Genotyping and Haplotype Inference of Asthenospermic Bulls

The two asthenospermic bulls were genotyped at 54,001 SNPs using the Illumina BovineSNP50 Bead chip using DNA purified from semen samples following standard DNA extraction protocols. To facilitate haplotype inference, we also considered genotypes of 119 fertile bulls from the Nordic Red dairy cattle breed, including the sires (n = 2) and 17 paternal half-sibs of the affected bulls. Genotypes for these 119 bulls were also determined using the Illumina BovineSNP50 Bead chip comprising genotypes at 54,001 (version 1) or 54,609 SNPs (version 2). The chromosomal positions of the SNPs corresponded to the University of Maryland reference sequence of the bovine genome (UMD3.1) [49 (link)]. Following quality control, we retained 41,594 autosomal SNPs with a call-rate greater than 95%. The per-individual call-rate was between 96.07 and 100% with an average call-rate of 99.73%. The Beagle [50 (link)] software (version 3.2.1) was used to impute sporadically missing genotypes and infer haplotypes. Genotype data are available in plink binary format [51 (link)] (.bed/.bim/.fam) as Additional file 4.

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Iso-Touru T., Wurmser C., Venhoranta H., Hiltpold M., Savolainen T., Sironen A., Fischer K., Flisikowski K., Fries R., Vicente-Carrillo A., Alvarez-Rodriguez M., Nagy S., Mutikainen M., Peippo J., Taponen J., Sahana G., Guldbrandtsen B., Simonen H., Rodriguez-Martinez H., Andersson M, & Pausch H. (2019). A splice donor variant in CCDC189 is associated with asthenospermia in Nordic Red dairy cattle. BMC Genomics, 20, 286.

Publication 2019

BovineSNP50 Bead chip

Asthenospermic Bovine Chip Chromosomal Fertile Genome Genotype Haplotypes Semen Snps

Corresponding Organization :

Other organizations : Natural Resources Institute Finland, Technical University of Munich, University of Helsinki, ETH Zurich, Linköping University, University of Pannonia, Aarhus University

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Variable analysis

independent variables

Genotyping asthenospermic bulls and fertile bulls at 54,001 SNPs using the Illumina BovineSNP50 Bead chip

dependent variables

Genotypes of asthenospermic bulls and fertile bulls

control variables

DNA purified from semen samples following standard DNA extraction protocols
Chromosomal positions of the SNPs corresponding to the University of Maryland reference sequence of the bovine genome (UMD3.1)
Retaining 41,594 autosomal SNPs with a call-rate greater than 95%
Per-individual call-rate between 96.07 and 100% with an average call-rate of 99.73%
Using Beagle software (version 3.2.1) to impute sporadically missing genotypes and infer haplotypes

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