Chromosome restriction enzyme digestion in domestic pig (Sus scrofa) constitutive heterochromatin arrangement

The bimodal karyotype of pig appears to contain two types of constitutive heterochromatin, reflecting different satellite DNA families: GC-rich heterochromatin located mainly in the centromeric regions of the biarmed chromosomes, and less-GC-rich heterochromatin in the centromeric regions of the one-armed chromosomes. In order to better discriminate this constitutive heterochromatin, we treated pig chromosome preparations with eight different restriction endonucleases, followed by C-banding. This technique allowed an expedited characterization of the constitutive heterochromatin and demonstrated its great heterogeneity in pig chromosomes. Our work allowed the detection and identification of twenty-two heterochromatin subclasses (twelve centromeric, four interstitial, five telomeric, and the Yq band). Moreover, several cryptic interstitial and telomeric bands were revealed. The work presented here is useful not only for fundamental studies of chromosome banding and constitutive heterochromatin, but also offers a new approach for pig clinical cytogenetics.     

Design and development of exome capture sequencing for the domestic pig (Sus scrofa)

Background

The domestic pig (Sus scrofa) is both an important livestock species and a model for biomedical research. Exome sequencing has accelerated identification of protein-coding variants underlying phenotypic traits in human and mouse. We aimed to develop and validate a similar resource for the pig.

Results

We developed probe sets to capture pig exonic sequences based upon the current Ensembl pig gene annotation supplemented with mapped expressed sequence tags (ESTs) and demonstrated proof-of-principle capture and sequencing of the pig exome in 96 pigs, encompassing 24 capture experiments. For most of the samples at least 10x sequence coverage was achieved for more than 90% of the target bases. Bioinformatic analysis of the data revealed over 236,000 high confidence predicted SNPs and over 28,000 predicted indels.

Conclusions

We have achieved coverage statistics similar to those seen with commercially available human and mouse exome kits. Exome capture in pigs provides a tool to identify coding region variation associated with production traits, including loss of function mutations which may explain embryonic and neonatal losses, and to improve genomic assemblies in the vicinity of protein coding genes in the pig.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-550) contains supplementary material, which is available to authorized users.     

Electron microscopic observations on absorption in the epithelium of the guinea pig gall bladder

Summary The fine structure of the epithelium of the gall bladder in the guinea pig has been examined after the resorption of Thorotrast. Vesicles at the apex of the epithelial cells containing Thorotrast give evidence of pinocytosis and particles are also found in the intercellular spaces and in dense cytoplasmic bodies. The epithelium exhibits interdigitating lateral cell membranes which are correlated with its function of resorbing large amounts of water.     

Characteristics of sodium transport in pig (Sus scrofa) erythrocytes

Sodium content, sodium transport (ouabain-sensitive efflux rate of sodium, oMosNa; and ouabain-sensitive efflux rate constant of sodium, oKosNa), [3H]ouabain binding capacity, and Na+, K+-ATPase activity were measured in erythrocytes from young pigs (Sus scrofa). The sodium content, sodium transport, and the number of sodium pumps (assessed by ouabain binding capacity) were lower in the pig compared to the human erythrocytes. The efflux rate constant of sodium, oKosNa was 36% and the ouabain binding capacity was 60% of those in human, suggesting the degree of activation of sodium pump units is much lower.     

A chromosome 1-specific DNA library from the domestic pig (Sus scrofa domestica).

Chromosomes were prepared from lymphocytes of a male domestic pig and flow-sorted on a dual-laser FACS. Twenty spots were observed, corresponding to the known pig karyotype of 18 pairs of autosomes plus the X and Y. DNA was isolated from 10,000 copies of the presumed chromosome 1 spot, restricted with Sau3A, ligated into the vector pGEM4z, and PCR amplified using universal primers; the products were then re-ligated into pUC18. After transformation into Escherichia coli, 210,000 independent colonies were obtained, 5% of which contained only vector DNA. The average insert size of the library was 405 bp. Southern blotting revealed that 36% of the clones contained single-copy DNA and that the remainder contained moderately or highly repetitive DNA. Screening with a (CA)n probe revealed that roughly 1% of the clones contained microsatellite sequences. A bulk insert of the library was biotinylated by PCR and used as a probe for chromosomal in situ suppression hybridization to pig chromosomes, which confirmed that the library is specific for chromosome 1. However, sequences from the centromeric and telomeric regions seem to be underrepresented in the library.     

