bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of a novel ovine PrP polymorphism and scrapie-resistant genotypes for St. Croix White and a related composite breed
Authors: Seabury C.M. , Derr J.N.
Published: February 2004

Susceptibility to scrapie is primarily controlled by polymorphisms in the ovine prion protein gene (PRNP). Here, we report a novel ovine exon three PRNP polymorphism (SNP G346C; P116), its association with the ovine ARQ allele (P116A136R154Q171), and two new genotypes (PARQ/ARR; PARQ/ARQ) for the St. Croix White (SCW) breed and a related composite (CMP) breed developed for meat production. The (P116) polymorphism occurs between the N-terminal cleavage site and the hydrophobic region of the ovine prion protein, a region which exhibits extreme conservation across mammalian taxa. The relatively high frequency (0.75) of resistant ARR alleles and the absence of ARQ alleles for the SCW ewes used as breeding stock for CMP resulted in significant genic differentiation (P = 0.0123; S.E. = 0.00113). Additionally, the majority of the SCW (66.7%) and CMP (65.4%) sampled possessed genotypes considered resistant or nearly resistant to scrapie and experimental BSE (bovine spongiform encephalopathy.
Allelic variants of ovine prion protein gene (PRNP) in Oklahoma sheep
Authors: DeSilva U. , Guo X. , Kupfer D.M. , Fernando S.C. , Pillai A.T.V. , Najar F.Z. , So S. , Fitch G.Q. , Roe B.A.
Published: February 2004

1,144 sheep belonging to 21 breeds and known crosses were sequence analyzed for polymorphisms in the ovine PRNP gene. Genotype and allele frequencies of polymorphisms in PRNP known to confer resistance to scrapie, a fatal neurodegenerative disease of sheep, are reported. Known polymorphisms at codons 136 (A/V), 154 (H/R) and 171 (Q/R/H/K) were identified. The frequency of the171R allele known to confer resistance to type C scrapie was 53.8% and the frequency of the 136A allele known to influence the resistance to type A scrapie was 96.01%. In addition, we report the identification of five new polymorphisms at codons 143 (H/R), 167 (R/S), 180 (H/Y), 195 (T/S) and 196 (T/S). We also report the identification of a novel allele (S/R) at codon 138.
A new contribution to the integration of human and porcine genome maps: 623 new points of homology
Authors: Robic A. , Faraut T. , Iannuccelli N. , Lahbib-Mansais Y. , Cantegrel V. , Alexander L. , Milan D.
Published: February 2004

In this study we examined homologies between 1,735 porcine microsatellites and human sequence. For 1,710 microsatellites we directly used the sequence flanking the repeat available in GenBank. For a set of 305 microsatellites, a BAC library was screened and end-sequencing provided 461 additional sequences. Altogether 2,171 porcine sequences were tentatively aligned with the sequence of the human genome using the fasta program. Human homologies were observed for 652 microsatellite loci and porcine chromosome assignments available for 623 microsatellites provide useful links in the human and pig comparative map. Moreover for 92 STS, a significant sequence similarity was detected using at least two sequences and in all cases corresponding human locations were consistent. The present study allowed the integration of anonymous markers and the porcine linkage map into the framework of the comparative data between human and porcine genomes (http://w3.toulouse.inra.fr/lgc/pig/msat/). Moreover all conserved syntenic segments were defined on human chromosomes.
Construction of a high-resolution comparative gene map between swine chromosome region 6q11→q21 and human chromosome 19 q-arm by RH mapping of 51 genes
Authors: Bosak N. , Faraut T. , Mikawa S. , Uenishi H. , Kiuchi S. , Hiraiwa H. , Hayashi T. , Yasue H.
Published: February 2004

A comprehensive and comparative map was constructed for the porcine chromosome (SSC) 6q11→q21 region, where the gene(s) responsible for the maldevelopment of embryos are localized using swine populations of the National Institute of Animal Industry, Japan (NIAI). Since the chromosomal region corresponds to a region of human chromosome (HSA) 19q13.1→q13.3 based on bi-directional chromosome painting, primer pairs were designed from porcine cDNA sequences identified, on a sequence comparison basis, as being transcripts from genes orthologous to those in the HSA region. Fifty-one genes were successfully assigned to a swine radiation hybrid (RH) map with LOD scores greater than 6. ERF and PSMD8 genes were assigned to SSC4 and SSC1, respectively. The remaining 49 genes were assigned to SSC6, demonstrating that the synteny between the SSC6 and HSA19 chromosomal regions is essentially conserved, therefore confirming, the results of bi-directional chromosome painting. However, when examined precisely, rearrangements have apparently occurred within the region of conserved synteny. For the ERF and PSMD8 genes assigned to SSCs other than SSC6, additional mapping using somatic cell hybrid (SCH) panels was performed to confirm the results of RH-mapping.
Generation of a 5.5-Mb BAC/PAC contig of pig chromosome 6q1.2 and its integration with existing RH, genetic and comparative maps
Authors: Martins-Wess F. , Rohrer G. , Voß-Nemitz R. , Drögemüller C. , Brenig B. , Robic A. , Yerle M. , Milan D. , Leeb T.
Published: February 2004

