Syntenic Group Research Articles

Regional Mapping of Loci from Human Chromosome 2q to Sheep Chromosome 2q

The human chromosome 2q loci, fibronectin 1 (FN1), the alpha 1 chain of type III collagen (COL3A1), and the delta subunit of the muscle acetylcholine receptor (CHRND) have been regionally assigned to sheep chromosome 2q by in situ hybridization. COL3A1 is pericentromeric (2q12-q21), while FN1 and CHRND are in the subterminal region at 2q41-q44 and 2q42-qter, respectively. The mapping of FN1 assigns the sheep syntenic group U11, which contains FN1, villin 1 (VIL1), isocitrate dehydrogenase 1 (IDH1), and gamma subunit of the muscle acetylcholine receptor (CHRNG), to sheep chromosome 2q. Inhibin-alpha (INHA) is also assigned to sheep chromosome 2q as FN1 and INHA compose sheep linkage group 3. These seven loci are members of a conserved chromosomal segment in human, mouse, and sheep.

Gene mapping from a bovine 1;29 DNA library prepared with chromosome microdissection.

Bovine gene mapping is progressing rapidly using syntenic group mapping based on somatic cell hybrids and linkage, and to a lesser extent on in situ hybridization. Single chromosome DNA libraries are a logical next step, and this was, therefore, the aim of our laboratory. Since we have access to several cattle with t(1;29) and this chromosome is readily distinguishable, we chose this as our first target--recognizing that we would not produce a "single" chromosome library in the strict sense because two autosomes are represented. We utilized an inverted microscope and a micromanipulator fitted with glass instruments pulled specifically to dissect off approximately 100 t(1;29) chromosomes per microdrop. A glass chamber made to accommodate a hanging drop was used to extract the DNA under a dissecting microscope. The DNA was then cleaved with EcoRI and inserted in lambda gtwes arms. Host cells were then infected with these phage and positive clones obtained. The first clone, isolated from this library by hybridization with a human collagen 6A1 cDNA, was mapped by in situ hybridization to bovine Chromosome some (Chr) 1q12-q14, near the centromere. The second clone, an anonymous DNA fragment (D1S11), was mapped to 1q43-q46, near the terminal end.

A genetic linkage map for cattle.

We report the most extensive physically anchored linkage map for cattle produced to date. Three-hundred thirteen genetic markers ordered in 30 linkage groups, anchored to 24 autosomal chromosomes (n = 29), the X and Y chromosomes, four unanchored syntenic groups and two unassigned linkage groups spanning 2464 cM of the bovine genome are summarized. The map also assigns 19 type I loci to specific chromosomes and/or syntenic groups and four cosmid clones containing informative microsatellites to chromosomes 13, 25 and 29 anchoring syntenic groups U11, U7 and U8, respectively. This map provides the skeletal framework prerequisite to development of a comprehensive genetic map for cattle and analysis of economic trait loci (ETL).

A new marker (NGFB) on pig chromosome 4, isolated by using a consensus sequence conserved among species

The nerve growth factor beta gene (NGFB) belongs to a conserved syntenic group on human chromosome 1 and mouse Chromosome 3. The objective of this study was the isolation of a part of the porcine NGFB gene and its use as a genetic and physical marker in the pig genome. On the basis of a nucleotide sequence comparison among different species, NGFB-specific primers were chosen to amplify the corresponding porcine sequence by PCR. A pig genomic DNA fragment of 763 bp was isolated, and its DNA sequence, containing the complete coding sequence of mature NGFB, was determined. It was demonstrated that pig NGFB is largely homologous with NGFB of other species (mouse, cattle, chicken) and especially with human NGFB; the isolated clone shows 91% nucleotide and 99% translated amino acid sequence identity to the human NGFB sequence. The porcine DNA clone allowed us to identify an RFLP marker for genetic mapping in pigs and was used to map the NGFB gene to pig chromosome region 4q1.6-->q2.3 by radioactive in situ hybridization. Previously, we had localized to the same chromosome another member of this syntenic group, the gene encoding alpha 1 Na+,K+ ATPase (ATP1A1). These results show that a portion of the homologous region between human chromosome 1 and mouse Chromosome 3 is also conserved on pig chromosome 4.

