Whole Genome DNA Sequencing of Bull Breeds

Whole genome DNA sequences were generated as described in [40 (link)]. In brief: DNA was isolated from blood samples of 155 bulls using a DNA Isolation System, then libraries were generated from 1 μg of genomic DNA using the Illumina TruseqDNA PCR, and sequenced on the IlluminaHiSeq2000 with a 100 cycles of paired-end sequencing module using the Truseq SBS kit v3. All animals were selected and sequenced within the frame of the Gene2Farm project and represented 13 breeds: Brown Swiss (48), Fleckvieh (31), Norwegian Red (26), Guernsey (20), Simmental (16), Parda de la Montaña (4), Pezzata Rossa Italiana (3), Avileña (2), Bruna Italiana (1), Albera (1), Rubia Gallega (1), Toro de Lidia (1) and Pirenaica (1). The total number of raw reads obtained for a single bull varied between 83,423,880 (a Norwegian Red bull) and 763,594,929 (a Brown Swiss bull). The number of reads per individual was shown on Additional file 3: Figure S3 The length of single read was 101 bp and the corresponding insert size was 350 bp. Data were paired-end type and the average quality of reads per bull ranged from 28.11 to 36.69.