Two Different Copy Number Variations of the CLCN2 Gene in Chinese Cattle and Their Association with Growth Traits

SIMPLE SUMMARY: Compared with traditional breeding methods, molecular marker breeding can greatly speed up the process of livestock breeding to improve the production performance of economic traits. As one form of genetic variation, copy number variations could be used for molecular marker breeding. This study explored CNVs in bovine CLCN2 genes on account of this gene possibly being involved in cell volume regulation, transepithelial transport and cell proliferation. We investigated their association with growth traits in four Chinese cattle breeds. Our results provide evidence that there are two different copy number variations in CLCN2, which are associated with growth traits in two different Chinese cattle populations and could be used as candidate markers for cattle molecular breeding. ABSTRACT: Copy number variation (CNV) can affect gene function and even individual phenotypic traits by changing the transcription and translation level of related genes, and it also plays an important role in species evolution. Chloride voltage-gated channel 2 (CLCN2) encodes a voltage-gated chloride channel (CLC-2), which has a wide organ distribution and is ubiquitously expressed. Based on previous studies, we hypothesize that CLCN2 could be a candidate gene involved in cell volume regulation, transepithelial transport and cell proliferation. This study aimed to explore CNVs in the CLCN2 gene and investigate its association with growth traits in four Chinese cattle breeds (Yunling cattle, Xianan cattle, Qinchuan cattle and Pinan cattle). We identified there are two copy number variation regions (CNV1: 3600 bp, including exon 2–11; CNV2: 4800 bp, including exon 21–22) of the CLCN2 gene. The statistical analysis showed that the CNV1 mutation in the YL cattle population was significantly associated with cannon circumference (p < 0.01). The CNV2 mutation in the XN cattle population had a significant effect on body slanting length, chest girth and body weight (p < 0.05). In the YL cattle, the association analysis of CLCN2 gene CNV1 and CNV2 combination with cannon circumference was significant (p < 0.01). Our results provide evidence that CNV1 and CNV2 in CLCN2 are associated with growth traits in two different cattle populations and could be used as candidate markers for cattle molecular breeding.