Assignment of the growth hormone gene locus to 19q26-qter in cattle and to 11q25-qter in sheep by in situ hybridization

The growth hormone gene locus (GH) of cattle and sheep was mapped to a chromosomal region in each species by using in situ hybridization. The probe employed was an 830-bp cDNA sequence from the ovine growth hormone gene. Based on QFQ chromosome preparations, our results show that the GH locus is on cattle chromosome 19 in the region of bands q26-qter and in sheep on chromosome region 11q25-qter. The GH assignments together with previous localizations of type I cytokeratin genes (KRTA) and one homeobox (HOX2) gene in cattle and one type I cytokeratin gene (KRTA) in sheep identify a strongly conserved chromosomal segment on human chromosome 17, bovine chromosome 19, and sheep chromosome 11.     

Five regional localizations to the sheep genome: first assignments to chromosomes 5 and 12

The regional localization of five reference loci to sheep chromosomes is reported. The newly mapped loci are the T-cell receptor, beta ( TCRB ), coagulation factor X ( F10 ), laminin gamma 1 ( LAMC1 ), cyclic GMP rod phosphodiesterase, alpha ( PDEA ) and fibroblast growth factor 2 ( FGF2 ). The assignments of PDEA and LAMC1 to chromosomes 5q23–q31 and 12q22–q24 respectively provide the first markers physically assigned to these chromosomes. They also allow the provisional assignment of sheep syntenic group U19 to chromosome 5 and U1 to chromosome 12. The mapping of FGF2 to chromosome 17q23–q25 anchors the unassigned linkage group 'A' to chromosome 17, and the assignment of TCRB to chromosome 4q32–qter facilitates the orientation of a linkage group on sheep chromosome 4. The mapping of F10 to sheep chromosome 10q23–qter supports the recent assignment of bovine syntenic group U27 to cattle chromosome 12, as sheep chromosome 10 and cattle chromosome 12 are banded homologues.     

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.     

Chromosome mapping of the owl monkey CSF1R and IL5 genes.

We mapped the owl monkey colony-stimulating factor 1 receptor (CSF1R) locus to the proximal region of chromosome 3q of karyotype VI(K-VI) and karyotype V(K-V) and the interleukin 5 (IL5) locus to the mid-region of chromosome 3q(K-VI) and 19q(K-IV) using a combination of Southern hybridization of somatic cells and in situ chromosomal hybridization methodologies. The findings support the proposed evolution of owl monkey chromosome 3(K-VI) from a fusion of two smaller structures, the homologs of chromosomes 6 and 19 (K-IV). The data also indicate genomic conservation of the HSA 5q23-q35 segment in the higher primates.     

Six loci mapped on to human chromosome 2p are assigned to sheep chromosome 3p

Six loci, apoliproprotein B (including Ag(x) antigen), immunoglobulin kappa constant region (IGKC), luteinizing hormone/choriogonadotrophin receptor, avian myelocytomatosis viral related oncogene, neuroblastoma derived, ornithine decarboxylase, and proopiomelanocortin (adrenocorticotropin/beta-lipotropin) (POMC), were newly assigned to sheep chromosome 3p using a chromosomally characterized minipanel of sheep-hamster cell hybrids. Isotopic in situ hybridization of IGKC to sheep chromosome 3p22–p17 is reported, confirming the cell hybrid assignment. As these loci are all known to map to human chromosome 2p, this study demonstrates that this chromosomal segment is extensively conserved in sheep. Only POMC has been previously assigned to cattle chromosome 11, which is the equivalent of sheep chromosome 3p. Therefore, we predict that the other loci assigned in this study to sheep 3p are likely to be located on cattle 11. The provisional assignment of an additional locus, annexin-like to sheep chromosome 3p is also reported.     

