Equivalent effective population size mating as a useful tool in the genetic management of the Ibicenco rabbit breed (Conill Pages d’Eivissa)

The Ibicenco rabbit (Conill Pages D’Eivissa) is a rare breed mainly located on Ibiza Island, in rural areas. Today breeders are looking for a sustainable use and alternative routes for profitability of the population to avoid its extinction. The breed presents some variety in coat colour (brown, black, orange, and grey), and breeders would like to maintain these characteristics. The objectives of this study were to develop a method to design matings in a population with unbalanced pedigree depth in a scenario of maintaining the variety of coat colours, and to analyze the genealogical information of the Ibicenco rabbit to ascertain the genetic structure of the population. Equivalent effective population size mating was developed as a useful parameter to design the mating in this particular scenario. Results obtained by the initial application showed that this population was properly managed for maintaining the maximum genetic variability. This mating method is recommended to manage the genetic variability of this small rabbit population in a scenario of partial permanent colour structure. For the pedigree analysis, a reference population formed by 143 animals available for reproduction was used. A demographic study, a probability gene origin analysis, computation of inbreeding and effective size, and an analysis of genetic structure were done. The generation interval was approximately one year (11.8 months). The average number of equivalent generations was 3.4. The effective numbers of founders and ancestors were 10 and 11, respectively, and the founder genome equivalent was 6. The average inbreeding was 10.8%, but the mean inbreeding seems to have stopped increasing as a consequence of deeper monitoring in the mating design. The realized effective size was 9.6 (via inbreeding) and 17.5 (via coancestry). Regarding the genetic structure, the orange and black groups are the most distant genetically while grey and blacks are closer.