performance data used in the analyses were the estimated breeding values (EBV) of the Show Jumping sport discipline of 12,197 horses in the CDE pedigree, available from the 2020 routine genetic evaluations of the CDE breeding program (starting in 2004). Dressage and Eventing EBV values were also assessed. Results showed values of F higher than expected under random mating; this pointed to some degree of inbred matings. With regard to the evolution of breeding values, we found that, in general, EBVs of offspring were higher than the EBVs of parents. Notwithstanding, there is still a need for improvement in population management and the coordination of the breeders to get higher responses but controlling the loss of genetic diversity in the CDE breed. Animals 2022,12, 1635. https://doi.org/10.3390/ani12131635 https://www.mdpi.com/journal/animals Animals 2022,12, 1635 2 of 15 Keywords: pedigree; open breed; breeding program; founders; show jumping; equine 1. Introduction The equine breeding industry for sports performance has evolved in recent years into a fairly profitable economic activity. Thus, horse breeds have been selected to find the animal that is best suited for the equestrian discipline they participate in. This is true for pure breeds as well as for mixed breeds. In fact, different horse breeds, such as the Irish Sport Horse, Brazilian Sport Horse, Polish Sport Horse or, more recently, the Caballo de Deporte Español, were created as composite breeds, with the horses’ capacity for a certain sports performance as the objective or selection criterion [ 1 ]. In particular, the Caballo de Deporte Español (Spanish Sport Horse; CDE) is bred for Dressage, Eventing and Endurance disciplines with a special focus on Show Jumping discipline, taking advantage of the probable heterosis effect that results from this multiple breed combination [ 2 , 3 ]. The breed is managed by the Caballo de Deporte Español Breeders Association (ANCADES, www.ancades.com (accessed on 25 February 2022)), and its breeding program was officially approved in 2004 and updated in 2020 [ 4 ]. Its main goal is to select a horse with a suitable functional conformation, temperament and health, able to attain a high performance at either national or international sports events in which it participates. When the CDE Official Stud Book was created, an animal could be registered in the Foundational Registry (and thus be identified as a CDE animal) up until 2004 if it came from any of the “permitted” cross-breeds (established by Spanish laws APA/3318/2002 and APA/1646/2004) and was born between 1992 and 1998. Since the Foundational Registry was closed in 2004, an animal is considered to be a CDE either when both parents are registered as CDE, when only one of them is a CDE with the other parent from any of the “permitted” breeds included in these laws, or when both parents belong to any of these “permitted” breeds (even when both parents are from foreign breeds, their offspring could be inscribed as CDE at the owner’s request if they are not inscribed in any other official Stud Book). Although CDE is an open breed that allows animals of different breeds on its Stud Book [ 1 ], since the establishment of its breeding program, breeders are being encouraged to use animals already registered as CDE as reproducers. Notwithstanding, although heterosis falls in the F2 generation if purebred animals are no longer incorporated, an advantage in the phenotype of animals with a more “mixed” genetic background can still be manifested, with crosses being directed to obtain CDE horses showing a lot of heterosis [ 5 ]. However, no studies have been developed before about CDE breeders’ real preferences when selecting horses to create the next generation, i.e., whether they choose animals with the best estimated breeding values (EBV) for sport performance or just animals from the geographically nearest studs. Different criteria may have different repercussions on the outcome of the CDE breeding program. The selection process and mating are a consequence of a conscious decision, usually intended only for short-term achievements in intensively managed domesticated species [ 6 ]. In a crossbreed like the CDE horse, decisions are also influenced by breed preferences when choosing the individuals selected for breeding and, consequently, the evolution of performance and of the genetic parameters across time could also show this effect. The main aim of this study was to determine/characterize the effects of 15 years of selection on this breed and find out whether it has been effective and adequate regarding the main CDE breeding objectives. 