Localization of the glucose phosphate isomerase gene to the p12----q21 segment of chromosome 6 in pig by in situ hybridization

Mutation discovery for Mendelian traits in non-laboratory animals: a review of achievements up to 2012

Within two years of the re-discovery of Mendelism, Bateson and Saunders had described six traits in non-laboratory animals (five in chickens and one in cattle) that show single-locus (Mendelian) inheritance. In the ensuing decades, much progress was made in documenting an ever-increasing number of such traits. In 1987 came the first discovery of a causal mutation for a Mendelian trait in non-laboratory animals: a non-sense mutation in the thyroglobulin gene (TG), causing familial goitre in cattle. In the years that followed, the rate of discovery of causal mutations increased, aided mightily by the creation of genome-wide microsatellite maps in the 1990s and even more mightily by genome assemblies and single-nucleotide polymorphism (SNP) chips in the 2000s. With sequencing costs decreasing rapidly, by 2012 causal mutations were being discovered in non-laboratory animals at a rate of more than one per week. By the end of 2012, the total number of Mendelian traits in non-laboratory animals with known causal mutations had reached 499, which was half the number of published single-locus (Mendelian) traits in those species. The distribution of types of mutations documented in non-laboratory animals is fairly similar to that in humans, with almost half being missense or non-sense mutations. The ratio of missense to non-sense mutations in non-laboratory animals to the end of 2012 was 193:78. The fraction of non-sense mutations (78/271 = 0.29) was not very different from the fraction of non-stop codons that are just one base substitution away from a stop codon (21/61 = 0.34).

Isolation, characterization and chromosomal assignment of a partial cDNA for porcine 6-phosphogluconate dehydrogenase

A partial cDNA for 6-phosphogluconate dehydrogenase (PGD, EC 1.1.1.44) was isolated from a porcine liver cDNA library using a rat PGD cDNA. The identity of the PGD cDNA was confirmed by DNA sequencing and comparison of the amino acid sequence with the corresponding ovine sequence. The PGD cDNA was assigned to 6q2.5-2.7 by in situ hybridization.

Chromosomal localization of the glucose phosphate isomerase (GPI) gene in cattle, sheep and goat by in situ hybridization--chromosomal banding homology versus molecular conservation in Bovidae

A porcine genomic glucose phosphate isomerase (GPI) DNA probe was used for in situ hybridization with metaphase chromosomes in cattle, sheep and goat. The probe gave distinct signals on the q22----proximal part of the q24 segment of chromosome 18, 14 and 18 in cattle, sheep and goat, respectively, indicating the location of GPI gene. The three species belong to the family Bovidae and have high resemblance in chromosome banding patterns. The localization of the GPI locus to the same site on chromosomes with almost similar banding patterns suggests high degree of homology at these sites in the three species. Correlation between banding homologies and possible similarities at the molecular level is discussed.

Localization of the citrate synthase (CS) gene to the p12-p13 bands of chromosome 5 in pigs by in situ hybridization

Citrate synthase (CS) is a key enzyme of the Krebs tricarboxylic acid cycle. A 1.4 kb porcine CS cDNA probe was used to chromosomally localize the CS gene in pigs by in situ hybridization. Two in situ hybridization experiments were conducted. Although the first experiment indicated a distinct signal on the 5p12-p13 bands, a secondary signal was observed on the 13q24-q32 bands. Hence, a second in situ hybridization experiment was conducted at higher stringency. The results demonstrated a consistent signal on the 5p12-p13 bands, and the signal on chromosome 13 was scattered with no prominent secondary peak. The CS gene was therefore assigned to the p12-p13 bands of chromosome 5 in pigs.

The porcine PGD gene is preferentially lost from chromosome 6 in pig x rodent somatic cell hybrids

The 6-phosphogluconate dehydrogenase (PGD) and glucose phosphate isomerase (GPI) genes are both located on chromosome 6 in the pig (Sus scrofa domestica). Nonetheless, the PGD gene was absent in a total of 17 GPI-positive cell lines found in three independently derived panels of pig x rodent somatic cell hybrids. In most of these cell lines we found an apparently normal pig chromosome 6 at cytogenetic analysis. These results suggest instability of the porcine PGD gene region in interspecies hybrid cells.