Sarcocystis miescheriana infection in domestic pigs (Sus scrofa) in the Philippines

Sarcocystis miescheriana sarcocysts were identified in skeletal muscles of 9 (27%) of 33 swine slaughtered for human consumption. Sarcocysts were 144-180 microm x 20-38 microm in size. Ultrastructurally, the cyst wall resembled the type 10 sarcocyst wall. The villar protrusions (VP) were 3-4.5 microm long and 0.6-1.2 microm wide and had prominent longitudinally arranged microtubules extending from the VP tips to the granular layer (=ground substance). The parasitophorous vacuolar membrane with its underlying electron-dense layer (EDL) measured 25 nm in thickness. The base of the VP exhibited minute (0.42-0.87 microm) bulblike inpocketings. Each VP had 80-90 microtubules situated underneath the EDL. The granular layer was 0.5-1.2 microm thick, and contained hairlike microtubules continuous with those of the VP core. This is the first report of S. miescheriana in Philippine domestic pigs Sus scrofa.     

Pre- and perinatal oxygen transport in mammals: the embryonic hemoglobins of the domestic pig (Sus scrofa domestica)

Pigs express two globin genes of beta-type, the epsilon- and chains during their embryonic stage. With the alpha- and epsilon-chains they form four embryonic hemoglobins. We describe here in detail the experimental procedures for sequencing the epsilon- and chains from the pig (Sus scrofa domestica) and we discuss the data with respect to their special functional properties. From the components Gower I and Heide I, we obtained all embryonic chains by chromatography on CM-Cellulose. The sequence of the tryptic peptides of the beta-type chains was established by automatic Edman-Begg degradation. They were aligned by comparison with the corresponding human chains. The epsilon-chains from man and pig differ in 20 positions, porcine and epsilon-chains only in 4 positions. Up to now these have only been found in pigs. A fetal hemoglobin (gamma-chains) was not observed. As a result of this work the sequences of all peptide chains of pig's hemoglobin are determined.     

Genetic diversity in wild (Sus scrofa scrofa) and domestic (Sus scrofa domestica) pigs and their hybrids based on polymorphism of a fragment of the D-loop region in the mitochondrial DNA

We examined the variation in mitochondrial DNA by sequencing the D-loop region in wild and domestic (large-white breed) pigs, in hybrids between domestic and wild pigs, and in Monteiro pigs. A D-loop fragment of approximately 330 bp was amplified by PCR. Sequencing of DNA amplicons identified haplotypes previously described as European and Asian types. Monteiro pigs and wild pigs had European haplotypes and domestic pigs had both European and Asian haplotypes.     

The PiGMaP consortium linkage map of the pig (Sus scrofa)

A linkage map of the porcine genome has been developed by segregation analysis of 239 genetic markers. Eighty-one of these markers correspond to known genes. Linkage groups have been assigned to all 18 autosomes plus the X Chromosome (Chr). As 69 of the markers on the linkage map have also been mapped physically (by others), there is significant integration of linkage and physical map data. Six informative markers failed to show linkage to these maps. As in other species, the genetic map of the heterogametic sex (male) was significantly shorter (16.5 Morgans) than the genetic map of the homogametic sex (female) (21.5 Morgans). The sex-averaged genetic map of the pig was estimated to be 18 Morgans in length. Mapping information for 61 Type I loci (genes) enhances the contribution of the pig gene map to comparative gene mapping. Because the linkage map incorporates both highly polymorphic Type II loci, predominantly microsatellites, and Type I loci, it will be useful both for large experiments to map quantitative trait loci and for the subsequent isolation of trait genes following a comparative and candidate gene approach.     

The high resolution R-banded karyotype of the domestic pig, Sus scrofa domestica L

A representative haploid R-banded karyotype of the domestic pig, and a diagrammatic representation of the banding patterns at the 550 band level are presented.