Genetic diversity and population structure of U.S. Suffolk sheep participating in the national sheep improvement program

Authors: Wilson, Carrie; MURDOCH, BRENDA - University Of Idaho; BRITO, LUIZ - Purdue University; Taylor, Joshua; ROCHA, ARTUR - Purdue University; Freking, Bradley; Murphy Jr, Thomas; LEWIS, RONALD - University Of Nebraska

Submitted to: Genetics Selection Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/12/2025
Publication Date: 1/14/2026
Citation: Wilson, C.S., Murdoch, B.M., Brito, L.F., Taylor, J.B., Rocha, A.O., Freking, B.A., Murphy Jr, T.W., Lewis, R.M. 2026. Genetic diversity and population structure of U.S. Suffolk sheep participating in the national sheep improvement program. Genetics Selection Evolution. 58. article 7. https://doi.org/10.1186/s12711-025-01027-4.
DOI: https://doi.org/10.1186/s12711-025-01027-4

Interpretive Summary: The Suffolk is the primary terminal sire sheep breed in the U.S. As the sheep industry moves toward the use of genomic data in national genetic evaluations, we need an understanding of the current levels of genetic diversity present in each breed to establish a baseline for future comparisons. The the primary objective of this study was to assess the current genetic diversity of U.S. Suffolk sheep using both pedigree- and genomic-based methods. Based on the pedigree (n = 75,161) and animals genotyped with the GGP Ovine 50K SNP chip (n = 1,878), measures of genetic diversity were computed, including inbreeding, effective population size, and differentiation among flocks. Primary findings showed that the rate of inbreeding was at an acceptable level, but the effective population size was modest, indicating that monitoring of genetic diversity and strategic mating of less related animals in the breed should continue. As the sheep industry moves forward, assessments of genetic diversity are needed every 10-15 years.

Technical Abstract: The Suffolk is the primary terminal sire breed in the U.S. with rapid early growth, heavy muscling, and superior feed efficiency. As a breed that participates in the National Sheep Improvement Program (NSIP), Suffolk breeders are attempting to accumulate enough genomic information to provide genomic-enhanced estimated breeding values as part of the national genetic evaluations. The genetic gains achieved from genomic selection may be accompanied by a loss in genetic diversity. Therefore, the primary objective of this study was to assess the current genetic diversity and population structure of U.S. Suffolk sheep included in the NSIP using both pedigree- and genomic-based methods. A secondary objective was to compare the levels of genomic diversity of U.S. Suffolk to those from other countries. Based on the pedigree (n = 75,161), the generation interval was 2.8 years, the effective number of founders and ancestors were 504 and 300, respectively. Effective population size ranged from 28 to 194 based on pedigree-based measures and 75 based on a genomic-based measure. When inbreeding was compared for the 1,878 genotyped animals (GGP Ovine 50K BeadChip) that passed quality control, pedigree-based inbreeding, Wright’s inbreeding, inbreeding based on runs of homozygosity, and inbreeding based on the genomic relationship matrix were 4.8, 3.3, 4.6, and 3.3%, respectively. Of the 16 flocks with genotyped animals, four had fixation index values that exceeded 0.10, but the model-based population structure showed admixture across all flocks. For the principal component analysis and the model-based population structure with international genomic datasets, the U.S. Suffolks were distinct, the United Kingdom Suffolks were placed in-between but distinct from the other countries, and the Australian, Irish, and New Zealand Suffolks were grouped together. In this study, the current level of genetic diversity and population structure was quantified for the U.S. Suffolk breed. While the rate of inbreeding was at an acceptable level, the effective population size was modest, indicating that monitoring of genetic diversity and strategic mating of less related animals in the breed should continue. As the sheep industry moves forward, assessments of genetic diversity and population structure are needed every decade.