New gene assignments and syntenic groups in the baboon (Papio papio)

MDH2, SOD2, PEPS, and ITPA were assigned to Papio papio chromosomes 3, 4, 5, and 10, respectively, by their concordant segregation with previously assigned gene markers in a set of baboon X mouse somatic cell hybrids. The linkage of NP, IDH2, SORD, MPI, and PKM2 was confirmed, and three other independently segregating markers (MDH1, ACY1, and PEPB) were identified. Syntenic groups described in the baboon are compared to those found in man and in the rhesus monkey.     

New gene assignments in the baboon and new chromosome homoeologies with man

Eight new gene assignments were demonstrated in the baboon (Papio papio, PPA) by cosegregation analysis of twelve hybrid clones obtained by fusion between PPA fibroblasts and a mouse cell line deficient in thymidine kinase. The following markers and syntenic groups were assigned: SOD1 to PPA3, GLO-ME1 to PPA-4, PGM2 to PPA5, CKBB-SORD to PPA7, LDHB to PPA11 and LDHA to PPA14. These localizations are in agreement wit hthe following homoeologies with the human karyotype: PPA3-HSA21, PPA4-HSA6, PPA5-HSA4, PPA7-HSA14 and 15, PPA11-HSA12, PPA14-HSA11.     

New gene assignments in the rabbit (Oryctolagus cuniculus). Comparison with other species

Nineteen cell hybrids were obtained by fusing rabbit (Oryctolagus cuniculus, OCU) fibroblasts and a Chinese hamster cell line HGPRT-. Eleven enzymatic markers were previously investigated (Soulié and Grouchy 1982); seven of these could be assigned (LDHA, LDHB, TPI, PEPB, NP, ITP, and G6PD). Two assignments were uncertain (MDH2 and GUK). Two markers could not be assigned (MDH1 and PGD). Seven further markers were investigated and are the subject of this report. Six could be assigned: GALT to chromosome OCU1, GAPD to OCU4, GPX and ACY to OCU9, PGM1 to OCU13, and GSR to OCU19. One could not be assigned (GPI). MDH2 and GUK were previously considered uncertain. Now MDH2 was found impossible to assign and GUK was mapped on OCU15. These assignments were compared with those known in man, Cebus capucinus, Microcebus murinus, cat, and mouse. It was impossible to assign any enzymatic marker belonging to the ten linkage groups known in the rabbit. The esterase locus could not be investigated since the rabbit enzyme migrates in the same position as the hamster enzyme.     

Complex chromosome homologies between the rhesus monkey (Macaca mulatta) and man

The chromosome localization and gene synteny of soluble malate dehydrogenase (MDH1), soluble isocitrate dehydrogenase (IDH1), mitochondrial superoxide dismutase (SOD2), phosphoglucomutase-3 (PGM3), mitochondrial malate dehydrogenase (MDH2), beta-glucuronidase (GUSB), nucleoside phosphorylase (NP), pyruvate kinase M2 (PKM2), hexosaminidase A (HEXA), inosine triphosphatase (ITPA), and N-acetyl-alpha-D-galactosaminidase (NAGA) were determined in the rhesus monkey using somatic cell hybrids. Comparison with the human and Pongidae syntenic groups shows that chromosome banding homologies do not always correlate with gene mapping data.     

A genomewide linkage scan for quantitative trait loci influencing the craniofacial complex in baboons (Papio hamadryas spp.)

Numerous studies have detected significant contributions of genes to variation in development, size, and shape of craniofacial traits in a number of vertebrate taxa. This study examines 43 quantitative traits derived from lateral cephalographs of 830 baboons (Papio hamadryas) from the pedigreed population housed at the Southwest National Primate Research Center. Quantitative genetic analyses were conducted using the SOLAR analytic platform, a maximum-likelihood variance components method that incorporates all familial information for parameter estimation. Heritability estimates were significant and of moderate to high magnitude for all craniofacial traits. Additionally, 14 significant quantitative trait loci (QTL) were identified for 12 traits from the three developmental components (basicranium, splanchnocranium, and neurocranium) of the craniofacial complex. These QTL were found on baboon chromosomes (and human orthologs) PHA1 (HSA1), PHA 2 (HSA3), PHA4 (HSA6), PHA11 (HSA12), PHA13 (HSA2), PHA16 (HSA17), and PHA17 (HSA13) (PHA, P. hamadryas; HSA, Homo sapiens). This study of the genetic architecture of the craniofacial complex in baboons provides the groundwork needed to establish the baboon as an animal model for the study of genetic and nongenetic influences on craniofacial variation.     

