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We report an extended river buffalo (Bubalus bubalis, 2n = 50; BBU) cytogenetic map including 388 loci, of which 68 have been FISH-mapped on autosomes in the present study. Ovine and caprine BAC clones containing both type I loci (known genes) and type II loci (simple sequence repeats (SRs), microsatellite marker, sequence-tagged sites (STSs)), previously assigned to sheep chromosomes, have been localized on R-banded river buffalo chromosomes (BBU), which expands the cytogenetic map of this important domestic species and increases our knowledge of the physical organization of its genome. The loci mapped in the present study correspond to loci already localized on homoeologous cattle (and sheep) chromosomes and chromosome bands, further confirming the high degree of chromosome homoeologies among bovids. The comparison of the integrated cytogenetic maps of BBU2p/BBU10 and BBU5p/BBU16 with those of human chromosomes (HSA) 6 and 11, respectively, identified, at least, nine conserved chromosome segments in each case and complex rearrangements differentiating river buffalo (and cattle) and human chromosomes.

Presented herein is an updated sheep cytogenetic map that contains 452 loci (291 type I and 161 type II) assigned to specific chromosome bands or regions on standard R-banded ideograms. This map, which significantly extends our knowledge of the physical organization of the ovine genome, includes new assignments for 88 autosomal loci, including 74 type I loci (known genes) and 14 type II loci (SSRs/microsatellite marker/STSs), by FISH-mapping and R-banding. Comparison of the ovine map to the cattle and goat cytogenetic maps showed that common loci were located within homologous chromosomes and chromosome bands, confirming the high level of conservation of autosomes among ruminant species. Eleven loci that were FISH-mapped in sheep (B3GAT2, ASCC3, RARSL, BRD2, POLR1C, PPP2R5D, TNRC5, BAT2, BAT4, CDC5L and OLA-DRA) are unassigned in cattle and goat. Eleven other loci (D3S32, D1S86, BMS2621, SFXN5, D5S3, D5S68, CSKB1, D7S49, D9S15, D9S55 and D29S35) were assigned to specific ovine chromosome (OAR) bands but have only been assigned to chromosomes in cattle and goat.

Background: Comparative mapping provides new insights into the evolutionary history of genomes. In particular, recent studies in mammals have suggested a role for segmental duplication in genome evolution. In some species such as Drosophila or maize, transposable elements (TEs) have been shown to be involved in chromosomal rearrangements. In this work, we have explored the presence of interspersed repeats in regions of chromosomal rearrangements, using an updated high-resolution integrated comparative map among cattle, man and mouse., Results: The bovine, human and mouse comparative autosomal map has been constructed using data from bovine genetic and physical maps and from FISH-mapping studies. We confirm most previous results but also reveal some discrepancies. A total of 211 conserved segments have been identified between cattle and man, of which 33 are new segments and 72 correspond to extended, previously known segments. The resulting map covers 91% and 90% of the human and bovine genomes, respectively. Analysis of breakpoint regions revealed a high density of species-specific interspersed repeats in the human and mouse genomes., Conclusion: Analysis of the breakpoint regions has revealed specific repeat density patterns, suggesting that TEs may have played a significant role in chromosome evolution and genome plasticity. However, we cannot rule out that repeats and breakpoints accumulate independently in the few same regions where modifications are better tolerated. Likewise, we cannot ascertain whether increased TE density is the cause or the consequence of chromosome rearrangements. Nevertheless, the identification of high density repeat clusters combined with a well-documented repeat phylogeny should highlight probable breakpoints, and permit their precise dating. Combining new statistical models taking the present information into account should help reconstruct ancestral karyotypes.

Although the European rabbit (Oryctolagus cuniculus) is used both in agronomics and in research, genomic resources for this species are still limited and no microsatellite-based genetic map has been reported. Our aim was to construct a rabbit genetic map with cytogenetically mapped microsatellites so as to build an integrated genetic and cytogenetic map. A reference population of 187 rabbits comprising eight three-generation families with 10-25 offspring per family was produced. One hundred and ninety-four of 305 previously identified microsatellites were included in this study. Of these, 158 were polymorphic with two to seven alleles. The map reported here comprises 111 markers, including 104 INRA microsatellites, five microsatellites from another source and two phenotypic markers (angora and albino). Ninety markers were integrated into 20 linkage groups. The remaining 21 microsatellites mapped to separate linkage groups, 19 with a precise cytogenetic position and two with only a chromosomal assignment. The genetic map spans 2766.6 cM and covers 20 rabbit chromosomes, excluding chromosomes 20, 21 and X. The density of this map is limited, but we used it to verify the location of angora and albino on chromosomes 15q and 1q, respectively, in agreement with previously published data. This first generation genetic/cytogenetic map will help gene identification and quantitative trait loci mapping projects in rabbit.

