Whole genome short read data from 567 bulls of 14 breeds provides insight into genetic diversity of French cattle.

Abstract

Technological developments in high-throughput sequencing and advances in bioinformatic analysis allowed to sequence and study a very large number of genomes from a single species (cattle). Analyzing this data set enabled to generate the corresponding genomic variant database, especially for single nucleotide polymorphisms (SNPs) and small insertion or deletion (Indels) variations. These variants and genotypes allowed to better characterize the genetic diversity of these breeds. In this work, we sequenced 567 bulls from 14 different breeds (Holstein, Montbéliarde, Normande, Brown Swiss, Simmental, Abondance, Tarentaise, Vosgienne, Blonde d'Aquitaine, Charolaise, Limousine, Aubrac, Flamande, Parthenaise). Each sample was sequenced at an approximately 15x depth on the Illumina Novaseq6000 platform. We detected 34,252,080 variants, 25,115,987 of which were already known in the Ensembl variation database version 110 and 9,136,093 were absent and were considered as novel variants. This data set represents a useful resource for the community to better identify SNPs or indels such as mutation anticipation and provides new insights into bovine genetic diversity.