Domestication of wild boar (Sus scrofa) and subsequent selection have resulted in dramatic phenotypic changes in domestic pigs for a number of traits, including behavior, body composition, reproduction, and coat color. Here we have used whole-genome resequencing to reveal some of the loci that underlie phenotypic evolution in European domestic pigs. Selective sweep analyses revealed strong signatures of selection at three loci harboring quantitative trait loci that explain a considerable part of one of the most characteristic morphological changes in the domestic pig-the elongation of the back and an increased number of vertebrae. The three loci were associated with the NR6A1, PLAG1, and LCORL genes. The latter two have repeatedly been associated with loci controlling stature in other domestic animals and in humans. Most European domestic pigs are homozygous for the same haplotype at these three loci. We found an excess of derived nonsynonymous substitutions in domestic pigs, most likely reflecting both positive selection and relaxed purifying selection after domestication. Our analysis of structural variation revealed four duplications at the KIT locus that were exclusively present in white or white-spotted pigs, carrying the Dominant white, Patch, or Belt alleles. This discovery illustrates how structural changes have contributed to rapid phenotypic evolution in domestic animals and how alleles in domestic animals may evolve by the accumulation of multiple causative mutations as a response to strong directional selection.

BackgroundReal-time quantitative PCR (qPCR) is a method for rapid and reliable quantification of mRNA transcription. Internal standards such as reference genes are used to normalise mRNA levels between different samples for an exact comparison of mRNA transcription level. Selection of high quality reference genes is of crucial importance for the interpretation of data generated by real-time qPCR.ResultsIn this study nine commonly used reference genes were investigated in 17 different pig tissues using real-time qPCR with SYBR green. The genes included beta-actin (ACTB), beta-2-microglobulin (B2M), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), hydroxymethylbilane synthase (HMBS), hypoxanthine phosphoribosyltransferase 1 (HPRT1), ribosomal protein L4 (RPL4), succinate dehydrogenase complex subunit A (SDHA), TATA box binding protein (TPB)and tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta polypeptide (YWHAZ). The stability of these reference genes in different pig tissues was investigated using the geNorm application. The range of expression stability in the genes analysed was (from the most stable to the least stable): ACTB/RPL4, TBP, HPRT, HMBS, YWHAZ, SDHA, B2M and GAPDH.ConclusionExpression stability varies greatly between genes. ACTB, RPL4, TPB and HPRT1 were found to have the highest stability across tissues. Based on both expression stability and expression level, our data suggest that ACTB and RPL4 are good reference genes for high abundant transcripts while TPB and HPRT1 are good reference genes for low abundant transcripts in expression studies across different pig tissues.

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A cattle genetic linkage map was constructed which covers more than 95 percent of the bovine genome at medium density. Seven hundred and forty six DNA polymorphisms were genotyped in cattle families which comprise 347 individuals in full sibling pedigrees. Seven hundred and three of the loci are linked to at least one other locus. All linkage groups are assigned to chromosomes, and all are orientated with regards to the centromere. There is little overall difference in the lengths of the bull and cow linkage maps although there are individual differences between maps of chromosomes. One hundred and sixty polymorphisms are in or near genes, and the resultant genome-wide comparative analyses indicate that while there is greater conservation of synteny between cattle and humans compared with mice, the conservation of gene order between cattle and humans is much less than would be expected from the conservation of synteny. This map provides a basis for high-resolution mapping of the bovine genome with physical resources such as Yeast and Bacterial Artificial Chromosomes as well as providing the underpinning for the interpolation of information from the Human Genome Project.

