Canine Genome Mapping : Current Scenario - Part 2

Retinitis pigmentosa
Retinitis pigmentosa is marked by abnormal retinal cGMP metabolism due to a deficiency in cGMP-PDE activity. The enzyme - cGMP-phosphodiesterase (PDE) is made of two catalytic (alpha and beta) and two identical inhibitory (gamma) subunits.

Wang et al at the James Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University have characterized the canine PDE6D gene. It has been found to be about 4.2kb and has four exons interrupted by three introns.

The canine PDE6D gene has been localized to canine radiation hybrid group 14-a. Identification of the gene has helped to provide a link with the genes which cause canine retinal degenerations, especially rod-cone dysplasia 2 (rcd2) in collie dogs.

X-linked progressive retinal atrophy (XLPRA) in the Siberian husky dog is another naturally occurring X-linked retinopathy which is very similar to X-linked retinitis pigmentosa (XLRP) in humans. Efforts are on to identify the mutant loci involved in causing the condition.

Early retinal degeneration
Early retinal degeneration (erd) is marked by early onset progressive retinal atrophy. The disease is quite similar to human retinitis pigmentosa (RP). Acland et al at the Baker Institute for Animal Health, College of Veterinary Medicine, Ithaca, New York have identified a novel retinal degenerationl locus.

The gene causing erd has been localized to a single linkage group made up of two previously identified canine linkage groups, 20 and 26, corresponding to canine radiation hybrid groups RH.34-a and RH.40-a. After comparing the similar sites on human chromosome 12p13-q13, several candidate genes for erd have been identified.

APOH gene ruled out as candidate for pcrd!
Progressive rod-cone degeneration (prcd) is an autosomal recessive retinal degeneration of dogs. Some of the signs seen include abnormalities in lipid metabolism.

Gu et al at the James Baker Institute, College of Veterinary Medicine, Cornell University, Ithaca have studied the role APOH gene as a positional candidate for prcd ( progressive rod cone degeneration).

The gene has found to map to the centromeric region of canine chromosome 9, homologous to human 17q, which contains the apolipoprotein H (apoH, protein; APOH, gene) gene involved in lipid metabolism and regulation of triglycerides. Canine-rodent hybrid cell lines were analyzed to detect canine APOH. ApoH has been localized to the photoreceptor outer segment layer by immunocytochemistry. Its expression in the retina of normal and prcd-affected dogs was confirmed by RT-PCR.

The APOH gene has been found to be well expressed in the retina and tightly linked to the prcd locus. In this study, on the basis of linkage analysis, Gu et al, have excluded the APOH gene as a primary candidate for prcd in canines.

Canine chromosome 5
Thomas et al at the Genetics Section, Animal Health Trust, have carried out an integrated cytogenetic, radiation-hybrid, and comparative map of dog Chromosome (Chr) 5 . The map has 14 gene markers, mapped within the corresponding evolutionarily conserved chromosome segments (ECCS) of the human genome.

The T gene
Haworth et al at the Human Biochemical Genetics Unit, University College, London have investigated the genetic basis of a short-tail trait. The investigators have focussed on the T gene, which encodes a T-box transcription factor important for normal posterior mesoderm development.

The investigators have cloned the canine homolog of the T gene and mapped the locus to canine Chromosome (Chr) 1q23. The investigators have analyzed the full sequence analysis of the T gene from a number of different dog breeds identified several polymorphisms and identified a unique missense mutation in a bob-tailed dog and its bob-tailed descendants.

It appears that the offspring from several independent bobtail x bobtail crosses have the homozygous phenotype which is lethal at the embryo stage.

Calcitonin gene
Wende et al at the Institute of Veterinary Medicine, University of Gottingen, Germany have identified a recombinant phage which has the canine CALC-I/alpha-CGRP gene. The gene covers a region of nearly 5.3 kb and consists of six exons with sizes ranging from 95 bp (exon 2) and 494 bp (exon 4).

It appears that the gene encodes either the 32-amino acid-long hormone calcitonin (CALC) or the neurotransmitter calcitonin gene-related peptide (alpha-CGRP) with a length of 37 amino acids after proteolytic processing of precursor molecules.

