Removal of undesirable MC1R gene alleles from ‘Berrenda en Negro’, an endangered Spanish cattle breed, to enhance breed conservation programs

‘Berrenda en Negro’ (BN) is an endangered Spanish cattle breed with substantial ecological and cultural value and meat quality. Phenotypically, it is differentiated by its black-sided coat pattern. The goal of this study were to analyse the presence of unwanted alleles at the MC1R locus (E⁺ and e) and propose appropriate selective strategies for their eradication from the population. Both goals were based on the identification of genotypes of the MC1R locus using genetic markers and DNA microsatellites, to identify changes in the genetic variability of the resulting populations after applying selective strategies to decrease the frequency of red and wild-type alleles. Introgression and crossbreeding of BN with other Iberian cattle breeds in the past has left undesirable E⁺ and e alleles, with frequencies of 7 and 12%, respectively. The extent to which the genetic variability of the BN population could be affected by selection strategies was quantified in terms of the number of affected animals and farms, effective population size (Ne) of the remaining genetic variability, and loss of gene diversity and allelic richness. The neutral genetic diversity found in BN suggested that selection strategies for the MC1R gene are possible. These strategies should be implemented progressively, in combination with extensive mating control. The best strategy to eliminate unwanted MC1R alleles in the short term would be to remove all cattle with the Eᴰe genotype in the first phase, followed by a second phase, in which the EᴰE⁺ genotype would be eradicate after the recovery of the population to its effective size. The results of this study will assist the BN Breeders Association to managing the conservation program for the breed.