2. Materials and Methods 2.1. Population Description Since the creation of the CDE Official Stud Book (in 2002) until 2004, an animal could have been inscribed in the Foundational Registry (and thus be identified as a CDE animal) if it fulfilled two requirements: (i) coming from any of the admitted horse breeds (established by Spanish laws APA/3318/2002 and APA/1646/2004); and (ii) being born between 1992 Animals 2022,12, 1635 3 of 15 and 1998. Since the closing of the Foundational Registry in 2004, not only animals with both parents registered as CDE can be included in the CDE Official Stud Book, but horses with only one or neither parent registered as CDE can also be included and considered CDE. In the latter cases, the “external” parents (i.e., non-CDE horses) should belong to any of the admitted breeds established in the CDE Stud Book. Obviously, their offspring can be inscribed in the CDE Stud Book if they are not already registered in any other official Stud Book. Furthermore, the non-CDE parents can be inscribed in the Auxiliary Registry of the CDE Stud Book as Foreign CDE (CDEx), and from that point, their descendants would be registered as CDE directly in the Principal Registry of the CDE Stud Book. The pedigree information used in this study was gathered from the Caballo de Deporte Español official Stud Book, provided by ANCADES. For analysis purposes, no differences between CDE registrations were considered, thus counting 21,163 CDE horses for this study (19,045 registered as CDE in the Principal Registry and 2118 registered as Foreign CDE in the Auxiliary Registry of the Stud Book), representing 44.7% males and 55.3% females. The whole pedigree included 47,884 animals (18,799 males and 29,085 females). According to the composite nature of this breed, different horse breeds were included in the CDE Stud Book via the relatives of the CDE animals (55.8% of the whole pedigree). These breeds were considered independently according to their representation in the CDE pedigree. Breeds with fewer than 500 animals (less than 1.5%) in the pedigree were grouped together in an “Other Horse Breeds” group (OHB). A total of 14 breed groups were assessed, 12 of them corresponding to majority horse breeds (>500 animals) present in the CDE Stud Book, together with the OHB and the CDE horses groups: Belgian Warmblood breed (BWP; 624 animals), Oldenburger breed (OLDBG; 642 animals), Westphalian breed (WESTF; 653 animals), Lusitano breed (LUS; 875 animals), Holsteiner breed (HOLST; 1269 animals), Anglo-Arab Horse breed (AAH; 1561 animals), Hanoverian breed (HANN; 1742 animals), Arab Horse breed (AH; 1835 animals), Dutch Warmblood (KWPN; 2120 animals), Selle Français (SF; 2311 animals), Thoroughbred (TH; 2924 animals), Other Horse Breeds group (OHB; 4731 animals), Pura Raza Española (PRE; 5434 animals) and the Caballo de Deporte Español breed group (CDE; 21163). In order to study the evolution of these breeds over time (in terms of the proportion of individuals belonging to each breed) and their influence on CDE pedigree, five different periods were considered according to the year of birth of the animals. The first period (P0), including animals born before 2000, was settled before the Foundational Registry of the CDE Stud Book was created in 2002. Consequently, P0 only has animals from the Foundational Registry, and thus, no CDE animals were found in this period. Then, the second period (P1) included animals born between 2000 and 2004, the third period (P2), between 2005 and 2009, the fourth period (P3) involved individuals born between 2010 and 2014, and finally, the fifth and last period (P4), between 2015 and 2021. Figure 1shows the distribution across these periods of the breed groups considered, showing different size and color of the circles according to the number of animals represented in each period. Furthermore, in order to confirm that all breeds considered for this study were genetically different between them, a principal component