Copy number variations of MICAL-L2 shaping gene expression contribute to different phenotypes of cattle

Copy number variations (CNVs) recently have been recognized as an important source of genetic variability. Compelling evidence has indicated that CNVs are responsible for phenotypic traits by altering the copy numbers of functional genes. The molecule interacting with CasL-like protein 2 (MICAL-L2) gene plays a critical role in muscle fiber development and has been identified in the CNV region by comparative genomic hybridization array. In the present study, we detected the different distributions of MICAL-L2 gene copy numbers in four Chinese cattle breeds (QC, NY, LX, and CY) and investigated the functional effects of MICAL-L2 CNVs on the gene’s expression level and the phenotypic traits in QC and NY cattle. The results showed that the copy number loss (relative to Angus cattle) was more frequent in CY than in the other breeds. The MICAL-L2 gene copy number presented a moderate negative correlation with the transcriptional expression in fetal skeletal muscles (P < 0.05). Statistical analysis revealed that the MICAL-L2 CNVs were significantly associated with body weight, body height, and body length of NY cattle in the early stages (6 and 12 months old), and the copy number loss showed better traits than the gain and/or median groups (P < 0.05). No significance was found at the late stages in QC (24 months old) and NY cattle (18 and 24 months old). These observations provided further insight into the associations between cattle CNVs and economic traits, suggesting that the CNVs may be considered promising markers for the molecular breeding of Chinese beef cattle.