Bovinehd beadchip array

High‐density SNP genotyping was carried out for seven cases (cases 1–7) and eight obligate carriers (three dams and five sires) (Online Resource 1) on the Illumina BovineHD BeadChip array including 777.962 SNPs. All given SNP positions correspond to the bovine ARS-UCD1.2 genome assembly. The PLINK v1.9 software (Chang et al. 2015 (link)) was used to perform basic quality filtering of the dataset. Even though no sample was excluded, a total of 146.440 variants were removed owing to minor allele thresholds. The total genotyping rate was approximately 0.98. With a total of 631.522 remaining markers, homozygosity mapping was performed for the 7 IC-affected animals using the software PLINK v1.9 (Purcell et al. 2007 (link)) with the commands ‐‐homozyg‐kb 100 (considering homozygous segments of at least 100 kb), ‐‐homozyg‐match 0.95 (for allelic matching between both cases) and ‐‐homozyg‐group (for generating an overlap‐file), resulting in shared runs of homozygosity (ROH) indicating chromosomal region of identity-by-descent (IBD).

We evaluated the genotype concordance between the SNVs and SNP panel genotype data of Gyr_1, Gyr_2, Girolando_1, Girolando_2, Girolando_3, and Guzerat_2 samples to verify and validate the quality of the identified SNVs. The genotype quality control (QC) was not carried out. A python script was used to compare the SNV calling to the Bovine HD BeadChip array (Illumina, San Diego, USA). The script stored the final report file output from the Illumina Bead Express software used with the BovineHD BeadChip and compared each called locus to its counterpart in the variant calling format (VCF) file containing the SNV calling from the whole-genome sequencing.

Whole blood was collected from each cow, and genomic DNA was isolated using the Easy-DNA kit (Invitrogen, Cat. #K1800-01). All sample were genotyped using the using the Illumina BovineHD BeadChip Array (Illumina, Cat. #WG-450-1002), which contains 735,293 autosomal SNPs [42 (link)], according to the manufacturer’s instructions. SNP clustering and genotype calling was performed using GenomeStudio V2011 (Illumina, version 1.9.4), and all markers passed quality control (call rate >98%). The UMD3.1 assembly was used to map SNPs position [43 ]. CNVR were detected as previouly reported [9 (link)], detected using PennCNV software (version June 2011) [44 (link), 45 ], which incorporates factors including log R ratio (LRR), B allele frequency (BAF), marker distance, and the population frequency of B allele (PFB) into a hidden Markov model.

Blood was collected from 791 Japanese Black cows. Genomic DNA was extracted using the Easy-DNA kit (Invitrogen, Cat. #K1800–01). All samples were genotyped using the BovineHD BeadChip Array (Illumina, Cat. #WG-450-1002) [41 (link)]. SNPs genotype calling were performed using GenomeStudio V2011 (Illumina, version 1.9.4). The ARS-UCD1.2 assembly was used to map the SNP position [42 ]. CNVR was detected as previously reported [15 (link)], using PennCNV software (version June 2011) [43 (link)].