Sequence-based genome-wide association study of individual milk mid-infrared wavenumbers in mixed-breed dairy cattle

Fourier-transform mid-infrared (FT-MIR) spectroscopy provides a high-throughput and inexpensive method for predicting milk composition and other novel traits from milk samples. Whilst there have been many genome-wide association studies (GWAS) conducted on FT-MIR predicted traits, there have been few GWAS for individual FT-MIR wavenumbers. Here we examine associations between genomic regions and individual FT-MIR wavenumber phenotypes within a population of 38,085 mixed-breed New Zealand dairy cattle with imputed whole-genome sequence. GWAS were conducted for each of 895 individual FT-MIR wavenumber phenotypes and three FT-MIR predicted milk composition traits, and gene annotation and mammary tissue gene expression datasets were employed to identify candidate causative genes and variants. This resulted in the identification of 38 co-locating, co-segregating expression QTL (eQTL), and 31 protein-sequence mutations for FT-MIR wavenumber phenotypes, the latter including a null mutation in ...