Genome mapping of the silver fox. I. Determination of the chromosomal location of 8 fox genes and the search for homologous regions on fox and human chromosomes

Twenty-three silver fox-Chinese hamster somatic cell hybrids were analysed for the expression of fox enzyme loci and the segregation of fox chromosomes. This analysis made it possible to assign the gene PGD to chromosome 2, MDH2 to chromosome 3. NP to chromosome 10. APRT, ENO1, PGM1 to chromosome 12, MDH1 and IDH1 to chromosome 16. Possible use of the above-mentioned clone panel for fox gene mapping is analysed. An attempt to reveal homologous regions on fox and human chromosomes was made by comparative analysis of prometaphase fox and human chromosomes containing the homologous genes. The means and perspectives of verification of the hypothesis proposed are discussed.     

Genome mapping in silver fox. Syntenic genes in Carnivora

Hamster X fox somatic cell hybrids segregating individual fox chromosomes in different combinations were used to assign seven structural loci to fox chromosomes. The gene for ME1 was mapped on the VFU1 chromosome, the genes for ADK and PP being located on the VFU4 chromosome. The gene for GSR was assigned to the VFU7 chromosome and the genes for MPI and COT1 were assigned to the VFU15 chromosome. Localization of these genes enhances the established fox genetic map and extends the known syntenic homologies between the fox and other mammalian. The comparison of data on gene mapping has provided basis for suggestion that there are significant differences in rates of karyotypic evolution in many mammalian taxa.     

Silver fox gene mapping: conserved chromosome regions in the order Carnivora

Twenty-three silver fox x hamster somatic cell hybrid clones were used to assign 15 fox genes: GPI to chromosome 1; PGD to chromosome 2; MDH2 to chromosome 3; ESD to chromosome 6; LDHB to chromosome 8; NP to chromosome 10; LDHA to chromosome 11; APRT, ENO1, and PGM1 to chromosome 12; IDH1 and MDH1 to chromosome 16; and GLA, G6PD, and HPRT to the X chromosome. High-resolution G-banding of human, cat, mink, and fox chromosomes containing homologous regions (according to genetic maps) revealed regions of putative homology. The results lend support to the suggestion that the most considerable karyotypic reorganization of the ancestral genome in the order Carnivora occurred during Canidae formation. The details of karyotypic evolution in mammals are discussed.     

A comparative analysis of MC4R gene sequence, polymorphism, and chromosomal localization in Chinese raccoon dog and Arctic fox

Numerous mutations of the human melanocortin receptor type 4 (MC4R) gene are responsible for monogenic obesity, and some of them appear to be associated with predisposition or resistance to polygenic obesity. Thus, this gene is considered a functional candidate for fat tissue accumulation and body weight in domestic mammals. The aim of the study was comparative analysis of chromosome localization, nucleotide sequence, and polymorphism of the MC4R gene in two farmed species of the Canidae family, namely the Chinese raccoon dog (Nycterutes procyonoides procyonoides) and the arctic fox (Alopex lagopus). The whole coding sequence, including fragments of 3'UTR and 5'UTR, shows 89% similarity between the arctic fox (1276 bp) and Chinese raccoon dog (1213 bp). Altogether, 30 farmed Chinese raccoon dogs and 30 farmed arctic foxes were searched for polymorphisms. In the Chinese raccoon dog, only one silent substitution in the coding sequence was identified; whereas in the arctic fox, four InDels and two single-nucleotide polymorphisms (SNPs) in the 5'UTR and six silent SNPs in the exon were found. The studied gene was mapped by FISH to the Chinese raccoon dog chromosome 9 (NPP9q1.2) and arctic fox chromosome 24 (ALA24q1.2-1.3). The obtained results are discussed in terms of genome evolution of species belonging to the family Canidae and their potential use in animal breeding.     

A novel imprinted gene, HYMAI, is located within an imprinted domain on human chromosome 6 containing ZAC

Transient neonatal diabetes mellitus (TNDM) is a rare disease characterized by intrauterine growth retardation, dehydration, and failure to thrive due to a lack of normal insulin secretion. This disease is associated with paternal uniparental disomy or paternal duplication of chromosome 6, suggesting that the causative gene(s) for TNDM is imprinted. Recently, Gardner et al. (1999, J. Med. Genet. 36: 192-196) proposed that a candidate gene for TNDM lies within chromosome 6q24.1-q24.3. To find human imprinted genes, we performed a database search for EST sequences that mapped to this region, followed by RT-PCR analysis using monochromosomal hybrid cells with a human chromosome 6 of defined parental origin. Here we report the identification of a novel imprinted gene, HYMAI. This gene exhibits differential DNA methylation between the two parental alleles at an adjacent CpG island and is expressed only from the paternal chromosome. A previously characterized imprinted gene, ZAC/LOT1, is located 70 kb downstream of HYMAI and is also expressed only from the paternal allele. In the pancreas, both genes are moderately expressed. HYMAI and ZAC/LOT1 are therefore candidate genes involved in TNDM. Furthermore, the human chromosome 6q24 region is syntenic to mouse chromosome 10 and represents a novel imprinted domain.     

