Recombination map of male germline cell for a single Holstein bull

Using Illumina® BovineHD Genotyping BeadChip assay, we applied single sperms genotyping from one single Holstein bull to preliminarily describe its recombination map. We received 56 single sperms with qualified genotype information and totally detected 1,526 autosomal crossovers. Sperm cells were obtained from a single Holstein bull. The active single sperms were picked up by pipetting into a reaction tube under micromanipulator. Whole genome amplification was performed according to the protocol of Single Cell Whole Genome Amplification Kit (Yikon Genomics, Shanghai, China) based on the MALBAC (Multiple Annealing and Looping Based Amplification Cycles) technology.PCR products were purified and sent to Neogen/GeneSeek (Lansing, MI, USA) for genotyping by the Illumina® BovineHD Genotyping BeadChip assay. Heterozygous SNPs (hetSNPs) of the semen donor (the bull) were phased to two haploids (paternal and maternal) based on the genotypes of two parents. We applied the Viterbi algorithm in hidden Markov model (HMM) in R to identify crossovers in the sperm haplotype as a transition between paternal and maternal status.