bluuebunny/crossref_metadata_2025 huggingface dataset:
Potential causes of arrested succession in Kibale National Park, Uganda: growth and mortality of seedlings
Authors: Chapman Colin A. , Chapman Lauren J. , Kaufman Les , Zanne Amy E.
Published: March 2003

Recent studies suggest that regeneration following large‐scale disturbance in Kibale National Park, Uganda, is slow or possibly arrested. Here, data is provided on the growth and mortality of seedlings in the forest understory, treefall gaps, and in large gaps that suggest that this pattern of arrested succession can be attributed partially to the fact that this East African community lacks aggressive colonizing tree species. Growth and mortality rates were contrasted for seedlings of six tree species planted in the understory, small gaps, and large gaps for 36 months. Data suggest that species are adapted to gaps of particular sizes. For example, Uvariopsis congensis grew faster in the understory than in small gaps, whereas Warburgia ugandensis had the lowest mortality rate and highest growth rate in large gaps. Seedlings (n=170) of 15 species were transplanted to assess the response of the tree community to large gap conditions. The limited survival of seedlings in large gaps relative to the understory suggests that only a small proportion of the tree community in this forest regenerates best in gaps larger than those created by the collapse of a single tree. These findings differ from a number of studies conducted in other geographical regions, and suggests that tree communities differ with respect to the proportion of tree species adapted to gaps of particular sizes. This may relate to variation among regions in their history of disturbance and thus frequency of gap formation, size of gaps, and the duration of periods of release. Such variation could imply the existence of a corresponding pattern among tropical forests of differential vulnerability to human disturbance, which tends to create many large gaps.
Vegetation gradients around artificial water points in the Central Kalahari Game Reserve of Botswana
Authors: Makhabu Shimane W. , Marotsi Balisana , Perkins J.
Published: March 2003

Vegetation was assessed in plots sited at varying distances along two line transects radiating from each of nine artificial water points. Environmental variables such as distance from water point, soil type and ground cover were related to grass species composition. Grass species composition in calcrete soils differed significantly from that found in sandy soils. On calcrete soils, distance from water point did not have a significant effect on species composition. On sandy soils, distance from water point had a significant effect on species composition at two of the nine water points sampled. At these two water points, grass species that are usually associated with disturbed areas dominated close to the water points while those that dominated far from the water points were those that are usually associated with undisturbed sites. The results therefore indicate that there was no severe degradation of habitat around water points.
Cloning, sequencing and linkage mapping of the NRAMP1 gene of sheep and deer
Authors: Matthews G. D. , Crawford A. M.
Published: March 2003

The ovine NRAMP1 and cervine NRAMP1 cDNAs were cloned by RT PCR of RNA derived from macrophage enriched leukocyte preparations. The complete coding and 3′ regions were sequenced. Both sheep and deer NRAMP1 proteins are 548 amino acids long. There are 77 and 73 amino acid differences, respectively, compared to the mouse Nramp1 sequence. Dinucleotide repeats were found in both the ovine and cervine 3′ non‐coding sequence. Amplification of these regions in individual sheep and deer showed them to be polymorphic micro‐satellites. They have polymorphism information content values of 0·76 and 0·84 in sheep and deer, respectively. Using these microsatellites, the ovine NRAMP1 gene was mapped in a linkage group on ovine chromosome 2q and cervine NRAMP1 was mapped in a linkage group syntenic with human chromosome 2, mouse chromosome 1 and sheep chromosome 2.
Mapping of porcine genes belonging to two different cytochrome P450 subfamilies
Authors: Nissen P. H. , Winterø A. K. , Fredholm M.
Published: March 2003

Three cDNA clones from a porcine small intestine cDNA library, tentatively identified as transcripts of two different cytochrome P450 (CYP) gene subfamilies, were sequenced and mapped. One of the clones was found to comprise an open reading frame of 503 amino acids and showed up to an 80% similarity to genes from the CYP3A subfamily. Translation of the other two cDNA clones revealed high similarity to genes from the CYP2C subfamily. One of these clones was truncated, lacking a part of the 5′ end of the coding region, whereas the other encodes a putative pseudogene. The CYP3A gene was mapped cytogenetically by means of a pig/rodent somatic hybrid cell panel to pig chromosome 3, in the region p16–p17 or p11. The CYP2C pseudogene was mapped genetically to pig chromosome 14, using the PiGMaP shared reference pedigrees. The localisations provide information for the human/pig comparative map.
Tyrosine hydroxylase and insulin‐like growth factor II but not insulin are adjacent in the teleost species barramundi, Lates calcarifer
Authors: Collet C. , Candy J. , Sara V.
Published: March 2003

In humans, the genes encoding tyrosine hydroxylase (TH), insulin and insulin‐like growth factor II (IGF‐II) form an extremely tight linkage group on chromosome 11p15. Characterisation of the homologous genomic region of a teleost, the barramundi Lates calcarifer, revealed tight linkage of the TH and IGF‐II genes, and the absence of the gene encoding insulin.
NCAM: a polymorphic microsatellite locus conserved across eutherian mammal species
Authors: Moore S. S. , Hale P. , Byrne K.
Published: March 2003