Asynchronous Replication,Mono-Allelic Expression,and Long Range Cis-Effects of ASAR6

Mammalian chromosomes initiate DNA replication at multiple sites along their length during each S phase following a temporal replication program. The majority of genes on homologous chromosomes replicate synchronously. However, mono-allelically expressed genes such as imprinted genes, allelically excluded genes, and genes on female X chromosomes replicate asynchronously. We have identified a cis-acting locus on human chromosome 6 that controls this replication-timing program. This locus encodes a large intergenic non-coding RNA gene named Asynchronous replication and Autosomal RNA on chromosome 6, or ASAR6. Disruption of ASAR6 results in delayed replication, delayed mitotic chromosome condensation, and activation of the previously silent alleles of mono-allelic genes on chromosome 6. The ASAR6 gene resides within an ∼1.2 megabase domain of asynchronously replicating DNA that is coordinated with other random asynchronously replicating loci along chromosome 6. In contrast to other nearby mono-allelic genes, ASAR6 RNA is expressed from the later-replicating allele. ASAR6 RNA is synthesized by RNA Polymerase II, is not polyadenlyated, is restricted to the nucleus, and is subject to random mono-allelic expression. Disruption of ASAR6 leads to the formation of bridged chromosomes, micronuclei, and structural instability of chromosome 6. Finally, ectopic integration of cloned genomic DNA containing ASAR6 causes delayed replication of entire mouse chromosomes.     

Phylogenetic tests of the hypothesis of block duplication of homologous genes on human chromosomes 6, 9, and 1

There are 10 gene families that have members on both human chromosome 6 (6p21.3, the location of the human major histocompatibility complex [MHC]) and human chromosome 9 (mostly 9q33-34). Six of these families also have members on mouse chromosome 17 (the mouse MHC chromosome) and mouse chromosome 2. In addition, four of these families have members on human chromosome 1 (1q21-25 and 1p13), and two of these have members on mouse chromosome 1. One hypothesis to explain these patterns is that members of the 10 gene families of human chromosomes 6 and 9 were duplicated simultaneously as a result of polyploidization or duplication of a chromosome segment ("block duplication"). A subsequent block duplication has been proposed to account for the presence of representatives of four of these families on human chromosome 1. Phylogenetic analyses of the 9 gene families for which data were available decisively rejected the hypothesis of block duplication as an overall explanation of these patterns. Three to five of the genes on human chromosomes 6 and 9 probably duplicated simultaneously early in vertebrate history, prior to the divergence of jawed and jawless vertebrates, and shortly after that, all four of the genes on chromosomes 1 and 9 probably duplicated as a block. However, the other genes duplicated at different times scattered over at least 1.6 billion years. Since the occurrence of these clusters of related genes cannot be explained by block duplication, one alternative explanation is that they cluster together because of shared functional characteristics relating to expression patterns.      

The T6 Translocation in the Mouse: Its Use in Trisomy Mapping, Centromere Localization, and Cytological Identification of Linkage Group III

The occurrence of hairless piebald mice trisomic for the chromosome segments of the T6M chromosome has shown that the LG III loci hr and s are not located on T6M. The T6 breakpoint in LG III is therefore in the position hr-s-T6. T6M must carry the gene Fkl, which is located on the far side of the T6 breakpoint from hr in LG III.-T6 reduces recombination in the hr-s region.-Trisomy for the chromosome segments of the T6M chromosome appears to severely reduce viability.-The gene hr has been shown to lie between the centromere and the T6 breakpoint. The order of loci in LG III is therefore: centromere-hr-s-T6.-Equations are given for the relation between the frequency of adjacent-2 segregation and the frequency of recovery of complementation zygotes for the case in which the translocation heterozygote can form either quadrivalent or univalent-trivalent configurations at meiosis.-Linkage Group III is carried on chromosome 14. LG VI is the other linkage group involved in T6, and is carried on chromosome 15.     

