Pedigree analysis in the Andalusian horse: population structure, genetic variability and influence of the Carthusian strain

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The studbook of the Andalusian horse comprising a total of 75,389 individuals (6318 of them classified as Carthusians) was analysed in order to ascertain the genetic history of the breed and, specially, to evaluate its genetic variability and the influence of the Carthusian strain in the breed. Although there is no possible way to identify studs acting as Nucleus in the breed, there is a high concentration of genes and individuals' origin. The effective number of studs producing grandfathers was of 10.6. The equivalent number of founders was 1948.5 individuals (370.5 Carthusians). The effective number of founders was 39.6 and the effective number of ancestors 27. Only 6 ancestors were necessary to explain 50% of the genetic variability of the breed. The average values of inbreeding and average relatedness for the whole Andalusian horse population were, respectively, 8.48% and 12.25%. The same values for the Carthusian strain were higher (9.08% and 13.01%) even thought the generation interval for the strain was larger than that for the whole population (12.43 versus 10.11 years). In any case, inbreeding in Andalusian horse breed seems to have a remote origin and linked to the Carthusian individuals. The total contribution of the Carthusian founders to the populations accounted for up to 87.64% of the population. In turn the Carthusian ancestors explained 80.46% of the genetic variability of the breed. No differentiation was found between Carthusian and non-Carthusian reproductive individuals using genealogical FST (0.000026). It can be concluded that the distinction between Carthusian and non-Carthusian individuals within the Andalusian horse breed does not have genetic support. The unbalanced use of the Carthusian individuals with lower average relatedness values for reproduction is proposed to preserve the genetic variability of the breed.