Magmax system

Genomic DNA extraction for high-throughput genotyping was conducted using ear-punch tissue samples or blood, processed using Qiagen BioSprint kits (Qiagen) or a MagMAX system (Life Technologies). The former extraction method was performed by GeneMark (Hamilton, New Zealand), with the latter performed by GeneSeek (Lincoln, NE, USA). For whole genome sequencing, DNA was extracted using phenol-chloroform-based protocols, using semen samples from males, and blood or ear punch tissue samples from females. All high throughput genotyping was conducted by GeneSeek (Lincoln, NE, USA), with animals typed across a range of platforms including the GeneSeek Genomic Profiler BeadChip (Super GGP; GeneSeek/Illumina; N = 26,878), the Illumina BovineSNP50 BeadChip (Illumina; N = 36,266), or the Illumina BovineHD BeadChip (Illumina; N = 1,038). Most (N = 377) of the 406 RNA-seq animals were typed using the BovineHD BeadChip, with the remainder (N = 29) typed using the BovineSNP50 platform.

DNA was extracted either from ear-punch tissue samples or blood samples for the 124,364 animals included in our study. These samples were processed to extract DNA at GeneMark (Hamilton, New Zealand) using Qiagen BioSprint kits, or at GeneSeek (Lincoln, NE, USA) using the Life Technologies’ MagMAX system. Genotyping was performed using a variety of single nucleotide polymorphism (SNP) arrays including GeneSeek GGPv1 (8729 SNPs), GGPv2 (20,012 SNPs), GGPv2.1 (20,015 SNPs), GGPv3 (31,813 SNPs), GGPv3.1 (31,945 SNPs), GGPv4 (37,092 SNPs), GGP50kv1 (48,156 SNPs), GGP50kv1.1 (48,161 SNPs), Illumina BovineSNP50v1 (53,126 SNPs), Illumina BovineSNP50v2 (53,629 SNPs), or the BovineHD (772,235 SNPs) chips.