Chromosomal localization of human, rat, and mouse protein phosphatase type 1 beta catalytic subunit genes (PPP1CB) by fluorescence in situ hybridization.

Using fluorescent in situ hybridization (FISH) method, gene encoding the catalytic subunit of protein phosphatase type 1 beta (PPP1CB) in human and its corresponding gene in rat (PP1 delta) and mouse (dis2m2) were mapped to human 2p23, rat 6q21-q23, and mouse 12D, respectively. These results indicate that PPP1CB is a member of conserved syntenic group. It is shown that the genes encoding catalytic subunit of protein phosphatase type 1 family (PP1 alpha, PP1 beta, and PP1 gamma in human and those corresponding genes in rat and mouse), in spite of their high identity, are located to different chromosomes in these three species.

Somatic cell mapping and in situ localization of the bovine uridine monophosphate synthase gene (UMPS).

Uridine monophosphate synthase (UMPS) catalyzes the final two steps of de novo pyrimidine synthesis, converting orotic acid to uridine 5' monophosphate. In Holstein and Red Holstein cattle, deficiency of UMPS (DUMPS) is inherited as a monogenic autosomal recessive trait. Heterozygous animals are phenotypically normal but have decreased UMPS activity in a number of tissues, whereas the homozygous genotype is lethal in utero. The cDNA for UMPS has recently been cloned in cattle (Sch6ber et al. 1993). A C ~ T point mutation in codon 405 results in a premature stop codon in DUMPS cattle (Schwenger et al. 1993), providing a DNA test for the detection of heterozygous bulls prior to entry into artificial insemination programs. UMPS has previously been mapped to human Chromosome (Chr) 3q13 (Qumsiyeh et al. 1989), Chinese hamster Chr 4p2 (Qumsiyeh and Suttle 1990), and sheep Chr lq (Burkin et al. 1993). Using somatic celt hybrid analysis and fluorescence in situ hybridization (FISH), we have assigned UMPS to cattle syntenic group U10 and sublocalized the gene to bovine Chr (BTA) 1 band 31. This represents the first assignment of a U10 marker to cattle chromosomes. BUS 6, a 1.5-kb fragment of the bovine UMPS cDNA representing amino acids 133-480 and the 3' untranslated region, was isolated from the E c o R I site of the plasmid pTZl9R (Sch6ber et al. 1993). The insert was radiolabeled with a-32p-dCTP and hybridized to EcoRI -d iges t ed bovine rodent hybrid somatic cell DNAs under high strin-

Regional localization of the bovine interleukin-2 (IL2) gene to chromosome 17q22→q23 by in situ hybridization

The interleukin-2 (IL2) gene was localized to the q22-->q23 bands of chromosome 17 in cattle using radioactive in situ hybridization. The localization confirms the recent provisional assignment of syntenic group U23 to this bovine chromosome. Increasing evidence for chromosomal banding and gene location homology within the Bovidae suggests that the IL2 gene most likely also maps to chromosome 17 in sheep, goats and buffaloes.

Isolation and Mapping of a Single-Locus Minisatellite Sequence Marker to 1q36-qter and Synteny Group 10 in Cattle and to 1q36-qter in Sheep

A minisatellite sequence (RD1613) was isolated from a bovine cosmid genomic library and its chromosomal location determined in cattle and sheep. In cattle, somatic cell hybrid panel analysis assigned RD1613 to the syntenic group U10 with a concordancy of 100%. In situ hybridization placed RD1613 onto bovine chromosome 1 in the region of bands q36-qter. This is the first in situ localization to chromosome 1 in cattle and allows the provisional assignment of syntenic group U10 to this chromosome. It was also found that RD1613 hybridized strongly to sheep genomic DNA. In situ hybridization localized RD1613 to sheep chromosome 1q36-qter, which is consistent with homology between cattle chromosome 1 and sheep chromosome 1q. The RD1613 probe detects a polymorphic single locus marker (designated D1S1) in both cattle and sheep and will be very useful in linkage studies.