analysis was developed, using a matrix with the proportion of the individual genome coming from each original founder’s breed, calculated from the pedigree-derived relationship matrix (Figure A1). Animals 2022,12, 1635 4 of 15 Animals 2021, 11, x FOR PEER REVIEW 4 of 15 Figure 1. Distribution of horse breeds from the Caballo de Deporte Español Official Stud Book according to the period considered. Different sizes and colors of the circles indicate the number of animals of a certain breed within periods. Where AAH is Anglo-Arab Horse, AH is Arab Horse, BWP is Belgian Warmblood, CDE is Caballo de Deporte Español, HANN is Hanoverian Horse, HOLST is Holsteiner Horse, KWPN is KWPN Horse, LUS is Lusitano Purebred, OLDBG is Oldenburg Horse, OHB is Other Horse Breeds, PRE is Pura Raza Española, TH is Thoroughbred, SF is Selle Français, WESTF is Westphalian Horse; P0 is the period with animals born before 2000, P1 between 2000 and 2004, P2 between 2005 and 2009, P3 between 2010 and 2014, and P4 after 2015. 2.2. Pedigree Analyses Pedigree analyses were computed using the program ENDOG (v.4.8, [7]). In order to ascertain the circumstances affecting the genetic history of the CDE horse breed population, some parameters were calculated to determine the amount of available information, the pedigree completeness level, the number of complete generations (t) and the generation interval (GI) as a measure of the speed of genetic transmission due to the physiology of the species and the particular management performed. The first one was assessed as the proportion of ancestors known per generation for each offspring [8]. The t value was computed as the sum of (1/2)n, where n is the number of generations separating the individual from each known ancestor [9]. The GI was calculated as the average age of parents at the birth of their offspring kept for reproduction [10]. The three parameters were computed for the whole population and for a reference population, including only animals born in the last 10 years (between 2011 and 2021), which mostly corresponds to animals from the last generation. These will also be referred to as “active animals”. In order to monitor the animal genetic resources for this breed, the effective population size (Ne) was also computed. PopRep 1.0. software’s [11] decision tree was used for picking the best method to calculate Ne for our data. After the analyses, the Ne calculated by individual increase in inbreeding, following Ref [12], appeared as the method that best fitted our data. Ne was calculated as 𝑁𝑒 = 1 2∗∆𝐹, 𝑤ℎ𝑒𝑟𝑒 ∆𝐹 = 𝐹𝑡 − 𝐹𝑡 − 1 1 − 𝐹 t - 1 , where Ft is the inbreeding coefficient of the offspring, and Ft-1 is the inbreeding coefficient of the parents. 2.3. Performance Data The EBV of 12,197 horses for Show Jumping, 5253 horses for Eventing and 7790 horses for Dressage disciplines, from the CDE pedigree, were available for this study, including the performance data of animals from 2004 to 2020 [13]. Figure 1. Distribution of horse breeds from the Caballo de Deporte Español Official Stud Book according to the period considered. Different sizes and colors of the circles indicate the number of animals of a certain breed within periods. Where AAH is Anglo-Arab Horse, AH is Arab Horse, BWP is Belgian Warmblood, CDE is Caballo de Deporte Español, HANN is Hanoverian Horse, HOLST is Holsteiner Horse, KWPN is KWPN Horse, LUS is Lusitano Purebred, OLDBG is Oldenburg Horse, OHB is Other Horse Breeds, PRE is Pura Raza Española, TH is Thoroughbred, SF is Selle Français, WESTF is Westphalian Horse; P0 is the period with animals born before 2000, P1 between 2000 and 2004, P2 between 2005 and 2009, P3 between 2010 and 2014, and P4 after 2015. 