Sequencing of mitochondrial DNA from 53 Slovenian Lipizzans revealed 17 distinct mtDNA haplotzpes: ten haplotypes (Capriola, Allegra, Monteaura, Slavina, Batosta, Gratiosa, Wera, Betalka, Dubovina and Gaetana) were present in classical mare families, haplotype Thais in the new Slovenian mare family Rebecca and haplotypes C, M, Strana, Trompeta, Boka and Y in mare families of Croatian, Romanian or Hungarian origin. We expected large amount of "classical" haplotypes, because after 1947 the Lipizzan breed in Slovenia was re-established using mainly Lipizzans from classical mare families. However, Lipizzans from incorrect mare families were probably used for the recovery of three classical families and therefore in these three families Slovenian Lipizzans had different haplotypes than other European Lipizzans. Additional pedigree errors were detected in four families showing more than one haplotype. We suggested that pedigree errors should be corrected by introduction of several new mare families and by minor re-distributions of Lipizzans among mare families. Geographical origin of the Lipizzan haplotypes remains uncertain, but haplotypes Allegra and Monteaura could be of Spanish origin due to the highest frequency of these haplotypes in Iberian (Andalusian and Lusitano) and North African horses (Barbs). Kladrubian origin of haplotypes Batosta and Slavina, which are characteristic for Lipizzan mare families of Kladrubian origin, Africa and Almerina, could be supported by the presence of both haplotypes in the present Kladruber horses. The Arabic origin of haplotype Gaetana, which is characteristic for the Lipizzan mare family of Arabic origin, could be supported by the high frequency of the haplotype Gaetana in Arabian horses.
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