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

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 US and international sheep breeds. We considered genotypes of 667 NSIP Rambouillet from a 50 K single nucleotide polymorphism (SNP) array and 600 K SNP genotypes on 64 each of NSIP Rambouillet, Suffolk, and Katahdin sheep. Pedigree analyses were also conducted on the NSIP Rambouillet. International comparisons incorporated 50 K 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 years, respectively. This pedigree and genomic assessment of genetic diversity provides the basis for genomic selection and monitoring of the NSIP Rambouillet.