Mapping of the interferon gamma (IFNG) gene in river and swamp buffaloes by in situ hybridization

In situ hybridization technique was applied using a tritiated (3H) bovine IFNG cDNA probe to regionally localize the gene on river and swamp buffalo chromosomes. The hybridization signals peaked on the 4q23-->q26 bands in river buffaloes and on the 1p24-->p26 bands in swamp buffaloes. The results are compared to the localization of the same gene in cattle. Possible evolutionary conservation in the Bovidae is discussed.

Localization of the ceruloplasmin (CP) gene to the q32-q33 bands of chromosome 13 in pigs by in situ hybridization

Ceruloplasmin (CP) is a copper-binding protein in vertebrate plasma. In the present study, the porcine ceruloplasmin gene was localized to the 13q32-q33 bands by in situ hybridization, using a human CP cDNA probe. This confirmed the localization of the porcine linkage group V to chromosome 13. The CP locus is closely linked to the transferrin locus in pigs. Their relative physical order on chromosome 13 is discussed. Comparisons are made with the order of these two loci in other mammalian species.

The gene for bovine interferon gamma (IFNG) maps to the q22-q24 bands of chromosome 5 in cattle

A approximately 700 bp bovine IFNG cDNA probe was used for the chromosomal localization of the IFNG gene in cattle using in situ hybridization technique. This locus has previously been assigned to chromosome 5 by analysis of a somatic cell hybrid panel. The in situ hybridization results obtained in the present study allow us to map the locus at the 5q22-q24 bands. Relative location of the IFNG gene and the class II cytokeratin and HOX3 gene clusters in cattle and humans is discussed.

Genetics and pathogenesis of malignant hyperthermia

Malignant hyperthermia (MH) is a potentially life-threatening event in response to anesthetic triggering agents, with symptoms of sustained uncontrolled skeletal muscle calcium homeostasis resulting in organ and systemic failure. Susceptibility to MH, an autosomal dominant trait, may be associated with congenital myopathies, but in the majority of the cases, no clinical signs of disease are visible outside of anesthesia. For diagnosis, a functional test on skeletal muscle biopsy, the in vitro contracture test (IVCT), is performed. Over 50% of the families show linkage of the IVCT phenotype to the gene encoding the skeletal muscle ryanodine receptor and over 20 mutations therein have been described. At least five other loci have been defined implicating greater genetic heterogeneity than previously assumed, but so far only one further gene encoding the main subunit of the voltage-gated dihydropyridine receptor has a confirmed role in MH. As a result of extensive research on the mechanisms of excitation-contraction coupling and recent functional characterization of several disease-causing mutations in heterologous expression systems, much is known today about the molecular etiology of MH.

First international workshop on porcine chromosome 6. Report and abstracts

Recent advances in the use of microsatellite markers and the development of comparative gene mapping techniques have made the construction of high resolution genetic maps of livestock species possible. Framework and comprehensive genetic linkage maps of porcine chromosome 6 have resulted from the first international effort to integrate genetic maps from multiple laboratories. Eleven highly polymorphic genetic markers were exchanged and mapped by four independent laboratories on a total of 583 animals derived from four reference populations. The chromosome 6 framework map consists of 10 markers ordered with high local support. The average marker interval of the framework map is 15.1 cM (sex averaged). The framework map is 135, 175 and 109 cM in length (for sex averaged, female and male maps, respectively). The comprehensive map includes a total of 48 type I and type II markers with a sex averaged interval of 3.5 cM and is 166, 196 and 126 cM (for sex averaged, female and male maps, respectively). Additional markers within framework map marker intervals can thus be selected from the comprehensive map for further analysis of quantitive trait loci (QTL) located on chromosome 6. The resulting maps of swine chromosome 6 provide a valuable tool for analysing and locating QTL.

cDNA sequence and chromosome localization of pig alpha 1,3 galactosyltransferase

Human serum contains natural antibodies (NAb), which can bind to endothelial cell surface antigens of other mammals. This is believed to be the major initiating event in the process of hyperacute rejection of pig to primate xenografts. Recent work has implicated galactosyl alpha 1,3 galactosyl beta 1,4 N-acetyl-glucosaminyl carbohydrate epitopes, on the surface of pig endothelial cells, as a major target of human natural antibodies. This epitope is made by a specific galactosyltransferase (alpha 1,3 GT) present in pigs but not in higher primates. We have now cloned and sequenced a full-length pig alpha 1,3 GT cDNA. The predicted 371 amino acid protein sequence shares 85% and 76% identity with previously characterized cattle and mouse alpha 1,3 GT protein sequences, respectively. By using fluorescence and isotopic in situ hybridization, the GGTA1 gene was mapped to the region q2.10-q2.11 of pig chromosome 1, providing further evidence of homology between the subterminal region of pig chromosome 1q and human chromosome 9q, which harbors the locus encoding the AB0 blood group system as well as a human pseudogene homologous to the pig GGTA1 gene.