A new genetic locus, Bevi, on human chromosome 6 which controls the replication of baboon type C virus in human cells.

Somatic cell hybrids derived from seven independent fusions between mouse X human and hamster X human parental cells were examined for their ability to support the replication of the baboon endogenous type C virus. These hybrids preferentially segregated human chromosomes while retaining rodent chromosomes, as demonstrated by karyotypic and isozyme analysis. A total of 41 primary colonies and 33 secondary subclones were analyzed for viral replication, as well as for the presence of enzyme structural gene markers for 19 of 23 human chromosomes. A syntenic association was seen between the ability of the baboon type C virus to infect and replicate in hybrid cultures and the expression of human malic enzyme-1 (assigned to human chromosome 6). Analysis of 86 highly segregated subclones derived from cells preinfected with baboon type C virus showed that the continued production of baboon type C virus segregated concordantly with the expression of three enzyme genes assigned to human chromosome 6 (malic enzyme-1, phosphoglucomutase-3 and superoxide dismutase-2). Subclones of infected hybrids which lost chromosome 6 and failed to release virus also failed to synthesize the virus-coded major structural protein p30. No syntenic association between baboon virus expression and any of 18 other human chromosomes was observed. These studies define a new gene (designated Bevi) on human chromosome 6 which dominantly controls the replication of baboon type C virus. The data suggest that Bevi may be a preferred integration site for the baboon type C DNA provirus in the human genome.     

Of rabbit and man: Comparative gene mapping

Summary Nineteen cell hybrids were obtained by fusing rabbit (Oryctolagus cuniculus, OCU) fibroblasts and a Chinese hamster cell line HGPRT. Eleven enzymatic markers were investigated for cosegregation analysis. Seven could be assigned to OCU chromosomes: LDHA to OCU1; LDHB and TPI to OCU4; PEPB, NP, and ITP to OCU16; and G6PD to OCUX. Two assignments were considered possible: MDH2 to OCU15, and GUK to OCU3 or 15. Two could not be assigned: MDH1 and PGD. These results are consistent with the OCU-HSA chromosome homocologies previously reported, except for PEPB.     

Synteny mapping in the bovine: genes from human chromosome 4.

Genes homologous to those located on human chromosome 4 (HSA4) were mapped in the bovine to determine regions of syntenic conservation among humans, mice, and cattle. Previous studies have shown that two homologs of genes on HSA4, PGM2 and PEPS, are located in bovine syntenic group U15 (chromosome 6). The homologous mouse genes, Pgm-1 and Pep-7, are on MMU5. Using a panel of bovine x hamster hybrid somatic cells, we have assigned homologs of 11 additional HSA4 loci to their respective bovine syntenic groups. D4S43, D4S10, QDPR, IGJ, ADH2, KIT, and IF were assigned to syntenic group U15. This syntenic arrangement is not conserved in the mouse, where D4s43, D4s10, Qdpr, and Igj are on MMU5 while Adh-2 is on MMU3. IL-2, FGB, FGG, and F11, which also reside on MMU3, were assigned to bovine syntenic group U23. These data suggest that breaks and/or fusions of ancestral chromosomes carrying these genes occurred at different places during the evolution of humans, cattle, and mice.     

Gene mapping in the Chinese hamster and conservation of syntenic groups and Q-band homologies between Chinese hamster and mouse chromosomes

Using Chinese hamster/mouse somatic cell hybrids segregating hamster chromosomes, we assigned 15 enzyme genes to six different Chinese hamster autosomes. Of the 15 loci, three genes, HK1, PEPC, and SORD, were newly assigned to chromosomes 1, 5, and 6, respectively, while ENO1, PGD, and PGM1 were assigned to the long arm of chromosome 2, in the segment 2q113----qter. The locations of the following loci were confirmed: ESD, NP, and PEPB on chromosome 1, ME1 and MPI on chromosome 4, AK1 on chromosome 6, and GPI and PEPD on chromosome 9. Comparative mapping of Chinese hamster and laboratory mouse chromosomes revealed conservation of syntenic groups and extensive banding homology between the Chinese hamster and mouse chromosomes on which homologous enzyme markers have been mapped.     

