Abstract
BackgroundCopy Number Variations (CNVs) are gain or loss of DNA segments that are known to play a role in shaping a wide range of phenotypes. In this study, we used two dairy cattle populations, Holstein Friesian and Jersey, to discover CNVs using the Illumina BovineHD Genotyping BeadChip aligned to the ARS-UCD1.2 assembly. The discovered CNVs were investigated for their functional impact and their population genetics features.ResultsWe discovered 14,272 autosomal CNVs, which were aggregated into 1755 CNV regions (CNVR) from 451 animals. These CNVRs together cover 2.8% of the bovine autosomes. The assessment of the functional impact of CNVRs showed that rare CNVRs (MAF < 0.01) are more likely to overlap with genes, than common CNVRs (MAF ≥ 0.05). The Population differentiation index (Fst) based on CNVRs revealed multiple highly diverged CNVRs between the two breeds. Some of these CNVRs overlapped with candidate genes such as MGAM and ADAMTS17 genes, which are related to starch digestion and body size, respectively. Lastly, linkage disequilibrium (LD) between CNVRs and BovineHD BeadChip SNPs was generally low, close to 0, although common deletions (MAF ≥ 0.05) showed slightly higher LD (r2 = ~ 0.1 at 10 kb distance) than the rest. Nevertheless, this LD is still lower than SNP-SNP LD (r2 = ~ 0.5 at 10 kb distance).ConclusionsOur analyses showed that CNVRs detected using BovineHD BeadChip arrays are likely to be functional. This finding indicates that CNVs can potentially disrupt the function of genes and thus might alter phenotypes. Also, the population differentiation index revealed two candidate genes, MGAM and ADAMTS17, which hint at adaptive evolution between the two populations. Lastly, low CNVR-SNP LD implies that genetic variation from CNVs might not be fully captured in routine animal genetic evaluation, which relies solely on SNP markers.
Highlights
Copy Number Variations (CNVs) are gain or loss of DNA segments that are known to play a role in shaping a wide range of phenotypes
A previous study using PennCNV on BovineHD data, of which 47 Holstein Friesian (HOL) animals overlapped with our study, showed high rate of CNV confirmation based on qPCR validation (91.7% for CNVs found in multiple animals, 40% for singleton CNVs) [24]
Using commercial high-density Single nucleotide polymorphism (SNP) arrays, we identified 14,272 CNVs, that built 1755 CNV regions (CNVR), and the CNVRs were further used as genetic loci this study
Summary
Copy Number Variations (CNVs) are gain or loss of DNA segments that are known to play a role in shaping a wide range of phenotypes. In the early phase of their discovery, CNVs were expected to resolve the missing heritability (significant SNPs identified from genome-wide association studies (GWAS) together account small part of the heritability) [6, 7]. It was because, as in terms of base pairs, they cover a larger proportion of the genome, compared to SNPs. With the accumulation of data and analyses, the occurrence of CNVs in the genome was shown to be biased outside of functional elements [5]. Numerous studies have shown that CNVs play a role in determining a wide range of
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