Assessing losses of genetic variability in the endangered Mallorquí horse

Information contained in the studbook of the endangered Mallorquí horse was analysed to assess the genetic variability of the breed. Also, the effect of selection for coat colour variation was assessed using a set of 15 microsatellites genotyped on 68 Mallorquí reproductive individuals previously diagnosed for the presence of the chestnut allele on the melanocortin-1 receptor gene. Mean inbreeding for the whole pedigree (310 individuals) was 2.5% while that for the individuals born during the last three years of recording (reference population) was 4.7%. Only 70% of all the founders have genetic representation in the reference population. A comparison of the parameters such as effective number of founders, effective number of ancestors and founder genome equivalents documented that the losses of founder genes occurred very soon after the implementation of conservation strategies. The parameter FIS computed from genealogical information was positive (0.029) for the whole population and negative (-0.024) for the reference population, thus illustrating the effort of the Mallorquí horse breeders to avoid matings between relatives in later generations. A total of 14 individuals were heterozygotes for the chestnut allele (allele frequency of 10.6%). The rejection for reproduction of the chestnut heterozygote individuals would not affect the overall gene diversity of the population. However, the total allelic richness would decrease both at the within-subpopulation (1.2%) and total contribution level (0.4%). The chestnut heterozygote individuals are a within-breed reservoir of rare alleles that should be preserved to avoid risks for the future viability of the breed.