Characterization of Copy Number Variants in Cattle Population
This study focuses on analyzing copy number variants in a diverse population of beef and dairy cattle using high-density genotype data. Various methods such as QuantiSNP and PennCNV were employed to study CNVs, providing insights into the genomic landscape and breed comparisons.
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Characterization of copy number variants in a large multi-breed population of beef and dairy cattle using high-density single nucleotide polymorphism genotype data P. Rafter* , D. C. Purfield*, D. P. Berry*2, A. C. Parnell , I.C. Gormley ,J.F. Kearney#, M.P. Coffey ,T. R. Carthy* *Teagasc, Animal & Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland. UCD School of Mathematics and Statistics, Insight Centre for Data Analytics, University College Dublin, Belfield, Dublin 4, Ireland. Animal & Veterinary Sciences, SRUC, Roslin Institute Building, Easter Bush, Midlothian, Scotland. EH25 9RG. # ICBF, Highfield House, Shinagh, Bandon, Co.Cork, Ireland. 1
What is a copy number variant (CNV)? A A A A A A Deletion Duplication C B B B B B C C C C B D D D D D C D
Copy number analysis 1 B allele Frequency 0.5 0 Log R Ratio 0.5 0 -0.5 4
Genotype data Illumina BovineHD, 777,962 SNPs non-autosomal SNPs SNPs with a call-rate non-Mendelian SNPs (0.2%) < 95% 713,162 SNPs
The CNV dataset QuantiSNP PennCNV > 3 SNPs PennCNV QuantiSNP Remove double counting Final dataset 6
Non-Mendelian Inheritance Parental Genotypes A B B Parental Alleles A B B Progeny Genotypes A B B Observed Progeny Genotypes Non- B A B B Mendelian Mendelian 18
Conclusions For most animals a small proportion of their genome were composed of CNVs. Small differences did exist between some breeds for mean length of CNVs, and mean number of CNVs per animal. The presence of CNVs can give rise to apparent Mendelian inconsistencies in SNP genotype data. 19
