GWAS for Productive and Udder Traits Using CNV in Brown Swiss Dairy Cattle

CNVs are DNA sequences of 0.5 bp, up to several Mb long, which can vary in copy number in comparison with a reference genome.

The objective of this study was to perform a GWAS with udder traits (Fore Udder Attachment-FUA, Rear Udder Height-RUH, Rear Udder Width-RUW, Udder Composite-UDC), Somatic Cell Score (SCS), and production traits (Milk, protein and Fat Yield – MY, FY, PY) using CNV previously mapped in 1,410 samples of Brown Swiss with the Illumina Bovine HD SNP chip.

Analyses were performed using SVS 8.4.4 software using the CNAM algorithm for CNV detection and a correlation-trend test model for the GWAS. Genes within significant associated CNVRs were annotated with a GO analysis using DAVID 6.7 on the Ensembl v.86 autosomal UMD3.1 gene set.

The quality control filtered out 294 samples and a total of 25,030 CNVs were identified in 1,116 individuals. After summarizing the CNVs in non-redundant CNV regions (CNVRs) a total of 398 CNVRs were identified, comprising 30 gains, 344 losses and 24 complex CNVRs (i.e. containing both losses and gains), covering 3.92% of the bovine autosomes.

The GWAS disclosed 11, 22 and 12 CNVRs significantly associated with MY FY and PY respectively. For the type traits, there were 22 CNVRs significantly associated with FUA, 1 with RUH, 17 with RUW, and 4 with UDD. No CNVR were found in association with SCS.

The associated regions overlap with 22 different genes annotated on the Bos taurus genome assembly (UMD3.1).