-A set of eleven pig breeds originating from six European countries, and including a small sample of wild pigs, was chosen for this study of genetic diversity. Diversity was evaluated on the basis of 18 microsatellite markers typed over a total of 483 DNA samples collected. Average breed heterozygosity varied from 0.35 to 0.60. Genotypic frequencies generally agreed with Hardy-Weinberg expectations, apart from the German Landrace and Schwäbisch-Hällisches breeds, which showed significantly reduced heterozygosity. Breed differentiation was significant as shown by the high among-breed fixation index (overall F ST = 0.27), and confirmed by the clustering based on the genetic distances between individuals, which grouped essentially all individuals in 11 clusters corresponding to the 11 breeds. The genetic distances between breeds were first used to construct phylogenetic trees. The trees indicated that a genetic drift model might explain the divergence of the two German * Correspondence and reprints E-mail: glaval@toulouse.inra.fr 188 G. Laval et al.breeds, but no reliable phylogeny could be inferred among the remaining breeds. The same distances were also used to measure the global diversity of the set of breeds considered, and to evaluate the marginal loss of diversity attached to each breed. In that respect, the French Basque breed appeared to be the most "unique" in the set considered. This study, which remains to be extended to a larger set of European breeds, indicates that using genetic distances between breeds of farm animals in a classical taxonomic approach may not give clear resolution, but points to their usefulness in a prospective evaluation of diversity.genetic diversity / molecular marker / conservation / pig / European breed Résumé -Diversité génétique de onze races porcines européennes. Un ensemble de onze races porcines en provenance de six pays européens, et incluant un petit echantillon de sangliers, aété choisi pour uneétude de diversité génétique. Cette diversité aétéévaluée sur la base de 18 marqueurs microsatellites typés sur un total de 483échantillons d'ADN. Les racesétudiées manifestent un taux d'hétérozygotie allant de 0,35à 0,60. Les locus sont enéquililibre de Hardy-Weinbergà l'exception du cas des races allemandes Landrace et Schwäbisch-Hällisches, qui manifestent un déficit d'hétérozygotes. L'indice de différenciation entre races estélevé (F ST global de 0,27) et les distances génétiques entre individus permettent de les regrouper pratiquement en 11 ensembles distincts, correspondant aux 11 races considérées. Les distances génétiques entre races ont d'abordété utilisées pour construire des arbres phylogénétiques. Ces arbres suggèrent qu'un modèle de dérive génétique pourrait expliquer la divergence des deux races allemandes, mais aucune phylogénie fiable n'a puêtreétablie entre les races restantes. Les mêmes distances ont ensuiteété utilisées pour mesurer la diversité génétique globale de l'ensemble etévaluer la perte marginale de diversité associéeà chacune des racesétudiée...

In 1995, Edfors-Lilja and coworkers mapped the locus for the E. coli K88ab (F4ab) and K88ac (F4ac) intestinal receptor to pig chromosome 13 (SSC13). Using the same family material we have refined the map position to a region between the microsatellite markers Sw207 and Sw225. Primers from these markers were used to screen a pig BAC library and the positive clones were used for fluorescent in situ hybridization (FISH) analysis. The results of the FISH analysis helped to propose a candidate gene region in the SSC13q41→q44 interval. Shotgun sequencing of the FISH-mapped BAC clones revealed that the candidate region contains an evolutionary breakpoint between human and pig. In order to further characterise the rearrangements between SSC13 and human chromosome 3 (HSA3), detailed gene mapping of SSC13 was carried out. Based on this mapping data we have constructed a detailed comparative map between SSC13 and HSA3. Two candidate regions on human chromosome 3 have been identified that are likely to harbour the human homologue of the gene responsible for susceptibility towards E. coli F4ab/ac diarrhoea in pigs.

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. The Sino-Danish PigEST resource

A resource consisting of one million porcine ESTs is described, providing an essential resource for annotation, comparative genomics, assembly of the pig genome sequence, and further porcine transcription studies.

Aggregated distributions of macroparasites within their host populations are characteristic of most natural and experimental infections. We designed this study to measure the amount of variation that is attributable to host genetic factors in a pig-helminth system. In total, 195 piglets were produced after artificial insemination of 19 sows (Danish LandraceYorkshire crossbreds) with semen selected from 13 individual Duroc boars (1 or 2 sows per boar; mean litter size: 10.3; 5-14 piglets per litter). Starting at 10 weeks of age, piglets were repeatedly infected with the gastrointestinal helminths Trichuris suis and Ascaris suum by administering eggs in the feed for 14 weeks until necropsy. Faecal egg counts (FECs) were estimated regularly and A. suum worm burden was obtained at necropsy. Heritability calculations for log (FEC þ 1) at weeks 7-10 post-infection (p.i.) showed that 0.32-0.73 of the phenotypic variation for T. suis could be attributed to genetic factors. For A. suum, heritabilities of 0.29-0.31 were estimated for log (FEC þ 1) at weeks 7-14 p.i., whereas the heritability of log worm counts was 0.45. Strong positive genetic correlations (0.75-0.89) between T. suis and A. suum FECs suggest that resistance to both infections involves regulation by overlapping genes. Our data demonstrate that there is a strong genetic component in resistance to A. suum and T. suis infections in pigs. Identification of responsible genes would enhance our understanding of the host immune response to these common nematodes and for the closely related species (T. trichiura and A. lumbricoides) in man infecting more than a billion people.