Newly annotated genomic features for biology-driven genome selection: the BovReg contribution

International audience

English. Transcriptome (mRNA, totalRNA, small-RNA and CAGE), ATAC- and ChIP-Seq (H3K4me3, H3K4me1, H3K27me3, H3K27ac and CTCF) assays were compiled in a catalogue of 129 tissue samples collected from six individuals of both sexes, different ages, kept in different environments and from three divergent dairy and beef cattle breeds/crosses. From the de novo transcriptome assembly, 43,117k gene models including ≥15k potentially novel transcripts were assembled. 1,265 (638 known and 627 novel) miRNAs were detected, and for the majority, potential primary transcripts were identified. We fine mapped 51,295 transcription start sites (TSS) and 2,328 TSS-Enhancer regions shared across the three populations. On average, we dentified 105,245, 28,187, 152,646, 127,855, 77,967 and 71,868 peaks (q-value≥ 0.05) per sample for ATAC, H3K4me3, H3K4me1, H3K27me3, H3K27ac and CTCF, respectively, covering 2.89%, 1.52%, 7.96%, 5.16%, 3.95% and 2.49% of the bovine genome on average. Regulatory regions are being characterized by virtue of epigenetic features including open chromatin regions, histone marks and transcription factor as well as, expression data from the different RNA-Seq assays compiled in the diverse catalogue of tissue samples. Moreover, using WGS data from different breeds, a catalogue of unfixed mobile genetics elements was built and a panel of tests for 727 selected insertion sites have been deployed at the public part of EuroGenomics array, widely used in European cattle breeding. The newly annotated genomic features will be used on biology-driven genomic predictions within and across different cattle breeds. The BovReg project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 815668.