Founder and present maternal diversity in two endangered Spanish horse breeds assessed via pedigree and mitochondrial DNA information.

Pedigree information and 179 mtDNA sequences from two endangered Spanish horse breeds, the Asturcón pony (143) and the Mallorquí horse (36), were analysed to asses: (i) the pedigree and molecular maternal genetic diversity of the two breeds; (ii) the concordance between the dam lines recorded in the corresponding studbooks and the mtDNA haplotypes identified; and (iii) to assess the losses of maternal genetic variability occurred from the foundation of the studbooks to present. Up to 50 Asturcón and 18 Mallorquí founder dam lines were identified in the studbooks analysed. Up to 315 Asturcón mares and 51 Mallorquí mares that foaled in the last 5 years of recording formed a reference population. Only 35 Asturcón and 13 Mallorquí founder dam lines were represented in their reference populations. Sequences from a total of 38 Asturcón and 12 Mallorquí dam lines could be obtained. The 179 sequences obtained gave 15 different haplotypes, 11 and 9 of them being identified, respectively, in the Asturcón pony and in the Mallorquí horse. Five different haplotypes (roughly two-thirds of the sequences) were shared by the two horse breeds. Most dam lines analysed had a single mtDNA haplotype. However, more than one haplotype was detected within eight of the dam lines in Asturcón pony. The found inconsistencies are likely to result from deficiencies in genebank management. The maternal N(e) (mN(e)) computed using the dam line information was higher in the Asturcón pony (20.5) than in the Mallorquí horse (15.9), while these figures were on the opposite direction for the haplotypic line information (6.4 and 9.4, respectively). The ratio of the computed mN(e) values to the actual number of founder dam lines were always higher in the Mallorquí horse probably due to a more balanced distribution of individuals kept for reproduction among studs. Consequences for the conservation programmes of the analysed breeds are discussed.