2.2. Pedigree Analyses Pedigree analyses were computed using the program ENDOG (v.4.8, [7]). In order to ascertain the circumstances affecting the genetic history of the CDE horse breed population, some parameters were calculated to determine the amount of available information, the pedigree completeness level, the number of complete generations (t) and the generation interval (GI) as a measure of the speed of genetic transmission due to the physiology of the species and the particular management performed. The first one was assessed as the proportion of ancestors known per generation for each offspring [ 8 ]. The t value was computed as the sum of (1/2) n , where n is the number of generations separating the individual from each known ancestor [ 9 ]. The GI was calculated as the average age of parents at the birth of their offspring kept for reproduction [ 10 ]. The three parameters were computed for the whole population and for a reference population, including only animals born in the last 10 years (between 2011 and 2021), which mostly corresponds to animals from the last generation. These will also be referred to as “active animals”. In order to monitor the animal genetic resources for this breed, the effective population size (Ne) was also computed. PopRep 1.0. software’s (PopRep.tzv.fal.de (accessed on 15 June 2022)) [ 11 ] decision tree was used for picking the best method to calculate Ne for our data. After the analyses, the Ne calculated by individual increase in inbreeding, following Ref [ 12 ], appeared as the method that best fitted our data. Ne was calculated as Ne =1 2∗∆F , where ∆F=Ft−Ft−1 1−Ft−1 , where F t is the inbreeding coefficient of the offspring, and Ft−1is the inbreeding coefficient of the parents. 2.3. Performance Data The EBV of 12,197 horses for Show Jumping, 5253 horses for Eventing and 7790 horses for Dressage disciplines, from the CDE pedigree, were available for this study, including the performance data of animals from 2004 to 2020 [13]. Animals 2022,12, 1635 5 of 15 Genetic parameters for the Show Jumping, Eventing and Dressage sport disciplines used in this study were obtained from the 2020 routine genetic evaluation information of the CDE breeding program. Genetic evaluation implies a multivariate BLUP analysis using the following genetic model: y=Xb +Za +Wp +Qr +e, where y was the vector of observations for the analyzed traits of each discipline; b was the vector of fixed effects; a was the vector of additive genetic effects; p the vector of riderhorse interaction effect (for Show Jumping discipline) or the rider effect (for Eventing and Dressage disciplines); r the vector of permanent environmental effects (for Show Jumping and Dressage disciplines); and e the vector of random residual terms, X, Z, W and Q were the incidence matrices assigning observations to the fixed, animal, rider-horse interaction or rider and permanent environmental effects, respectively. In respect of the Show Jumping discipline, the analyzed traits were (i) penalty score transformed to a positive scale (ranging from 50 to 100, with 100 representing the highest punctuation in the competition “0 penalties” and 50 the lowest “maximum penalties”) and (ii) weighted total ranking (calculated on a positive points scale by assigning a value of 100 to the first classified animal (within the same event, penalty scale and competition level) and a value of 0 to the last) for Show Jumping. The fixed effects considered were: age, breed, gender, event, height of fences and category type of test interaction. The general index for this discipline combined both variables considered with a weight of 50% each. For the Endurance discipline, the analyzed traits were (i) penalty score transformed to a positive scale of the Show Jumping exercise, (ii) final points obtained in the Dressage exercise and (iii) penalty score transformed to a positive scale of the Cross exercise. The fixed effects considered in this genetic model were: age, breed, gender, event, level of the event and owner, whereas the general index combined with a weight of 25% for (i), 35% for (ii) and 40% for (iii). Finally, in the Dressage discipline, the analyzed traits were (i) points obtained at the dressage reprise, (ii) points for walk, (iii) points for trot, (iv) points for gallop, (v) points for submission and vi) points for general impression. This model considered the following fixed effects: age, breed, gender, event, level of the event and stud. Additionally, all traits were combined in the following general index: 70% for (i), 10% for (ii) and 10% for (iii), 5% for (iv), 2.5% for (v) and 2.5% for (vi). It must be highlighted that, in all genetic evaluations, EBVs were standardized for an interval of 80–120 with a population average of 100. All BLUP genetic evaluations were carried out with the VCE software—version 6.0.2 (Nashville Video Production Company/Podcast Studio, Nashville, TN, USA) [ 14 ]. In addition, for the official genetic evaluations of the three disciplines considered, the accuracy of EBVs (r), was calculated as r=q1 –PEV δ2 a , where PEV is the prediction error variance and δ2 a was the additive genetic variance. 