We generated a sequence-ready BAC/PAC contig spanning approximately 5.5 Mb on porcine chromosome 6q1.2, which represents a very gene-rich genome region. STS content mapping was used as the main strategy for the assembly of the contig and a total of 6 microsatellite markers, 53 gene-related STS and 116 STS corresponding to BAC and PAC end sequences were analyzed. The contig comprises 316 BAC and PAC clones covering the region between the genes GPI and LIPE. The correct contig assembly was verified by RH-mapping of STS markers and comparative mapping of BAC/PAC end sequences using BLAST searches. The use of microsatellite primer pairs allowed the integration of the physical maps with the genetic map of this region. Comparative mapping of the porcine BAC/PAC contig with respect to the gene-rich region on the human chromosome 19q13.1 map revealed a completely conserved gene order of this segment, however, physical distances differ somewhat between HSA19q13.1 and SSC6q1.2. Three major differences in DNA content between human and pig are found in two large intergenic regions and in one region of a clustered gene family, respectively. While there is a complete conservation of gene order between pig and human, the comparative analysis with respect to the rodent species mouse and rat shows one breakpoint where a genome segment is inverted.
Improving the comparative map of porcine chromosome 10 with respect to human chromosomes 1, 9 and 10
Authors: Aldenhoven J. , Chen Y. , Backofen B. , Moran C.
Published: February 2004

ZOO-FISH mapping shows human chromosomes 1, 9 and 10 share regions of homology with pig chromosome 10 (SSC10). A more refined comparative map of SSC10 has been developed to help identify positional candidate genes for QTL on SSC10 from human genome sequence. Genes from relevant chromosomal regions of the public human genome sequence were used to BLAST porcine EST databases. Primers were designed from the matching porcine ESTs to assign them to porcine chromosomes using the INRA somatic cell hybrid panel (INRA-SCHP) and the INRA-University of Minnesota Radiation Hybrid Panel (IMpRH). Twenty-eight genes from HSA1, 9 and 10 were physically mapped: fifteen to SSC10 (ACO1, ATP5C1, BMI1, CYB5R1, DCTN3, DNAJA1, EPHX1, GALT, GDI2, HSPC177, OPRS1, NUDT2, PHYH, RGS2, VIM), eleven to SSC1 (ADFP, ALDHIB1, CLTA, CMG1, HARC, PLAA, STOML2, RRP40, TESK1, VCP and VLDLR) and two to SSC4 (ALDH9A1 and TNRC4). Two anonymous markers were also physically mapped to SSC10 (SWR1849 and S0070) to better connect the physical and linkage maps. These assignments have further refined the comparative map between SSC1, 4 and 10 and HSA1, 9 and 10.
Improving the comparative map of porcine chromosome 9 with respect to human chromosomes 1, 7 and 11
Authors: Middleton R. , Aldenhoven J. , Chen Y. , Backofen B. , Moran C.
Published: February 2004

Conserved segments have been identified by ZOO-FISH between pig chromosome 9 (SSC9) and human chromosomes 1, 7 and 11. To assist in the identification of positional candidate genes for QTL on SSC9, the comparative map was further developed. Primers were designed from porcine EST sequence homologous to genes in regions of human chromosomes 1, 7 and 11. Porcine ESTs were then physically assigned using the INRA somatic cell hybrid panel (INRASCHP) and the high-resolution radiation hybrid panel (IMpRH). Seventeen genes (PEPP3, RAB7L1, FNBP2, MAPKAPK2, GNAI1, ABCB1, STEAP, AKAP9, CYP51A1, SGCE, ROBO4, SIAT4C, GLUL, CACNA1E, PTGS2, C1orf16 and ETS1) were mapped to SSC9, while GUSB, CPSF4 and THG-1 were assigned to SSC3.
A refined comparative map between porcine chromosome 13 and human chromosome 3
Authors: van Poucke M. , Yerle M. , Chardon P. , Jacobs K. , Genêt C. , Mattheeuws M. , van Zeveren A. , Peelman L.J.
Published: February 2004

We report here the localisation of BAIAP1 (13q24), HTR1F (13q45), PTPRG (13q23) and UBE1C (13q24) by fluorescence in situ hybridisation (FISH), and BAIAP1 (Swr2114; 21 cR; LOD = 11.03), GATA2 (Sw2448; 37 cR; LOD = 8.26), IL5RA (Swr2114; 64 cR; LOD = 3.85), LMCD1 (Sw2450; 61 cR; LOD = 4.73), MME (CP; 50 cR; LOD = 7.75), RYK (Swc22; 12 cR; LOD = 18.62) and SGU003 (Sw1876; 6 cR; LOD = 16.99) by radiation hybrid (RH) mapping to porcine chromosome 13 (SSC13). The mapping of these 10 different loci (all mapped to human chromosome 3; HSA3) not only confirms the extended conservation of synteny between HSA3 and SSC13, but also defines more precisely the regions with conserved linkage. The syntenic region of the centromeric part of SSC13 was determined by isolating porcine bacterial artificial chromosome (BAC) clones (842D4 and 1031H1) using primers amplifying porcine microsatellite markers S0219 and S0076 (mapped to this region). Sequence comparison of the BAC end sequences with the human genome sequence showed that the centromeric part of SSC13 is homologous with HSA3p24.
Study of candidate genes for glycolytic potential of porcine skeletal muscle: identification and analysis of mutations, linkage and physical mapping and association with meat quality traits in pigs
Authors: Fontanesi L. , Davoli R. , Nanni Costa L. , Scotti E. , Russo V.
Published: February 2004

