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.     

Sheep linkage mapping: RFLP markers for comparative mapping studies

Restriction fragment length polymorphisms (RFLPs) detected using cDNA probes for conserved genes provide an important set of markers that anchor or link syntenic groups in a range of divergent mammalian species. DNA probes from sheep, cattle, pig, human and mouse were screened against sheep DNA samples and 24 new RFLP markers for sheep were identified. Among the loci tested, 22 had a homologue that has been mapped in humans. An RFLP for fibronectin (FN1) was linked to α-inhibin (INHA) at a distance of 5cM. The FN1 locus has been assigned to sheep chromosome 2q41–q44 and linkage between FN1 and INHA assigns INHA to the same chromosome in sheep. In addition to the new loci reported here, 28 RFLPs have been published previously by this group and these are collated together with RFLPs published from other laboratories. RFLPs have been reported for 86 loci in sheep. Fifty-four loci have been mapped to 16 different chromosomes.     

FISH mapping of the IGF2 gene in horse and donkey—detection of homoeology with HSA11

Three genomic subclones derived from a phage clone containing the equine IGF2 gene were used to FISH map the gene on horse (ECA) and donkey (EAS) metaphase chromosomes. The gene mapped on ECA 12q13 band and is the first locus mapped to this horse chromosome. In donkey the gene mapped very terminal on the long arm of one small submetacentric chromosome that shows almost identical DAPI-banding pattern with ECA12. This is the first locus mapped in donkey genome. Cross species chromosome painting of equine metaphase chromosomes with human Chromosome (Chr) 11-specific probe showed homoeology of this human chromosome with ECA12 and ECA7. The novel ECA12 comparative painting results are thus in accordance with the localization of the equine IGF2 gene. Comparison of the hitherto known physical locations of IGF2 in different species, viz. human, cattle, sheep, horse, and donkey, shows that this gene tends to maintain a terminal location on the chromosome arm. Received: 12 January 1997 / Accepted: 17 March 1997     

The complete map of the Ig heavy chain constant gene region reveals evidence for seven IgG isotypes and for IgD in the horse

This report contains the first map of the complete Ig H chain constant (IGHC) gene region of the horse (Equus caballus), represented by 34 overlapping clones from a new bacterial artificial chromosome library. The different bacterial artificial chromosome inserts containing IGHC genes were identified and arranged by hybridization using overgo probes specific for individual equine IGHC genes. The analysis of these IGHC clones identified two previously undetected IGHC genes of the horse. The newly found IGHG7 gene, which has a high homology to the equine IGHG4 gene, is located between the IGHG3 and IGHG4 genes. The high degree of conservation shared between the nucleotide sequences of the IGHG7 and IGHG4 genes is unusual for the IGHG genes of the horse and suggests that these two genes duplicated most recently during evolution of the equine IGHG genes. Second, we present the genomic nucleotide sequence of the equine IGHD gene, which is located downstream of the IGHM gene. Both the IGHG7 and IGHD genes were found to be expressed at the mRNA level. The order of the 11 IGHC genes in the IGH-locus of the horse was determined to be 5'-M-D-G1-G2-G3-G7-G4-G6-G5-E-A-3', confirming previous studies using lambda phage clones, with the exception that the IGHG5 gene was found to be the most downstream-located IGHG gene. Fluorescence in situ hybridization was used to localize the IGHC region to Equus caballus (ECA) 24qter, the horse chromosome corresponding to human chromosome 14, where the human IGH locus is found.     

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).     

Linkage of bilateral convergent strabismus with exophthalmus (BCSE) to BTA5 and BTA18 in German Brown cattle

Bilateral convergent strabismus with exophthalmus (BCSE) is a widespread inherited eye defect in several cattle populations. Its progressive condition often leads to blindness in affected cattle and decreases their usability. Furthermore, the German animal welfare laws prevent breeding with animals whose progeny are expected to be affected by genetic defects. Identifying genes involved in the heredity of BCSE should lead to insights into the molecular pathogenesis of this eye disease and permit the establishment of a genetic test for this disease. A whole-genome scan for 10 families containing a total of 159 genotyped individuals identified two BCSE loci. One BCSE locus mapped to the centromeric region on bovine chromosome (BTA) 5 and the other BCSE locus mapped to the telomeric region of BTA18. Thus, it is possible that two genes are involved in the development of BCSE. Alternatively, one of these loci could be the cause for the development of BCSE and the other locus could affect the progression and severity of the defect.     