Regional localization of the human genes for aldehyde dehydrogenase-1 and aldehyde dehydrogenase-2

We have used the cDNA probes for human aldehyde dehydrogenase-1 (ALDH1) and aldehyde dehydrogenase-2 (ALDH2) to determine regional chromosomal locations of these two genes by in situ hybridization. Results presented here allow localization of ALDH1 to band q21 on chromosome 9 and ALDH2 to band q24 on chromosome 12.     

Four human Chromosome 3q and four human Chromosome 21 loci map onto sheep Chromosome 1q

Eight new loci have been assigned to sheep Chromosome (Chr) 1q by use of a chromosomally characterized minipanel of sheep x hamster cell hybrids. Four loci, which have been mapped to the distal region of human Chr 3q, are ceruloplasmin (CP), sucrase isomaltase (SI), glucose transporter 2 (GLUT2), and ectopic viral integration site 1 (EVI1). The other four loci, on human Chr 21, include interferon alpha receptor (IFNAR); interferon inducible protein p78, murine (MX1); collagen type VI, alpha 1 (COL6A1); and S100 protein, beta polypeptide (S100B). All of these loci, except GLUT2 and MX1, have been mapped onto bovine Chr 1 or are syntenic with loci on this chromosome. The in situ localization of transferrin (TF) to sheep Chr 1q42-q45 confirms our previous assignment of this locus and independently anchors the eight new syntenic loci to sheep Chr 1q.     

Physical mapping of the bovine, caprine and ovine homologues of the paired box gene PAX8.

The PAX8 gene, a member of the human paired box gene family, was mapped by FISH to chromosome 11 in cattle and goat and to the short arm of chromosome 3 in sheep. The cytogenetic position of PAX8 on BTA 11 and on its homologue OAR 3p lies in the region where the interleukin beta (IL1B) gene has been previously located, (BTA 11q22. 1-->q22.3 and OAR 3p25-->q26 respectively; Lòpez-Corrales et al., 1998). The results indicated that PAX8 as well as interleukin beta and interleukin alpha (IL1B and IL1A) genes detected on the human chromosome segment HSA 2q13-->q21 maintain a similar order and location in these three related species. In addition, the breakpoint in conserved synteny can now be narrowed to a position between the protein C (PROC) and PAX8 genes, which lie in close proximity on HSA 2.     

An integrated radiation hybrid map of bovine chromosome 18 that refines a critical region associated with multiple ocular defects in cattle

Congenital multiple ocular defects (MOD) of Japanese black cattle is a hereditary ocular disorder with an autosomal recessive mode of inheritance showing developmental defects of the lens, retina and iris, persistent embryonic eye vascularization and microphthalmia. The MOD locus has been mapped by linkage analysis to a 6.6-cM interval on the proximal end of bovine chromosome 18, which corresponds to human chromosome 16q and mouse chromosome 8. To refine the MOD region in cattle, we constructed an integrated radiation hybrid (RH) map of the proximal region of bovine chromosome 18, which consisted of 17 genes and 10 microsatellite markers, using the SUNbRH7000 panel. Strong conservation of gene order was found among the corresponding chromosomal regions in cattle, human and mouse. The MOD-critical region was fine mapped to a 59.5-cR region that corresponds to a 6.3-Mb segment of human chromosome 16 and a 4.8-Mb segment of mouse chromosome 8. Several positional candidate genes, including FOXC2 and USP10, were identified in this region.     

Ribonucleotide reductase M2 subunit sequences mapped to four different chromosomal sites in humans and mice: functional locus identified by its amplification in hydroxyurea-resistant cell lines

