Chromosomal localization of sixty autosomal loci in sheep (OVIS ARIES, 2n = 54) by fluorescence in situ hybridization and R-banding

Sixty autosomal loci (5 type I and 55 type II) from 24 bovine syntenic groups, and previously FISH-mapped to goat and river buffalo chromosomes, were localized by fluorescence in situ on sheep (OVIS ARIES, 2n = 54) chromosomes, thereby notably extending the cytogenetic map of this economically important species. Caprine BAC clones were hybridized to R-banded chromosome preparations. FITC-signals and RBPI- banding (R-banding by late BrdU-incorporation and propidium iodide staining) were simultaneously visualized and captured by a colour CCD-camera. All mapped loci were localized on homoeologous chromosomes and chromosome regions (bands) of sheep, goat and river buffalo, further supporting chromosome and genetic (loci) homoeologies among bovids.     

The river buffalo (Bubalus bubalis, 2n = 50) cytogenetic map: assignment of 64 loci by fluorescence in situ hybridization and R-banding

Sixty-four genomic BAC-clones mapping five type I (ADCYAP1, HRH1, IL3, RBP3B and SRY) and 59 type II loci, previously FISH-mapped to goat (63 loci) and cattle (SRY) chromosomes, were fluorescence in situ mapped to river buffalo R-banded chromosomes, noticeably extending the physical map of this species. All mapped loci from 26 bovine syntenic groups were located on homeologous chromosomes and chromosome regions of river buffalo and goat (cattle) chromosomes, confirming the high degree of chromosome homeologies among bovids. Furthermore, an improved cytogenetic map of the river buffalo with 293 loci from all 31 bovine syntenic groups is reported.     

Comparative FISH mapping in river buffalo and sheep chromosomes: assignment of forty autosomal type I loci from sixteen human chromosomes.

Forty autosomal type I loci earlier mapped in goat were comparatively FISH mapped on river buffalo (BBU) and sheep (OAR) chromosomes, noticeably extending the physical map in these two economically important bovids. All loci map on homoeologous chromosomes and chromosome bands, with the exception of COL9A1 mapping on BBU10 (homoeologous to cattle/goat chromosome 9) and OAR9 (homoeologous to cattle/goat chromosome 14). A FISH mapping control with COL9A1 on both cattle and goat chromosomes gave the same results as those obtained in river buffalo and sheep, respectively. Direct G- and R-banding comparisons between Bovinae (cattle and river buffalo) and Caprinae (sheep and goat) chromosomes 9 and 14 confirmed that a simple translocation of a small pericentromeric region occurred between the two chromosomes. Comparisons between physical maps obtained in river buffalo and sheep with those reported in sixteen human chromosomes revealed complex chromosome rearrangements (mainly translocations and inversions) differentiating bovids (Artiodactyls) from humans (Primates).     

Comparative FISH-mapping of twelve loci in river buffalo and sheep chromosomes: comparison with HSA8p and HSA4q

Twelve loci (11 of type I and 1 of type II) previously FISH-mapped in cattle were comparatively FISH-mapped in both river buffalo chromosome 1p (BBU1p) and homologous chromosome 26 of sheep (OAR26), extending the cytogenetic maps in both chromosome species and providing a more precise localization of these loci in single chromosome bands than previous locations on BTA27. Bovine BAC clones containing DCTD, C4orf20, CASP3, TLR3, MSR1, FAT, LONRF1, DLC1, C8orf41, CSSM036, LSM1 and EIF4EBP1 were used for FISH on RBPI-banded chromosomes. All loci were located on the same homologous chromosome bands (R-band positive) of both species further confirming the high degree of banding and gene (order of loci) homologies among bovids. Detailed cytogenetic maps of OAR26 and BBU1p were performed and compared with that of BTA27 as well as with those of both HSA8p and HSA4q, revealing complex chromosome rearrangements differentiating OAR26/BBU1p/BTA27 from human chromosomes.     

Comparative FISH mapping of mucin 1, transmembrane (MUC1) among cattle, river buffalo, sheep and goat chromosomes: comparison between bovine chromosome 3 and human chromosome 1

Four bovine BAC clones (0494F01, 0069D07, 0060B06, and 0306A12) containing MUC1, as confirmed by mapping MUC1 on a RH3000 radiation hybrid panel, were hybridised on R-banded chromosomes of cattle (BTA), river buffalo (BBU), sheep (OAR) and goat (CHI). MUC1 was FISH-mapped on BTA3q13, BBU6q13, OAR1p13 and CHI3q13 and both chromosomes and chromosome bands were homoeologous confirming the high degree of chromosome homoeologies among bovids and adding more information on the pericentromeric regions of these species' chromosomes. Indeed, MUC1 was more precisely assigned to BTA3 and assigned for the first time to BBU6, OAR1p and CHI3. Moreover, detailed and improved cytogenetic maps of BTA3, CHI3, OAR1p and BBU6 are shown and compared with HSA1.     

