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Jeongwoen Shin,Dong Jae Lee,Dongwon Seo,SooHyun Lee,You-Sam Kim,박명흠,Cedric Gondro,구양모,이승환 한국동물유전육종학회 2021 한국동물유전육종학회지 Vol.5 No.4
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 occurred. The BovineSNP50 BeadChip series and Hanwoo SNP50K BeadChip are based on the older version of the bovine reference assembly UMD3.1. In a recent bovine reference genome of ARS-UCD1.2, SNP positions changed in the map file of a commercial SNP chip. Hence, this study assessed SNP re-positioning in the updated reference genome 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 3.5~4.0% of the SNPs failed the lift-over 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, the map file of SNP chip data based on UMD3.1 needs to use the position information of ARS-UCD1.2, a new reference genome, for accurate comparison with other currently published studies.