The sites of sequences homologous to a murine cDNA for ribonucleotide reductase (RR) subunit M2 were determined on human and murine chromosomes by Southern blot analysis of interspecies somatic cell hybrid lines and by in situ hybridization. In the human genome, four chromosomal sites carrying RRM2-related sequences were identified at 1p31----p33, 1q21----q23, 2p24----p25, and Xp11----p21. In the mouse, M2 sequences were found on chromosomes 4, 7, 12, and 13 by somatic cell hybrid studies. By Southern analysis of human hydroxyurea-resistant cells that overproduce M2 because of gene amplification, we have identified the amplified restriction fragments as those that map to chromosome 2. To further confirm the site of the functional RRM2 locus, two other cDNA clones, p5-8 and S7 (coding for ornithine decarboxylase; ODC), which are coamplified with RRM2 sequences in human and rodent hydroxyurea-resistant cell lines, were mapped by Southern and in situ hybridization. Their chromosomal map positions coincided with the region of human chromosome 2 (p24----p25) that also contains one of the four RRM2-like sequences. Since this RRM2 sequence and p5-8 and ODC are most likely part of the same amplification unit, the RRM2 structural gene can be assigned to human chromosome 2p24----p25. This region is homologous to a region of mouse chromosome 12 that also carries one of numerous ODC-like sequences. In an RRM2-overproducing mouse cell line, we found amplification of the chromosome 12-specific restriction fragments. Thus, we conclude that mouse chromosome 12 carries the functional locus for RRM2.     

Assignment of the genes encoding human interleukin-8 receptor types 1 and 2 and an interleukin-8 receptor pseudogene to chromosome 2q35.

Two human cDNA clones that encode different interleukin-8 (IL8) receptors have recently been isolated. The interleukin-8 receptor type 1 (IL8R1) binds IL8 only, whereas the interleukin-8 receptor type 2 (IL8R2) (previously designated IL8RA) also binds growth regulated gene (GRO), and neutrophil activating protein-2 (NAP-2) with high affinity. In the process of screening a genomic library with these cDNAs to obtain large clones for use in chromosomal localization studies, we isolated an interleukin-8 receptor pseudogene (IL8RP) that bears greatest similarity to IL8R2. Using Southern hybridization analysis of human x rodent somatic cell hybrid DNAs with cDNA probes for IL8R1 and IL8R2 and probes from the IL8RP locus, we assigned the three loci to chromosome 2; fluorescence in situ hybridization (FISH) to metaphase chromosome preparations using genomic clones from each locus refined this localization to chromosome 2, band q35, for all three. By virtue of their chromosomal location, IL8R1 and IL8R2 may be considered candidate genes for several human disorders in which the involved locus has been mapped to distal 2q or that are associated with structural abnormalities of this segment, including van der Woude syndrome and the neoplastic diseases rhabdomyosarcoma and uterine leiomyomata. In addition, because this region of chromosome 2q is homologous to proximal mouse chromosome 1 in the segment containing the Lsh-Ity-Bcg locus involved in mediating host resistance to infection with intracellular pathogens, examination for abnormalities of the murine homologues of the IL8R genes should be considered in mice affected by mutations of this locus.     

Assignment of the HOX2 and HOX3 gene clusters to the bovine chromosome regions 19q17-qter and 5q14-23

The homeobox 2 (HOX2) and homeobox 3 (HOX3) clusters have been chromosomally assigned in cattle by in situ hybridization. The probes employed were a murine probe for the mapping of HOX2 to 19q17-qter and human probes for the mapping of HOX3 to 5q14-q23. These assignments confirm the chromosomal assignment of two syntenic groups, consisting of loci located on human chromosome 12 (bovine chromosome 5) and the long arm of human chromosome 17 (bovine chromosome 19).     

Assignment of 35 single-copy and 17 repetitive sequence DNA probes to human chromosome 3: high-resolution physical mapping of 7 DNA probes by in situ hybridization

