A high density recombination map of the pig reveals a correlation between sex-specific recombination and GC content

Abstract

BackgroundThe 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.ResultsFour 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.ConclusionsThe 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.

Intraindividual Variation of Meiotic Recombination Parameters in Pig Spermatocytes: A Preliminary Study

“…This was consistent with the lack of intraindividual variation observed for IFD ( p > 0.05). Although some minor differences have been found between different mouse strains Baier et al, 2014], our observations confirm that the overall distribution of recombination events is highly regulated and almost invariable [Tortereau et al, 2012;Mary et al, 2014;Zhou et al, 2016].…”

Genome-wide analysis of CpG islands in some livestock genomes and their relationship with genomic features

“…This feature may be the reason of positive correlation between CGI density and recombination rate. Several GC related measures (GC-rich repeats, CpG dinucleotide sites, and CpG islands) were positively correlated with recombination rate in previous studies Tortereau et al 2012;Rao et al 2013). The same result was obtained in this study.…”

Artificial selection on introduced Asian haplotypes shaped the genetic architecture in European commercial pigs

“…The recombination map from Tortereau et al [25] was used to obtain the recombination frequency per Mb. To test whether the probability of introgression decreases with an increase in the number of genes in a region, we used the Pearson's product-moment correlation in R.…”