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논문 기본 정보
- 자료유형
- 학술저널
- 저자정보
- 저널정보
- 한국동물유전육종학회 Journal of Animal Breeding and Genomics Journal of Animal Breeding and Genomics Vol.5 No.4
- 발행연도
- 2021.12
- 수록면
- 255 - 266 (12page)
- DOI
- 10.12972/jabng.20210026
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초록· 키워드
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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.
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참고문헌 (18)
참고문헌 신청
Boddhireddy, P. / 2014 / Genomic predictions of economically important traits in Nelore cattle of Brazil / Paper presented at the Proceedings of the 10th World Congress of Genetics Applied to Livestock Production
Braun, M. / 2019 / Study of congenital Morgagnian cataracts in Holstein calves / PLoS One 14(12):e0226823
Chen, Y. / 2010 / Ensembl variation resources / BMC Genomics 11(1):293
Cingolani, P. / 2012 / A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff / Fly 6(2):80~92
Grada, A. / 2013 / Next-generation sequencing: methodology and application / The Journal of investigative dermatology 138(8):e11
Braun, M. / 2019 / Study of congenital Morgagnian cataracts in Holstein calves / PLoS One 14(12):e0226823
Chen, Y. / 2010 / Ensembl variation resources / BMC Genomics 11(1):293
Cingolani, P. / 2012 / A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff / Fly 6(2):80~92
Grada, A. / 2013 / Next-generation sequencing: methodology and application / The Journal of investigative dermatology 138(8):e11
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