Journal of Animal Breeding and Genomics (J Anim Breed Genom)
Jeongwoen Shin1†, Dong Jae Lee1†, Dongwon Seo1, Soo Hyun Lee2, You-Sam Kim3, Myung Hum Park3, Cedric Gondro4, Yang-Mo Koo5* and 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
Correspondence to Seung Hwan Lee, E-mail: slee46@cnu.ac.kr
Volume 5, Number 4, Pages 255-266, December 2021.
Journal of Animal Breeding and Genomics 2021, 5(4), 255-266. https://doi.org/10.12972/jabng.20210026
Received on 16 December, 2021, Revised on 29 December, 2021, Accepted on 29 December, 2021, Published on 31 December, 2021.
Copyright © 2021 Korean Society of Animal Breeding and Genetics.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0).
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.
Annotation, ARS–UCD1.2, Lift-over, SNP BeadChip, UMD3.1
This work was supported by Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, Forestry and Fisheries (IPET) funded by Ministry of Agriculture, Food and Rural Affairs (MAFRA) (321082-3)