Polymorphism Analysis of NOTCH2 and CD1A Genes and Their Association with Wool Traits in Subo Merino Sheep

To identify molecular markers associated with wool traits in fine-wool sheep, we examined genetic polymorphisms in the <i>NOTCH2</i> and <i>CD1A</i> genes in 944 Subo Merino sheep in this study. Subsequently, we performed association analyses between mutation sites in the <i>NOTCH2</i> and <i>CD1A</i> genes and wool traits using SAS 9.4 software, followed by linkage disequilibrium (LD) analysis of different mutation sites using Haploview 4.2 software. Additionally, bioinformatics tools were employed to predict the potential impacts of missense mutations on protein secondary and tertiary structures. Finally, quantitative PCR (qPCR) was used to assess the expression levels of the <i>NOTCH2</i> and <i>CD1A</i> genes. Genetic analysis revealed six polymorphic sites in <i>NOTCH2</i> and <i>CD1A</i>, all of which were missense mutations. Two SNPs in <i>NOTCH2</i> (SNP1 and SNP2) showed significant associations with the coefficient of variation of fibre diameter, and SNP1 was also associated with greasy fleece weight. Four SNPs in <i>CD1A</i> (SNP3-SNP6) were significantly associated with fibre diameter standard deviation, and SNP3, SNP4, and SNP5 were additionally associated with crimp number. LD analysis revealed that SNP3, SNP4, and SNP5 were closely linked. Bioinformatics analysis indicated that the mutations caused alterations in the secondary and tertiary structures of the <i>NOTCH2</i> and <i>CD1A</i> proteins. qPCR results showed that the <i>CD1A</i> gene was highly expressed in the fine wool fibre group compared with the ultra-fine wool fibre group. In conclusion, this study revealed a genetic association between <i>NOTCH2</i> and <i>CD1A</i> and wool traits. The results are expected to provide a theoretical foundation for breeding wool traits in Subo Merino sheep, thereby enhancing the economic value of fine wool.