Submitted to: Biomed Central (BMC) Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/9/2012
Publication Date: 11/15/2012
Publication URL: http://handle.nal.usda.gov/10113/57922
Citation: Tortereau, F., Servin, B., Frantz, L., Megens, H.-J., Milan, D., Rohrer, G., Wiedmann, R., Beever, J., Archibald, A.L., Schook, L.B., Groenen, M.A.M. 2012. A high density recombination map of the pig reveals a correlation between sex-specific recombination and GC content. BMC Genomics. 13:586. Interpretive Summary: Comprehensive placement of specific sequences in the pig genome is an essential tool for the further characterization of chromosomal regions associated with a variety of traits and for a better understanding of the evolution of the pig genome. Four different pig families were genotyped with the Illumina PorcineSNP60 BeadChip and the inheritance of Beadchip markers within each family was used to place the markers throughout the pig genome. The resulting genetic maps comprised 38,599 genetic markers, including 928 markers that are not positioned on a chromosome in the current assembly of the pig genome (build 10.2). The predicted sizes of each chromosome based on recombination of genetic markers were larger in females than males, with a notable exception for swine chromosome 1. Recombination rates also varied among chromosomes and along individual chromosomes, with regions of high recombination rate tending to cluster close to chromosome ends. Correlations between DNA sequence composition and recombination rate were significant. The correlations were higher in females than in males, and the recombination rate was found to be greater in females than males particularly where the concentration of DNA guanine plus cytosine bases was higher than 0.4. In conclusion, the analysis of genetic marker recombination rate along the pig genome indicated that the rate was higher near the ends of the chromosomes, and that major sex-differences in recombination rate were observed.
Technical Abstract: Background: The availability of a high-density SNP chip and a reference genome sequence of the pig have enabled the construction of a high-density linkage map. A high density linkage map is an essential tool for the further fine-mapping of QTL for a variety of traits in the pig and for a better understanding the mechanisms underlying genome evolution. Results: Four different pig pedigrees were genotyped with the Illumina PorcineSNP60 BeadChip. Recombination maps 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 rate 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 rate were investigated and significant correlations were obtained for all the studied motifs. Regions characterized by a high recombination rate 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 higher than 0.4. Conclusions: The analysis of the recombination rate along the pig genome highlighted that the more recombinant regions tend to cluster around the telomeres irrespective of the location of the centromere. Major sex-differences in recombination were observed with a higher recombination rate in the females only within GC-rich regions, with females exhibiting a much stronger correlation between recombination rate and specific sequence features.