- S.C. Liefers (1)
- H.J.W.C. Megens (1)
- D. Milan (1)
- G. Rohrer (1)
- L.B. Schook (1)
- B. Servin (1)
- F.J.D. Tortereau (1)
- H.J. Wijk van (1)
A high density recombination map of the pig reveals a correlation between sex-specific recombination and GC content
Tortereau, F.J.D. ; Servin, B. ; Frantz, L.A.F. ; Megens, H.J.W.C. ; Milan, D. ; Rohrer, G. ; Schook, L.B. ; Groenen, M.A.M. - \ 2012
BMC Genomics 13 (2012). - ISSN 1471-2164
biased gene conversion - multipoint linkage analysis - porcine genome - hot-spots - sus-scrofa - evolution - rates - humans - mice - interference
Background: 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. Results: 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. Conclusions: 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.
In silico identification and mapping of microsatellite markers on Sus scrofa chromosome 4
Wijk, H.J. van; Liefers, S.C. ; Buschbell, H. ; Dibbits, B.W. ; Harlizius, B. ; Groenen, M.A.M. - \ 2007
Animal Biotechnology 18 (2007)4. - ISSN 1049-5398 - p. 251 - 261.
carcass composition - porcine genome - linkage map
Apolipoprotein B (APOB) serves an essential role in the assembly and secretion of triglyceride-rich lipoproteins and lipids transport. This study was designed to clone the full-length cDNA of the chicken APOB gene, to characterize the expression profile, and investigate the differential expression between layer and broiler of the chicken APOB gene. The full-length cDNA sequence (14,150-bp) that contained a 13,896-bp ORF encoding 4,631 amino acids was obtained by RT-PCR, RACE, and bioinformatics analysis. qReal-Time PCR analysis showed that the chicken APOB gene was highly expressed in kidney, liver, and intestine. The results of differential expression showed that the APOB gene was more highly expressed in intestine and kidney in Bai'er layer than in broiler, but there was no significant difference in liver between the two breeds. The results of this study provided basic molecular information for studying the role of APOB in the energy transportation in avian species.