Identification and functional assessment of CDSN gene variants associated with horn phenotypes in sheep.

backgroundHorn phenotype is an important trait in sheep breeding, yet the genetic factors contributing to horn variation remain incompletely understood. In this study, we focused on the Corneodesmosin (CDSN) gene to evaluate its potential involvement in horn development and phenotypic divergence.

resultsUsing RNA-seq data from horn tissue, we observed consistently higher CDSN expression in small-horn individuals compared with large-horn sheep. Analysis of public transcriptomes further confirmed a stable skin- and horn-biased expression pattern across breeds.Whole-genome sequencing datasets were used to identify single-nucleotide polymorphisms (SNPs) within and around CDSN. A total of 29 functional variants were detected, including missense, synonymous, intronic and 3'UTR sites. Several SNPs showed clear allele-frequency differences between horned and polled populations, and multiple sites were significantly associated with horn length under a dominant model. Linkage disequilibrium analysis revealed distinct haplotype blocks encompassing both regulatory and coding variants. Allele-specific expression analysis identified eight cis-acting sites clustered within exon 2, suggesting that this region plays a key regulatory role in controlling CDSN transcription.

conclusionThe convergence of differential expression, associated SNPs, and allele-specific patterns supports CDSN as a promising candidate gene associated with horn-related phenotypic variation in sheep. These results provide useful candidate markers and a foundation for future functional studies of horn biology and breeding applications.