2.4. Effect of Genetic Selection on Inbreeding and Average Relatedness Coefficient of the Caballo de Deporte Español Population The level of genetic variability in the whole CDE population and within each breed group defined was assessed considering the following parameters: Mean inbreeding coefficient (F), defined as the probability that an individual has two identical alleles by descent in any locus [15]. Average relatedness coefficient (AR) of each individual, interpreted as the representation of the animal in the whole pedigree, or the amount of the animal genetic information it shares. Thus, it is equivalent to the average relationship of an individual with the rest of the population, i.e., the marginal of the relationship matrix divided by the number of individuals. Furthermore, the average of all AR values is also equivalent to twice 1—the expected heterozygosity, which is a common measure of genetic diversity [ 16 , 17 ]. When Animals 2022,12, 1635 6 of 15 AR is calculated for a founder, it expresses the proportion of the genetic information arising from it, and thus, its relevance in the development of the pedigree. In order to check the effect that breeders’ decisions have had when selecting the breeding stock on the genetic merit of the CDE population, the genetic variability was assessed for the whole population and also according to a hypothetical breeding scenario, where only CDE horses with CDE breed parents were allowed to register as CDE in the CDE official Stud Book. Furthermore, using results from the Pedigree analyses developed before with the program ENDOG (v.4.8, [ 7 ]), the evolution across time of F and AR values for animals with best EBVs for the performance ability for Show Jumping, was also evaluated. The EBVs values used were described previously in Section 2.3. 2.5. Probability of Gene Origin of the CDE Horse Breed Ancestors with both unknown parents in the available database were considered founders, as it is a common practice (unless molecular information exists for those animals). In order to check the genetic representation of the founder individuals in the CDE population and in all the breed groups considered, the genetic contribution of founders to the descendant gene pool of the population [ 18 ] was assessed, classified by breed of origin and per period. This way the evolution of the relative influence of each breed in the composition of the CDE population could be studied. Additionally, for the 10 most contributing founders on each period (P0 to P4) their mean EBV for Show Jumping performance and that of their descendants on each period was computed to determine the genetic trend with time. 3. Results 3.1. Population Description Breed groups’ distribution appearing in Figure 1showed PRE and OHB as majority horse breeds in P0, with 4387 (19.2%) and 4076 (17.8%) animals born in this period (percentage within period), respectively. Afterwards, from P1 to P4, CDE was the majority horse breed, showing an increasing tendency from 79.4% (8804) animals in P1 to 98.2% (3986) in P4. On the other hand, PRE, OHB, KWPN, HANN, AH and SF breeds showed higher representation after CDE in P1, with 5.4% (596), 4.0% (442), 2.5% (276), 1.5% (169), 1.3% (144) and 1.1% (123) animals, respectively. All of them showed a decreasing tendency over the periods, with PRE still showing the highest representation in every period (after CDE), with 310 animals in P2 (4.9%), 121 in P3 (3.4%) and 20 in P4 (0.5%). The rest of the breeds showed fewer than 100 animals in P3 and P4 periods. 