Several genes (PRKAA2, PRKAB1, PRKAB2, PRKAG3, GAA, GYS1, PYGM, ALDOA, GPI, LDHA, PGAM2 and PKM2), chosen according to their role in the regulation of the energy balance and in the glycogen metabolism and glycolysis of the skeletal muscle, were studied. Eleven single nucleotide polymorphisms (SNPs) were identified in six of these genes (PRKAB1, GAA, PYGM, LDHA, PGAM2 and PKM2). Allele frequencies were analyzed in seven different pig breeds for these loci and for a polymorphism already described for GPI and for three polymorphic sites already reported at the PRKAG3 locus (T30N, G52S and I199V). Linkage mapping assigned PYGM and LDHA to porcine chromosome (SSC) 2, PKM2 to SSC7, GAA to SSC12, PRKAB1 to SSC14 and PGAM2 to SSC18. Physical mapping, obtained by somatic cell hybrid panel analysis, confirmed the linkage assignments of PRKAB1 and GAA and localized ALDOA, PRKAB2 and GYS1 to SSC3, SSC4 and SSC6, respectively. Pigs selected for the association study, for which several meat quality traits were measured, were first genotyped at the PRKAG3 R200Q polymorphic site (RN locus), in order to exclude carriers of the 200Q allele, and then were genotyped for all the mutations considered in this work. Significant associations (P ≤ 0.001) were observed for the PRKAG3 T30N and G52S polymorphic sites with meat colour (L* at 24 h post mortem). PGAM2 and PKM2 were significantly associated (P = 0.01) with drip loss percentage and glycogen content at one hour post mortem, respectively.
Mapping, identification of polymorphisms and analysis of allele frequencies in the porcine skeletal muscle myopalladin and titin genes
Authors: Davoli R. , Braglia S. , Lama B. , Fontanesi L. , Buttazzoni L. , Baiocco C. , Russo V.
Published: February 2004

Genes coding for sarcomeric proteins may play a key role in muscle mass accretion and meat production. Screening a skeletal muscle cDNA library we isolated two partial sequences coding for the sarcomeric myopalladin and titin genes. In the present work we identified three SNPs in the 3′ untranslated region, two at the myopalladin locus and one at the titin locus. Myopalladin was mapped on porcine chromosome (SSC) 14 using a somatic cell hybrid panel, a radiation hybrid panel and by linkage mapping. The linkage mapping of titin confirmed the position on SSC15. Then we analysed the allelic distribution of the alleles at both loci in six different porcine breeds. The analysis of the allele frequencies for these two loci in extremely divergent groups of pigs selected according to lean cuts (LC) and average daily gain (ADG) approached the significance level for myopalladin and LC trait. Further studies are needed to test the presence of a putative effect of myopalladin on lean meat content.
Linkage and comparative mapping of the locus controlling susceptibility towards E. coli F4ab/ac diarrhoea in pigs
Authors: Jørgensen C.B. , Cirera S. , Anderson S.I. , Archibald A.L. , Raudsepp T. , Chowdhary B. , Edfors-Lilja I. , Andersson L. , Fredholm M.
Published: February 2004

In 1995, Edfors-Lilja and coworkers mapped the locus for the E. coli K88ab (F4ab) and K88ac (F4ac) intestinal receptor to pig chromosome 13 (SSC13). Using the same family material we have refined the map position to a region between the microsatellite markers Sw207 and Sw225. Primers from these markers were used to screen a pig BAC library and the positive clones were used for fluorescent in situ hybridization (FISH) analysis. The results of the FISH analysis helped to propose a candidate gene region in the SSC13q41→q44 interval. Shotgun sequencing of the FISH-mapped BAC clones revealed that the candidate region contains an evolutionary breakpoint between human and pig. In order to further characterise the rearrangements between SSC13 and human chromosome 3 (HSA3), detailed gene mapping of SSC13 was carried out. Based on this mapping data we have constructed a detailed comparative map between SSC13 and HSA3. Two candidate regions on human chromosome 3 have been identified that are likely to harbour the human homologue of the gene responsible for susceptibility towards E. coli F4ab/ac diarrhoea in pigs.
Comparative sequence analysis of the PRKAG3 region between human and pig: evolution of repetitive sequences and potential new exons
Authors: Amarger V. , Erlandsson R. , Pielberg G. , Jeon J.-T. , Andersson L.
Published: February 2004

The PRKAG3 gene encodes the γ3 chain of AMP-activated protein kinase (AMPK). A non-conservative missense mutation in the PRKAG3 gene causes a dominant phenotype involving abnormally high glycogen content in pig skeletal muscle. We have determined >126 kb (in 13 contigs) of porcine genomic sequence surrounding the PRKAG3 gene and the corresponding mouse region covering the gene. A comparison of these PRKAG3 sequences and the human sequence was conducted and used to predict evolutionarily conserved regions, including regulatory regions. A comparison of the human genomic sequence and a porcine BAC sequence containing the PRKAG3 gene, revealed a conserved organization and the presence of three additional genes, CYP27A1 (cytochrome P450, family 27, subfamily A, polypeptide 1), STK36 (Serine Threonine Kinase 36), and the homolog of the unidentified human mRNA KIAA0173. Interspersed repetitive elements constituted 51.4 and 38.6% of this genomic region in human and pig, respectively. We were able to reliably align 12.6 kb of orthologous repeats shared between pig and human and these showed an average sequence identity of 72.4%. Our analysis revealed that the human KIAA0173 gene harbors alternative 5′ untranslated exons originating from repetitive elements. This provides an obvious example how transposable elements may affect gene evolution.
Chromosome location, genomic organization of the porcine COL10A1 gene and model structure of the NC1 domain
Authors: Madsen L.B. , Petersen A.H. , Nielsen V.H. , Nissen P.H. , Dunø M. , Krejci L. , Bendixen C. , Thomsen B.
Published: February 2004

