Copy Number Variations of the NSMF Gene and Their Associations with Growth Traits in Three Chinese Sheep Breeds

Background/Objectives: Copy number variations (CNVs) are a significant source of genetic variation and have been shown to influence growth traits in livestock. This study aimed to validate previous CNV candidates within the NSMF gene (XM_015093798.1) and identify novel CNV markers for molecular breeding in sheep. Methods: Using quantitative PCR (qPCR), we genotyped NSMF CNVs (chr3: 586,001-601,000) and assessed their associations with growth traits in three Chinese sheep breeds: Chaka sheep (CKS, n = 312), Hu sheep (HS, n = 67), and Small-tailed Han sheep (STHS, n = 70). Results: Our results revealed significant differences in NSMF CNV genotype frequencies across the three breeds, with the highest proportion of deletions observed in STHS (98.44%) and CKS (90.57%), while HS exhibited a higher frequency of duplications (14.06%). No significant associations were observed between NSMF CNV genotype and CKS growth traits (p-value > 0.05). However, the CNV could markedly affected cannon circumference in HS (p-value = 0.021), with individuals carrying the normal genotype showing a larger cannon circumference. Additionally, a marginally significant association was found between the CNV and body diagonal length in HS (p-value = 0.050). Conclusions: Future investigations employing larger cohorts of Hu sheep are warranted to definitively establish the utility of NSMF CNVs as genetic markers for growth traits in Hu sheep breeding programs.