Genome-wide associations with body and fleece weight in United States sheep

Authors: BECKER, GABRIELLE - University Of Idaho; SCHAUB, DANIEL - University Of Idaho; Taylor, Joshua; Mousel, Michelle; Wilson, Carrie; SMITCHGER, JAMIN - University Of Idaho; THORNE, JACOB - Texas A&M Agrilife; MURDOCH, BRENDA - University Of Idaho

Submitted to: Frontiers in Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/23/2025
Publication Date: 6/24/2025
Citation: Becker, G.M., Schaub, D., Taylor, J.B., Mousel, M.R., Wilson, C.S., Smitchger, J., Thorne, J., Murdoch, B. 2025. Genome-wide associations with body and fleece weight in United States sheep. Frontiers in Genetics. 16(7). Article 733. https://doi.org/10.3390/genes16070733.
DOI: https://doi.org/10.3390/genes16070733

Interpretive Summary: Selection for average and lifetime fleece weights in sheep can improve profitability for producers. Understanding the SNPs and genes related to variation in wool growth would improve understanding of this important biological product and facilitate the creation of more accurate indices to balance fleece weight gains with other production goals. This study used GWAS to identify genetic variants potentially associated with relevant traits, including lifetime and average greasy fleece weight and average post-lambing ewe weight. Many of the genes proposed by these analyses are involved in pathways crucial for hair follicle initiation and cycling, or have been implicated by previous signatures of selection or association studies for body weight and related traits. This study provides further evidence towards the importance of these genes and suggests SNPs of interest for further consideration.

Technical Abstract: Wool is an important product in sheep production, but the genetic mechanisms underpinning variation in wool growth are not fully understood. Identifying the genes and genomic variants that play a role in increasing fleece weight may allow for increased selection accuracy and improved economic return to producers. A genome-wide association study (GWAS) was conducted to investigate genetic associations with lifetime fleece weight, average fleece weight and average post-lambing ewe weight for Rambouillet, Polypay, Suffolk and Columbia ewes (N = 1,125). The GWAS were conducted with GCTA using mixed linear model association (MLMA) with 501,560 autosomal markers. Additionally, Weir-Cockerham FST and runs of homozygosity (ROH) analyses were conducted to improve detection of putative wool-related signatures. Fifteen genome-wide significant (P-value < 9.97e-08) and nine chromosome-wide significant (P-value < 8.87e-07) SNPs were identified through GWAS. Chromosomes 2 and 6 contained ROH islands present in more than 70% of the Rambouillet, and chromosomes 2, 3, and 10 contained ROH islands in more than 70% of the Suffolk sheep. The FST analysis identified 725 SNPs in proximity to 1,005 genes of interest. Many of the genes implicated by GWAS have been previously reported in sheep transcriptomics or signature of selection studies for follicle growth or wool fineness, including ADAR, KCNN3, NTN1, SETBP1, TP53 and TNFSF12. The highly conserved ROH on chromosome 6 in Rambouillet contains the genes LCORL, NCAPG and LAP3, which have been previously implicated through signatures of selection and association analyses with production traits in sheep. Review of the genes identified through FST revealed pathways important for hair follicle initiation and development, including JAK-STAT, MAPK, mTOR, Notch, NF-'B, PI3K/AKT, Sonic hedgehog signaling and Wnt signaling. Together, these findings support many of the current candidate genes for wool growth and contribute to understanding of the genetic basis for wool development. The SNPs implicated by GWAS may be used to predict ewes’ potential for lifetime wool production and are suggested as candidates for further study to continue to elucidate the genetic mechanisms underlying wool production traits in United States rangeland sheep breeds.