A genome-wide association study using CNVs for production traits in Brown Swiss dairy cattle

Summary

Detecting genetic variation such as Copy Number Variation (CNV) in cattle provides the opportunity to study their association with productive traits. The aim of this study was to investigate CNVs in 1,410 samples of the Brown Swiss cattle breed using Illumina BovineHD Genotyping BeadChip data and to perform a genomewide association analysis for three production traits: milk yield (MY), fat yield (FY) and protein yield (PY).
After severe quality control, CNVs were called with the Golden Helix SVS 8.3.1 and PennCNV software and were summarized to CNV regions (CNVRs) at a population level, i.e. overlapping CNVs, using BEDTools.
Additionally common CNVRs between the two software were set as consensus. CNV-association studies were executed with the CNVRuler software using a linear regression model. Genes within significant associated CNVRs for each trait were annotated with a GO analysis using the DAVID Bioinformatics Resources 6.7. The quality control filtered out 294 samples. The GoldenHelix software identified 25,030 CNVs summarized to 398 CNVRs while PennCNV identified 62,341 CNVs summarized to 5,578 CNVRs. A total of 132 CNVRs were identified to be significantly associated with one or more of the three evaluated traits. The greatest association signal was given by a CNVR on chromosome 4 for MY. The associated regions overlap with 256 genes annotated on the Bos taurus genome assembly (UMD3.1). The result of this study is a comprehensive genomic analysis of the Brown Swiss breed, which enriches the bovine CNV map in its genome. Finally, the results of the association studies deliver new information for productive traits considered in selection programs of the Brown Swiss breed.