The porcine COL10A1 gene, encoding the α1(X) chain of type X collagen, has been sequenced. The gene structure is evolutionarily conserved, consisting of three exons and two introns spanning 7100 bp. Linkage mapping localized the gene to chromosome 1, which is in agreement with human-pig homology maps. Furthermore, protein structure comparison of the functionally important carboxyl domain between species revealed that amino acid changes were few and mainly situated in loop regions.
Aneuploidy detection in porcine embryos using fluorescence in situ hybridization
Authors: Zudova D. , Rezacova O. , Kubickova S. , Rubes J.
Published: February 2004

In contrast to human embryos, there are very few studies published on the frequency of chromosomal aneuploidy in farm animals. The objectives of this study were to apply a three-color fluorescent in situ hybridization (FISH) method for evaluating aneuploidy in porcine embryos using chromosome-specific DNA probes, establish baseline frequencies of aneuploidy in embryos and compare the results with our previous findings of aneuploidy in spermatozoa and oocytes. The embryos were collected from superovulated gilts, which were slaughtered 48 h after insemination. FISH was performed using probes specific for the centromeric regions of porcine chromosomes 1, 10 and Y. Altogether 403 blastomeres from 114 porcine embryos were successfully investigated. Diploidy was observed in 101 (88.6%) embryos, triploidy in 2 (1.8%) embryos, mosaicism/mixoploidy in 9 (7.9%) embryos, and trisomy for chromosomes 1 or 10 in 2 (1.8%) embryos. No blastomere showed aneuploidy for chromosome Y. These findings correspond with the frequencies of aneuploidy we have found previously in porcine germ cells.
Equine genomics: galloping to new frontiers
Authors: Chowdhary B.P. , Bailey E.
Published: February 2004

Analysis of the horse genome is proceeding at a rapid pace. Within a short span of 6–7 years, ∼1,500 markers have been mapped in horse, of which at least half are genes/ESTs. Health, performance and phenotypic characteristic are of major concern/interest to horse breeders and owners. Current efforts to analyze the equine genome are primarily aimed at developing critical resources (including an advanced gene map) that could readily be used in the near future to i) identify genes and mutations responsible for inherited equine diseases/disorders and to formulate approaches for accurate diagnostics, therapeutics and prevention, ii) discover genes associated with various other traits of significance, e.g. fertility, disease resistance, coat color and athletic performance etc., and iii) use functional genomic approaches to identify gene regulatory events involved in the manifestation of various diseases.
An ordered BAC contig map of the equine major histocompatibility complex
Authors: Gustafson A.L. , Tallmadge R.L. , Ramlachan N. , Miller D. , Bird H. , Antczak D.F. , Raudsepp T. , Chowdhary B.P. , Skow L.C.
Published: February 2004

A physical map of ordered bacterial artificial chromosome (BAC) clones was constructed to determine the genetic organization of the horse major histocompatibility complex. Human, cattle, pig, mouse, and rat MHC gene sequences were compared to identify highly conserved regions which served as source templates for the design of overgo primers. Thirty-five overgo probes were designed from 24 genes and used for hybridization screening of the equine USDA CHORI 241 BAC library. Two hundred thirty-eight BAC clones were assembled into two contigs spanning the horse MHC region. The first contig contains the MHC class II region and was reduced to a minimum tiling path of nine BAC clones that span approximately 800 kb and contain at least 20 genes. A minimum tiling path of a second contig containing the class III/I region is comprised of 14 BAC clones that span approximately 1.6 Mb and contain at least 34 genes. Fluorescence in situ hybridization (FISH) using representative clones from each of the three regions of the MHC localized the contigs onto ECA20q21 and oriented the regions relative to one another and the centromere. Dual-colored FISH revealed that the class I region is proximal to the centromere, the class II region is distal, and the class III region is located between class I and II. These data indicate that the equine MHC is a single gene-dense region similar in structure and organization to the human MHC and is not disrupted as in ruminants and pigs.
Comparative sequence analysis of equine and human MHC class II DQB genes
Authors: Mashima S.
Published: February 2004

The MHC class II DQB gene of horse was isolated and characterized. No obvious mutations causing frame shifts, or destruction of putative protein structure and splicing machinery were detected. Nucleotide sequence of exon 2 was consistent with an allelic sequence of the W23 haplotype. The cytoplasmic region of the equine DQB gene comprised two exons and an intron. A novel fragment of the gene was identified at the 3′ intergenic region proximal to the ELA-DQB gene by sequence comparison between the human and horse DQB genes. This sequence showed the highest identity to exon 3 region of the DQB gene, however the 5′ half of this exon was truncated as compared with the intact exon. This gene fragment was also identified in the same site of the HLA-DQB gene.
Genetic mapping of GBE1 and its association with glycogen storage disease IV in American Quarter horses
Authors: Ward T.L. , Valberg S.J. , Lear T.L. , Guérin G. , Milenkovic D. , Swinburne J.E. , Binns M.M. , Raudsepp T. , Skow L. , Chowdhary B.P. , Mickelson J.R.
Published: February 2004

