Biomedical subjects

Denis Milan

Publications and source records attributed to Denis Milan.

25 records · Page 2Linked to original sources

PubMed2003

Contribution to high-resolution mapping in pigs with 101 type I markers and progress in comparative map between humans and pigs.

In the frame of the European program GenetPig, we localized on the Pig map 105 coding sequences (type I markers) from different origins, using INRA-University of Minnesota porcine Radiation Hybrid Panel (IMpRH, 101 markers) and somatic cell hybrid panel (SCHP, 93 markers, of which only four were not also mapped using IMpRH). Thus, we contributed to the improvement of the porcine high-resolution map, and we complemented the integration between the RH and cytogenetic maps. IMpRH tools allowed us to map 101 new markers relatively to reference markers of the first generation radiation hybrid map. Ninety out of 101 markers are linked to an already mapped marker with a LOD score greater than 4.8. Seventy-eight markers were informative for comparative mapping. Comparison of marker positions on the RH map with those obtained on the cytogenetic map or those expected by Human-Pig comparative map data suggested to us to be cautious with markers linked with a LOD lower than 6. These results allowed us to specify chromosomal fragments well conserved between humans and pigs and also to suggest new correspondences (Sscr1-Hsap3, Sscr9-Hsap9, Sscr13-Hsap11, Sscr15-Hsap6) confirmed by FISH on pig chromosomes. We examined in more detail the comparative map between Hsap12 and Sscr5 considering gene order, which suggests that rearrangements have occurred within the conserved synteny.

Animals↗

PubMed2003

Rearranged gene order between pig and human in a QTL region on SSC 7.

On porcine Chromosome 7, the region surrounding the MHC region contains QTL influencing many traits including growth, back fat thickness, and carcass composition. Towards the identification of the responsible gene(s), this article describes an increase of density of the radiated hybrid map of SSC 7 in the q11-q14 region and the comparative analysis of gene order on the porcine RH map and human genome assembly. Adding 24 new genes in this region, we were able to build a framework map that fills in gaps on the previous maps. The new software Carthagene was used to build a robust framework in this region. Comparative analysis of human and porcine maps revealed a global conservation of gene order and of distances between genes. A rearranged fragment of around 3.7 Mb was, however, found in the pig approximately 20 Mb upstream from the expected location on the basis of the human map. This rearrangement, found by RH mapping on the IMpRH 7.000 rads panel, has been confirmed by two-color FISH and by mapping on the high resolution IMNpRH2 12.000 rads panel. The rearranged fragment contains two microsatellites found at the most likely QTL location in the INRA QTL experiment. It also contains the BMP5 gene, which, together with CLPS, could be considered as a possible candidate.

Animals↗

PubMed2002

A first-generation EST RH comparative map of the porcine and human genome.

We have constructed a first-generation EST radiation hybrid comparative map of the porcine genome by assigning 1,058 markers to the IMpRH(7000) panel. Chromosomal localization was determined with a 2pt LOD of 4.8 for 984 markers, using the IMpRH mapping tool. Annotated ESTs represent 46.2% or 489 of the markers. Marker distribution was not stochastic and ranged from 0.41 for SSC8 to 1.77 for SSC12, respectively. Two hundred fifty-one markers assigned to the physical map of the pig did not find a homologous sequence in V22 of the human genome assembly, indicative of gaps in the assembled human genome sequence. The comparative porcine/human map covers 3,290 MB, or 98.3% of the presumed size of the human genome. However, 60 breakpoints were identified between chromosomes, as well as 90 micro-rearrangements within synteny groups. Six porcine chromosomes-SSC2, 5, 6, 7, 12, and 14-correspond to the three gene-richest human chromosomes, HSA17, 19, and 22, and show above average marker density. Porcine Chrs 1, 8, 11, and X display a low DNA/marker ratio and correspond to the 'genome deserts' on HSA 18, 4, 13, and X.

Animals↗

PubMedDate not supplied

A further look at quantitative trait loci affecting growth and fatness in a cross between Meishan and Large White pig populations.