Rabbit (Oryctolagus cuniculus) represents a valuable source of biomedical models and corresponds to a small but active economic sector in Europe for meat and fur. The rabbit genome has not been thoroughly studied until recently, and high-resolution maps necessary for identification of genes and quantitative trait loci (QTL) are not yet available. Our aim was to isolate over 300 new and regularly distributed (TG)n or (TC)n rabbit microsatellites. To achieve this purpose, 164 microsatellite sequences were isolated from gene-containing bacterial artificial chromosome (BAC) clones previously localized by fluorescence in situ hybridization (FISH) on all the rabbit chromosomes. In addition, 141 microsatellite sequences were subcloned from a plasmid genomic library, and for 41 of these sequences, BAC clones were identified and FISH-mapped. TC repeats were present in 62% of the microsatellites derived from gene-containing BAC clones and in 22% of those from the plasmid genomic library, with an average of 42.9% irrespective of the microsatellite origin. These results suggest a higher proportion of (TC)n repeats and a nonhomogeneous distribution of (TG)n and (TC)n repeats in the rabbit genome compared to those in man. Among the 305 isolated microsatellites, 177 were assigned to 139 different cytogenetic positions on all the chromosomes except rabbit Chromosome 21. Sequence similarity searches provided hit locations on the Human Build 35a and hypothetical assignments on rabbit chromosomes for ten additional microsatellites. Taken together, these results report a reservoir of 305 new rabbit microsatellites of which 60% have a cytogenetic position. This is the first step toward the construction of an integrated cytogenetic and genetic map based on microsatellites homogeneously anchored to the rabbit genome.

Rabbit, a domestic species exploited both in animal production and medical research has only recently begun to be included in gene mapping projects, in particular by the French National Institute of Agronomics. By 2002, less than 60 genes had been precisely localised on rabbit chromosomes, which led us to start a large-scale project on gene mapping in rabbit with the publication of 133 gene localisations in 2003 (Chantry-Darmon et al., 2003). Here, we report the localisation of 102 new genes resulting in good coverage of the rabbit genome and an eight-fold enrichment of the gene map. In addition, we have detected a new conserved segment between rabbit chromosome 4q15.3 and part of human chromosome 22 and thus improved the comparative map with the human genome.

In this study, we present a comprehensive 3000-rad radiation hybrid (RH) map of bovine Chromosome (Chr) 26 (BTA26) with 80 markers including 50 genes or ESTs: 44 have an ortholog mapping to human Chr 10 (HSA10) and 29 to mouse Chr (MMU) 7, 10, and 19. Moreover, 12 other HSA10 genes were integrated in a newly developed RH map of BTA28 (seven represent new assignments). The available draft of the mouse genome allowed us to present a detailed picture of the distribution of conserved synteny segments among the three species (human, cattle, and mouse) and to propose a simple model of the comparative chromosomal organization between the long arm of HSA10 and BTA26 and 28. Finally, the INRA bovine BAC library was screened for most of the BTA26 markers considered in this study to provide anchors for the bovine physical map.

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.

Rabbit (Oryctolagus cuniculus), besides its interest for medical research and biotechnological applications, has a small agronomic production in southern European countries. However, it is still a "map-poor" species with about 80 genes mapped. Recently, useful tools for research on this species have been developed, such as heterologous human-rabbit chromosome painting data and a rabbit BAC library. In this study, our aim is to enrich the rabbit cytogenetic map using the FISH technique. Towards this, we have used cDNAs (rabbit and non rabbit) present in the public databases to determine intra-exon primers used to screen our three-genome equivalent BAC library, by standard PCR directly on DNA pools, and by hybridization of high-density filters. 133 BAC clones containing the genes of interest were isolated and FISH-mapped to the rabbit chromosomes. We present the localization of new genes on all rabbit chromosomes except OCU20 and OCUY and some preliminary data on the rabbit/human comparative map. In addition, this set of BAC clones quite regularly distributed on the rabbit genome will be useful to isolate microsatellites, in order to construct a first generation genetic map., (Copyright 2003 S. Karger AG, Basel)

As part of the human genome study, large-scale cDNA sequencing has produced thousands of Expressed Sequence Tags (ESTs). Généthon has mapped in human 10,000 of these ESTs and has shown that the primers of about 1000 ESTs could amplify bovine DNA. In this work, we have analyzed 233 primer pairs provided by Genethon, to assign type I sequences to the bovine genome by using a hamster-bovine somatic cell hybrid panel. Among these 233 primer pairs, 109 gave a specific PCR product with bovine genomic DNA, but for 50% the size of the PCR product was the same in cattle and hamster, requiring SSCP analysis. Finally, 60 ESTs were assigned to the bovine genome, and among them 46 were found on the bovine chromosome expected from heterologous painting data between cattle and human.