Regional Assignment of Conserved Reference Loci Anchors Unassigned Linkage and Syntenic Groups to Ovine Chromosomes

Seven loci that have been previously mapped to human and mouse chromosomes have now been regionally assigned to six sheep chromosomes. Nerve growth factor β (NGFB), antigen CD3 ζ polypeptide (CD3Z), inhibin β A (INHBA), estrogen receptor (ESR), rhodopsin (RHO), insulin-like growth factor 2 (IGF2), and myelin basic protein (MBP) were mapped by in situ hybridization to sheep chromosomes 1p24-p21, 1p14-p11, 4q26-q31, 8q25-q27, 19q23-qter, 21q21-qter, and 23q11-q12.3, respectively. ESR, RHO, IGF2, and MBP are the first markers to be assigned to their respective sheep chromosomes. These new data allow the previously unassigned sheep linkage groups H, J, K, and S to be provisionally assigned to chromosomes 21, 19, 4, and 8, respectively. The unassigned sheep syntenic groups U8 and U13 are provisionally assigned to sheep chromosomes 8 and 21, respectively. The new assignments support the emerging picture that there is extensive conservation of human chromosomal segments in the sheep and cattle genomes. The position of another evolutionary breakpoint on human chromosome 1q is suggested.     

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.     

Sheep gene mapping: assignment of ALDOB, CYP19, WT and SOX2 by somatic cell hybrid analysis

Twenty-four hamster-sheep hybrid cell lines representing eleven ovine synteny groups were used to make syntenic assignments for seven loci ALDOB (aldolase B, fructose biphosphate); AMH (anti-Müllerian hormone); CYP19 [cytochrome P₄₅₀ aromatase, subfamily XIX (aromatization of androgens)]; WT (Wilms' tumour gene); SOX2 (SRY-related HMG-box gene 2); FSHB (follicle-stimulating hormone, beta polypeptide); and SRY (sex region of Y chromosome). These loci were assigned to synteny groups U11(chr2) ( ALDOB ); U19 ( AMH ); U3(chr7) ( CYP19 ); and to chromosomes 15 ( WT ) and 1 ( SOX2 ). SRY defines the hybrids containing the Y chromosome.     

Human aminoacylase-1: cloning, regional assignment to distal chromosome 3p21.1, and identification of a cross-hybridizing sequence on chromosome 18.

Aminoacylase-1 (ACY1, EC 3.5.1.14) is a cytosolic enzyme with a wide range of tissue expression and has been postulated to function in the catabolism and salvage of acylated amino acids. ACY1 has been assigned to chromosome 3p21, a region reduced to homozygosity in small-cell lung cancer and renal cell carcinoma, and has been reported to exhibit reduced or absent expression in small-cell lung cancer cell lines and tumors. Using monoclonal antibodies to human ACY1, we have isolated cDNA clones from a liver lambda gt11 cDNA library. As proof of identity, the fusion protein encoded by a putative ACY1 cDNA displayed ACY1 enzymatic activity. Additionally, it was determined that the putative ACY1 cDNA clones hybridize to an EcoR1 restriction fragment that has been mapped to chromosome 3p. Both ACY1 activity and this restriction fragment have been further demonstrated to be syntenic to distal 3p21.1 through the use of a panel of human-rodent somatic cell hybrids containing fragments of chromosome 3. An additional EcoR1 restriction fragment to which the probe hybridizes has been assigned to chromosome 18. The major mRNA species to which the ACY1 cDNA hybridizes is 0.9 kb; faint hybridization to a 4.2-kb mRNA species is also detected. These studies further refine a region of interest in the investigation of gene inactivation in small-cell lung cancer and provide a new marker on chromosome 18.     

Red cell antigen, serum protein and red cell enzyme polymorphisms in Eastern Highlanders of New Guinea

A series of 1,187 blood samples from eight population groups in the Eastern Highlands of Papua New Guinea were tested for genetic variation in blood groups, serum proteins and red cell enzyme systems. The populations belonged to the language groups Gahuku-Asarc-Bena Bena, Kamano, Yagaria, Keiagana, Fore, Agarabe, Auyana and Tairora. Polymorphic variation was found in the ABO, MNS, P1, Rh, Hp, Tf, SEP, 6-PGD, ADA, MDH, and PGM genetic systems. East to West variation was shown in the language groups; the O, S, R2, and R0 genes increase in frequency from East to West and the A, R1, and M genes decrease in the same direction. In the East higher frequencies were found for the Du antigen, for the PGM21 gene and for a PGM second locus variant. The MDH 3 variant was found in all the populations, its highest value being in the Tairora.     

Differential staining of hamadryas baboon chromosomes with Romanovsky-Giemsa dye (G-discs)]

The pattern of G-discs in the chromosomes of baboon (Papio hamadryas) was studied after staining by means of ASG method. On the basis of these data all the 20 pairs of autosomes and sex chromosomes were identified. According to the distinctness of the discs all the chromosomes were classified into 3 groups: well differentiated, faintly differentiated and moderately differentiated. The most distinct pattern of discs was obtained in slightly spiralized chromosomes. Dimorphism of the disc pattern in homologous chromosomes was observed, which is, possibly, indicative of their different functional activity.     

