Probe-based association analysis identifies several deletions associated with average daily gain in beef cattle

BackgroundAverage daily gain (ADG) is an important trait that contributes to the production efficiency and economic benefits in the beef cattleindustry. The molecular mechanisms of ADG have not yet been fully explored because most recent association studies for ADG are based on SNPs or haplotypes. We reported a systematic CNV discovery and association analysis for ADG in Chinese Simmental beef cattle.ResultsOur study identified 4912 nonredundant CNVRs with a total length of 248.7Mb, corresponding to 8.9% of the cattle genome. Using probe-based CNV association, we identified 24 and 12 significant SNP probes within five deletions and two duplications for ADG, respectively. Among them, we found one common deletion with 89kb imbedded in LHFPL Tetraspan Subfamily Member 6 (LHFPL6) at 22.9Mb on BTA12, which has high frequency (12.9%) dispersing across population. CNV selection test using V-ST statistic suggested this common deletion may be under positive selection in Chinese Simmental cattle. Moreover, this deletion was not overlapped with any candidate SNP for ADG compared with previous SNPs-based association studies, suggesting its important role for ADG. In addition, we identified one rare deletion near gene Growth Factor Receptor-bound Protein 10 (GRB10) at 5.1Mb on BTA4 for ADG using both probe-based association and region-based approaches.ConclusionsOur results provided some valuable insights to elucidate the genetic basis of ADG in beef cattle, and these findings offer an alternative perspective to understand the genetic mechanism of complex traits in terms of copy number variations in farm animals.