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J E Womack

Publications and source records attributed to J E Womack.

At least 37 records · Page 2Linked to original sources
PubMed2001

Isolation and characterization of hepatic and intestinal expressed sequence tags potentially involved in trait differentiation between cows of different metabolic type.

mRNA differential display was applied to identify hepatic and intestinal expressed sequence tags (ESTs) in lactating cows of different metabolic types (milk type, meat/milk type, meat type) that are potentially associated with energy turnover and involved in the regulation of these processes. Altogether, 277 ESTs (liver: 161, intestine: 116) were identified. For 150 transcripts (liver: 99, intestine: 51), the sequences showed similarity to previously described genes and ESTs. Many of these homologous sequences are reported to be involved in hepatic metabolism. Ninety-four ESTs (liver: 43, intestine: 51) did not match with any database entries. Semi-quantitative RT-PCR revealed quantitative differences in transcript represented by randomly chosen ESTs in liver samples of animals of the Holstein and Charolais breeds. One hundred twenty-two ESTs were mapped physically by using a bovine-hamster somatic cell hybrid panel (SCP) and a 5000-rad bovine whole genome radiation hybrid panel (WGRH). These ESTs were assigned to the bovine syntenic groups and positioned in the recently established RH-based ordered comparative map of the cattle and human genomes. The mapped, differentially expressed sequence tags are a useful prerequisite for cloning of genetic variation underlying economic traits.

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PubMed2001

Physical mapping of CSF2RA, ANT3 and STS on the pseudoautosomal region of bovine chromosome X.

The pseudoautosomal region (PAR) of bovine chromosome X (BTA X) has a particularly low representation of genes and markers, making comparative gene mapping in this region difficult. We describe the localization of three genes, colony-stimulating factor 2 receptor alpha (CSF2RA), ADP/ATP translocase 3 (ANT3) and steroid sulphatase (STS) on PAR of BTA X using a 5000 rad whole-genome radiation hybrid panel. The relationship of these genes to a number of previously mapped simple sequence repeat (microsatellite) markers is determined by physical and radiation hybrid mapping methods. The resulting radiation hybrid map resolves a discrepancy between the two major bovine linkage maps in the PAR of BTA X.

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PubMed2001

Mapping of 12 bovine ribosomal protein genes using a bovine radiation hybrid panel.

Twelve bovine ribosomal protein genes, for which sequence data had been acquired from complementary deoxyribonucleic acid (cDNA) clones isolated from a cattle skin cDNA library, were mapped. As ribosomal protein genes are a group of highly conserved house keeping genes, specific primers were designed to span the intron-exon splice sites and to amplify intronic sequences, in order to obtain bovine-specific polymerase chain reaction (PCR) products. Two of 12 ribosomal protein genes were genotyped in this way and the remaining 10 were mapped using additional primers designed from within the intron. Eleven previously unmapped ribosomal protein genes were localized and one previously reported ribosomal protein gene localization was confirmed. The 12 ribosomal protein genes mapped in this study are spread over 10 chromosomes, including the X chromosome. The locations show conservation of comparative map position in cattle and human.

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PubMed2001

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.

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PubMed2001

Comparative mapping of five coding DNA sequences on cattle chromosomes 7 and 25.

Comparative mapping of four genes and one unknown coding DNA sequence in breakpoint positions of bovine chromosomes (BTA) 7 and 25 are presented. Performing a genome data base search five bovine expressed sequence tags from the MARC library matched with human genes coding for the general transcription factor IIIC polypeptide 1 (GTF3C1), the hypothetical protein KIAA0556, the interleukin 4 receptor (IL4R), the regulatory factor X-associated ankyrin-containing protein (RFXANK), and with an unknown human coding sequence partially homologous to the genomic cosmid clone R30923. Loci for these sequences were COMPASS predicted on BTA7 or BTA18 and to BTA18 or BTA25. Mapping was performed in a cattle-hamster somatic hybrid cell panel and a cattle-hamster 5000 rad whole genome radiation hybrid panel. GTF3C1, KIAA0556 and IL4R were assigned to the centromere region of BTA25 and RFXANK and R30923 close to the centromere of BTA7. The assignments contribute to the identification of evolutionary chromosome break points between human chromosomes 16 and 19 and BTA7, BTA18, and BTA25.

