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The aim of this study was to detect the novel copy number variation (CNV) locus of  NCAM2  gene in Chinese Holstein, and to analyze the effect of the novel CNV locus in  NCAM2  gene on milk composition traits. The novel CNV locus of  NCAM2  gene in 310 Chinese Holstein was detected by real-time quantitative fluorescent PCR (qPCR) and association analysis was performed between the novel CNV locus in  NCAM2  gene and milk composition traits in Chinese Holstein. There are three CNV types of  NCAM2  gene in Chinese Holstein: gain (increased copy number), median (normal copy number) and loss (deleted copy number). Statistical analysis revealed that there was a significant association between CNV types and milk fat rate ( p  &lt; 0.05). Moreover, we also discovered that the milk production and milk protein rate of gain type is higher than that of loss type, but that of mediate type is lower than that of loss type. However, in terms of somatic cell score, loss type is higher than that of gain type, but that of mediate type is lower than that of gain type. These observations suggested that gain type can be used as a candidate molecular genetic marker of milk fat rate.HighlightsThe CNVs of the  NCAM2  gene were detected and validated in Chinese Holstein.The type of CNV was successfully implemented using qPCR.The statistical analysis indicated that the CNV of the  NCAM2  gene are significantly associated with milk fat rate. The CNVs of the  NCAM2  gene were detected and validated in Chinese Holstein. The type of CNV was successfully implemented using qPCR. The statistical analysis indicated that the CNV of the  NCAM2  gene are significantly associated with milk fat rate.

A molecular marker of milk composition traits in NCAM2 gene of Chinese Holstein