BovReg TWAS Annotation File BovReg_RNA-Seq_CAGE_merged_track_sorted_LIEGE.gtf

Transcriptome annotation file used for manuscript: A novel, reusable transcriptome-wide association study workflow used to map key genes linked to important cattle traits

The BovReg consortium has recently generated an updated gene and transcript annotation of the cattle genome, the version used for the analysis presented in this manuscript is BovReg_RNA-Seq_CAGE_merged_track_sorted_LIEGE.gtf (Costa-Monteiro-Moreira et al. unpublished). The pipeline used to generate the new annotation is available via the BovReg GitHub repository (https://github.com/BovReg/rnaseq). This new annotation was generated from PolyA+ RNA, total RNA, small RNA and CAGE data from a diverse set of 24 tissue types from six individual cattle of different breeds, and sexes.

In the manuscript we demonstrate the utility of our TWAS workflow by applying it to both novel and publicly available GWAS cohorts for cattle, detecting novel gene-trait associations for complex traits. Using this new transcriptome annotation of the cattle genome generated for the BovReg project we also illustrate how previously un-assayable associations can be detected. The results and the workflow we present, provide a new resource for the community and contribute to a better understanding of the molecular drivers of complex traits in cattle with the goal of eventually leveraging this information in future breeding decisions.