Thirty-five single-copy and 17 repetitive sequence DNA probes specific for human chromosome 3 were isolated from human chromosome 3-derived genomic libraries. Seven DNA clones, including three that are polymorphic for BglII or MspI, were mapped by in situ hybridization. Four probes were mapped to 3p subregions and 3 were mapped to 3q subregions. Three of the DNA sequences map to regions overlapping a segment of chromosome 3 (3p14-23) frequently deleted in small cell lung cancer cells. By Southern blot analysis on a deletion hybrid panel, we previously mapped 6 of these probes to three distinct chromosome 3 subregions. Our in situ data support these assignments and more precisely determine the localization of each clone to the following regions: D3S34 (3p14-21), D3S35 (3p21), D3S39 (3p21), D3S40 (3p12-13), D3S37 (3q21-23), and D3S36 (3q21). Clone pL84c, a low repeat sequence clone (approximately 30 copies), was mapped to the 3q21-29 subregion. These DNA clones mapped by in situ hybridization can provide useful landmarks for the ordering and localization of other clones.     

Human Chromosome 10 loci map to three different sheep chromosomes

The interleukin 2 receptor (IL2RA), a human Chromosome (Chr) 10p locus, was mapped to sheep Chr 13q12-q15 by in situ hybridization. Two loci from human Chr 10q, cytochrome P450 subfamily XVII (CYP17) and the tachykinin 2 receptor (TAC2R), were assigned to sheep Chrs 22q21-q23 and 25q14-q23 respectively. The assignment of IL2RA allows the provisional assignment of the previously unassigned sheep syntenic group U15 to sheep Chr 13. Sheep linkage group 5 is predicted to be located on sheep Chr 25 on the basis of the TAC2R assignment.     

Remarkable synteny conservation of melanocortin receptors in chicken,human, and other vertebrates

The melanocortin receptors (MCR) belong to the superfamily of G-protein-coupled receptors that participate in both peripheral and central functions, including regulation of energy balance. Genomic clones of the five chicken (GGA) MCRs were isolated and used to find the chromosomal location of each of the loci. The genes encoding MC2R and MC5R mapped to the middle part of the long arm of chromosome 2 (GGA2q22-q26) and MC4R proximally on the same chromosome arm, close to the centromere (2q12). This arrangement seems to be conserved on chromosome 18 in the human (HSA18). The MC1R and MC3R genes mapped to different microchromosomes that also appear to share homology with the respective human localization. The conserved synteny of the MC2R, MC5R, and MC4R cluster in chicken (GGA2), human (HSA18), and other mammals suggests that this cluster is ancient and was formed by local gene duplications that most likely occurred early in vertebrate evolution. Analysis of conserved synteny with mammalian genomes and paralogon segments prompted us to predict an ancestral gene organization that may explain how this family was formed through both local duplication and tetraploidization processes.     

Fluorescence in situ hybridization mapping of six loci containing genes involved in the dioxin metabolism of domestic bovids

Six loci containing genes involved in the dioxin metabolism (ARNT, AHR, CYP1A1, CYP1A2, CYP1B1 and AHRR) were assigned, for the first time, to cattle (Bos taurus, 2n = 60, BTA), river buffalo (Bubalus bubalis, 2n = 50, BBU), sheep (Ovis aries, 2n = 54, OAR) and goat (Capra hircus, 2n = 60, CHI) chromosomes by comparative FISH-mapping and R-banding using bovine BAC-clones. The following chromosome locations were found: ARNT to BTA3q21, BBU6q21, OAR1p21 and CHI3q21, AHR to BTA4q15, BBU8q15, OAR4q15 and CHI4q15; CYP1A1 and CYP1A2 to BTA21q17, BBU20q17, OAR18q17 and CHI21q17; CYP1B1 to BTA11q16, BBU12q22, OAR3p16 and CHI11q16, AHRR to BTA20q24, BBU19q24, OAR16q24 and CHI20q24. All loci were mapped at the same homoeologous chromosomes and chromosome bands of the four bovid species. Comparisons with corresponding human locations were also reported.     

Chromosome banding and gene localizations support extensive conservation of chromosome structure between cattle and sheep.