Based on their observations, Wende et al have found the CALC-I/alpha-CGRP gene to be a member of the calcitonin gene family. The researchers have localized the gene to chromosome CFA 16q25.1. Based on comparative analysis of different dog breeds the investigators have identified a breed-specific allelic d(CAGGAG)-hexanucleotide expansion in exon 3.

Chromosome 20
TBreen et al at the Institute of Veterinary Medicine, University of Gottingen, Germany have studied the genomic sequence from canine chromosome 20q15.1--> q15.2. The investigators have successfully identified two closely linked genes from this specific genomic sequence. The two genes appear to be the canine orthologs of human aminomethyltransferase (AMT) and the human T-cell leukemia translocation associated (TCTA) gene.

The canine AMT gene spans a region of 5 kb and has nine exons. The gene has been found to code for a protein of 403 amino acids which bears 88% identity to human aminomethyltransferase. The investigators believe that the 4-kb canine TCTA gene, situated very near to AMT is a pseudogene.

TSC 2 gene
Jonasdottir et al at the department of morphology, Norwegian School of Veterinary Science have mapped the canine tuberous sclerosis 2 (TSC2) gene to canine chromosome 6, using a canine whole genome radiation hybrid panel. According to the investigators, there appears to be a close linkage between canine TSC2 and the polycystic kidney disease 1 gene (PKD1), as has been observed in humans and other mammalian species.

Pituitary hormone deficiency
Combined pituitary hormone deficiency (CPHD) is an autosomal recessive inherited disease of German shepherd dogs. The disease is marked primarily by dwarfism. In mice and humans, a similar genetic disorder has been noticed that occurs due to an alteration in the gene encoding the transcription factor Pit-1.

Abnormalities in the genes encoding Pit-1 and Prop-1 have been reported to cause combined pituitary hormone deficiency (CPHD) in mice and humans.

However, some rather intriguing and interesting observations have resulted from this study. Lantinga-van Leeuwen et al at the Department of Clinical Sciences, University of Utrecht, Netherlands used a Pit-1 BAC clone as probe, to map the gene by FISH to canine Chromosome (Chr) 31.

Rather surprisingly, the investigators observed that in dwarf German shepherd dogs a C to A transversion was presented, causing a Phe (TTC) to Leu (TTA) substitution at codon 81. This alteration was present neither in other canine breeds analyzed nor in other mammalian species.

Another finding was that healthy German shepherd dogs were also homozygous for the mutant allele. This finding has led the investigators to conclude that the identified gene Pit -1 gene (POU1F1) is not the one responsible for causing syndrome of dwarfism seen in German shepherd dogs

.In addition, linkage analysis of polymorphic DNA markers flanking the Pit-1 gene, 41K19 and 52L05, revealed no co-segregation between the Pit-1 locus and the CPHD phenotype.

In another study, the same team has reported the isolation and mapping of the canine Prop-1 gene (PROP1). By fluorescence in situ hybridization ( FISH), PROP1 was mapped to canine chromosome 11. The researchers found by sequence analysis of genomic DNA from dwarf German shepherd dogs no alterations in the PROP1 gene. Besidest this, the investigators have observed no co-segregation between the PROP1 locus and the CPHD phenotype. In conclusion, Lantinga-van Leeuwen and colleagues have dismissed the gene as a candidate for canine CPHD.

Keratin genes
The keratin family of proteins are classified as being a part of the superfamily of intermediate filaments. The keratins are important structural proteins of the epidermis, hair, and nail.

Researchers have observed that mutations in genes encoding epithelial keratins cause various diseases in humans. Similar findings have been reported in dogs. The keratin proteins have been found to belong to two groups, type I (acidic) and type II (basic). In humans, the genes encoding the acidic and basic keratins have been located on chromosomes 17 and 12, respectively while in mice it has been located on chromosome 11 and 15, respectively.

Miller et al at the Feinstone Institute of Molecular Biology, University of Memphis have found out through, identified using FISH clones from a canine genomic library that indicate that the acidic keratin gene cluster is situated on CFA9 and the basic keratin gene cluster is located on CFA27.

Conclusion
In this age of modern biology, where the cause and cure for a disease is being tracked for its molecular and genetic origins, the more one searches, the more one gets entangled in a maze of loci and codons, some really causing the disease while others leading in to blind alleys, making one search afresh.

References