3.2. Pedigree Analyses In order to study the quality of the pedigree information, for both the individuals included in the entire CDE Stud Book and those in the defined reference population (active animals), the pedigree completeness level was assessed. When the whole CDE population was considered, tracing back just two generations yielded a completeness level of 50%. The same level (50%) was obtained when analyzing the reference population, even when four generations were accounted for. Therefore, the quality of the pedigree information is higher for the reduced set of animals. The number of animals, number of equivalent complete generations, average generation interval and effective population size, computed via individual increase in inbreeding for both the entire and the reference populations considered, were included in Table 1. The reference population represented 14.1% of the entire CDE pedigree and showed 1.91 more equivalent complete generations (3.86) and a generation interval 1.02 years longer (11.89) than the whole pedigree (with values of 1.95 and 10.87, respectively). On the other hand, Ne was 4% smaller in the reference population considered (Ne = 196) than in the whole pedigree (Ne = 204). Animals 2022,12, 1635 7 of 15 Table 1. Number of animals, number of equivalent complete generations (t), average generation interval (GI) and effective population size computed via individual increase in inbreeding (Ne) for the whole Caballo de Deporte Español Studbook and for the animals born between 2011 and 2021 (reference population). Population Number of Animals tGI Ne Whole Pedigree 47,884 1.95 10.87 204 Born between 2011 and 2021 6743 3.86 11.89 196 3.3. Effect of Genetic Selection on Inbreeding and Average Relatedness Coefficient of the Caballo de Deporte Español Population The mean inbreeding coefficient (F) and average relatedness (AR) for the whole CDE population were 0.32% and 0.09%, respectively, and for the reference population, they were 0.79% and 0.19%, respectively, whereas the population with animals showing an EBV over the population mean (EBV > 100) showed 0.27% and 0.19% for F and AR values, respectively. The hypothetical scenario where only CDE horses were allowed to be registered and reproduced, showed an F coefficient of 2.18% and an AR of 0.19%. The evolution of the above parameters in all the sets considered and of the Ne computed via individual increase in inbreeding over the five periods analyzed is shown in Figure 2. Considering that in an ideal population with random matings, F would be half the AR, the larger than expected F-values would indicate an important subdivision and/or non-random mating pattern in the population. Animals 2021, 11, x FOR PEER REVIEW 7 of 15 the other hand, Ne was 4% smaller in the reference population considered (Ne = 196) than in the whole pedigree (Ne = 204). Table 1. Number of animals, number of equivalent complete generations (t), average generation interval (GI) and effective population size computed via individual increase in inbreeding (Ne) for the whole Caballo de Deporte Español Studbook and for the animals born between 2011 and 2021 (reference population). Population Number of animals t GI Ne Whole Pedigree 47884 1.95 10.87 204 Born between 2011 and 2021 6743 3.86 11.89 196 3.3. Effect of Genetic Selection on Inbreeding and Average Relatedness Coefficient of the Caballo de Deporte Español Population The mean inbreeding coefficient (F) and average relatedness (AR) for the whole CDE population were 0.32% and 0.09%, respectively, and for the reference population, they were 0.79% and 0.19%, respectively, whereas the population with animals showing an EBV over the population mean (EBV > 100) showed 0.27% and 0.19% for F and AR values, respectively. The hypothetical scenario where only CDE horses were allowed to be registered and reproduced, showed an F coefficient of 2.18% and an AR of 0.19%. The evolution of the above parameters in all the sets considered and of the Ne computed via individual increase in inbreeding over the five periods analyzed is shown in Figure 2. Considering that in an ideal population with random matings, F would be half the AR, the larger than expected F values would indicate an important subdivision and/or non-random mating pattern in the population. Figure 2. Evolution of average global inbreeding coefficient (F; orange solid line), for animals with breeding value over the mean for Show Jumping discipline (FEBV>100; orange dashed line) and for animals with both parents from CDE (FCDE; orange dotted line). Evolution of average global relatedness coefficient (AR; green solid line), for animals with breeding value over the mean for Show Jumping discipline or (AREBV>100; green dashed line) and for animals with both parents from CDE (ARCDE; green dotted line). All values are in percentage. Evolution of effective population