Assessing population structure and genetic diversity in U.S. Suffolk sheep to define a framework for genomic selection

Authors: Wilson, Carrie - Welsh; PETERSEN, J - University Of Nebraska; Blackburn, Harvey; LEWIS, R - University Of Nebraska

Submitted to: Journal of Heredity
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/13/2022
Publication Date: 5/16/2022
Citation: Wilson, C.S., Petersen, J.L., Blackburn, H.D., Lewis, R.M. 2022. Assessing population structure and genetic diversity in U.S. Suffolk sheep to define a framework for genomic selection. Journal of Heredity. 113(4):431-443. https://doi.org/10.1093/jhered/esac026.
DOI: https://doi.org/10.1093/jhered/esac026

Interpretive Summary: Long-term sustainability of breeds depends on having sufficient genetic diversity for adaptability to change. Genetic diversity in U.S. Suffolk sheep was evaluated using pedigree and molecular methods. We observed a decline in genetic diversity over time. Genetic differences among flocks was evident and was not due to geographic distance. An international comparison of U.S., Australian, and Irish Suffolk showed each countries population was distinct. The results provide a framework for establishing a genomic reference population in U.S. engaged in the national evaluation program. This research also provides a baseline for genetic diversity prior to the implementation of genomic selection and the opportunity for the breed to assess the impact of genomic selection on the population over time.

Technical Abstract: Long-term sustainability of breeds depends on having sufficient genetic diversity for adaptability to change, whether driven by climatic conditions or by priorities in breeding programs. Genetic diversity in Suffolk sheep in the U.S. was evaluated in four ways: 1) using genetic relationships from pedigree data [(n=64,310 animals recorded in the U.S. National Sheep Improvement Program (NSIP)]; 2) using molecular data (n=304 Suffolk genotyped with the OvineHD BeadChip); 3) comparing Australian (n=109) and Irish (n=55) Suffolk sheep to those in the U.S. using molecular data; and 4) assessing genetic relationships (connectedness) among active Suffolk flocks (n=18) in NSIP. By characterizing genetic diversity, a goal was to define the structure of a reference population for use for genomic selection strategies in this breed. Pedigree-based mean inbreeding level for the most recent year of available data was 5.5%. Ten animals defined 22.8% of the current gene pool. The effective population size ranged from 27.5 to 244.2 based on pedigree, and was 79.5 based on molecular, data. Expected and observed heterozygosity were 0.317 and 0.306, respectively. Model-based population structure included 7 subpopulations. Principal Component Analysis of country populations demonstrated their unique structure. Within the U.S. population, flocks formed genetically disconnected clusters. A decline in genetic diversity over time was observed from both pedigree and genomic-based derived measures with evidence of population substructure as measured by Fst. Using these measures of genetic diversity, a framework for establishing a genomic reference population in U.S. Suffolk sheep engaged in NSIP was proposed.