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PubMed2000

Comparative organization of cattle chromosome 5 revealed by comparative mapping by annotation and sequence similarity and radiation hybrid mapping.

A whole genome cattle-hamster radiation hybrid cell panel was used to construct a map of 54 markers located on bovine chromosome 5 (BTA5). Of the 54 markers, 34 are microsatellites selected from the cattle linkage map and 20 are genes. Among the 20 mapped genes, 10 are new assignments that were made by using the comparative mapping by annotation and sequence similarity strategy. A LOD-3 radiation hybrid framework map consisting of 21 markers was constructed. The relatively low retention frequency of markers on this chromosome (19%) prevented unambiguous ordering of the other 33 markers. The length of the map is 398.7 cR, corresponding to a ratio of approximately 2.8 cR(5,000)/cM. Type I genes were binned for comparison of gene order among cattle, humans, and mice. Multiple internal rearrangements within conserved syntenic groups were apparent upon comparison of gene order on BTA5 and HSA12 and HSA22. A similarly high number of rearrangements were observed between BTA5 and MMU6, MMU10, and MMU15. The detailed comparative map of BTA5 should facilitate identification of genes affecting economically important traits that have been mapped to this chromosome and should contribute to our understanding of mammalian chromosome evolution.

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PubMed2000

Mapping of 16 ESTs expressed in the bovine mammary gland during lactation.

A bovine mammary gland cDNA-library was used to characterize and map genes expressed during lactation. Fifty cDNA clones selected by differential hybridization were sequenced from both ends, and sequences were examined for similarities with database sequences. For 34 of the transcripts, the sequences showed more than 80% similarity to previously characterized genes or expressed sequence tags (ESTs). Twenty cDNAs that could be of interest as candidate genes for milk production are selected for genetic or chromosomal mapping. Twenty-three out of the 39 designed primer pairs representing 16 cDNA clones amplified the expected fragments and were used for subsequent fluorescent single-strand conformation polymorphism analysis (F-SSCP) in the International Bovine Reference Panel families (IBRP). Ten polymorphic loci could be identified and used to genotype the IBRP animals, and nine of them were subsequently genetically mapped on nine chromosomes. In addition, eight loci from the 16 cDNA clones could be mapped by somatic cell hybrids, bringing the total number of mapped genes to 16, one of which was mapped genetically as well as physically. The mapped mammary gland ESTs are potentially useful for cloning economic trait loci by a positional candidate gene cloning approach.

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PubMed2000

RH maps of bovine chromosomes 15 and 29: conservation of human chromosomes 11 and 5.

Comparative mapping data on evolutionary conserved coding sequences and synteny maps between human and cattle are insufficient to define the extent and distribution of conserved segments between these two species, because the order of loci is often rearranged. A 5000-rad cattle whole-genome radiation hybrid (WG-RH) panel was constructed to provide high-resolution comparative maps and also to integrate linkage maps of microsatellites with evolutionary conserved genes and transcripts in a single ordered map. We used the WG-RH panel to construct radiation hybrid maps of bovine Chromosomes (Chrs) 15 and 29 (BTA15 and BTA29), integrating microsatellites from published linkage maps with selected genes. The comprehensive map of BTA15 consists of 24 markers, 13 of which were placed in the framework map. Eleven molecular markers compose the comprehensive map of BTA29, seven of which were placed in the framework map. We identified the homologous regions between bovine Chr 15 (BTA15) and human Chrs 5 and 11 (HSA5 and HSA11), as well as between BTA29 and HSA11. The present study demonstrates that WG-RH mapping is an efficient method for integrating multiple genetic maps into one map and for incorporating monomorphic Type I loci into ordered maps for comparison between species.