Comparative biochemical and histopathological data suggest that a deficiency in the glycogen branching enzyme (GBE) is responsible for a fatal neonatal disease in Quarter Horse foals that closely resembles human glycogen storage disease type IV (GSD IV). Identification of DNA markers closely linked to the equine GBE1 gene would assist us in determining whether a mutation in this gene leads to the GSD IV-like condition. FISH using BAC clones as probes assigned the equine GBE1 gene to a marker deficient region of ECA26q12→q13. Four other genes, ROBO2, ROBO1, POU1F1, and HTR1F, that flank GBE1 within a 10-Mb segment of HSA3p12→p11, were tightly linked to equine GBE1 when analyzed on the Texas A&M University 5000 rad equine radiation hybrid panel, while the GLB1, MITF, RYBP, and PROS1 genes that flank this 10-Mb interval were not linked with markers in the GBE1 group. A polymorphic microsatellite (GBEms1) in a GBE1 BAC clone was then identified and genetically mapped to ECA26 on the Animal Health Trust full-sibling equine reference family. All Quarter Horse foals affected with GSD IV were homozygous for an allele of GBEms1, as well as an allele of the most closely linked microsatellite marker, while a control horse population showed significant allelic variation with these markers. This data provides strong molecular genetic support for the candidacy of the GBE1 locus in equine GSD IV.
The epitheliogenesis imperfecta locus maps to equine chromosome 8 in American Saddlebred horses
Authors: Lieto L.D. , Cothran E.G.
Published: February 2004

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 α3, laminin β3 and laminin γ2). 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.
FISH analysis comparing genome organization in the domestic horse (Equus caballus) to that of the Mongolian wild horse (E. przewalskii)
Authors: Myka J.L. , Lear T.L. , Houck M.L. , Ryder O.A. , Bailey E.
Published: February 2004

Przewalski’s wild horse (E. przewalskii, EPR) has a diploid chromosome number of 2n = 66 while the domestic horse (E. caballus, ECA) has a diploid chromosome number of 2n = 64. Discussions about their phylogenetic relationship and taxonomic classification have hinged on comparisons of their skeletal morphology, protein and mitochondrial DNA similarities, their ability to produce fertile hybrid offspring, and on comparison of their chromosome morphology and banding patterns. Previous studies of GTG-banded karyotypes suggested that the chromosomes of both equids were homologous and the difference in chromosome number was due to a Robertsonian event involving two pairs of acrocentric chromosomes in EPR and one pair of metacentric chromosomes in ECA (ECA5). To determine which EPR chromosomes were homologous to ECA5 and to confirm the predicted chromosome homologies based on GTG banding, we constructed a comparative gene map between ECA and EPR by FISH mapping 46 domestic horse-derived BAC clones containing genes previously mapped to ECA chromosomes. The results indicated that all ECA and EPR chromosomes were homologous as predicted by GTG banding, but provide new information in that the EPR acrocentric chromosomes EPR23 and EPR24 were shown to be homologues of the ECA metacentric chromosome ECA5.
Genetic variation in Przewalski’s horses, with special focus on the last wild caught mare, 231 Orlitza III
Authors: Bowling A.T. , Zimmermann W. , Ryder O. , Penado C. , Peto S. , Chemnick L. , Yasinetskaya N. , Zharkikh T.
Published: February 2004

In our continuing efforts to document genetic diversity in Przewalski’s horses and relatedness with domestic horses, we report genetic variation at 22 loci of blood group and protein polymorphisms and 29 loci of DNA (microsatellite) polymorphisms. The loci have been assigned by linkage or synteny mapping to 20 autosomes and the X chromosome of the domestic horse (plus four loci unassigned to a chromosome). With cumulative data from tests of 568 Przewalski’s horses using blood, hair or tooth samples, no species-defining markers were identified, however a few markers were present in the wild species but not in domestic horses. Inheritance patterns and linkage relationships reported in domestic horses appeared to be conserved in Przewalski’s horses. A derived type for the last wild caught mare 231 Orlitza III provided evidence for markers apparently not found in (or not currently available by descent from) the other species founders that were captured at the end of the nineteenth century. This information has been critical to the development of parentage analyses in the studbook population of Przewalski’s horses at Askania Nova, at one time the largest herd of captive animals and the source of stock for reintroduction efforts. Some horses in the study showed genetic incompatibilities with their sire or dam, contradicting published studbook information. In many cases alternative parentage could be assigned from living animals. To assist in identification of correct parentage, DNA marker types for deceased horses were established from archived materials (teeth) or derived from offspring. Genetic markers were present in pedigreed animals whose origin could not be accounted for from founders. Genetic distance analysis of erythrocyte protein, electrophoretic and microsatellite markers in Przewlaski’s horses and ten breeds of domestic horse place the Przewalski’s horse as an outgroup to domestic horses, introgression events from domestic horses not withstanding.
Karyotypic relationships of horses and zebras: results of cross-species chromosome painting
Authors: Yang F. , Fu B. , O’Brien P.C.M. , Robinson T.J. , Ryder O.A. , Ferguson-Smith M.A.
Published: February 2004

Complete sets of chromosome-specific painting probes, derived from flow-sorted chromosomes of human (HSA), Equus caballus (ECA) and Equus burchelli (EBU) were used to delineate conserved chromosomal segments between human and Equus burchelli, and among four equid species, E. przewalskii (EPR), E. caballus, E. burchelli and E. zebra hartmannae (EZH) by cross-species chromosome painting. Genome-wide comparative maps between these species have been established. Twenty-two human autosomal probes revealed 48 conserved segments in E. burchelli. The adjacent segment combinations HSA3/21, 7/16p, 16q/19q, 14/15, 12/22 and 4/8, presumed ancestral syntenies for all eutherian mammals, were also found conserved in E. burchelli. The comparative maps of equids allow for the unequivocal characterization of chromosomal rearrangements that differentiate the karyotypes of these equid species. The karyotypes of E. przewalskii and E. caballus differ by one Robertsonian translocation (ECA5 = EPR23 + EPR24); numerous Robertsonian translocations and tandem fusions and several inversions account for the karyotypic differences between the horses and zebras. Our results shed new light on the karyotypic evolution of Equidae.
Isolation and chromosomal assignment of canine genomic BAC clones representing 25 cancer-related genes
Authors: Thomas R. , Bridge W. , Benke K. , Breen M.
Published: February 2004

