Genetic diversity, admixture and the effect of inbreeding on milk performance in two autochthonous goat breeds

For the development of an appropriate program for the conservation of animal genetic resources, careful evaluation of the current genetic diversity in endangered breeds was performed. Pedigree data from a total of 38,288 animals registered in studbooks between 1970 and 2017 from two autochthonous Czech goat breeds, White and Brown Shorthair goats, were analysed to identify factors that may have affected the genetic variability of the breeds. Because the populations of both breeds are closed, there is concern about the loss of genetic variation. The average numbers of equivalent complete generations were 10 and 11 for White Shorthair goat and Bowen Shorthair goat, respectively. The effective numbers of founders contributing to the current genetic pool were 323 and 45, and the effective numbers of ancestors were 90 and 24, respectively. The average inbreeding and relatedness coefficients for the reference populations of the two breeds were 2% and 5.3%, respectively, for White Shorthair goats and 3.7 and 11.5% for Brown Shorthair goats. The corresponding estimates of the effective population size based on an increase in inbreeding or coancestry were 244 and 311, respectively, for White Shorthair goats and 82 and 87 for Brown Shorthair goats. Three kinds of inbreeding coefficients, the classical inbreeding coefficient, the new inbreeding coefficient and the ancestral inbreeding coefficient, were used to quantify the effects of inbreeding and purging on milk production in both analysed breeds. All tested inbreeding coefficients (F-x, F-n(ew)) showed a significantly negative influence on milk performance in the White Shorthair goat breed. The purging effect was confirmed based on the difference between F-x and F-new, in White Shorthair goats and on the suitability of the statistical model in Brown Shorthair goats. These statistics suggest that genetic variability has decreased and inbreeding depression has occurred and that without changes in the breeding strategy, genetic variability might continue to decline.