Abstract
Understanding how genomes, particularly genetic variants, instruct animals to develop and function is crucial for animal breeders. Copy number variants (CNVs), the gain or loss of DNA segments, can affect gene expression and alter phenotypes. However, most large-scale genetic analyses in animal breeding use single nucleotide polymorphism (SNP) genotypes from genotyping arrays, and efforts to incorporate CNVs are limited. In theory, variation from CNVs can be captured by SNPs, if they are in high linkage disequilibrium (LD). We evaluated the LD of CNV-SNP pairs in whole genome sequencing and genotyping array data. Our whole genome sequencing data showed that most CNVs have tagging SNPs. However, CNV-SNP pairs from genotyping array data were mostly in low LD, because most CNV-SNP pairs had unmatching allele frequencies. We conclude that most rare CNVs may not be fully captured by genotyping arrays.
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