90 whole genomes of international Holstein-Freisian dairy cattle sires sequenced using the HiSeqX

Cattle breeding programs aim for the genetic improvement of phenotypic traits of interest. To achieve this genetic evaluations are carried to calculate estimated breeding values (EBVs) – the measure of the genetic merit of an animal – which can then be used to identify sires with highly favourable genetics. Many popular cattle sires have been genotyped using SNP chip arrays allowing the genetic information to be included in the breeding programs. The genetic data can also be used to investigate the genetic basis of phenotypic traits, for example through a genome-wide association study. These popular sires are now increasingly being whole-genome sequenced to supplement the existing databases of genetic variants. A new trait considered in UK genetic evaluations is resistance to bovine tuberculosis (bTB). Called TB Advantage, it allows farmers to select for increased resistance to bTB in their herds (https://dairy.ahdb.org.uk/resources-library/technical-information/breeding-genetics/genetic-evaluations-for-tb-advantage/#.Ww66E2fA6uI). Sires with robust EBVs for bTB resistance were used to create a shortlist of popular international Holstein-Freisian dairy cattle sires for whole genome sequencing. The robustness of the EBVs was determined by considering those with reliability > 80% and that had records for 20 herds with at least one daughter cow diagnosed as infected. Semen straws for the shortlist of international Holstein-Freisian dairy cattle sires were purchased from commercial breeding companies. Genomic DNA was extracted from the semen straws using a dithiothreitol (DTT)/proteinase K protocol and sequenced on the Illumina HiSeqX Next-Generation Sequencing platform at a mean depth of 30X. A total of 88 international Holstein-Freisian dairy cattle sires were sequenced, with 2 sires sequenced twice, thus providing 90 whole genome sequences. These sequences provide a database of genetic variants for highly popular international Holstein-Freisian dairy cattle sires and allows for in-depth characterisation of genetic variation associated with bTB resistance along with other phenotypic traits beyond the existing bovine SNP arrays.