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PubMed2000

Differences between the radiation hybrid and genetic linkage maps of bovine chromosome 5 resolved with a quasi-phylogenetic method of analysis.

Two major differences were detected in gene order between the radiation hybrid map and the genetic linkage map of bovine Chromosome (Chr) 5, and these were resolved by analyzing the raw radiation hybrid data by a quasi-phylogenetic method. Seventeen loci were typed on the new cattle whole genome radiation hybrid panel. Most of these loci are framework loci and include AGLA293, BM315, BM6026, BP1, BZRP, CD9, CSSM22, CSSM34, CYP2D@, ETH2, ETH10, ETH152, IGF1, LALBA, SLC2A3, SYT1, and TPI1. BP1 was found to be closer to the centromere than either BM6026 or SYT1 with two standard computer software packages for analyzing radiation hybrid panel data. This is inconsistent with any of the genetic linkage maps as well as their consensus. CYP2D@ was placed between ETH2 and BZRP, and this is also inconsistent with the genetic linkage maps, since CYP2D@ should be the most telomeric of the loci tested in this study. Resolution was reached by analyzing the raw radiation hybrid data for clones that bind some but not all of the loci, and the binding pattern was more consistent with the linkage maps and less consistent with the software-generated radiation hybrid map. The comparative mapping data confirm the relative inversion of gene order of SYT1 compared with humans and mice. A non-polymorphic fragment for CD9 indicates the conservation of gene order for three loci located on human Chr 12p. The genes of bovine Chr 5 conserved on human Chr 12p are located separately from the genes conserved on human Chr 12q. It is recommended that the raw data for radiation hybrid maps be made publicly available so that conflicts in gene order can be evaluated explicity.

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PubMed2000

A 12,000 rad whole genome radiation hybrid panel for high resolution mapping in cattle: characterization of the centromeric end of chromosome 1.

We have constructed a 12,000 rad bovine whole-genome radiation hybrid panel (BovR12) to complement the 5000 rad panel (BovR5) currently available to the bovine genomics research community. Initial characterization with markers from chromosome 1 reveals a higher frequency of breakage between adjacent markers and subsequently a larger number of 'linkage' groups on this chromosome. For this set of markers, the retention frequency is also higher than in BovR5.

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PubMed2000

An ordered comparative map of the cattle and human genomes.

A cattle-human whole-genome comparative map was constructed using parallel radiation hybrid (RH) mapping in conjunction with EST sequencing, database mining for unmapped cattle genes, and a predictive bioinformatics approach (COMPASS) for targeting specific homologous regions. A total of 768 genes were placed on the RH map in addition to 319 microsatellites used as anchor markers. Of these, 638 had human orthologs with mapping data, thus permitting construction of an ordered comparative map. The large number of ordered loci revealed > or =105 conserved segments between the two genomes. The comparative map suggests that 41 translocation events, a minimum of 54 internal rearrangements, and repositioning of all but one centromere can account for the observed organizations of the cattle and human genomes. In addition, the COMPASS in silico mapping tool was shown to be 95% accurate in its ability to predict cattle chromosome location from random sequence data, demonstrating this tool to be valuable for efficient targeting of specific regions for detailed mapping. The comparative map generated will be a cornerstone for elucidating mammalian chromosome phylogeny and the identification of genes of agricultural importance."Ought we, for instance, to begin by discussing each separate species-in virtue of some common element of their nature, and proceed from this as a basis for the consideration of them separately?" from Aristotle, On the Parts of Animals, 350 B.C.E.

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PubMed1999

The promise of comparative genomics in mammals.

