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

Abstract Background The Suffolk is the primary terminal sire breed in the U.S. 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 effective implementation of genomic selection and management of genetic diversity in the breed require a comprehensive assessment of current genetic diversity and population structure. Therefore, the primary objective of this study is to assess the genetic diversity and population structure present in U.S. Suffolk sheep included in the NSIP using both pedigree- and genomic-based methods. A secondary objective is to compare the levels of genomic diversity of U.S. Suffolk to those from other selected countries. Results Based on pedigree (n = 75,161) analyses, the generation interval was 2.8 years, and 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 to 85 based on genomic-based metrics. When the mean inbreeding was compared for the 1,878 genotyped animals (GGP Ovine 50 K BeadChip) that passed quality control, pedigree-based inbreeding; and, inbreeding based on heterozygosity, runs of homozygosity, diagonal of the genomic relationship matrix, and homozygous-by-descent segments were 4.8%, 3.3%, 4.6%, 3.3%, and 3.4%, 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. Conclusions 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, regular assessments of genetic diversity and population structure are needed.