Update physical genomic information for commercial bovine SNP chip based on recent reference genome sequences (ARS-UCD1.2)

With rapid advances in next-generation sequencing technology, previously released reference genomes are being upgraded, and new genome assemblies for novel organisms are being published. In recent updates of the bovine reference genome, changes in single-nucleotide polymorphism (SNP) position and gene location have occurred. The BovineSNP50 BeadChip series and HanwooSNP50K BeadChip are based on UMD3.1, an older version of the bovine reference assembly. In a recent update of the bovine reference genome, SNP positions changed in the map file of commercial SNP chip. Hence, this study assessed SNP re-positioning in the current ARS-UCD1.2 reference using the LiftoverVcf tool. We annotated SNP variants, which were mapped to both reference genomes, to compare SNP information such as position and adjacent genes between assemblies. The results showed that approximately 70% of the SNPs failed the liftover procedure. Moreover, , the number of SNPs successfully lifted over that affect protein expression, number of effects according to SNP type, and locations of Hanwoo economic trait-related candidate genes differed between reference genomes. In conclusion, a new <italic>Bos taurus</italic> genotyping chip should be developed for the current bovine reference assembly, and the results of studies that used UMD3.1 should be re-assessed after another round of mapping with ARS-UCD1.2. Additionally, as each genotype chip serves a different purpose, an appropriate SNP chip should be selected according to the objectives of the study.