Genetic Diversity and Trends of Ancestral and New Inbreeding in German Sheep Breeds by Pedigree Data

Simple Summary Sheep breeding is a long-standing tradition throughout Germany. Due to breeding in marginal and harsh sites, sheep developed into a large number of unique breeds adapted to many different ecosystems. In this work, we study demographic measures of genetic diversity and inbreeding trends in 35 sheep breeds using the national database of herdbook breeders in Germany. This database is a valuable resource to manage and monitor diversity in breeding populations. The loss of genetic diversity was found in all breeds studied, mainly due to genetic drift rather than unequal use of founders. The analysis of pedigree data from more than 1.4 million sheep revealed an overall measure of inbreeding of F = 0.031, an individual rate of inbreeding of ΔFi = 0.0074, and a realized effective population size of Ne = 91.4 with 25–75% quartiles of 0.019–0.040, 0.0040–0.0086, and 57.9–125.3, respectively. Trends in individual inbreeding were significantly positive in meat and mountain sheep, but trends in the individual rate of inbreeding were only slightly positive. Country sheep showed significantly negative trends in the rate of individual inbreeding. Ancestral inbreeding had increasing trends in all sheep breeds. Our results demonstrate the efficiency of genetic diversity management and should help to conserve endangered breeds and maintain high genetic diversity in breeds used for wool, meat, and milk production. Abstract In Germany, many autochthonous sheep breeds have developed, adapted to mountain, heath, moorland, or other marginal sites, but breeds imported from other countries have also contributed to the domestic breeds, particularly improving wool and meat quality. Selective breeding and the intense use of rams may risk losing genetic diversity and increasing rates of inbreeding. On the other hand, breeds with a low number of founder animals and only regional popularity may not leave their endangered status, as the number of breeders interested in the breed is limited. The objective of the present study was to determine demographic measures of genetic diversity and recent as well as ancestral trends of inbreeding in all autochthonous German sheep breeds and sheep of all breeding directions, including wool, meat, and milk. We used pedigree data from 1,435,562 sheep of 35 different breeds and a reference population of 981,093 sheep, born from 2010 to 2020. The mean number of equivalent generations, founders, effective founders, effective ancestors, and effective founder genomes were 5.77, 1669, 123.2, 63.5, and 33.0, respectively. Genetic drift accounted for 69% of the loss of genetic diversity, while loss due to unequal founder contributions was 31%. The mean inbreeding coefficient, individual rate of inbreeding (∆Fi), and realized effective population size across breeds were 0.031, 0.0074, and 91.4, respectively, with a significantly decreasing trend in ∆Fi in 11/35 breeds. New inbreeding, according to Kalinowski, contributed to 71.8% of individual inbreeding, but ancestral inbreeding coefficients showed an increasing trend in all breeds. In conclusion, in our study, all but one of the mountain-stone sheep breeds and the country sheep breed Wald were the most vulnerable populations, with Ne < 50. The next most endangered breeds are exotic, country, and heath breeds, with average Ne of 66, 83, and 89, respectively. The wool, meat, and milk breeds showed the highest genetic diversity, with average Ne of 158, 120, and 111, respectively. The results of our study should help strengthen conservation program efforts for the most endangered sheep breeds and maintain a high genetic diversity in all sheep breeds.