Genetic diversity of US Rambouillet in the National Sheep Improvement Program compared to other sheep breeds

Authors: SCHULZ, EMILY - University Of Nebraska; NILSON, SARA - University Of Nebraska; Murphy Jr, Thomas; MURDOCH, BRENDA - University Of Idaho; BRITO, LUIZ - Purdue University; LEWIS, RONALD - University Of Nebraska; PETERSEN, JESSICA - University Of Nebraska

Submitted to: Journal of Heredity
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/2/2025
Publication Date: 3/1/2026
Citation: Schulz, E.J., Nilson, S.M., Murphy, T.W., Murdoch, B.M., Brito, L.F., Lewis, R.M., Petersen, J.L. 2026. Genetic diversity of US Rambouillet in the National Sheep Improvement Program compared to other sheep breeds. Journal of Heredity. 117(2):211-221. https://doi.org/10.1093/jhered/esaf079.
DOI: https://doi.org/10.1093/jhered/esaf079

Interpretive Summary: The Rambouillet breed has been the foundation of the western U.S. sheep industry since the late 1800s. Known for its high quality wool production, hardiness, and long breeding season, the Rambouillet is not only reared as a purebred but has contributed to the development of many composite sheep breeds throughout the world. The National Sheep Improvement Program (NSIP) is the only U.S. provider of estimated breeding values (EBV), or predictions of individual genetic merit, for economically important traits. Rambouillet account for 11% of total NSIP records, the third most among purebred sheep. Future breeding strategies within Rambouillet, including the incorporation of genomic-enhanced EBV, rely on understanding its population structure. The objective of this study was to evaluate genetic diversity in Rambouillet enrolled in the NSIP in comparison to other sheep breeds using both pedigree and genomic relatedness metrics. The NSIP Rambouillet were both distinct from and more diverse than the NSIP Suffolk and Katahdin. The NSIP Rambouillet also had lower mean inbreeding coefficient, providing further support of their greater diversity compared to the NSIP Suffolk and Katahdin. However, the NSIP Rambouillet had lower genetic diversity than the international breeds considered, including several populations of Merino which is a close relative to Rambouillet. These results provide a basis for monitoring and maintaining genetic diversity while continuing to genetically improve performance and health within NSIP going forward.

Technical Abstract: Breed management and genomic evaluation rely on understanding population structure and genetic diversity. The primary objective of this study was to evaluate genetic diversity in Rambouillet enrolled in the National Sheep Improvement Program (NSIP) in comparison to other U.S. and international sheep breeds. We considered genotypes of 667 NSIP Rambouillet from a 50K single nucleotide polymorphism (SNP) array and an additional 600K SNP genotypes on 64 each of NSIP Rambouillet, Suffolk, and Katahdin sheep. Pedigree analyses were also conducted on the NSIP Rambouillet. International comparisons incorporated 50K SNP data from nine international breeds. After genomic quality control measures to reduce bias in analyses, the NSIP Rambouillet had the greatest diversity among the three NSIP breeds (expected heterozygosity: 0.404; average individual inbreeding: 9.94%). Conversely, the NSIP Rambouillet had the lowest genetic diversity when compared to the international breeds. Based on principal component analyses, NSIP Rambouillet were divergent from the international populations except for evidence of connectivity between the NSIP and European Rambouillet. Population structure within the NSIP Rambouillet, demonstrated by cluster analysis and a significant loss of heterozygosity (FIS) was driven primarily by one flock. Using complete pedigrees of the NSIP population, effective population size, effective number of founders, and average generation interval was 87 to 218, 95, and 3.4 yr, respectively. This pedigree and genomic assessment of genetic diversity provides the basis for genomic selection and monitoring of the NSIP Rambouillet.