Genomic diversity of U.S. katahdin hair sheep

Authors: NILSON, SARA - University Of Nebraska; Burke, Joan; BECKER, GABRIELLE - University Of Idaho; MURDOCH, BRENDA - University Of Idaho; PETERSEN, JESSICA - University Of Nebraska; LEWIS, RON - University Of Nebraska

Submitted to: Journal of Animal Breeding and Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/15/2024
Publication Date: 11/27/2024
Citation: Nilson, S., Burke, J.M., Becker, G.M., Murdoch, B., Petersen, J., Lewis, R.M. 2024. Genomic diversity of U.S. katahdin hair sheep. Journal of Animal Breeding and Genetics. https://doi.org/10.1111/jbg.12914.
DOI: https://doi.org/10.1111/jbg.12914

Interpretive Summary: Sheep producers using genetic/genomic selection through programs such as the National Sheep Improvement Program strive to improve traits such as parasite resistance and increased lamb growth. It is important to understand and maintain genetic diversity within a breed which can be compromised with intense selection. The objective of collaborators from University of Nebraska, USDA-ARS, and University of Idaho was to characterize the genomic population structure and diversity present in the breed and determine the subsequent impact on the accuracies of genomic predictions. It was determined that flocks within NSIP are genetically connected which improves accuracy of genomic predictions. The breed has adequate diversity so that genetic selection should yield favorable responses, but intense selection has the potential to cause loss of genetic diversity. These results are important to the U.S. sheep industry, the producers and consultants, geneticists and other scientists involved in improving sheep production.

Technical Abstract: In the late 1950s, Katahdin hair sheep were developed as a composite breed of medium size and moderate prolificacy, with potential to express resistance to gastrointestinal nematodes. With its increasing popularity and the recent adoption of genomic prediction in the breeding program, monitoring the genetic diversity of this breed is necessary as there is a risk of decreasing variation with selection based on genomically-enhanced estimated breeding values. While Katahdin pedigrees are readily available sources for estimating diversity, they may not capture the entirety of genetic relationships available compared to genomic data. We aimed to characterize the genomic population structure and diversity present in the breed and determine the subsequent impact on the accuracies of genomic predictions. Genotypes on Katahdin sheep from 81 member flocks in the National Sheep Improvement Program (NSIP) were used. After quality control, there were 9,705 animals and 31,984 autosomal single nucleotide polymorphisms remaining. Population structure was minimal; based on principal component (PC) analysis, the first two PC explained only 9% of the variation in the population. Subpopulations were not detectable, as a single ancestral population explained 99.9% of the genetic variation among animals and identity-by-state clustering placed all animals into a single cluster. At the founding of the breed, effective population size (Ne) was estimated to be 310 while the current Ne was estimated to be 150. Despite differences in trait heritabilities, the current effect of Ne on the accuracy of genomic predictions suggested that the breed should aim for a reference population size of 15k. The average degree of inbreeding estimated from runs of homozygosity (ROH) was 16.59% ± 4.66%. Across the breed, 18.4% of the chromosomes were covered by ROH. Four genomic regions, previously associated with production traits, contained ROH shared among > 50% of the breed. Across four methods, average genomic inbreeding coefficients ranged from 0.011 to 0.012. Overall, the Katahdin breed has no detectable population structure and has low levels of inbreeding. The current diversity of the breed reflects genetic connectedness across flocks due to the sharing of animals which will reduce bias in genomic predictions. Shared regions of interest should be further explored for incorporation of functional effects into genomic predictions to increase selection gains. Negative impacts on genetic diversity due to genomic selection are not of immediate concern for Katahdin sheep engaged in NSIP.