Whole-Genome Resequencing Reveals Selection Signal Related to Sheep Wool Fineness

SIMPLE SUMMARY: Wool is a very important agricultural product and an ideal raw material for the production of high-quality textiles and clothing. In addition, the wool industry provides important support for economic development and the livelihoods of rural communities, creating employment opportunities and sources of income for farmers. Whole-genome sequencing technology has important applications in the study of genetic diversity, population structure, and selection pressure in the sheep genome. In this study, we analyzed the population structure and genomic differences of eight breeds. In addition, we identified a series of candidate genes that may be related to hair follicle development, wool traits, lipid metabolism, and androgen metabolism. This study provides valuable genomic resources and a theoretical basis for future wool improvement. ABSTRACT: Wool fineness affects the quality of wool, and some studies have identified about forty candidate genes that affect sheep wool fineness, but these genes often reveal only a certain proportion of the variation in wool thickness. We further explore additional genes associated with the fineness of sheep wool. Whole-genome resequencing of eight sheep breeds was performed to reveal selection signals associated with wool fineness, including four coarse wool and four fine/semi-fine wool sheep breeds. Multiple methods to reveal selection signals (Fst and θπ Ratio and XP-EHH) were applied for sheep wool fineness traits. In total, 269 and 319 genes were annotated in the fine wool (F vs. C) group and the coarse wool (C vs. F) group, such as LGR4, PIK3CA, and SEMA3C and NFIB, OPHN1, and THADA. In F vs. C, 269 genes were enriched in 15 significant GO Terms (p < 0.05) and 38 significant KEGG Pathways (p < 0.05), such as protein localization to plasma membrane (GO: 0072659) and Inositol phosphate metabolism (oas 00562). In C vs. F, 319 genes were enriched in 21 GO Terms (p < 0.05) and 16 KEGG Pathways (p < 0.05), such as negative regulation of focal adhesion assembly (GO: 0051895) and Axon guidance (oas 04360). Our study has uncovered genomic information pertaining to significant traits in sheep and has identified valuable candidate genes. This will pave the way for subsequent investigations into related traits.