The scurs locus in cattle maps to bovine chromosome 19

Polled, or the absence of horns, is a desirable trait for many cattle breeders. However, the presence of scurs, which are small horn-like structures that are not attached to the skull, can lower the value of an animal. The scurs trait has been reported as sex influenced. Using a genome scan with 162 autosomal microsatellite markers genotyped across three full-sib families, the scurs locus was mapped near BMS2142 on cattle chromosome 19 (LOD = 4.21). To more precisely map scurs, the families from the initial analysis and three additional families were genotyped for 16 microsatellite markers and SNPs in three genes on chromosome 19. In this subsequent analysis, the scurs locus was mapped 4 cM distal of BMS2142 (LOD = 4.46) and 6 cM proximal to IDVGA46 (LOD = 2.56). ALOX12 and MFAP4 were the closest genes proximal and distal, respectively, to the scurs locus. Three microsatellite markers on the X chromosome were genotyped across these six families but were not linked to scurs, further demonstrating that this trait was not sex linked. Because the polled locus has been mapped to the centromeric end of chromosome 1 and scurs has now been mapped to chromosome 19, these two traits are not linked in Bos taurus.     

Comparative mapping ofIGHG,IGHM, FES,andFOS in domestic cattle

The immunoglobulin genes have not been genetically characterized as thoroughly in cattle as in other mammals, particularly humans and mice. Comparative gene mapping in mammals suggests that the bovine immunoglobulin heavy chain genes,IGHG4 andIGHM might be syntenic with theFOS oncogene. Interestingly, however, when these genes were assigned to bovine syntenic groups utilizing a panel of bovine: hamster hybrid somatic cells,IGH genes were shown to be syntenic with theFES oncogene rather thanFOS. In this studyIGH andFES were assigned toBos taurus chromosome 21 whileFOS was assigned to chromosome 10. In addition, bovine-specific immunoglobulin-like sequences were observed in the hybrid somatic cells, and one, IGHML1, was mapped to bovine syntenic group U16. The probes used for somatic-cell mapping were also used to screen a small number of cattle of several different breeds for restriction fragment length polymorphisms.IGHG4 andIGHM were shown to be highly polymorphisms. whileFOS andFES were not. Address correspondence and offprint requests to: J. E. Womack.     

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.     

Development of microsatellite markers and comparative mapping for bovine chromosome 19

Previous research has mapped an ovulation rate quantitative trait locus (QTL) to bovine chromosome 19. In an effort to enhance comparative mapping information and develop additional markers for refined QTL mapping, microsatellite markers were developed in a targeted approach. A bovine bacterial artificial chromosome (BAC) library was screened for loci with either known or predicted locations on bovine chromosome 19. An average of 6.4 positive BAC were identified per screened locus. A total of 10 microsatellite markers were developed for five targeted loci with heterozygosity of 7-83% in a sample of reference family parents. The newly developed markers were typed on reference families along with four previously mapped marker loci and used to create a linkage map. Comparison of locus order between human and cattle provides support for previously observed rearrangement. One of the mapped loci myotubularin related protein 4 (MTMR4) potentially extends the proximal boundary of a conserved linkage group.     

Benign familial infantile convulsions: mapping of a novel locus on chromosome 2q24 and evidence for genetic heterogeneity

In 1997, a locus for benign familial infantile convulsions (BFIC) was mapped to chromosome 19q. Further data suggested that this locus is not involved in all families with BFIC. In the present report, we studied eight Italian families and mapped a novel BFIC locus within a 0.7-cM interval of chromosome 2q24, between markers D2S399 and D2S2330. A maximum multipoint HLOD score of 6.29 was obtained under the hypothesis of genetic heterogeneity. Furthermore, the clustering of chromosome 2q24-linked families in southern Italy may indicate a recent founder effect. In our series, 40% of the families are linked to neither chromosome 19q or 2q loci, suggesting that at least three loci are involved in BFIC. This finding is consistent with other autosomal dominant idiopathic epilepsies in which different genes were found to be implicated.     

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.     

The bovine pancreatic spasmolytic polypeptide gene maps to syntenic group U10: implications for the evolution of the human breast cancer estrogen inducible locus.

Recently, homology has been reported for pS2, a protein expressed in many human breast cancers, and a hormonogastric protein known as pancreatic spasmolytic polypeptide (SPP; formerly designated as PSP). The breast cancer estrogen inducible locus (BCEI), which encodes pS2, maps to human chromosome 21 (HSA 21). The SPP locus has not been mapped in humans. Several loci from HSA 21 have been mapped in cattle to syntenic group U10, but a BCEI bovine homolog was not detected. If a bovine BCEI locus does exist, map comparisons predict BCEI will reside on syntenic group U10. The assignment of bovine SPP to syntenic group U10 supports the postulated evolutionary relationship between BCEI and SPP.     

