An update of physical genomic information for commercial bovine SNP chip based on the ARS-UCD1.2 reference genome

Jeongwoen Shin1   Dong Jae Lee1   Dongwon Seo1   Soo Hyun Lee2   You-Sam  Kim3   Myung Hum  Park3   Cedric  Gondro4   Yang-Mo  Koo5   Seung Hwan  Lee1,*   

1Division of Animal and Dairy Science, Chungnam National University, Daejeon, 34134, Korea

2Division of Animal Breeding and Genetics, National Institute of Animal Science, RDA, Cheonan, 31000, Korea

3TNT Research. Co., Ltd., Anyang, 14059, Korea

4Department of Animal Science, Michigan State University, East Lansing, MI, 48824, USA

5Korea Animal Improvement Association (KAIA), Seoul, 06668, Korea

Abstract

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.

Figures & Tables

Fig. 1. Structure of Hanwoo 50K SNP Illumina BeadChip v1, Bovine 50K SNP Illumina BeadChip v2 and Bovine 50K SNP Illumina BeadChip v3. 47,450 SNPs were identified as common among the three panels (Hanwoo v1, Bovine v2, and Bovine v3). Each pair of panels shares SNPs ranged from 64 to 3,458. Hanwoo v1 and Bovine v2 do not shared 4,042 and 3,637, respectively, with the other panels.