size computed via individual increase in inbreeding was also included (Ne; blue solid line). Where P0 is the period with animals born before 2000, P1 between 2000 and 2004, P2 between 2005 and 2009, P3 between 2010 and 2014, and P4 after 2015. The results showed this subdivision in the three groups considered (total population, reference population and a hypothetical scenario with only CDE horses as reproducers), Figure 2. Evolution of average global inbreeding coefficient (F; orange solid line), for animals with breeding value over the mean for Show Jumping discipline (F EBV > 100 ; orange dashed line) and for animals with both parents from CDE (F CDE ; orange dotted line). Evolution of average global relatedness coefficient (AR; green solid line), for animals with breeding value over the mean for Show Jumping discipline or (AR EBV > 100 ; green dashed line) and for animals with both parents from CDE (AR CDE ; green dotted line). All values are in percentage. Evolution of effective population size computed via individual increase in inbreeding was also included (Ne; blue solid line). Where P0 is the period with animals born before 2000, P1 between 2000 and 2004, P2 between 2005 and 2009, P3 between 2010 and 2014, and P4 after 2015. The results showed this subdivision in the three groups considered (total population, reference population and a hypothetical scenario with only CDE horses as reproducers), with a progressive increase over periods for the whole population, going from almost 0% F and AR values in P0 to 0.86% and 0.19%, respectively, in P4. For animals with EBV > 100, Animals 2022,12, 1635 8 of 15 the F-values remained below 0.8% until P3, increasing considerably to almost 3.0% in P4, whereas the AR values remained below 0.4% over the four periods. Regarding the hypothetical scenario considered for the CDE population, the F-values increased considerably from almost 0.0% in P0 to almost 2.0% in P1 and P2 and continued increasing to 2.8% in P4. However, the AR values maintained a constant evolution with quite low values that went from 0.0% in P0 to a maximum of 0.25% in P4. In respect of Ne results, values in P0 and P4 were the lowest (around 180 animals), whereas P2 showed the highest Ne, with 237 horses. 3.4. Effects of Genetic Selection on the CDE Horse Breed Genetic variances and heritability values from the genetic models used in the routine genetic evaluations of Show Jumping, Eventing and Dressage disciplines, are shown in Table 2. Heritability values were higher for Dressage than for Eventing or Show Jumping disciplines, ranging from 0.26 for Points obtained at the Dressage Reprise (P R ), to 0.32 for Points for Gallop (P G ) and Points for General Impression (P GI ). On the other hand, Show Jumping discipline showed the highest variance values for all the genetic model components. Table 2. Estimation of variance components and heritability (h2) for the genetic evaluations computed for Show Jumping (SJ), Eventing (E) and Dressage (D) disciplines. Variables Variance Genetic Components h2(±SE) Animal Rider Rhi Pe Res TV SJ PS 93.22 - 193.43 55.58 1988.22 2330.44 0.04 (±0.0009) WTR 112.86 - 73.21 49.44 893.06 1128.57 0.10 (±0.0007) E PSSJ 8.70 1.26 - - 33.63 43.60 0.12 (±0.2635) FPD11.93 13.01 - - 36.19 61.12 0.12 (±1.0982) PSc 41.83 30.04 - - 281.05 352.91 0.12 (±2.9944) D PR4.09 5.53 - 6.28 9.38 25.29 0.26 (±0.0574) PW0.15 0.14 - 0.18 0.23 0.70 0.20 (±0.0002) PT0.14 0.11 - 0.19 0.21 0.65 0.31 (±0.0085) PG0.14 0.11 - 0.18 0.19 0.62 0.32 (±0.0011) PS0.13 0.11 - 0.19 0.21 0.64 0.30 (±0.1520) PGI 0.14 0.11 - 0.19 0.19 0.62 0.32 (±0.0009) Where PS = penalty score transformed to a positive scale; WTR = weighted total ranking; PS SJ = penalty score transformed to a positive scale of the Show Jumping exercise; FP D = final points obtained in the Dressage exercise; PS C = penalty score transformed to a positive scale of the Cross exercise; P R = points obtained at the dressage reprise; P W = points for walk; P T = points for trot; P G = points for gallop; P S = points for submission; P GI = points for general impression; Animal = additive genetic effect; Rider = rider effect; Rhi = rider-horse interaction effect; Pe = permanent environment effect; Res = residual effect; TV = total variance; and h2 = heritability. In order to ascertain the genetic