FISH-mapping of LEP and SLC26A2 genes in sheep, goat and cattle R-banded chromosomes: comparison between bovine, ovine and caprine chromosome 4 (BTA4/OAR4/CHI4) and human chromosome 7 (HSA7)

Sheep (OAR), goat (CHI) and cattle (BTA) R-banded chromosome preparations, obtained from synchronized cell cultures, were used to FISH-map leptin (LEP) and solute carrier family 26 member 2 (SLC26A2) genes on single chromosome bands. LEP maps on OAR4q32 and CHI4q32, being the first assignment of this gene to these two species. SLC26A2 maps on BTA7q24, OAR5q24 and CHI7q24. This gene, too, was assigned for the fist time to both sheep and goat chromosomes, while it was more precisely localized on a single chromosome band in cattle. Improved cytogenetic maps of BTA4/OAR4/CHI4 were constructed and compared with HSA7 revealing five main conserved segments and complex chromosome rearrangements, including a centromere repositioning, differentiating HSA7 and BTA4/OAR4/CHI4.     

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.     

Physical mapping confirms that sheep chromosome 10 has extensive conserved synteny with cattle chromosome 12 and human chromosome 13

The following loci, on human chromosome 13, have been newly assigned to sheep chromosome 10 using chromosomally characterized sheep-hamster cell hybrids: gap junction protein, beta 2, 26 kDa (connexin 26) (GJB2); gap junction protein, alpha 3, 46 kDa (connexin 46) (GJA3), and esterase D/formylglutathione hydrolase (ESD). This assignment of ESD is consistent with comparative mapping evidence, but not with an earlier report of it on sheep chromosome 3p26-p24. Cell hybrid analysis confirmed the location of another human chromosome 13 locus, retinoblastoma 1 (including osteosar-coma) (RBI), and the anonymous ovine genomic sequence RP11 on sheep chromosome 10. Isotopic in situ hybridization was used to regionally localize RP11 on to sheep 10q15-q22. The location of microsatellites AGLA226, OarDB3, OarHH41, OarVH58, and TGLA441, previously assigned to sheep chromosome 10 by linkage analysis, was confirmed by polymerase chain reaction using the cell hybrid panel. These mapping data provide further evidence that sheep chromosome 10 is the equivalent of cattle chromosome 12, and that these chromosomes show extensive conserved synteny with human chromosome 13.     

A radiation hybrid map of bovine chromosome one

Radiation hybrid (RH) mapping has proven to be an extremely powerful approach to constructing high density maps of human chromosomes and is experiencing increased use in other animals, including cattle. A 5000 rad bovine whole-genome radiation hybrid panel was recently constructed in order to integrate existing cattle linkage maps with evolutionarily conserved genes and provide high resolution comparative maps relative to humans and mice. We utilized this panel to construct a 19 marker framework map of bovine chromosome 1 (BTA1), which included 8 Type I loci and 11 Type II loci ordered with at least 1000:1 odds. A 35 marker comprehensive map including 15 Type I loci and 20 Type II loci was also produced. Of the 15 Type I loci ordered on the comprehensive map, three are ordered on HSA3 and five are ordered in three blocks on HSA21 on the human cytogenetic maps.     

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.     

Fourteen chromosomal localizations and an update of the cytogenetic map of the rabbit

In order to improve the informativeness of the cytogenetic map of the rabbit genome, fourteen markers were regionally mapped to individual chromosomes. The localizations comprise eleven gene loci (PRLR, GHR, HK1, ACE, TF, 18S+28S rDNA, CYP2C4, PMP2, TCRB, ALOX15 and MT1) and three microsatellite loci (Sat13, Sol33 and D1Utr6). Five of the genes contain known microsatellite sequences. To achieve these localizations, homologous and heterologous small insert clones, and clones from a rabbit Bacterial Artificial Chromosome (BAC) library were used as probes for fluorescence in situ hybridization experiments. Results indicate that especially BAC clones are a valuable tool for cytogenetic mapping. Some of the genes were selected for mapping on the basis of human- rabbit comparative painting data, to achieve localizations on gene-poor rabbit chromosomes. Our data are, in general, in agreement with the human-rabbit comparative painting data. By mapping microsatellite sequences that have also been used in linkage studies, links are provided between the genetic and physical maps of the rabbit genome. Linkage groups I, VI and XI could be assigned to chromosomes 1, 5 and 3 respectively. Moreover, in this paper we give an overview of the current status of the rabbit cytogenetic map. This map now comprises 62 physically mapped genes, which are scattered over all autosomes, except chromosome 2, and the X chromosome.     