An extensive number of genes have been implicated in the initiation and progression of human cancers, aiding our understanding of the genetic aetiology of this highly heterogeneous disease. In order to facilitate extrapolation of such information between species, we have isolated and physically mapped the canine orthologues of 25 well-characterised human cancer-related genes. The identity of PCR products representing each canine gene marker was first confirmed by DNA sequencing analysis. Each product was then radiolabelled and used to screen a genomic BAC library for the domestic dog. The chromosomal location of each positive clone in the canine karyotype was determined by fluorescence in situ hybridisation (FISH) onto canine metaphase preparations. Of the 25 genes, the FISH localisation of 21 correlated fully with that expected on the basis of known regions of conserved synteny between the human and canine genomes. Three correlated less closely, and the chromosomal location of the remaining marker showed no apparent correlation with current comparative mapping data. In addition to generating useful comparative mapping information, this panel of markers will act as a valuable resource for detailed study of candidate genes likely to be involved in tumourigenesis, and also forms the basis of a canine cancer-gene genomic microarray currently being developed for the study of unbalanced genomic aberrations in canine tumours.
A canine cancer-gene microarray for CGH analysis of tumors
Authors: Thomas R. , Fiegler H. , Ostrander E.A. , Galibert F. , Carter N.P. , Breen M.
Published: February 2004

As with many human cancers, canine tumors demonstrate recurrent chromosome aberrations. A detailed knowledge of such aberrations may facilitate diagnosis, prognosis and the selection of appropriate therapy. Following recent advances made in human genomics, we are developing a DNA microarray for the domestic dog, to be used in the detection and characterization of copy number changes in canine tumors. As a proof of principle, we have developed a small-scale microarray comprising 87 canine BAC clones. The array is composed of 26 clones selected from a panel of 24 canine cancer genes, representing 18 chromosomes, and an additional set of clones representing dog chromosomes 11, 13, 14 and 31. These chromosomes were shown previously to be commonly aberrant in canine multicentric malignant lymphoma. Clones representing the sex chromosomes were also included. We outline the principles of canine microarray development, and present data obtained from microarray analysis of three canine lymphoma cases previously characterized using conventional cytogenetic techniques.
Identification of isoforms and RH mapping of canine KIT
Authors: Tsai K.L. , Guyon R. , Murphy K.E.
Published: February 2004

The proto-oncogene, c-kit (KIT), encodes a tyrosine kinase receptor, and mutations in this gene are causative for several mammalian diseases, including cancer and a form of pigmentation-associated hereditary deafness. Our laboratories are interested in a form of hereditary deafness that is associated with abnormalities in pigmentation and is common in the Dalmatian. Thus, KIT is being analyzed as a candidate gene for deafness in this breed. In addition to our interest in deafness, we are involved in mapping gene loci in the canine genome. Reported here is the identification of two isoforms of canine C-kit and radiation hybrid mapping of KIT to CFA13.
Comparative chromosomal localization of the canine-derived BAC clones containing LEP and IGF1 genes in four species of the family Canidae
Authors: Szczerbal I. , Rogalska-Niznik N. , Klukowska J. , Schelling C. , Dolf G. , Switonski M.
Published: February 2004

In the present report we show the chromosomal localization of two BAC clones, carrying the leptin (LEP) and insuline-like growth factor 1 (IGF1) genes, respectively, in four species belonging to the family Canidae: the dog, red fox, arctic fox and the Chinese raccoon dog. The assignments are in agreement with earlier data obtained from comparative chromosome painting for the dog, red fox and arctic fox.
Development of a cytogenetic map for the Chinese raccoon dog (Nyctereutes procyonoides procyonoides) and the arctic fox (Alopex lagopus) genomes, using canine-derived microsatellite probes
Authors: Szczerbal I. , Rogalska-Niznik N. , Schelling C. , Schläpfer J. , Dolf G. , Switonski M.
Published: February 2004

New chromosomal assignments of canine-derived cosmid clones containing microsatellites to the Chinese raccoon dog and arctic fox genomes are presented in the study. The localizations are in agreement with data obtained from comparative chromosome painting experiments between the dog and arctic fox genomes. However, paracentric inversions have been detected by comparing the loci order in canid karyotypes. The number of physically mapped loci increased to thirty-five both in the Chinese raccoon dog and in the arctic fox. Furthermore, the present status of the cytogenetic map of the Chinese raccoon dog and arctic fox is presented in this study.
Radiation hybrid mapping of 304 novel microsatellites in the domestic cat genome
Authors: Menotti-Raymond M. , David V.A. , Agarwala R. , Schäffer A.A. , Stephens R. , O’Brien S.J. , Murphy W.J.
Published: February 2004