The SOX gene family consists of a large number of embryonically expressed genes capable of encoding putative transcription factors and related by a DNA-binding domain, the HMG-box. We cloned and characterized the ovine SOX2 transcript using the screening of a testis (12dpp) cDNA library with a probe containing the SRY-HMG-box and we performed 3'RACE experiments. The ovine SOX2 sequence is strongly conserved in comparison to the human, mouse and chicken homologues and is located on sheep chromosome 1q33. The SOX2 expression pattern in developing gonads is consistent with the hypothesis that this gene plays a role in the germ cell line.

A comparative linkage map of human chromosome 13 and bovine chromosome 12 was constructed using eight polymorphic microsatellite markers associated with six specific genes. Linkage of these was also examined relative to five previously mapped anonymous microsatellite markers. Seven gene-linked markers were developed from bovine large-insert genomic clones containing one of five genes of interest (serotonin receptor subtype 2, fms-related tyrosine kinase, coagulation factor 10, retinoblastoma susceptibility gene, collagen type IV alpha 1), and one additional marker was developed from a microsatellite resident within an intron of the bovine dopachrome tautomerase gene. Four of these loci were previously assigned to bovine chromosome 12 by analysis of a somatic cell hybrid panel. This study provides linkage information for examining gene order in this conserved synteny group. The comparative linkage mapping results indicate that the q arm of human chromosome 13 is almost entirely conserved in bovine chromosome 12. One intrachromosomal rearrangement was detected in this linkage group relative to human, and this rearrangement was confirmed by fluorescence in situ hybridization results.

A beta-lactoglobulin (beta-LG) pseudogene has been isolated and sequenced (7634 bp) in goat. Its structure is remarkably similar to that of the beta-LG gene with all seven exons placed in the same relative position. The pseudogene seems to have originated by gene duplication, but a non uniform distribution of similarities along the sequence suggests that events of gene conversion have also occurred during its evolution. The comparison of the predicted ancestral protein encoded by the pseudogene shows its evolutionary relationship to the monomeric beta-LG II forms of the beta-LG reported in some non-ruminant species. Southern-blot analysis shows that similar pseudogenes are also found in the genome of sheep and cow. The pseudogene has been mapped by fluorescent in situ hybridization (FISH) to sheep chromosome 3p28 and cattle and goat chromosomes 11q28, in the same mapped position as that found for the beta-LG gene in all these species.

The six following genes: zinc finger proteins 164 (ZNF164) and 146 (ZNF146), alpha-galactosyltransferase 1 (GGTA1), SRY-related HMG-box 2 (SOX2), prolactin receptor (PRLR) and elongatin factor 2 (EEF2) have been localized by fluorescent in situ hybridization respectively on bovine and caprine chromosomes 17, 18, 11, 1, 20 and 7 and on sheep chromosomes 17, 14, 3, 1, 16, and 5. The comparison of the results with the localization of these genes in man (except for ZNF164) confirm the correspondences between human and bovine chromosomes established from heterologous chromosome painting data.

A clone carrying an open reading frame coding for a novel zinc finger protein of the Krüppel family was isolated from a bovine genomic library and designated ZNF 164 (zinc finger protein 164). Partial sequencing revealed that it contained at least 13 zinc finger motifs preceded by a lysine-rich region of 60 amino acids. The ZNF164 protein shared approximately 60% similarity with several zinc finger proteins but did not appear to be orthologous with a previously identified gene. Using fluorescence in situ hybridization, the ZNF164 gene was mapped to bovine chromosome band 17q24.

The RBG banded karyotype (2n = 38) of the blesbok (Damaliscus dorcas phillipsi) comprises 8 pairs of metacentric, 3 pairs of submetacentric and 7 pairs of acrocentric autosomes. The X and Y chromosomes are acrocentric. The 11 pairs of biarmed chromosomes correspond to Robertsonian translocations involving the chromosomes equivalent to goat and cattle chromosomes: 1;10, 4;5, 8;17, 7;9, 6;14, 13;15, 12;16, 20;22, 3;19, 2;27 and 11;23. The comparison of Blesbok karyotype with that of other species of Alcelaphinae and Hippotraginae reveals a high level of homoeology.

