Population genetic structure and conservation management of Retinta Extremeña goats

- We have found considerable gene diversity in the breed.
- The population is not at mutation-drift equilibrium under two-phase mutation model.
- It has been produced the introduction of new genetic material into the breed recently.
- The population is split into six differentiated small subpopulations.
- There is a certain degree of genetic flow among the sampled herds.

Genetic diversity, genetic Bottleneck hypothesis and population genetic structure were examined in the Retinta goat breed, endangered breed from Extremadura (Spain), with conservation management purposes. Twenty two microsatellite markers were used to genotype 271 animals belonging eight different sampling regions reproductively isolated. Estimates of genetic variability such as average number of alleles per locus (9.27 ± 0.54), effective number of alleles (ne = 4.01) and the expected gene diversity (He = 0.709 ± 0.025) revealed substantial genetic variation in the breed, even greater than other Spanish and European breeds not threatened. The global values obtained for the Wright's fixation index indicate the existence of a certain degree of inbreeding in the total population (FIT = 0.077). However, the decrease of heterozygotes is a consequence of the subdivision of the population (FST = 0.072), rather than to inbreeding in subpopulations (FIS = 0.006). The FST value found in this population was similar to obtained in other Spanish goat breeds. Population substructure was also confirmed by clustering analyses performed by STRUCTURE software and by the modal value of the distribution of the ΔK, showing clear membership of individuals in six clusters. The assignment of individuals to pre-defined sampling regions showed a clear drift of Retinta goat population, although it is also detected a certain degree of genetic flow (immigrant and admixed animals) among the sampled herds located in these regions. Recent bottleneck has not been detected in the Retinta goat population; however, the population experienced heterozygosity deficiency indicating that the population has undergone a size increase or expansion without immigration, or the introduction of unique alleles by immigrants. Based on the above results we designed a conservation program which aims the maintenance and sustainable use of the breed in its geographical and socioeconomic environment, preserving breed purity and maximum genetic variability. This program is based on maintaining live animals in a conservation nucleus with a minimum coancestry mating system and constant family sizes, and on the cryopreservation of germplasm.