Background: Copy number variation (CNV) can be identified using next-generation sequencing and microarray technologies, the research on the analysis of its association with meat traits in livestock breeding has significantly increased in recent years. Hanwoo is an inherent species raised in the Republic of Korea. It is now considered one of the most economically important species and a major food source mainly used for meat (Hanwoo beef). Methods: In this study, CNVs and the relationship between the obtained CNV regions (CNVRs) can be identified in the Hanwoo steer samples (n = 473) using Illumina Hanwoo SNP 50K bead chip and bioinformatic tools, which were used to locate the required data and meat traits were investigated. The PennCNV software was used for the identification of CNVs, followed by the use of the CNV Ruler software for locating the different CNVRs. Furthermore, bioinformatics analysis was performed. Results: We found a total of 2,575 autosomal CNVs (933 losses, 1,642 gains) and 416 CNVRs (289 gains, 111 losses, and 16 mixed), which were established with ranged in size from 2,183 bp to 983,333 bp and 10,004 bp to 381,836 bp, respectively. Upon analyzing the restriction of minor alleles frequency > 0.05 for meat traits association, 6 CNVRs in the carcass weight, 2 CNVRs in the marbling score, 3 CNVRs in the backfat thickness, and 2 CNVRs in the longissimus muscle area were related to the meat traits. In addition, we identified an overlap of 347 CNVRs. Moreover, 3 CNVRs were determined to have a gene that affects meat quality. Conclusions: Our results confirmed the relationship between Hanwoo CNVR and meat traits, and the possibility of overlapping candidate genes, annotations, and quantitative trait loci that results depended on to contribute to the greater understanding of CNVs in Hanwoo and its role in genetic variation among cattle livestock.

Since the Bovine sequencing and HapMap projects, there have been millions of genetic variations particularly including single nucleotide polymorphisms (SNPs) available throughout the cattle genome. While cataloguing substantial amounts of SNPs, copy number variation (CNV) has recently become getting great attention as an another form of genetic variation which is extensively distributed across the cattle genome. As it has been well known that CNVs can account for substantial proportions of phenotypic variance in other species including human, CNVs are highly expected to explain genetic variations of diverse economically important traits in cattle. Currently, two main approaches such as hybridization-based microarray and massively parallel sequencing-based method have been successfully applied to detect CNVs throughout the cattle genome. Although there is obvious difference of capabilities to detect genome-wide CNVs at fine scales between different platforms applied, all currently completed investigations exhibited that CNVs are extensively spread throughout the cattle genome as observed in other species. Despite these successes, there are still severe lacks of researches to identify multiple levels of CNVs from diverse cattle or multiple individuals, suggesting that there are a number of CNVs remained undiscovered. Furthermore, there are almost few investigations available to elucidate how each CNV is associated with traits of interest in cattle, so such functional study should be followed along with saturating most of potential CNVs on cattle genome.