Chromosome localization of the 31 type I Texas bovine markers in sheep and goat chromosomes by comparative FISH-mapping and R-banding

Bovine BAC clones containing the 31 genes, referred to as the Texas markers used earlier to definitively assign the 31 bovine syntenic groups (U) to cattle chromosomes, were mapped by fluorescent in situ hybridization to sheep and goat R-banded chromosomes according to ISCNDB2000. All 31 markers were localized on homoeologous chromosomes and chromosome bands of the two species in agreement with previous localizations obtained both in cattle and river buffalo, definitively confirming chromosome homoeologies between Caprinae and Bovinae. In addition, we have extended physical maps of sheep and goat as 11 genes (HSD3B1, INHBA, CSN10, IGF2R, PIGR, MAP1B, DSC1, ELN, TNFRSF6, CGN1, IGF2) and 14 genes (SOD1, HSD3B1, CSN10, IGF2R, RB1, TG, PIGR, MAP1B, IGH@, LTF, DSC1, TNFRSF6, CGN1, IGF2) were assigned for the first time to goat and sheep chromosomes, respectively.     

Crossing the Red Sea: phylogeography of the hamadryas baboon, Papio hamadryas hamadryas

The hamadryas baboon (Papio hamadryas hamadryas) is found both in East Africa and western Arabia and is the only free-ranging nonhuman primate in Arabia. It has been hypothesized that hamadryas baboons colonized Arabia in the recent past and were possibly even transported there by humans. We investigated the phylogeography of hamadryas baboons by sequencing a portion of the control region of mtDNA in 107 baboons from four Saudi Arabian populations and combing these data with published data from Eritrean (African) P. h. hamadryas. Analysis grouped sequences into three distinct clades, with clade 1 found only in Arabia, clade 3 found only in Africa, but clade 2 found in both Arabian and African P. h. hamadryas and also in the olive baboon, P. h. anubis. Patterns of variation within Arabia are neither compatible with the recent colonization of Arabia, implying that baboons were not transported there by humans, nor with a northerly route of colonization of Arabia. We propose that hamadryas baboons reached Arabia via land bridges that have formed periodically during glacial maxima at the straits of Bab el Mandab in the southern Red Sea. We suggest that the genetic differentiation of Arabian from African populations suggests that Arabian populations have a higher conservation status than recognized previously.     

Current status of the river buffalo (Bubalus bubalis L.) gene map.

Ninety-nine loci have been assigned to river buffalo chromosomes, 67 of which are coding genes and 32 of which are anonymous DNA segments (microsatellites). Sixty-seven assignments were based on cosegregation of cellular markers in somatic cell hybrids (synteny), whereas 39 were based on in situ hybridization of fixed metaphase chromosomes with labeled DNA probes. Seven loci were assigned by both methods. Of the 67 assignments in somatic cell hybrids, 38 were based on polymerase chain reaction (PCR), 11 on isozyme electrophoresis, 10 on restriction endonuclease digestion of DNA, 4 on immunofluorescence, and 4 on chromosomal identification. A genetic marker or syntenic group has been assigned to each arm of the five submetacentric buffalo chromosomes as well as to the 19 acrocentric autosomes, and the X and Y chromosomes. These same markers map to the 29 cattle autosomes and the X and Y chromosomes, and without exception, cattle markers map to the buffalo chromosome or chromosomal region predicted from chromosome banding similarity.     

Chromosomal mapping of lysosomal enzyme structural genes in the domestic cat

A panel of 42 rodent x cat somatic cell hybrids has been used to assign seven structural genes for lysosomal enzymes to specific chromosomes in the domestic cat. The assignments include alpha-glucosidase (GANAB) to chromosome D1, alpha-galactosidase (GLA) to the X chromosome, beta-galactosidase 1 (GLB1) to chromosome B3, beta-glucuronidase (GUSB) to chromosome E3, alpha-mannosidase A (MANA) to chromosome B3, alpha-L-fucosidase (FUCA) to chromosome C1, and hexosaminidase A (HEXA) to chromosome B3. In all cases, the feline lysosomal enzyme genes were located in linkage groups which were syntenic with their homologous positions in the human gene map. These assignments expand the genetic map of the cat and reaffirm the extensive syntenic homology between the chromosome maps of man and cat.