Chromosomal pericentric inversion detected in a sow and her piglets

Forty-four pigs with the suspicious symptoms of porcine stress syndrome (PSS) were selected for chromosome analysis. Cytogenetic evaluation by means of the G-banding technique revealed that one sow had an abnormal (38,XX, inv (1p+q-) (2.1;1.1) karyotype. The same abnormality was also detected in 8 of 13 offspring of this sow. However, there was no correlation between the chromosome abnormality and PSS. The chromosome abnormality did not give rise to a reduction in the fertility of this sow or in the viability of her offspring. This case represents the first reported instance of pericentric inversion in swine.

Localization of the IGHG, PRKACB, and TNP2 genes in pigs by in situ hybridization

The porcine genes encoding the immunoglobulin gamma heavy chain (IGHG), cAMP-dependent protein kinase catalytic beta subunit (PRKACB), and transition protein 2 (TNP2) were mapped to Chromosomes (Chrs) 7 q25-q26, 6q31-q33, and 3p13-cent, respectively, by in situ hybridization. Localization of the IGHG gene confirms the assignment of linkage group III to Chr 7. Our results show that the IGHG locus in pigs, similar to the situation in other mammalian species, viz. humans, mouse, cattle, and river buffaloes, is located on the terminal region of the chromosome. The assignment of the PRKACB gene extends the homology observed between porcine Chr 6q and human Chr 1p. Mapping of the TNP2 gene provides the first marker assigned to the p arm of Chr 3 in pigs. The present study contributes to the development of the physical gene map in pigs and also bears significance in terms of comparative gene mapping.

In situ hybridization mapping and restriction fragment length polymorphism analysis of the porcine albumin (ALB) and transferrin (TF) genes

In situ hybridization analyses were conducted on porcine metaphase chromosomes using porcine liver albumin (ALB) and transferrin (TF) cDNA probes. The ALB gene was assigned to the q12 band of chromosome 8 and the TF gene to the q31 band of chromosome 13. For the latter, a statistically significant secondary peak was observed on the 6p15 band. However, the TF probe predominantly hybridized to the 13q31 band, indicating that this band is the most likely site of the TF gene. Since the TF gene belongs to linkage group V, this linkage group can now be assigned to chromosome 13. The TF and ALB probes were also used for restriction fragment length polymorphism (RFLP) analysis. A screening of 10 unrelated animals revealed TaqI RFLPs for both ALB and TF. Family studies indicated that the ALB and TF polymorphisms were controlled by three and two alleles, respectively.

Assignment of the porcine calcium release channel gene, a candidate for the malignant hyperthermia locus, to the 6p11----q21 segment of chromosome 6

Several studies point to the possibility that malignant hyperthermia (MH) in pigs is caused by a defect in the calcium release channel (CRC) of skeletal muscle sarcoplasmic reticulum. The locus for MH is closely linked to the glucosephosphate isomerase (GPI) locus, near the centromere of chromosome 6. We demonstrate synteny of the genes for CRC and GPI using somatic cell hybrid lines, and assign the CRC gene to chromosome 6p11----q21 by in situ hybridization.

Localization of the PGD and TGF beta-1 loci to pig chromosome 6q

The TGF beta-1 and PGD loci have been localized by in situ hybridization to the C-greater than q2.1 and q2.2 -greater than q2.5 regions of pig chromosome 6. These assignments confirm that the conversation of syntenic groups around GPI and PGD extends to pigs where these two groups are uniquely found to be linked. Our data also support the hypothesis that the porcine and human inherited malignant hyperthermia syndromes are caused by mutations in homologous genes which map to human chromosome 19q, porcine chromosome 6q and murine chromosome 7.