Physically mapped, cosmid-derived microsatellite markers as anchor loci on bovine chromosomes.

To identify physical and genetic anchor loci on bovine chromosomes, 13 cosmids, obtained after the screening of partial bovine cosmid libraries with the (CA)n microsatellite motif, were mapped by fluorescence in situ hybridization (FISH). Eleven cosmid probes yielded a specific signal on one of the bovine chromosomes and identified the following loci: D5S2, D5S3, D6S3, D8S1, D11S5, D13S1, D16S5, D17S2, D19S2, D19S3, D21S8. Two cosmids produced centromeric signals on many chromosomes. The microsatellite-containing regions were subcloned and sequenced. The sequence information revealed that the two centromeric cosmids were derived from bovine satellites 1.723 and 1.709, respectively. A cosmid located in the subtelomeric region of Chromosome (Chr) 17 (D17S2) had features of a chromosome-specific satellite. Primers were designed for eight of the nonsatellite cosmids, and seven of these microsatellites were polymorphic with between three and eight alleles on a set of outbred reference families. The polymorphic and chromosomally mapped loci can now be used to physically anchor other bovine polymorphic markers by linkage analysis. The microsatellite primers were also applied to DNA samples of a previously characterized panel of somatic hybrid cell lines, allowing the assignment of seven microsatellite loci to defined syntenic groups. These assignments confirmed earlier mapping results, revealed a probable case of false synteny, and placed two formerly unassigned syntenic groups on specific chromosomes.

Assignment of five polymorphic ovine microsatellites to bovine syntenic groups.

A panel of bovine somatic cell hybrids was used to map ovine microsatellites. Five of seven microsatellites were assigned to five bovine syntenic groups. These microsatellites were designated D5S10 (MAF23), D1S4 (MAF46), D13S1 (MAF18), D4S3 (MAF50), and DXS2 (MAF45), mapped to syntenic groups U3 (chromosome 5), U10 (chromosome 1), U11, U13, and the X chromosome, respectively. Two remaining sheep microsatellites amplified rodent DNA in the hybrid somatic cell panel, and were not assigned to bovine syntenic groups. Assignment of ovine-derived microsatellites to bovine syntenic groups provides additional evidence of the usefulness of microsatellites for mapping closely related species. The use of ovine and bovine microsatellites will aid in development of comparative genomic maps for these two species.

A genetic map of DNA loci on bovine chromosome 1

We constructed a genetic map of most of the length of bovine chromosome 1 using the CSIRO and the Texas A&M University cattle reference families. Twelve loci are in a single linkage group, 9 of which are highly polymorphic loci. Four loci are of known biochemical function, α-1 crystallin (CRYA1), γ-s crystallin (CRYGS), superoxide dismutase 1 (SOD1), and uridine monophosphate synthase (LIMPS), and these have also been previously mapped in humans. The loci CRYA 1, CSRD 1613, GMBT 7, RM 95, SOD I, and LIMPS had been previously assigned to bovine syntenic group U10, while CSRD 1613 and LIMPS had also been assigned to chromosome 1 by in situ hybridization. All of the loci show statistically significant linkage to at least one other locus. The conserved loci indicate that there have been major rearrangements during the evolution of bovine chromosome 1 compared to other mammalian chromosomes. The estimate of the total length of the linkage group is 168 cM, which accords well with the predicted length based on chiasmata frequencies for the bovine genome and the relative size of chromosome 1 in the bovine genome.

