Genetic diversity of United States Rambouillet, Katahdin and Dorper sheep

Authors: BECKER, GABRIELLE - University Of Idaho; THORNE, JAKE - University Of Idaho; Burke, Joan; LEWIS, RON - University Of Nebraska; NOTTER, DAVID - Virginia Tech; MORGAN, JAMES - Round Mountain Consulting; SCHAUER, CHRIS - North Dakota State University; STEWART, WHIT - University Of Wyoming; REDDEN, REID - Texas A&M University; MURDOCH, BRENDA - University Of Idaho

Submitted to: Genetics Selection Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/23/2024
Publication Date: 7/30/2024
Citation: Becker, G., Thorne, J., Burke, J.M., Lewis, R.M., Notter, D., Morgan, J.L., Schauer, C., Stewart, W., Redden, R., Murdoch, B. 2024. Genetic diversity of United States Rambouillet, Katahdin and Dorper sheep. Genetics Selection Evolution. https://doi.org/10.1186/s12711-024-00905-7.
DOI: https://doi.org/10.1186/s12711-024-00905-7

Interpretive Summary: Managing genetic diversity is critically important for maintaining species health, including that of domestic sheep. Excessive homozygosity (extreme similarity of genes or traits) caused by the loss of genetic diversity can have detrimental effects on a breed’s reproduction and production ability. Analysis of genetic diversity can facilitate the identification of signatures of selection (regions in the genome that have been preferentially increased in frequency and fixed in a population because of their functional importance in specific processes) which may contribute to the specific health, production and visual characteristics of a breed or population. In this study, breeds with well-characterized traits such as fine wool production (Rambouillet, N = 745), parasite resistance (Katahdin, N = 581) and environmental hardiness (Dorper, N = 265) were evaluated for inbreeding, and other measures of genetic diversity. This study described signatures of selection within diverse and economically important U.S. sheep breeds. The genes contained within these signatures are proposed for further study to understand their relevance to biological traits and improve understanding of breed diversity.

Technical Abstract: Managing genetic diversity is critically important for maintaining species health. Excessive homozygosity caused by the loss of genetic diversity can have detrimental effects on a breed’s reproduction and production ability. Analysis of genetic diversity can facilitate the identification of signatures of selection which may contribute to the specific health, production and visual characteristics of a breed or population. In this study, breeds with well-characterized traits such as fine wool production (Rambouillet, N = 745), parasite resistance (Katahdin, N = 581) and environmental hardiness (Dorper, N = 265) were evaluated for inbreeding, runs of homozygosity (ROH) and Wright’s fixation index (FST) signatures of selection and effective population size (Ne) at 36,113 autosomal SNPs. Rambouillet sheep had the largest Ne and strongest linkage disequilibrium decay over distance in this analysis. The slope of Ne over time was greatest from 15 to 17 generations ago for Rambouillet (m = 9.00) and 80 to 98 generations ago for Katahdin (m = 5.11), which may indicate the presence and timing of historic bottleneck events. The most highly conserved ROH island was identified in Rambouillet with a signature of selection on chromosome 6 containing 202 SNPs called in an ROH in 50-94% of the breed. This region contained genes DCAF16, LCORL and NCAPG that have been reported to be under selection in other studies and have biological roles related to growth and body weight traits. Outlier regions identified through both FST comparisons with Katahdin contained genes with known roles in milk production and mastitis resistance or susceptibility, and regions identified through analyses of Rambouillet identified genes related to wool growth, suggesting these traits have been under natural or artificial selection pressure in these populations. Genes involved in the cytokine-cytokine receptor interaction pathways were identified in all FST breed comparisons, suggesting differences in allelic diversity at the genetic regions responsible for different components of this immune pathway. This study described signatures of selection within diverse and economically important U.S. sheep breeds. The genes contained within these signatures are proposed for further study to understand their relevance to biological traits and improve understanding of breed diversity.