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

BMC Genomics

Research Article

Jonathan Beever¹  Lawrence B Schook¹  Alan L Archibald²  Denis Milan³  Bertrand Servin³  Ralph Wiedmann⁴  Gary Rohrer⁴  Martien AM Groenen⁵  Laurent Frantz⁵  Hendrik-Jan Megens⁵  Flavie Tortereau⁶ 

[1] Department of Animal Sciences and Institute for Genomic Biology, University of Illinois, 382 ERML, 1201 W. Gregory Avenue, 61801, Urbana, IL, USA;Division of Genetics and Genomics, The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, EH25 9RG, Midlothian, Cedex, UK;INRA, Laboratoire de Génétique Cellulaire, 31320, Castanet-Tolosan, France;USDA, ARS, US Meat Animal Research Center, PO Box 166, Spur 18D, 68933-0166, Clay Center, NE, USA;Wageningen University, Animal Breeding and Genomics Centre, PO Box 338, 6700AH, Wageningen, The Netherlands;Wageningen University, Animal Breeding and Genomics Centre, PO Box 338, 6700AH, Wageningen, The Netherlands;INRA, Laboratoire de Génétique Cellulaire, 31320, Castanet-Tolosan, France;

关键词: Pig;    Recombination;    Genome;    SNP;    Linkage;    Meiosis;    Telomere;    Centromere;    Isochore;   

DOI  :  10.1186/1471-2164-13-586

 received in 2012-03-20, accepted in 2012-08-09,  发布年份 2012

来源: Springer

【 摘 要 】

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.

【 授权许可】

Unknown   
© Tortereau et al.; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License(http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.