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Abstract: Spanish heavy horses play a very important role in keeping up ecologically important rural areas. The interest in their conservation and characterization has increased over the last few years. The aim of this work is to contribute to the characterization of the endangered Spanish heavy horse populations in order to obtain useful information to implement conservation strategies for these genetic stocks. A total of 426 horses from six Spanish heavy horse populations corresponding to the four main heavy horse breeds (Hispano-Breton (HB) – with most animals located in three areas: Burgos (HBbu), León (HBle) and Palencia (HBpa) – Jaca Navarra (JN), Burguete (B) and the Cavall Pirinenc Català (CPC)) were analysed using 22 body measurements, 10 indices calculated from the body measurements and 16 microsatellite markers. From a morphological point of view, all the populations are clearly differentiated, except for the HBpa female population, which is located between the HBbu and JN populations. The HBle has greater body size than the other populations analysed, especially when compared to the JN. The genetic analysis provides us with information about the history of the analysed breeds. However, the most important point borne out by this analysis is the clear identification of different genetic backgrounds within the Spanish heavy horse populations. The overall information given in this work leads us to consider that the genetic scenario of the Spanish heavy horses is more likely to be due to ‘ancestrally’ different genetic backgrounds. Spanish heavy horse breeds resulted from the crosses between native mares and foreign stallions. The CPC population was the first in which this introgression occurred and the use of foreign stallions became more common. This work presents results based on neutral genetic variation, but also within- and between-population differences in morphological traits that have undergone artificial or natural (adaptive) selection. This information should be taken into account in future conservation strategies in order to contribute towards the efficiency of conservation measures. In this sense, the main problems are the small population size and genetic degeneration, with the consequent future loss of diversity. Therefore, the most immediate and effective conservation priorities would be (1) to avoid inbreeding within populations, (2) to increase the population size, and (3) to facilitate genetic exchange among the populations. [Copyright &y& Elsevier]

The genetic structure and level of diversity were assessed across 6 riding-horse breeds raised in Spain and born between 1989 and 2012 (Anglo-Arab, AA; Arab Purebred, PRA; Spanish Purebred, PRE; Menorca Purebred, PRMe; Spanish Sport horse, CDE; Spanish Trotter horse, TRO). The impact of selection on molecular diversity over time looking at 2 different cohorts in Crossbreds (AA, CDE and TRO) vs Purebreds (PRA, PRE and PRMe) has been also analysed. A total of 17 microsatellite loci were analysed in 2,530 horses from the cohort 1 (C1, born between 1989 and 2000) and 10,102 horses from the cohort 2 (C2, born between 2001 and 2012). The mean number of alleles per locus was the highest in C2 of TRO horses (11.76) and the lowest in C1 of PRMe breed (7.71). The lowest global values for the expected heterozygosity were found within Purebreds (0.71–0.76) compared to Crossbreds (0.76–0.78). For C2, the effective population size values based on linkage disequilibrium (from 4.9 in PRA to 668.3 in PRE) were higher than those computed for C1 (from 3.3 in PRA to 204.1 in CDE). Genetic distances and structure analysis showed that a significant amount of genetic variation is maintained due to an increase in the genetic uniformity across generations in Pure and Crossbreds. PRA, CDE and AA breeds seem to be the most genetically related, and for PRE, PRMe and TRO, both cohorts appeared closely related. In all populations, the genetic variability and effective population size have increased over time. Thus breeding policies have been properly managed to preserve diversity levels. Regarding the intense impact of selection in Purebreds across generations shown through the differences in the structure of the populations, no loss of genetic variability is expected in a short-term, although an extremely high degree of similarity and homogeneity between individuals of Purebreds compared to Crossbreds was shown. [ABSTRACT FROM AUTHOR]