A complete comparative chromosome map for the dog, red fox, and human and its integration with canine genetic maps

Cross-species reciprocal chromosome painting was used to delineate homologous chromosomal segments between domestic dog, red fox, and human. Whole sets of chromosome-specific painting probes for the red fox and dog were made by PCR amplification of flow-sorted chromosomes from established cell cultures. Based on their hybridization patterns, a complete comparative chromosome map of the three species has been built. Thirty-nine of the 44 synteny groups from the published radiation hybrid map and 33 of the 40 linkage groups in the linkage map of the dog have been assigned to specific chromosomes by fluorescence in situ hybridization and PCR-based genotyping. Each canine chromosome has at least one DNA marker assigned to it. The human-canid map shows that the canid karyotypes are among the most extensively rearranged karyotypes in mammals. Twenty-two human autosomal paints delineated 73 homologous regions on 38 canine autosomes, while paints from 38 dog autosomes detected 90 homologous segments in the human genome. Of the 22 human autosomes, only the syntenies of three chromosomes (14, 20, and 21) have been maintained intact in the canid genome. The dog-fox map and DAPI banding comparison demonstrate that the remarkable karyotype differences between fox (2n = 34 + 0-8 Bs) and dog (2n = 78) are due to 26 chromosomal fusion events and 4 fission events. It is proposed that the more easily karyotyped fox chromosomes can be used as a common reference and control system for future gene mapping in the DogMap project and CGH analysis of canine tumor DNA.     

Chromosomal localization of human glutathione transferase genes of classes alpha,mu and pi

Summary The numerous human glutathione transferases may be divided into three classes, mu, alpha and pi. Using a panel of human-rodent somatic cell hybrids and DNA probes specific for each of the three classes, we have mapped a class mu gene to chromosome 3, a class alpha gene to chromosome 6 and a class pi gene to chromosome 11. The two latter assignments confirm earlier reports, whereas the assignment of the class mu gene represents a new addition to the human gene map.     

An expressed beta-tubulin gene, TUBB, is located on the short arm of human chromosome 6 and two related sequences are dispersed on chromosomes 8 and 13

The chromosomal assignments of an expressed beta-tubulin gene and two related sequences have been determined by Southern blot analysis of DNA from a panel of human x Chinese hamster somatic cell hybrids cleaved with Hind III or EcoRI. Probes containing the 3' untranslated regions of the expressed gene M40 and of pseudogene 21 beta were used to localize the M40 sequence (gene symbol TUBB) to chromosome 6 region 6p21----6pter, the 21 beta pseudogene (TUBBP1) to chromosome 8 region 8q21----8pter and a third related sequence (TUBBP2) to chromosome 13. Asynteny of expressed genes and related processed pseudogenes has now been demonstrated for several gene families.     

Fine Mapping of the Blast Resistance Gene Pi15, Linked to Pii,

The gene Pi15 for resistance of rice to Magnaporthe grisea was previously identified as being linked to the gene Pii. However, there is a debate on the chromosomal position of the Pii gene, because it was originally mapped on chromosome 6, but recent work showed it might be located on chromosome 9. To determine the chromosomal location of the Pi15 gene, a linkage analysis using molecular markers was performed in a F2 mapping population consisting of 15 resistant and 141 susceptible plants through bulked-segregant analysis (BSA) in combination with recessive-class analysis (RCA). Out of 20 microsatellite markers mapped on chromosomes 6 and 9 tested, only one marker, RM316 on chromosome 9, was found to have a linkage with the Pi15 gene with a recombination frequency of (19.1 ± 3.7)%. To confirm this finding, four sequence-tagged site (STS) markers mapped on chromosome 9 were tested. The results suggested that marker G103 was linked to the Pi15 gene with a recombination frequency of (5.7 ± 2.1)%. To find marker(s) more closely linked to the Pi15 gene, random amplified polymorphic DNA (RAPD) analysis was performed. Out of 1 000 primers tested, three RAPD markers, BAPi15486, BAPi15782 and BAPi15844 were found to tightly flank the Pi15 gene with recombination frequencies of 0.35%, 0.35% and 1.1%, respectively. These three RAPD markers should be viewed as the starting points for marker-aided gene pyramiding and cloning. A new gene cluster of rice blast resistance on chromosome 9 was also discussed.     

Assignment of the rat parathyroid hormone-like peptide gene (PTHLH) to chromosome 4: evidence for conserved synteny between human chromosome 12, mouse chromosome 6, and rat chromosome 4

The gene coding for rat parathyroid hormone-like peptide (PTHLH) was previously assigned to rat chromosome 2 (Hendy et al., 1988). We reexamined this assignment. According to our results, the gene is on rat chromosome 4. Taking into account the known localizations of the KRAS2 (Kras-2) oncogene and the PTHLH gene, this assignment strongly suggests that a synteny group is conserved on rat chromosome 4, mouse chromosome 6, and human chromosome 12.     

