Whole-Genome Resequencing Reveals Selection Signatures Associated With Lambskin Patterns in Hu Sheep.

Abstract

In China, Hu sheep lambskin quality is largely determined by wool curvature, with wavy-wool lambs producing higher-quality pelts than straight-wool lambs. However, the genetic mechanisms underlying wool curvature formation remain poorly understood. To address this knowledge gap, we conducted whole-genome resequencing and transcriptomic analyses to identify candidate genes associated with wool curvature in Hu sheep. Phenotypic records from 3047 Hu lambs identified significant differences between wavy- and straight-wool groups. Twenty representative animals (10 per group) were selected for whole-genome resequencing. Selective sweep analyses based on the fixation index (FST), absolute log2-transformed nucleotide diversity ratio [|log2(π ratio)|], and Tajima's D (TajD) identified 157 genomic windows under positive selection. Four major genomic regions showing strong selective signatures were located on chromosomes 4, 7, 13, and 18. Several biologically relevant candidate genes were identified within these regions, including KRTDAP, FGF2, FGF7, OCLN, MAPK1, SHC4, LAMA2, and COL9A3. Functional enrichment analysis indicated that these genes are primarily associated with extracellular matrix (ECM) organization, focal adhesion, PI3K-Akt, MAPK, and Ras signaling pathways. In addition, RNA sequencing (RNA-seq) data from an independent cohort of eight lambs were integrated with genomic selection signals. This integrative analysis identified 61 overlapping genes, from which 12 high-confidence candidate genes were prioritized, including LUM, COL6A1, SPARC, ITGA11, and DCLK1. These findings highlight genomic regions and candidate genes potentially associated with ECM remodeling and other biological processes relevant to lambskin pattern formation, providing valuable genomic resources for future functional studies and marker-assisted selection in Hu sheep.