Male recombination map of the autosomal genome in German Holstein

Background: Recombination is a process by which chromosomes are broken and recombine to generate new combinations of alleles, therefore playing a major role in shaping genome variation. Recombination frequencies (theta) between markers are used to construct genetic maps, which have important implications in genomic studies. Here, we report a recombination map for 44,696 autosomal single nucleotide polymorphisms (SNPs) according to the coordinates of the most recent bovine reference assembly. The recombination frequencies were estimated across 876 half-sib families with a minimum number of 39 and maximum number of 4236 progeny, comprising over 367 K genotyped German Holstein animals. Results: Genome-wide, over 8.9 million paternal recombination events were identified by investigating adjacent markers. The recombination map spans 24.43 Morgan (M) for a chromosomal length of 2486 Mbp and an average of similar to 0.98 cM/Mbp, which concords with the available pedigree-based linkage maps. Furthermore, we identified 971 putative recombination hotspot intervals (defined as theta > 2.5 standard deviations greater than the mean). The hotspot regions were non-uniformly distributed as sharp and narrow peaks, corresponding to similar to 5.8% of the recombination that has taken place in only similar to 2.4% of the genome. We verified genetic map length by applying a likelihood-based approach for the estimation of recombination rate between all intra-chromosomal marker pairs. This resulted in a longer autosomal genetic length for male cattle (25.35 cM) and in the localization of 51 putatively misplaced SNPs in the genome assembly. Conclusions: Given the fact that this map is built on the coordinates of the ARS-UCD1.2 assembly, our results provide the most updated genetic map yet available for the cattle genome.