Extended cytogenetic maps of sheep chromosome 1 and their cattle and river buffalo homoeologues: comparison with the OAR1 RH map and human chromosomes 2, 3, 21 and 1q

Cytogenetic maps are useful tools for several applications, such as the physical anchoring of linkage and RH maps or genome sequence contigs to specific chromosome regions or the analysis of chromosome rearrangements. Recently, a detailed RH map was reported in OAR1. In the present study, we selected 38 markers equally distributed in this RH map for identification of ovine genomic DNA clones within the ovine BAC library CHORI-243 using the virtual sheep genome browser and performed FISH mapping for both comparison of OAR1 and homoeologous chromosomes BBU1q-BBU6 and BTA1-BTA3 and considerably extending the cytogenetic maps of the involved species-specific chromosomes. Comparison of the resulting maps with human-identified homology with HSA2q, HSA3, HSA21 and HSA1q reveals complex chromosome rearrangements differentiating human and bovid chromosomes. In addition, we identified 2 new small human segments from HSA2q and HSA3q conserved in the telomeric regions of OAR1p and homoeologous chromosome regions of BTA3 and BBU6, and OAR1q, respectively. Evaluation of the present OAR1 cytogenetic map and the OAR1 RH map supports previous RH assignments with 2 main exceptions. The 2 loci BMS4011 and CL638002 occupy inverted positions in these 2 maps.     

Twelve loci from HSA10, HSA11 and HSA20 were comparatively FISH-mapped on river buffalo and sheep chromosomes

Ten type I loci from HSA10 (IL2RA and VIM), HSA11 (HBB and FSHB) and HSA20 (THBD, AVP/OXT, GNAS1, HCK and TOP1) and two domestic cattle type II loci (CSSM30 and BL42) were FISH mapped to R-banded river buffalo (BBU) and sheep (OAR) chromosomes. IL2RA (HSA10) maps on BBU14q13 and OAR13q13, VIM (HSA10) maps on BBU14q15 and OAR13q15, HBB (HSA11) maps on BBU16q25 and OAR15q23, FSHB (HSA11) maps on BBU16q28 and OAR15q26, THBD (HSA20) maps on BBU14q15 and OAR13q15 while AVP/OXT, GNAS1, HCK, and TOP1 (HSA20) as well as CSSM30 and BL42 map on the same large band of BBU14q22 and OAR13q22. All loci were mapped on the same homologous chromosomes and chromosome bands of the two species, and these results agree with those earlier reported in cattle homologous chromosomes 15 and 13, respectively, confirming the high degree of both banding and physical map similarities among the bovid species. Indirect comparisons between physical maps achieved on bovid chromosomes and those reported on HSA10, HSA11 and HSA20 were performed.     

A genetic linkage map for the South African Angora goat

Despite their economical importance, relatively few molecular studies have been made on goats compared to other livestock species. The most recent goat map was published in 1998, and lacks complete genome coverage. A large number of discrepancies and especially inter-chromosomal re-assignments were reported between the 1998 goat linkage map and the sheep map. In this study 94 microsatellite markers were amplified in 12 half-sib South African Angora goat families for compilation of a genetic map, aiming to confirm or reject previously reported rearrangements and to improve the alignment between the ovine and caprine maps. The number of informative meiosis per marker ranged from 69 to 836, with an average of 518. The microsatellites were mapped to 23 chromosomes, spanning 1352 cM and resulting in an average marker interval of 23.0 cM. Marker orders were compared to the previously published goat maps, as well as to the ovine map. Six chromosomes (CHI 2, 4, 5, 11, 13 and 19) showed rearrangements in marker order compared to the 1998 Schibler et al. goat map, while nine previously unmapped markers were conclusively assigned to eight chromosomes. Four of the previously reported intra-chromosomal rearrangements between the goat and sheep maps were confirmed to be either population specific or mapping errors. The verification of rearrangements in loci order will lead to improved alignment between the two maps, as well as improved efficiency of genome and fine mapping efforts in goats.     

Cytogenetical anchoring of sheep linkage map and syntenic groups using a sheep BAC library

In order to simultaneously integrate linkage and syntenic groups to the ovine chromosomal map, a sheep bacterial artificial chromosome (BAC) library was screened with previously assigned microsatellites using a sheep-hamster hybrid panel and genetic linkage. Thirty-three BACs were obtained, fluorescently labelled and hybridised on sheep-goat hybrid metaphases (2n = 57). This study allowed us, (i), to anchor all linkage groups on sheep chromosomes, (ii), to give information on the probable position of the centromere on the linkage map for the centromeric chromosomes, (iii), to contradict the previous orientation of the ovine × linkage group by the mapping of BMS1008 on OARXq38. Concerning our somatic cell hybrid panel, this study resulted in the assignment of all the previously unassigned groups to ovine chromosomes and a complete characterisation of the hybrid panel. In addition, since hybridisations were performed on a sheep-goat hybrid, new marker/anchoring points were added to the caprine cytogenetic map.     

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.     

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.     

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.     

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.     

Comparative FISH-mapping of six expressed gene loci to river buffalo and sheep chromosomes.

Six expressed gene loci (NF1, CRYB1, CHRNB1, TP53, P4HB and GH1), recently assigned to cattle chromosome 19 by both radiation hybrid analysis and FISH-mapping, were comparatively FISH-mapped to river buffalo chromosome (BBU) 3p and sheep chromosome (OAR) 11, extending the physical map in these two important bovids. The six loci mapped to the same homoeologous chromosome bands of BBU 3p and OAR 11, and their gene order was centromere-NF1-CRYB1-CHNRB1-TP53-(GH1, P4HB).