Identification of Candidate Sequence Variants Driving Hotspots of Runs of Homozygosity in Nellore Cattle

We have recently reported hotspots of runs of homozygosity (ROH) on chromosomes 4, 7 and 12 in a sample of 1,278 Nellore cows genotyped for 777k SNPs. Based on ROH length (0.73 to 1.43 Mb), these hotspots were estimated to result from inbreeding events that may have occurred between 175 and 345 years ago. In an attempt to pinpoint candidate causal variants driving the formation of these hotspots, we sequenced 20 key Nellore founder bulls at 10x coverage each. After aligning paired-end reads to the UMDv3.1 reference genome, a standard variant calling and filtering procedure was performed. Only the bi-allelic SNPs were retained. The ROH were successfully validated, and we were able to narrow down the hotspots. Variants within these regions were annotated with the VEP software. On chromosome 4, two novel tolerated missense variants in the Lysine (K)-Specific Methyltransferase 2E (KMT2E) gene were found. The gene was previously shown to be associated with neonatal and postnatal lethality and reduced fertility and growth. In the glutathione peroxidase 4 (GPX4) gene, located on the chromosome 7 hotspot, we found four rare missense mutations, two of which are predicted to cause changes to the protein structure based on SIFT scores. This region was also previously found to be highly divergent between Bos taurus and Bos indicus. GPX4 is deemed to protect cells against membrane lipid peroxidation and it was also associated with early embryonic death. The chromosome 12 region is a desert gene region and therefore no candidate variants were annotated.