Commercially available human chromosome-specific DNA libraries covering the whole karyotype were hybridized to normal bovine metaphase spreads to characterize the conserved chromosomal segments between man and cattle. All chromosome libraries except the Y chromosome library displayed a signal on at least part of one or more bovine chromosomes. The labeling was clearly visualized and permitted precise delineation of the hybridized bovine chromosomal segments. This study indicates that the reorganization of the genetic material between human and bovine genomes is not as great as expected from classical comparative cytogenetics based on banding patterns. However, apart from interchromosomal rearrangements between ancestral forms of human and bovine chromosomes, a majority of intrachromosomal rearrangements must have occurred in these species during evolution to explain the differences in the banding patterns of their chromosomes. These results show that chromosome painting with heterologous chromosome-specific DNA libraries can provide useful information in comparative studies on karyotypes and gene maps of distantly related mammalian species. The observations are discussed in relation to published data on gene mapping in man and cattle.

The BLV receptor candidate gene has been localized precisely on cattle, goat, and sheep chromosomes using nonradioactive in situ hybridization and simultaneous fluorescent R-banding. The probe, a whole plasmid containing a 2.3-kb bovine cDNA fragment encoding part of this gene, was nick-translated in the presence of biotin-11-dUTP. It hybridized on band q15 of cattle chromosome 7, goat chromosome 7, and sheep chromosome 5, thus confirming the homoeology based on banding patterns among the chromosomes of these three species.

The lactoperoxidase (LPO), retinoblastoma (RB1), and alpha-lactalbumin (LALBA) genes have been mapped by fluorescent in situ hybridization respectively to cattle Chromosomes (Chrs) 19, 12, 5; goat Chrs 19, 12, 5; and sheep Chrs 11, 10, 3. The results confirm the homologies among cattle, sheep, and goat chromosomes, previously reported, and provide more information for the comparison between the bovine and human karyotypes and gene maps.

The alpha-S2-casein gene (CASAS2) has been mapped to the homoeologous cattle, sheep, and goat chromosomes 4 and to the long arm of a bovine chromosome translocation, t(4;8), using nonradioactive in situ hybridization and simultaneous fluorescent R-banding. The t(4;8) has been characterized by GTG-, GBG-, and RBG-banding and by silver staining of nucleolus organizer regions. These results confirm the previous (ISCNDA, 1989) localization of the casein gene group to chromosome 4 of cattle, sheep, and goats. We propose that the discrepancy between our results and earlier assignments of the casein gene group to chromosome 6 of cattle and sheep can be explained by the fact that the chromosome identified as No. 6 in the Reading Conference (1976) report was renamed chromosome 4 in the ISCNDA (1989) standardized karyotype of both species.

The ovine beta-casein gene (CNS2) has been mapped to a specific chromosome band using nonradioactive in situ hybridization and simultaneous fluorescent R-banding. The probe pTZ-E4 was a fragment of the ovine beta-casein gene inserted in the plasmid pTZ18R and labeled with biotin-11-dUTP. It hybridized to band q32 of ovine chromosome 4. The discrepancy between this result and the previous localization of this gene on cattle chromosome 6 may be explained by the very great similarity of the banding patterns of ovine and bovine chromosomes 4 and 6.

Human x mouse microcell hybrids resistant to G418 were constructed between mouse hepatoma cells and human x mouse whole cell hybrids containing only intact human chromosome 5 and 22 with an integrated neor-gene. Among these, microcell hybrid BG15 produced four subclones, BG15-4, BG15-6, BG15-7 and BG15-9, which contained variously sized complements of human chromosome 5. BG15-6 contained an intact human chromosome 5, BG15-7 a deleted human chromosome 5 (5pter-q22) and BG15-4 and BG15-9 a translocation between parts of human chromosome 5 (pter-qter? and pter-q23, respectively) and a mouse chromosome. Southern DNA blot analysis showed that the human dihydrofolate reductase (DHFR) gene was present in all four subclones, whereas the human homolog of the v-fms gene was present in BG15-4 and 15-6, but absent from BG15-7 and 15-9. BG15-4, 15-6 and 15-9 were sensitive to diphtheria toxin, and only BG15-7 was resistant to the toxin. We used these microcell hybrids to restrict further the regional location of the gene for diphtheria toxin sensitivity to the q23 region of human chromosome 5.