Sheep GEMS News Brief 8 – Early December 2024

The genetic diversity available within each sheep breed gives us tremendous opportunity to make genetic improvement. That snapshot of the genetic diversity currently available is extremely valuable since it provides a benchmark for comparing the consequences of selection over time in individual breeds. To establish that starting point, we used both pedigree- and molecular-based information to assess genetic diversity in the four breeds involved in Sheep GEMS.

For each of the breeds we evaluated—Katahdin, Polypay, Rambouillet, and Suffolk—we found substantial genetic diversity. That coincides with low inbreeding levels. So, what do we mean by inbreeding? Inbreeding arises from the mating of relatives, which leads to an increased chance that a lamb inherits identical copies of an allele from both its sire and dam. Such an increase in homozygosity is not necessarily bad. In fact, it is almost inevitable in a selection program where we retain rams and ewes with more favorable genotypes (or packages of alleles) for breeding. However, inbreeding does come with risks. Often, deleterious alleles are recessive. When that is the case, with inbreeding they will appear together in a homozygous state more often. That results in expression of their deleterious effects. Such negative consequences of inbreeding are most seen in fitness traits like health and reproductive success.

Increased inbreeding also coincides with reduced genetic diversity in a breed in general. Our ability to achieve good genetic progress in the long term depends on our having genetic variation to work with. So, in a well-designed breeding program, we need to balance an increase in inbreeding with strategies to track and maintain genetic diversity.

Another important concept related to genetic diversity is the effective population size (N_e), which is the number of individuals that effectively participate in producing the next generation. In other words, it is an estimate of the number of active breeding animals. The N_e is usually much less than the actual size of the population. We expect an N_e of 50 to lead to a rate of inbreeding of only 1% per generation. Consequently, we recommend an N_e of at least 50, although preferably at least 100.

For Katahdin, the inbreeding in the most recent generation averaged 1.7% with a rate of change of inbreeding of 0.025% per year. The N_e for the breed’s pedigree estimate ranged from 42 to 451 while the molecular-based estimate was 150 animals. These results are well within the recommended values and suggest the Katahdin breed has sufficient genetic diversity moving forward.

For Polypay, current pedigree-based inbreeding was 3.5% with an annual rate of inbreeding of 0.069% per year. The N_e ranged from 41 to 249 for pedigree-based methods and 118 for the molecular-based method. Furthermore, from our analyses of Polypay, the breed has become differentiated from the foundation flock at the U.S. Sheep Experiment Station, likely due to different selection objectives among NSIP flocks.

For Rambouillet, the current pedigree-based inbreeding was 2.0% and the rate of inbreeding per year was 0.079%. We estimated the average pedigree-based N_e to be 165 animals while the estimated molecular-based N_e was 392 animals. Therefore, like in Katahdin and Polypay, the Rambouillet is genetically diverse.

For Suffolk, the pedigree-based inbreeding was 5.5% for the most recent year while the annual rate of inbreeding was 0.015%. We computed the N_e using multiple pedigree-based methods, resulting in a range of 28 to 244. With the molecular-based method, the N_e was 79.5. The Suffolk analysis showed some disconnectedness within the breed, which is great for genetic diversity but less appealing for genetic evaluation, which relies on pedigree ties across flocks.

The take-home message from these studies is the genetic diversity of these four breeds is substantial and we can feel confident moving forward with genomic selection. However, we should repeat these analyses every 10 to 15 years to ensure we continue to maintain that genetic diversity.

For further information contact Dr. Carrie Wilson (carrie.wilson@usda.gov).

Acknowledgements. We thank U.S. sheep associations and breed organizations, the National Sheep Improvement Program, and sheep producers, for their contributions to this research. We supported this work through the Organic Agriculture Research and Extension Initiative (grant 2016-51300-25723/project accession no. 1010329), and by the Agriculture and Food Research Initiative Competitive Grant (grant 2022-67015-36073/project accession no. 1027785), from the USDA National Institute of Food and Agriculture. The USDA is an equal opportunity provider and employer. Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the USDA.