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. 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 ~ 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 ~ 5.8% of the recombination that has taken place in only ~ 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. 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.

中文翻译：

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德国荷斯坦牛常染色体基因组的男性重组图

重组是染色体断裂并重组以产生新的等位基因组合的过程，因此在塑造基因组变异中起主要作用。标记之间的重组频率（$$ \ theta $）用于构建遗传图谱，这在基因组研究中具有重要意义。在这里，我们根据最新的牛参考大会的坐标报告了44,696个常染色体单核苷酸多态性（SNP）的重组图。估计重组频率在876个半同胞科中进行，最少有39个同胞，最大有4236个后代，包括超过367 K基因分型的德国荷斯坦动物。在全基因组范围内，通过研究相邻标记物鉴定出超过890万个父系重组事件。重组图跨24个。43 Morgan（M）的染色体长度为2486 Mbp，平均〜0.98 cM / Mbp，与可用的基于谱系的连锁图一致。此外，我们确定了971个假定的重组热点时间间隔（定义为$$ \ theta $> 2.5标准偏差大于平均值）。热点区域不均匀地分布为尖锐和狭窄的峰，相当于仅在基因组的〜2.4％中发生的〜5.8％的重组。我们通过应用基于可能性的方法来估计所有染色体内标记对之间的重组率，从而验证了遗传图谱的长度。这导致雄性牛的常染色体遗传长度更长（25.35 cM），并且在基因组装配中定位了51个推定错位的SNP。鉴于此地图基于ARS-UCD1的坐标。