Effective utilization of the domestic cat as an animal model for hereditary and infectious disease requires the development and implementation of high quality gene maps incorporating microsatellites and conserved coding gene markers. Previous feline linkage and radiation hybrid maps have lacked sufficient microsatellite coverage on all chromosomes to make effective use of full genome scans. Here we report the isolation and genomic mapping of 304 novel polymorphic repeat loci in the feline genome. The new loci were mapped in the domestic cat radiation hybrid panel using an automated fluorescent Taq-Man based assay. The addition of these 304 microsatellites brings the total number of microsatellites mapped in the feline genome to 580, and the total number of loci placed onto the RH map to 1,126. Microsatellites now span every autosome with an average spacing of roughly one polymorphic STR every five centimorgans, and full genome coverage of one marker every 2.7 megabases. These loci now provide a useful tool for undertaking full-genome scans to identify genes associated with phenotypes of interest, such as those relating to hereditary disease, coat color, patterning and morphology. These resources can also be extended to the remaining 36 species of the cat family for population genetic and evolutionary genomic analyses.
Integration of animal linkage and BAC contig maps using overgo hybridization
Authors: Romanov M.N. , Price J.A. , Dodgson J.B.
Published: February 2004

The alignment of genome linkage maps, defined primarily by segregation of sequence-tagged site (STS) markers, with BAC contig physical maps and full genome sequences requires high throughput mechanisms to identify BAC clones that contain specific STS. A powerful technique for this purpose is multi-dimensional hybridization of “overgo” probes. The probes are chosen from available STS sequence data by selecting unique probe sequences that have a common melting temperature. We have hybridized sets of 216 overgo probes in subset pools of 36 overgos at a time to filter-spotted chicken BAC clone arrays. A four-dimensional pooling strategy, including one degree of redundancy, has been employed. This requires 24 hybridizations to completely assign BACs for all 216 probes. Results to date are consistent with about a 10% failure rate in overgo probe design and a 15–20% false negative detection rate within a group of 216 markers. Three complete rounds of overgo hybridization, each to sets of about 39,000 BACs (either BamHI or EcoRI partial digest inserts) generated a total of 1853 BAC alignments for 517 mapped chicken genome STS markers. These data are publicly available, and they have been used in the assembly of a first generation BAC contig map of the chicken genome.
Reversal and convergence in marsupial chromosome evolution
Authors: Rens W. , O’Brien P.C.M. , Fairclough H. , Harman L. , Graves J.A.M. , Ferguson-Smith M.A.
Published: February 2004

The karyotypes of marsupial species are characterized by their relatively low number of chromosomes, and their conservation. Most species have diploid numbers lying between the two modes, 2n = 14 and 2n = 22, but the karyotype of Aepyprymnus rufescens is exceptional in containing 2n = 32 chromosomes. Many differences in diploid number between marsupial species can be accounted for by particular fissions and fusions, which are easy to detect because of the low numbers of chromosomes in each karyotype. This should be a system in which it is possible to detect reversals and repeated chromosome rearrangements. We have used chromosome-specific paints derived from A. rufescens to compare the karyotypes of eight marsupial species, representing closely and distantly related taxa, to trace chromosome change during evolution, and especially to detect reversals and convergence. From these and other painting comparisons, we conclude that there have been at least three reversals of fusions by fissions, and at least three fusions or fissions that have occurred independently in different lineages.
Integration of chicken genomic resources to enable whole-genome sequencing
Authors: Aerts J. , Crooijmans R. , Cornelissen S. , Hemmatian K. , Veenendaal T. , Jaadar A. , van der Poel J. , Fillon V. , Vignal A. , Groenen M.
Published: February 2004

Different genomic resources in chicken were integrated through the Wageningen chicken BAC library. First, a BAC anchor map was created by screening this library with two sets of markers: microsatellite markers from the consensus linkage map and markers created from BAC end sequencing in chromosome walking experiments. Second, HindIII digestion fingerprints were created for all BACs of the Wageningen chicken BAC library. Third, cytogenetic positions of BACs were assigned by FISH. These integrated resources will facilitate further chromosome-walking experiments and whole-genome sequencing.
Identification of chicken lymphocyte antigen 6 complex, locus E (LY6E, alias SCA2) as a putative Marek’s disease resistance gene via a virus-host protein interaction screen
Authors: Liu H.-C. , Niikura M. , Fulton J.E. , Cheng H.H.
Published: February 2004

Marek’s disease virus (MDV) is a naturally occurring oncogenic avian herpesvirus that causes neurological disorders and T cell lymphoma disease in domestic chickens. Identification and functional characterization of the individual factors involved in Marek’s disease (MD) resistance or pathogenesis will enhance our understanding of MDV pathogenesis and further genetic improvement of chickens. To study the genetic basis for resistance to MD, a strategy that combined protein-protein interaction screens followed by linkage analysis was performed. The MDV protein US10 was used as the bait in an E. coli two-hybrid screening of a cDNA library derived from activated splenic T cells. The chicken LY6E, also known as SCA2 and TSA1, was found to specifically interact with US10. This interaction was confirmed by an in vitro protein-binding assay. Furthermore, LY6E was found to be significantly associated with MD traits in an MD resource population comprised of commercial chickens. Previously, LY6E was implicated in two independent DNA microarray experiments evaluating differential gene expression following MDV infection. Given that LY6E is involved in T cell differentiation and activation, we suggest that LY6E is a candidate gene for MD resistance and deserves further investigation on its role in MDV pathogenesis, especially with respect to the binding of US10.
The chicken telomerase RNA gene: conservation of sequence, regulatory elements and synteny among viral, avian and mammalian genomes
Authors: Delany M.E. , Daniels L.M.
Published: February 2004

