FAT atypical cadherin 1 (FAT1) is a member of the atypical cadherin superfamily and is involved in the planar cell polarity signalling pathway which regulates hair follicle morphogenesis, cycling, and orientation. The purpose of this study was to investigate the sheep FAT1 gene expression, polymorphisms and its association with wool quality traits in Chinese Merino sheep. Quantitative real-time PCR analysis showed that the FAT1 mRNA was differentially expressed in the adult skin of Chinese Merino and Kazak sheep. Seven SNPs (termed SNPs 1–7) were identified in exon 2 of sheep FAT1 gene by Sanger sequencing. SNPs 2 and 7 (novel SNPs) were significantly associated with wool crimp ( P 0.05). SNPs 4 and 5 (rs161528993 and rs161528992) were significantly associated with wool fibre length ( P 0.05). SNP 7 was highly significantly associated with average wool fibre diameter ( P 0.01). Similarly, FAT1 haplotypes were significantly associated with wool crimp ( P 0.05), and the haplotypes H1–H3 and H5 were significantly associated with higher wool crimp ( P 0.05). Bioinformatics analysis showed that the wool quality trait-associated SNPs (SNPs 2, 4, 5 and 7) might affect the pre-mRNA splicing by creating or abolishing the binding sites for serine/arginine-rich proteins, and in addition, SNPs 2 and 4 might alter the FAT1 mRNA secondary structure. Our results suggest that FAT1 influences wool quality traits and its SNPs 2, 4, 5 and 7 might be useful markers for marker-assisted selection and sheep breeding.
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