Crossbreeding can improve production performance and meat quality in sheep. The objective of this study was to look for genes related to sheep growth, development, and muscle. In this study, Dorper (DP) × Small Tailed Han (STH) sheep and Mongolia (MG) × Small-tailed Han (STH) sheep were used to estimate the productive performance and meat quality in a crossbreed. Subsequently, transcriptome analysis and bioinformatic analysis were performed on the Longissimus dorsi muscles of DP × STH and MG × STH sheep to identify differentially expressed genes (DEGs) related to growth, development, and meat quality. The presence of DEGs was confirmed by real-time PCR (qPCR). Productive performance and meat quality of the DP × STH sheep were better than the MG × STH sheep. Compared to DP × STH, a total of 1445 DEGs were identified in MG × STH sheep (1026 DEG were up-regulated and 419 DEG were down-regulated). Of these, 38 DEGs were related to growth, 161 to development, and 43 to muscle. In addition, 13 co-expressed genes (FGFRL1, SIX1, PLCB1, CRYAB, MYL2, ADIPOQ, GPX1, PPARD, GPC1, CDC42, LOC101106246, IGF1, and LARGE) were identified. The expression of DEGs was consistent with the comparative transcriptome analysis. This work provides genetics resources for future research on muscle development in sheep.

SNPs associated with important traits of fine-wool sheep that were previously obtained through genome-wide association analysis screening were verified and analyzed. A total of 20 SNPs related to birth weight, bundle strength, cleaning rate, and fiber diameter were screened using whole-genome resequencing, and the SNPshot assay was used to detect and analyze polymorphisms. This study found that, among the 20 SNPs associated with important traits in Alpine Merino sheep, 8 were monomorphic and 12 were polymorphic, of which 6 showed moderate polymorphisms and 6 showed low polymorphisms. The heterozygosity of the 12 polymorphic loci ranged from 0.10 to 0.49, the effective number of alleles ranged from 1.11 to 1.98, and the polymorphic information content ranged from 0.09 to 0.37. The chi-square test showed that only RHPN2:g.42678119T>G and RALYL:g.90030866A>G were in Hardy–Weinberg disequilibrium (p < 0.05); the other loci were in equilibrium (p > 0.05). These SNPs associated with important traits in Alpine Merino sheep provide a theoretical basis for genomic selection and molecular design breeding.

The sheep Y chromosome encodes genes essential for testicular development and spermatogenesis, yet their transcriptional dynamics across developmental and pathological states remain largely uncharacterized. Here, we profiled Y-linked gene expression using RNA-seq datasets from Hu sheep testes across postnatal development (0, 3, 6, 12 months) and from divergent testicular (large, normal, small, cryptorchid) and epididymal (large, small) weights. Developmental trajectory analysis of 134 expressed Y-linked genes revealed three distinct patterns: progressive activation from birth to sexual maturity (dominated by multicopy families ZNF280BY, HSFY, PRAMEY, TSPY3), progressive decrease, and stage-specific expression. Differential expression identified 41 Y-linked genes consistently downregulated in small, cryptorchid, and pre-pubertal testes compared with normal or large mature testes. Hierarchical clustering showed that 6-month-old small testes transcriptionally clustered with cryptorchid testes, not with immature or normal testes. In the epididymis, only one Y-linked gene was differentially expressed between large and small groups. Among X–Y gametolog pairs, most showed positive expression correlations in testes, whereas DDX3X/DDX3Y exhibited a significant negative correlation (ρ = −0.450, p = 0.0185); strikingly, this pair reversed to a positive correlation in the epididymis (ρ = 0.607, p = 3.29 × 10⁻⁵). In conclusion, Y-linked transcriptional profiles distinguish testicular pathology from normal maturation, and DDX3X/DDX3Y regulation is strictly tissue-specific.