Somatic cell mapping of conglutinin (CGN1) to cattle syntenic group U29 and fluorescence in situ localization to Chromosome 28

A 260-bp genomic PstI fragment, which encodes a portion of the carbohydrate recognition domain, was used along with hybrid somatic cells to map the conglutinin gene (CGN1) to domestic cow (Bos taurus) syntenic group U29. In turn, a cosmid containing the entire bovine CGN1 was used with fluorescence in situ hybridization to sublocalize this gene to cattle Chromosome (Chr) (BTA) 28 band 18. Since BTA 28 and several of the other small acrocentric autosomes of cattle are difficult to discriminate, we have also chromosomally sublocalized CGN1 to the p arm of the lone biarmed autosome of the gaur (Bos gaurus). The use of the gaur 2/28 Robertsonian as a marker chromosome and our assignment of CGN1 to BTA 28 should help resolve some of the nomenclatural questions involving this cattle chromosome.

Characterization of the hexaploid oat Avena byzantina cv. Kanota monosomic series using C-banding and RFLPs

The establishment of a C-banded karyotype of hexaploid oat (Avena spp., 2n = 6x = 42) has facilitated the cytological characterization of a monosomic series in 'Kanota', an A. byzantina (C. Koch) cultivar. The 'Kanota' series of monosomics analyzed in this study consists of only 12 of the 21 different chromosome-deficient lines possible plus potential translocated segments of two or three additional chromosomes. These findings were confirmed by RFLP mapping data from studies in which oat probes were assigned to syntenic groups using the 'Kanota' set of monosomic lines. Among the remaining nine monosomic lines analyzed, eight are missing chromosomes represented in the set of 12 unique lines and one line, monosomic K13, is missing a chromosome from the unique set of 12 that possesses a cytologically detectable translocation. This same translocation, involving chromosomes 7C and 14, is found in 5 of the 21 'Kanota' monosomics. The incompleteness of the set of 'Kanota' monosomics might be due to (i) difficulty in identifying individual oat chromosomes without C-banding, (ii) plant genotypic and phenotypic variability in the original source population of the 'Kanota' monosomics, and (or) (iii) a high frequency of monosomic shifts in progency of the original 'Kanota' monosomic lines.

Physical mapping of the lysozyme gene family in cattle.

Amplification of an ancestral lysozyme gene in artiodactyls is associated with the evolution of foregut fermentation in the ruminant lineage and has resulted in about ten lysozyme genes in true ruminants. Hybridization of a cow stomach lysozyme 2 cDNA clone to restricted DNAs of a panel of cow x hamster hybrid cell lines revealed that all but one of the multiple bovine-specific bands segregate concordantly with the marker for bovine syntenic group U3 [Chromosome (Chr) 5]. The anomalous band was subsequently mapped to bovine syntenic group U22 (Chr 7) with a second panel of hybrids representing all 31 bovine syntenic groups. By two-dimensional pulsed-field gel electrophoresis the lysozyme genes on cattle Chr 5 were shown to be clustered on a 2- to 3-Mb DNA fragment, while the lactalbumin gene and pseudogenes that are paralogous and syntenic with the lysozymes were outside the lysozyme gene cluster. Chromosomal fluorescence in situ hybridization of a cocktail of lysozyme genomic clones localized the lysozyme gene cluster to cattle Chr 5 band 23, corroborating the somatic cell assignment.

Chromosomal localization of HSP70 genes in cattle.

Five genomic clones representing three HSP70 genes of cattle were biotin labeled and independently hybridized to cattle chromosomes. Fluorescence in situ hybridization localized HSP70-2 to Chromosome (Chr) 23 band 22 (the BoLA region), HSP70-3 to Chr 10 band 34, and HSP70-4 to Chr 3 band 13. Since HSP70-1, a fourth HSP70 gene, is tightly linked with HSP70-2 and the BOLA, HSP70-1 was also localized to Chr 23 band 22. The localization of HSP70-4 is the first assignment of a cattle U6 marker; thus, this entire syntenic group is tentatively placed in cattle Chr 3.