Dense genetic maps of human, mouse, and rat genomes that are based on coding genes and on microsatellite and single-nucleotide polymorphism markers have been complemented by precise gene homolog alignment with moderate-resolution maps of livestock, companion animals, and additional mammal species. Comparative genetic assessment expands the utility of these maps in gene discovery, in functional genomics, and in tracking the evolutionary forces that sculpted the genome organization of modern mammalian species.

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PubMed1999

Fine-mapping of quantitative trait loci by identity by descent in outbred populations: application to milk production in dairy cattle.

We previously mapped a quantitative trait locus (QTL) affecting milk production to bovine chromosome 14. To refine the map position of this QTL, we have increased the density of the genetic map of BTA14q11-16 by addition of nine microsatellites and three single nucleotide polymorphisms. Fine-mapping of the QTL was accomplished by a two-tiered approach. In the first phase, we identified seven sires heterozygous "Qq" for the QTL by marker-assisted segregation analysis in a Holstein-Friesian pedigree comprising 1,158 individuals. In a second phase, we genotyped the seven selected sires for the newly developed high-density marker map and searched for a shared haplotype flanking an hypothetical, identical-by-descent QTL allele with large substitution effect. The seven chromosomes increasing milk fat percentage were indeed shown to carry a common chromosome segment with an estimated size of 5 cM predicted to contain the studied QTL. The same haplotype was shown to be associated with increased fat percentage in the general population as well, providing additional support in favor of the location of the QTL within the corresponding interval.

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PubMed1999

High-resolution, human-bovine comparative mapping based on a closed YAC contig spanning the bovine mh locus.

A closed YAC contig spanning the mh locus was assembled by STS content mapping with seven microsatellite markers, eight genes or EST, and nine STS corresponding to YAC ends. The contig comprises 27 YACs, has an average depth of 4.3 YACs, and spans an estimated 1.2 Mb. A linkage map was constructed based on five of the microsatellite markers anchored to the contig and shown to span 7 cM, yielding a ratio of 160 kb/1 cM for the corresponding chromosome region. Comparative mapping data indicate that the constructed contig spans an evolutionary breakpoint connecting two chromosome segments that are syntenic but not adjacent in the human. Consolidation of human gene order by means of whole genome radiation hybrids and its comparison with the bovine order as inferred from the contig confirm conservation of gene order within segments.

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PubMed1999

Parallel RH mapping of BTA1 with HSA3 and HSA21.

The development of radiation hybrid (RH) panels has elevated comparative gene mapping to a new level of resolution. In this study, we have constructed parallel RH maps defining rearrangements of gene order within conserved segments of bovine Chromosome (Chr) 1 (BTA1) and human Chrs 3 and 21 (HSA3, HSA21). Six new markers, including one gene, have been added to the bovine map, and 11 human genes were ordered with the human G3 panel. BTA1 is clearly a composite of genetic material conserved on these two human chromosomes with HSA21 homologs at each end of BTA1 flanking a large segment homologous to HSA3. Each of the three conserved segments of BTA1 contains rearrangements of gene order relative to their human counterparts.

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PubMed1999

Cytogenetic alignment of the bovine chromosome 13 genome map by fluorescence in-situ hybridization of human chromosome 10 and 20 comparative markers.

A bovine bacterial artificial chromosome (BAC) library was screened for the presence of six genes (IL2RA, VIM, THBD, PLC-II, CSNK2A1 and TOP1) previously assigned to human chromosomes 10 or 20 (HSA10 or HSA20). Four of the genes were found represented in the bovine BAC library by at least one clone. The identified BAC clones were used as probes in single-color fluorescence in-situ hybridization (FISH) to determine the chromosomal band location of each gene. As predicted by the human/bovine comparative map and comparative chromosome painting analysis, the four genes mapped to bovine chromosome 13 (BTA13). Dual-color FISH was then used to integrate these four type I markers into the existing BTA13 genome map. These FISH results anchor the BTA13 genome map from bands 14-23, and confirm the presence of a conserved HSA10 homologous synteny group on BTA13 centromeric to a HSA20 homologous segment.

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