Wageningen University, Animal Breeding and Genomics Centre, 6700AH, Wageningen, The Netherlands.
BMC Genomics. 2012 Nov 15;13:586. doi: 10.1186/1471-2164-13-586.
The availability of a high-density SNP genotyping chip and a reference genome sequence of the pig (Sus scrofa) enabled the construction of a high-density linkage map. A high-density linkage map is an essential tool for further fine-mapping of quantitative trait loci (QTL) for a variety of traits in the pig and for a better understanding of mechanisms underlying genome evolution.
Four different pig pedigrees were genotyped using the Illumina PorcineSNP60 BeadChip. Recombination maps for the autosomes were computed for each individual pedigree using a common set of markers. The resulting genetic maps comprised 38,599 SNPs, including 928 SNPs not positioned on a chromosome in the current assembly of the pig genome (build 10.2). The total genetic length varied according to the pedigree, from 1797 to 2149 cM. Female maps were longer than male maps, with a notable exception for SSC1 where male maps are characterized by a higher recombination rate than females in the region between 91-250 Mb. The recombination rates varied among chromosomes and along individual chromosomes, regions with high recombination rates tending to cluster close to the chromosome ends, irrespective of the position of the centromere. Correlations between main sequence features and recombination rates were investigated and significant correlations were obtained for all the studied motifs. Regions characterized by high recombination rates were enriched for specific GC-rich sequence motifs as compared to low recombinant regions. These correlations were higher in females than in males, and females were found to be more recombinant than males at regions where the GC content was greater than 0.4.
The analysis of the recombination rate along the pig genome highlighted that the regions exhibiting higher levels of recombination tend to cluster around the ends of the chromosomes irrespective of the location of the centromere. Major sex-differences in recombination were observed: females had a higher recombination rate within GC-rich regions and exhibited a stronger correlation between recombination rates and specific sequence features.
高密度 SNP 基因分型芯片和猪（Sus scrofa）参考基因组序列的可用性使得构建高密度连锁图谱成为可能。高密度连锁图谱是进一步精细定位猪各种性状数量性状基因座（QTL）以及更好地理解基因组进化机制的重要工具。
使用 Illumina PorcineSNP60 BeadChip 对四个不同的猪系进行了基因分型。使用一组共同的标记，为每个个体系计算了常染色体的重组图谱。所得遗传图谱包括 38599 个 SNP，其中 928 个 SNP 未定位在猪基因组当前组装（构建 10.2）的染色体上。总遗传长度根据系谱而变化，从 1797 到 2149cM。雌性图谱比雄性图谱长，除了 SSC1 之外，在 91-250Mb 区域，雄性图谱的重组率明显高于雌性。染色体之间和单个染色体上的重组率存在差异，高重组率区域往往聚集在染色体末端附近，而与着丝粒的位置无关。研究了主要序列特征与重组率之间的相关性，并在所有研究的基序中都获得了显著相关性。与低重组区域相比，高重组区域富含特定的 GC 丰富序列基序。与雄性相比，这些相关性在雌性中更高，并且在 GC 含量大于 0.4 的区域，雌性比雄性的重组率更高。
对猪基因组中重组率的分析表明，表现出更高水平重组的区域倾向于聚集在染色体的末端附近，而与着丝粒的位置无关。观察到主要的性别差异重组：雌性在 GC 丰富区域的重组率更高，并且在重组率与特定序列特征之间表现出更强的相关性。