Evolution of EF-hand calcium-modulated proteins. V. The genes encoding EF-hand proteins are not clustered in mammalian genomes

The chromosomal assignments of genes belonging to the EF-hand family which have a common origin are compiled in this article. So far data are available from 27 human gene loci belonging to 6 subfamilies and 8 murine loci belonging to 4 subfamilies. Chromosomal localization has been obtained by somatic-cell hybrid analysis using the Southern blot technique or PCR amplification, metaphase spread in situ hybridization, or isolation of the particular genes from chromosome-specific libraries. Except for genes of the S-100 alpha proteins which are grouped on human chromosome 1q12-25 and mouse chromosome 3, no linkage has been found for genes encoding EF-hand proteins, indicating absence of selective pressure for maintaining chromosomal clustering. Six of these genes map to known syntenic groups conserved in the human and mouse genomes. This suggests that chromosomal translocations occurred before divergence of these species. The possible significance of chromosomal positioning with respect to nearby located known genes and genetic disease loci is discussed.

The Human Urokinase-Plasminogen Activator Gene (PLAU) Is Located on Chromosome 10q24 Centromeric to the HOX11 Gene

Urokinase-plasminogen activator is one of two soluble serine proteases that are produced by humans and that convert plasminogen, an inactive proenzyme present in plasma and other extracellular fluids, to plasmin, a protease with broad substrate specificities. Its activity is involved in processes requiring localized extracellular proteolysis such as fibrinolysis, tissue remodeling, and cell migration. Increased production of urokinase has been associated with cancer metastases. The gene for urokinase-plasminogen activator, PLAU, was mapped to chromosome 10q24-qter. By employing somatic cell genetics, polymerase chain reaction (PCR), and Southern blot analysis, the authors assign PLAU to chromosome 10q24. Human chromosome segment 10q23-q25 contains the genes for terminal deoxynucleotidyltransferase, cytochrome P450IIC, glutamic-oxaloacetic transaminase, and plasma retinol binding protein, which form a syntenic group on murine chromosome 19. It is therfore of interest that PLAU and glutamate dehydrogenase, which are on murine chromosome 14, also map in or close to this region of human chromosome 10.

Somatic cell mapping of the bovine prion protein gene and restriction fragment length polymorphism studies in cattle and sheep.

Brains affected by the progressive neurological disease bovine spongiform encephalopathy (BSE) contain scrapie-associated fibrils and the protease-resistant isoform of prion protein. The gene encoding the normal host prion protein (PRNP) has been mapped to human chromosome 20 and mouse chromosome 2 with the hamster cDNA probe pEA974. Using this probe and a panel of bovine-rodent hybrid somatic cells, we have mapped PRNP to bovine syntenic group U11 (100% concordancy). PRNP restriction fragment length polymorphisms (RFLPs) were detected with five of six enzymes (BglII, EcoRI, HindIII, MspI and TaqI) in sheep, in contrast to one of 16 enzymes (HincII) in cattle. Codominant segregation of the bovine HincII RFLP was demonstrated in six backcross pedigrees. While PRNP RFLPs are tightly linked to scrapie incubation period, and consequently susceptibility or resistance to disease in rodents and sheep, the relationship between the PRNP RFLPs and BSE incubation period has not been determined.

Physical mapping of inhibin beta-A in domestic cattle.

The gene for the beta-A subunit of inhibin (INHBA) was assigned to bovine syntenic group U13 by bovine x rodent hybrid somatic cells and the polymerase chain reaction (PCR). A 482-bp PCR fragment was used to clone a 37-kb cosmid. This cosmid was assigned to bovine Chromosome (Chr) 4 (BTA 4) by fluorescence in situ hybridization (FISH). This is the first assignment of a U13 marker to a bovine chromosome. A restriction fragment length polymorphism (RFLP) was detected with PstI within the INHBA cosmid.

Somatic cell mapping of omega and trophoblast interferon genes to bovine syntenic group U18 and in situ localization to chromosome 8.

Bovine omega (IFNW) and trophoblast (IFNT) interferon genes were assigned to bovine syntenic group U18 by somatic cell genetics. Fluorescent in situ hybridization subsequently localized these genes to bovine chromosome 8 band 15. This assignment conflicts with a previous assignment of U17 genes to the same chromosome.