A detailed quantitative trait locus (QTL) analysis of growth and fatness data from a three generation experimental cross between Large White (LW) and Meishan (MS) pig breeds was carried out to search for sex x QTL interactions, imprinting effects and multiple linked QTLs. A total of 530 F(2) males and 573 F(2) females issued from 6 F(1) boars and 23 F(1) sows were typed for a total of 137 markers covering the entire porcine genome. Nine growth traits and three backfat thickness measurements were analysed. All analyses were performed using line cross regression procedures. A QTL with sex-specific expression was revealed in the proximal region of chromosome 8, although some confusion between herd and sex effects could not be discarded. This previously undetected QTL affected male growth during the fattening period, with a favourable additive effect of the LW allele. The analyses also revealed the presence of two linked QTLs segregating on chromosome 1, affecting growth traits during the post-weaning period. The first QTL, previously detected using a single QTL model, was located at the end of the q arm of chromosome 1 and had a favourable MS allele. The second QTL had a favourable LW allele and was located in the proximal extremity of the q arm of chromosome 1. Suggestive genomic imprinting was found in the distal region of chromosome 9 affecting growth during the fattening period.

Adipose Tissue↗

PubMedDate not supplied

A review on SNP and other types of molecular markers and their use in animal genetics.

During the last ten years, the use of molecular markers, revealing polymorphism at the DNA level, has been playing an increasing part in animal genetics studies. Amongst others, the microsatellite DNA marker has been the most widely used, due to its easy use by simple PCR, followed by a denaturing gel electrophoresis for allele size determination, and to the high degree of information provided by its large number of alleles per locus. Despite this, a new marker type, named SNP, for Single Nucleotide Polymorphism, is now on the scene and has gained high popularity, even though it is only a bi-allelic type of marker. In this review, we will discuss the reasons for this apparent step backwards, and the pertinence of the use of SNPs in animal genetics, in comparison with other marker types.

Alleles↗

PubMedDate not supplied

Detection of quantitative trait loci for carcass composition traits in pigs.

A quantitative trait locus (QTL) analysis of carcass composition data from a three-generation experimental cross between Meishan (MS) and Large White (LW) pig breeds is presented. A total of 488 F2 males issued from six F1 boars and 23 F1 sows, the progeny of six LW boars and six MS sows, were slaughtered at approximately 80 kg live weight and were submitted to a standardised cutting of the carcass. Fifteen traits, i.e. dressing percentage, loin, ham, shoulder, belly, backfat, leaf fat, feet and head weights, two backfat thickness and one muscle depth measurements, ham + loin and back + leaf fat percentages and estimated carcass lean content were analysed. Animals were typed for a total of 137 markers covering the entire porcine genome. Analyses were performed using a line-cross (LC) regression method where founder lines were assumed to be fixed for different QTL alleles and a half/full sib (HFS) maximum likelihood method where allele substitution effects were estimated within each half-/full-sib family. Additional analyses were performed to search for multiple linked QTL and imprinting effects. Significant gene effects were evidenced for both leanness and fatness traits in the telomeric regions of SSC 1q and SSC 2p, on SSC 4, SSC 7 and SSC X. Additional significant QTL were identified for ham weight on SSC 5, for head weight on SSC 1 and SSC 7, for feet weight on SSC 7 and for dressing percentage on SSC X. LW alleles were associated with a higher lean content and a lower fat content of the carcass, except for the fatness trait on SSC 7. Suggestive evidence of linked QTL on SSC 7 and of imprinting effects on SSC 6, SSC 7, SSC 9 and SSC 17 were also obtained.

Animals↗

PubMedDate not supplied

A gene-based radiation hybrid map of chicken microchromosome 14: comparison to human and alignment to the assembled chicken sequence.

We present a gene-based RH map of the chicken microchromosome GGA14, known to have synteny conservations with human chromosomal regions HSA16p13.3 and HSA17p11.2. Microsatellite markers from the genetic map were used to check the validity of the RH map and additional markers were developed from chicken EST data to yield comparative mapping data. A high rate of intra-chromosomal rearrangements was detected by comparison to the assembled human sequence. Finally, the alignment of the RH map to the assembled chicken sequence showed a small number of discordances, most of which involved the same region of the chromosome spanning between 40.5 and 75.9 cR(6000) on the RH map.

Animals↗