Telomerase RNA (TR) is essential for telomerase activity and the maintenance of telomere length in proliferating cell populations. The objective of the present research was to define the cytogenetic and molecular genomic organization of chicken TR (chTR). The chTR exists as a single copy gene (TERC, alias TR), mapping to chromosome 9 (GGA9). The loci on the q arm of GGA9 map to three chromosomes in human with five of the nine GGA9q loci mapping to HSA3q. Sequencing of the chTERC locus (3,763 bp) from the UCD 001 genome (Red Jungle Fowl) included: 604 bp 5′, 465 coding, and 2,694 bp 3′ (from –604 to +3159). Sequence analysis included homology searches conducted on several levels including comparisons among different chicken genotypes, Marek’s disease virus (MDV) sequences, plus human and murine. We provide evidence for distal 5′ and 3′ sequence homology between chTERC and the MDV genome among other known regions of homology (promoter and coding), elaborate on 5′ transcription factor binding motifs among the various genomes as well as show type and number of TERT-related motifs 3′ of chicken TR (e.g., Sp1, c-Myb, c-Myc, AP2, among others). Surrounding the gene are more than 25 Sp1 sites, over 20 oncogene transcription factor binding motifs and numerous hormonal and other specialized binding motifs. Knowledge of 5′ and 3′ chTERC regulatory elements will be useful for investigating normal control mechanisms during growth and development as well as investigating the potential for dysregulation of this important gene during oncogenesis, especially among different genotypes.
Dynamics of telomere erosion in transformed and non-transformed avian cells in vitro
Authors: Swanberg S.E. , Delany M.E.
Published: February 2004

Although vertebrate telomeres are highly conserved, telomere dynamics and telomerase profiles vary among species. The objective of the present study was to examine telomerase activity and telomere length profiles of transformed and non-transformed avian cells in vitro. Non-transformed chicken embryo fibroblasts (CEFs) showed little or no telomerase activity from the earliest passages through senescence. Unexpectedly, a single culture of particularly long-lived senescent CEFs showed telomerase activity after over 250 days in culture. Transformed avian lines (six chicken, two quail and one turkey) and tumor samples (two chicken) exhibited telomerase activity. Telomere length profiles of non-transformed CEF cultures derived from individual embryos of an inbred line (UCD 003) exhibited cycles of shortening and lengthening with a substantial net loss of telomeric DNA by senescence. The telomere length profiles of several transformed cell lines resembled telomere length profiles of senescent CEFs in that they exhibited little of the typical smear of terminal restriction fragments (TRFs) suggesting that these transformed cells may possess a reduced amount of telomeric DNA. These results show that avian telomerase activity profiles are consistent with the telomerase activity profiles of human primary and transformed cells. Further, monitoring of telomere lengths of primary cells provides evidence for a dynamic series of changes over the lifespan of any specific cell culture ultimately resulting in net telomeric DNA loss by senescence.
Allelic variation and genetic linkage of avian microsatellites in a new turkey population for genetic mapping
Authors: Reed K.M. , Chaves L.D. , Garbe J.R. , Da Y. , Harry D.E.
Published: February 2004

Efforts to build a comprehensive genetic linkage map for the turkey (Meleagris gallopavo) have focused on development of genetic markers and experimental resource families. In this study, PCR amplification was attempted for 772 microsatellite markers that had been previously developed for three avian species (chicken, quail and turkey). Allelic polymorphism at 410 markers (53.1% of total examined) was determined by genotyping ten individuals (six F1 parents and four grandparents) in a new resource population specifically developed for genetic linkage mapping. Of these 410 markers, 109 (26.6%) were polymorphic in the tested individuals, with an average of 2.3 alleles per marker. Higher levels of polymorphism were found for the turkey-specific markers (61.1%) than for the chicken (22.7%) or quail-specific markers (33.3%). To test the fidelity of the matings, demonstrate the power of these families for linkage analysis, and determine genetic linkage relationships, 86 polymorphic markers were genotyped for up to 224 birds including founder grandparents, parents and F2 progeny. Linkage relationships for many of the chicken markers elucidated in the turkey were comparable to those observed in the chicken. These data demonstrate that the new UMN/NTBF resource population will provide a solid foundation for constructing a comparative genetic map of the turkey.
Myosin light chain genes in the turkey (Meleagris gallopavo)
Authors: Chaves L.D. , Ostroski B.J. , Reed K.M.
Published: February 2004

Myosin light chains associate with the motor protein myosin and are believed to play a role in the regulation of its actin-based ATPase activity. Myosin light chain cDNA clones from the turkey (Meleagris gallopavo) were isolated and sequenced. One sequence corresponded to an alternative transcript, the skeletal muscle essential light chain (MYL1 isoform 1) and a second to the smooth muscle isoform of myosin light chain (MYL6). The DNA and predicted amino acid sequences of both light chain genes were compared to that of the chicken. Based on the cDNA sequence, oligonucleotide primers were designed to amplify genomic DNA from six of the seven introns of the MYL1 gene. Approximately 5 kb of DNA was sequenced (introns and 3′ UTR) and evaluated for the presence of single nucleotide polymorphisms (SNPs). SNPs were verified by sequencing common intron regions from multiple individuals and three polymorphisms were used to genotype pedigreed families. MYL1 is assigned to a turkey linkage group that corresponds to a region of chicken chromosome 7 (GGA7). The results of this study provide genomic reagents for comparative studies of avian muscle components and muscle biology.