change of the CDE breed regarding the objective trait, the EBV of Show Jumping, Eventing and Dressage performances characteristics and its evolution through the five periods considered was included in Table 3for the most influential founders and their descendants. Firstly, the 12 founders with the highest contributions to the entire CDE populations were included. Horses were ordered according to their year of birth. In the ‘Order’ column, the position of each founder in the ranking of global contributions and in each particular period was presented, showing the evolution of the ‘importance’ of each founder along time. Animals 2022,12, 1635 9 of 15 Table 3. Evolution of the genetic contribution of the twelve most contributing founders of the Caballo de Deporte Español breed in period 0, ordered by their contribution for each of the periods P1 to P4 (in percentage), with their mean estimated breeding value (EBV) and the mean EBV of its descendants (EBV d ) globally and per period, calculated based on the genetic evaluation of 2020 for Show Jumping (SJ), Eventing (Ev) and Dressage (Dr) disciplines. Founders F201 F464 F224 F445 F333 F203 F416 F1910 F229 F429 F430 F968 Year of Birth 1939 1950 1941 1950 1947 1939 1949 1963 1941 1949 1949 1956 Sex M F M F F F M M M M F M Breed TH OHB OHB SF SF TH TH HOLST AH PRE PRE PRE Contribution (%) 0.45 0.44 0.44 0.4 0.28 0.25 0.25 0.24 0.23 0.17 0.12 0.1 Order 1 2 3 4 5 6 7 8 9 10 11 12 Nd 5223 6641 6640 4632 3265 3672 3672 3233 1860 1623 1448 663 Global EBV SJ 101.3 101.5 101.5 101.7 102.4 103.2 103.2 98.9 98.6 98.7 99.3 99.9 Ev 108.4 106.1 106.1 105.1 109.8 107.4 107.4 107.8 108.2 107.6 108.9 111.1 Dr 98.7 97.2 97.5 96.8 100 99.4 99.4 100.7 100.4 107.2 102.7 - EBVd SJ 101.3 101.2 101.2 101.4 101.1 102.3 102.3 102.5 97.3 98.9 99.2 98.8 Ev 107.2 107.2 107.2 107.2 107.9 107.2 107.2 108.1 106.5 108.4 108.5 111 Dr 99.9 98.2 98.2 98.2 100.2 99.9 99.9 100 99.1 103 103 97.7 P0 Order 4 1 2 3 17 8 7 45 6 5 10 9 EBVd SJ 101.9 101.3 101.3 101.5 101.6 102.4 102.4 101.9 98.9 98.9 98.9 99.2 Ev 107.7 106.6 106.6 106.4 109 107.2 107.2 107.9 106.4 108.8 108.8 111.1 Dr 99.2 97.6 97.6 97.5 99.6 98.4 98.4 99.8 99.6 103 103 97 P1 Order 3 1 2 4 5 28 27 51 6 39 58 74 EBVd SJ 100.2 100 100 100.4 100.2 101.3 101.3 101.8 96.1 99.2 99.3 96.3 Ev 107.4 107.8 107.8 108 108.1 106.9 106.9 108.1 106.7 107 107.4 111 Dr 98.5 97.6 97.6 97.6 99 99.4 99.4 99.8 97.1 103.7 103.7 98.2 P2 Order 1 2 3 4 6 8 7 5 16 27 55 90 EBVd SJ 101.7 101.9 101.9 101.9 101.3 102.7 102.7 102.6 92.7 98.3 99.8 97.9 Ev 107.9 107.9 107.9 107.9 108.3 107.9 107.9 108 109.8 108.1 108.1 108.3 Dr 99.7 99.5 99.5 99.3 99.8 100.4 100.4 99.3 97.3 100.6 100.5 101.8 P3 Order 1 3 4 5 12 10 9 2 22 56 73 103 EBVd SJ 102.3 102.6 102.6 102.4 102.5 102.6 102.6 102.9 95.1 99.6 100.4 99.9 Ev 104.5 105.5 105.5 106.2 104.9 107 107 108.4 106.5 108 108 - Dr 104.5 104.9 104.9 104.7 104.5 104.2 104.2 101.6 97.5 104.6 104.6 103.6 P4 Order 1 3 4 2 18 16 17 5 109 101 129 461 EBVd SJ 102.2 102.9 102.9 102.7 103.7 103.3 103.3 104.9 94.3 - - - Ev 99 102.5 102.5 102.3 103.1 100.7 100.7 - - - - - Dr 104.3 103.2 103.2 103.2 104.5 100.5 100.5 102 - 106.3 106.3 104.7 Order indicates the order of the founder according to the percentage of contribution in the period/group considered, Nd is the number of all descendants of the founder throughout all periods, P0 is period with animals born before 2000, P1 between 2000 and 2004, P2 between 2005 and 2009, P3 between 2010 and 2014, and P4 after 2015. Results showed that the five most contributing founders for the whole CDE population were from TH (F201), OHB (F224 and F464) and SF (F333 and F445) breeds. They all showed an EBV for Show Jumping discipline above 101 (i.e., higher than the mean), and the mean EBVs of their descendants were between 101 and 102 (the superiority of these founders seems to be transmitted). In fact, there is a general upward trend through the periods for the EBVs of the descendants of the 12 founders listed, reaching up to 104. In respect of Eventing and Dressage disciplines, results showed that the ranking of individuals based on their EBVs was similar to the Show Jumping and Eventing performances but opposite to Dressage performance. These results are consistent with the negative genetic correlation found between Dressage and Eventing (−0.12 ±0.0199).