Mapping of the mouse fibronectin gene (Fn-1) to chromosome 1: conservation of the Idh-1-Cryg-Fn-1 synteny group in mammals

Restriction fragment length polymorphisms (RFLPs) were observed in BamHI-digested mouse DNA probed with a cDNA for human fibronectin. Analysis of the inheritance of fibronectin RFLPs in AKXD and SWXJ recombinant inbred strains of mice mapped the locus, Fn-1, to the midregion of mouse chromosome 1 about 4 cM distal from the loci encoding gamma-crystallins (Cryg). Loci homologous to genes in the centromeric third of mouse chromosome 1 are also syntenic in rats, humans, and cattle and may, therefore, mark a large conserved chromosomal segment of the mammalian genome.     

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.     

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.     

Physical mapping of four serpin genes: alpha 1-antitrypsin, alpha 1-antichymotrypsin, corticosteroid-binding globulin, and protein C inhibitor, within a 280-kb region on chromosome I4q32.1.

Alpha 1-antitrypsin (alpha 1AT; protease inhibitor [PI] locus), alpha 1-antichymotrypsin (alpha 1ACT; AACT locus), corticosteroid-binding globulin (CBG; CBG locus), and protein C inhibitor (PCI; PCI locus) are members of the serine protease inhibitor (serpin) superfamily. A noncoding PI-like (PIL) gene has been located 12 kb 3' of the PI gene. The PI, PIL, and AACT loci have been localized to 14q32.1, the CBG locus has been localized to 14q31-14q32.1, and PCI has been mapped to chromosome 14. Genetic linkage analysis suggests tight linkage between PI and AACT. We have used pulsed-field gel electrophoresis to generate a physical map linking these five serpin genes. The order of the genetic loci is AACT/PCI-PI-PIL-CBG, with a maximum distance of about 220 kb between the AACT/PCI and PI genes. These genes form a PI cluster at 14q32.1, similar to that of the homologous genes on murine chromosome l2. The close proximity of these genes has implications for disease-association studies.     

A Genetic Analysis of the Werner Syndrome Region on Human Chromosome 8p

Werner syndrome (WRN) is an inherited disorder that produces symptoms of premature aging. This disease is caused by a recessive mutation that has previously been mapped to chromosome 8p. We have now used genetic linkage analysis to map the WRN gene relative to chromosome 6 reference loci, to screen candidate genes, and to identify a novel dinucleotide repeat polymorphic marker closely linked to WRN. The WRN locus was mapped relative to the marker loci, PLAT, ANK1, D8S135, and D8S87 of the comprehensive chromosome 8 linkage map. The heregulin (HRG) and the fibroblast growth factor receptor 1 genes (FGFR1) have been mapped to chromosome 8p and are involved in cellular growth. Recombination events were detected between WRN and the HRG and FGFR1 genes, excluding them as candidates for the WRN gene. A polymorphic marker generated in this study, WT251, is linked to WRN at a recombination fraction of 0.006, with a lod score of 16.5.     

The epitheliogenesis imperfecta locus maps to equine chromosome 8 in American Saddlebred horses

Epitheliogenesis imperfecta (EI) is a hereditary junctional mechanobullous disease that occurs in newborn American Saddlebred foals. The pathological signs of epitheliogenesis imperfecta closely match a similar disease in humans known as Herlitz junctional epidermolysis bullosa, which is caused by a mutation in one of the genes (LAMA3, LAMB3 and LAMC2) coding for the subunits of the laminin 5 protein (laminin alpha3, laminin beta3 and laminin gamma2). The LAMA3 gene has been assigned to equine chromosome 8 and LAMB3 and LAMC2 have been mapped to equine chromosome 5. Linkage disequilibrium between microsatellite markers that mapped to equine chromosome 5 and equine chromosome 8 and the EI disease locus was tested in American Saddlebred horses. The allele frequencies of microsatellite alleles at 11 loci were determined for both epitheliogenesis imperfecta affected and unaffected populations of American Saddlebred horses by genotyping and direct counting of alleles. These were used to determine fit to Hardy-Weinberg equilibrium for control and EI populations using Chi square analysis. Two microsatellite loci located on equine chromosome 8q, ASB14 and AHT3, were not in Hardy-Weinberg equilibrium in affected American Saddlebred horses. In comparison, all of the microsatellite markers located on equine chromosome 5 were in Hardy-Weinberg equilibrium in affected American Saddlebred horses. This suggested that the EI disease locus was located on equine chromosome 8q, where LAMA3 is also located.