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 ...傅里叶变换中红外（Fourier-transform mid-infrared, FT-MIR）光谱法是一种高通量、低成本的技术，可通过牛乳样本预测乳成分及其他新型性状。尽管目前已有诸多针对FT-MIR预测性状的全基因组关联分析（genome-wide association studies, GWAS），但针对单个FT-MIR波数的全基因组关联分析仍较为匮乏。本研究以38085头携带经基因型填充的全基因组序列的新西兰混血奶牛为研究群体，探究基因组区域与单个FT-MIR波数表型之间的关联。研究针对895个单个FT-MIR波数表型与3个FT-MIR预测乳成分性状开展了全基因组关联分析，并借助基因注释与乳腺组织基因表达数据集，筛选潜在致病基因与致病变异。最终本研究共鉴定出38个共定位、共分离的表达数量性状位点（expression QTL, eQTL），以及31个与FT-MIR波数表型相关的蛋白质序列突变，其中后者包含一处无效突变……