Comprehensive Analyses of 723 Transcriptomes Enhance GWAS Biological Interpretation and Genomic Prediction for Complex Traits in Cattle

In this study, we generated 94 RNA-seq data that were colloced from different tissues in Hereford cow (L1 Dominette 01449) and its relatives. By combining these RNA-seq data with our other data and published data, we uniformly assembled and analyzed a total of 723 transcriptomes from 91 tissues and cell types in cattle, to identify tissue-specific genes with the highest specific expression. We then detected the trait-relevant tissues and cell types, and improved genomic prediction for milk production traits. Overall design: All the tissues were collocted in a previous study (Harhay et al. 2010). total RNA was extracted from snap frozen tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's instructions. The quantity and purity of RNA were measured using a NanoDrop 8000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE) and Agilent 2100 Bioanalyzer System (Agilent, Santa Clara, CA, USA).