MYO6, the human homologue of the gene responsible for deafness in Snell's waltzer mice, is mutated in autosomal dominant nonsyndromic hearing loss

Mutations in the unconventional myosin VI gene, Myo6, are associated with deafness and vestibular dysfunction in the Snell's waltzer (sv) mouse. The corresponding human gene, MYO6, is located on chromosome 6q13. We describe the mapping of a new deafness locus, DFNA22, on chromosome 6q13 in a family affected by a nonsyndromic dominant form of deafness (NSAD), and the subsequent identification of a missense mutation in the MYO6 gene in all members of the family with hearing loss.     

Chromosomal and regional localization of the genes for UMPH2, APRT, PEPD, PEPS, PSP, and PGP in mink: comparison with man and mouse

Segregation of mink biochemical markers uridine 5'-monophosphate phosphohydrolase-2 (UMPH2), adenine phosphoribosyltransferase (APRT), phosphoserine phosphatase (PSP), phosphoglycolate phosphatase (PGP), peptidases D (PEPD) and S (PEPS), as well as mink chromosomes, was investigated in a set of mink x mouse hybrid clones. The results obtained allowed us to make the following mink gene assignments: UMPH2, chromosome 8; PEPD and APRT, chromosome 7; PEPS, chromosome 6; and PSP and PGP, chromosome 14. The latter two genes are the first known markers for mink chromosome 14. For regional mapping, UMPH2 was analyzed in mouse cell clones transformed by means of mink metaphase chromosomes (Gradov et al., 1985) and also in mink x mouse hybrid clones carrying fragments of mink chromosome 8 of different sizes. Based on the data obtained, the gene for UMPH2 was assigned to the region 8pter----p26 of mink chromosome 8. The present data is compared with that previously established for man and mouse with reference to the conservation of syntenic gene groups and G-band homoeologies of chromosomes in mammals.     

Localization of the human vascular endothelial growth factor gene,VEGF, at Chromosome 6p12

Using overlapping cosmids representing the vascular endothelial growth factor (VEGF) locus, the VEGF gene was mapped by fluorescence in situ hybridization to chromosome 6p12. This localization permits linkage analysis and the identification of gene interaction in the region, as well as alterations of the VEGF structure or expression in cancer cells with chromosome abnormalities.     

Mapping of silver fox genes: chromosomal localization of the genes for GOT2, AK1, ALDOC, ACP1, ITPA, PGP, and BLVR.

Evidence is presented for the chromosome localization of seven silver fox genes by the use of a panel of fox x Chinese hamster somatic cell hybrids. AK1, GOT2, and ALDOC are assigned to chromosome VFU2, PGP to chromosome VFU38, BLVR to chromosome VFU5, ACP1 to chromosome VFU8, and ITPA to chromosome VFU14. The genetic map of 29 fox genes is compared with those reported for man and other mammals. The results we obtained support and extend our previous suggestion that the formation of the Canidae branch of the Carnivora phylogenic tree was associated with a great increase in the rate of reorganization of the ancestral karyotype.     

A Novel Imprinted Gene, HYMAI, Is Located within an Imprinted Domain on Human Chromosome 6 Containing ZAC

Transient neonatal diabetes mellitus (TNDM) is a rare disease characterized by intrauterine growth retardation, dehydration, and failure to thrive due to a lack of normal insulin secretion. This disease is associated with paternal uniparental disomy or paternal duplication of chromosome 6, suggesting that the causative gene(s) for TNDM is imprinted. Recently, Gardner et al. (1999, J. Med. Genet. 36: 192–196) proposed that a candidate gene for TNDM lies within chromosome 6q24.1–q24.3. To find human imprinted genes, we performed a database search for EST sequences that mapped to this region, followed by RT-PCR analysis using monochromosomal hybrid cells with a human chromosome 6 of defined parental origin. Here we report the identification of a novel imprinted gene, HYMAI. This gene exhibits differential DNA methylation between the two parental alleles at an adjacent CpG island and is expressed only from the paternal chromosome. A previously characterized imprinted gene, ZAC/LOT1, is located 70 kb downstream of HYMAI and is also expressed only from the paternal allele. In the pancreas, both genes are moderately expressed. HYMAI and ZAC/LOT1 are therefore candidate genes involved in TNDM. Furthermore, the human chromosome 6q24 region is syntenic to mouse chromosome 10 and represents a novel imprinted domain.