By using three gene probes, one derived from the porcine major histocompatibility complex (MHC) and two from bovine cytokeratin genes, type I (KRTA) and type II (KRTB), the hypothesis of conservation of genome structure in two members of the family Bovidae was examined. Gene mapping data revealed the MHC to be in chromosome region 23q15----q23 in cattle (BOLA) and 20q15----q23 in sheep (OLA). KRTA was localized to chromosome region 19q25----q29 in cattle and 11q25----q29 in sheep and KRTB to 5q14----q22 in cattle and 3q14----q22 in sheep. The banding patterns of the chromosome arms to which the loci were assigned were identical in both species. Moreover, the resemblances of GTG- or QFQ-banding patterns between the cattle and sheep karyotypes illustrated further chromosome homologies. These studies, based on gene mapping comparisons and comparative cytogenetics, document that within bovid chromosomes, homology of banding patterns corresponds to a homologous genetic structure. Hence, we propose that gene assignments on identified chromosomal segments in one species of the Bovidae can be extrapolated, in general, to other bovid species based on the banding homologies presented here.     

Chromosomal mapping of the gene for the type II insulin-like growth factor receptor/cation-independent mannose 6-phosphate receptor in man and mouse

The gene for insulin-like growth factor II (IGF-II) receptor (IGF2R) that has recently been found, by DNA sequencing, to be identical to the cation-independent mannose 6-phosphate receptor (CIM6PR) has been mapped in the human and murine species. Cloned cDNAs for human and rat IGF-II receptors were used to probe Southern blots of somatic cell hybrid DNA and for in situ chromosomal hybridization. The genes are located in a region of other conserved syntenic genes on the long arm of human chromosome 6, region 6q25----q27, and mouse chromosome 17, region A-C. The CIM6PR/IGF2R locus in man is asyntenic with the genes encoding IGF-II (IGF2), the IGF-I receptor (IGF1R), and the cation-dependent mannose 6-phosphate receptor (CDM6PR).     

Comparative mapping of genes from human chromosome 12 by genetic linkage mapping in cattle.

Loci from human chromosome 12 were mapped in cattle to compare the gene order between species. Polymorphisms were detected in cattle in six loci that had been mapped with high precision in humans. Four of these loci, LALBA, SLC2A3, SYT1, and TPI1, mapped to bovine chromosome 5, and one, PLA2G1B, mapped to bovine chromosome 17. The sixth locus, SLC2A3L, due to a fragment produced by the SLC2A3 primers, maps to the telomeric region of BTA18. The differences in gene order between human chromosome 12 and cattle chromosome 5, when these loci are added to others already mapped in cattle, show evidence of significant rearrangement in gene order requiring several evolutionary events. There is also evidence in cattle chromosome 5 of the interspersal of material conserved on human chromosome 22 into the material conserved on human chromosome 12, consistent with ZOOFISH analyses. This analysis indicates that the larger block near the centromere is conserved on the long arm of human chromosome 12 and the smaller block near the telomere is conserved as part of the short arm of human chromosome 12. The level of variation detected in the amplified cattle DNA was approximately 1 variant per 464 nucleotides of haploid DNA using single-strand conformation polymorphism analysis. This corresponds to a per individual level of 1 variant per 1, 961 nucleotides of haploid DNA. This confirms lower genetic variability in cattle compared to humans but indicates the potential for millions of single nucleotide polymorphisms in cattle.     

Localization of the murine macrophage colony-stimulating factor gene to chromosome 3 using interspecific backcross analysis

The chromosomal location of the murine macrophage colony-stimulating factor (Csfm) gene was determined by interspecific backcross analysis. We mapped Csfm to mouse chromosome 3, 2.5 cM distal to Ngfb and Nras and 1.3 cM proximal to Amy-2. CSFM maps to human chromosome 5q, while AMY2, NGFB, and NRAS map to human chromosome 1p. The chromosomal location of Csfm thus disrupts a previously identified conserved linkage group between mouse chromosome 3 and human chromosome 1. The location of Csfm also identifies yet another mouse chromosome that shares synteny with human chromosome 5q, a region involved in several different types of myeloid disease.