A dinucleotide microsatellite was found to be conserved at the 3′ untranslated end of the neural cell adhesion molecule (NCAM) gene in cattle, rat and human. The high level of sequence conservation found in this gene allows the use of a single set of PCR primers to amplify sequence spanning the repeat in many species. Sequence analysis revealed the conservation of the dinucleotide repeat in all eutherian mammal species studied with variation in length as well as internal structure caused by base substitutions. Polymorphisms were seen across five mammalian orders, in rat, buffalo, sheep, cow, whale and dolphin, with polymorphisms predicted in pig and dugong based on the length of the uninterrupted dinucleotide repeat.
Effectiveness of bovine microsatellites in resolving paternity cases in American bison, Bison bison L.
Authors: Mommens G. , Van Zeveren A. , Peelman L. J.
Published: March 2003

A set of 33 cattle microsatellite primer pairs was tested with the DNA of American bison from a captive population in Belgium and evaluated for usefulness in parentage testing. Two primer sets did not amplify and three were monomorphic. Among the polymorphic markers, the number of alleles ranged from two to nine. Heterozygosity, polymorphism information content (PIC) and probability of exclusion (PE) values were low by comparison with those obtained with the same markers in cattle. Two methods of estimating PE were used, one which assumed equal allele frequencies between parental sexes and another which took into account differences in allele frequencies between parental sexes. An internationally accepted set of nine microsatellites gives cumulative PE values of 0·98 and 0·97, respectively, for the two methods. The potential of this marker set to identify bison × cattle hybrids is discussed. Because bison and cattle have a common ancestor, these microsatellites are a useful way to establish genetic distances and can lead to the construction of phylogenetic trees.
A low rate of replacement substitutions in two major Ovis aries mitochondrial genomes
Authors: Hiendleder S.
Published: March 2003

Two mitochondrial DNA molecules which represent major Ovis aries mtDNA haplogroups were cloned and comparatively sequenced to assess the degree of intraspecific variation. A total of 9623 bp that correspond to 58% of both mitochondrial genomes were determined. The control region, the Cytb, ND2, ND3, ND4L, COIII and 12 tRNA genes, including the origin of L‐strand replication, were completely characterized. Partial sequence information was obtained from the 12S and 16S rRNA and an additional six protein coding and six tRNA genes. The control regions of the two mtDNAs showed a nucleotide divergence of 4·34% while coding regions differed by 0·44%. The number of sheep coding region substitutions was similar to values observed in intraspecific comparisons of mitochondrial DNAs that represent remote points in genealogical trees of mice and humans. However, replacement substitutions were only observed at ∼30% of the rate in mice and ∼20% of the rate in humans. Nucleotide substitutions with a potential for phenotypic effects were found in the 12S and 16S rRNA and in the ND1 and COIII genes.
Mapping of the natural resistance‐associated macrophage protein 1 (NRAMP1) gene to pig chromosome 15
Authors: Sun H. S. , Wang L. , Rothschild M. F. , Tuggle C. K.
Published: March 2003

The natural resistance‐associated macrophage protein 1 (NRAMP1) was mapped in the pig for study as a potential candidate gene in controlling pig resistance to Salmonella infection. Primers were designed from the pig cDNA to amplify a 1·6 kb fragment between exons 1 and 3. By using a pig‐rodent somatic cell hybrid panel, NRAMP1 was mapped to pig chromosome 15 (SSC15) with 100% probability, and the regional assignment was SSC15q23‐26 with 87% concordance. A polymerase chain reaction‐restriction fragment length polymorphism (PCR‐RFLP) marker was developed by using the HinfI enzyme and three alleles were identified from a population including 11 breeds. Linkage analysis confirmed the physical assignment by using the PiGMaP reference families. Pig NRAMP1 was linked to SSC15 markers S0088, S0149 and S0284 (LOD > 3). A small population study revealed large allele frequency differences among tested breeds. An A allele is only observed in dam (white) lines whereas a similar exclusivity of the C allele was seen in sire (colored) breeds.
Reduced bovine leukaemia virus proviral load in genetically resistant cattle
Authors: Mirsky M. L. , Olmstead C. , Da Y. , Lewin H. A.
Published: March 2003

The bovine leukaemia virus (BLV) is an exogenous retrovirus that is closely related to the human T cell leukaemia viruses. Genetic resistance and susceptibility to persistent lymphocytosis (PL), an advanced subclinical stage of infection characterized by a polyclonal expansion of the infected B cell population, have been mapped to structural motifs in bovine MHC DRB3 (class II) alleles. To determine whether alleles of DRB3 influence the number of BLV‐infected B cells in peripheral blood, seven pairs of Holstein cows naturally infected with BLV were matched on the basis of DRB3 genotype (resistance or susceptibility to PL), age, and year of seroconversion. Flow cytometry was used to separate B cell populations that then were tested for the presence of provirus by a single‐cell PCR methodology. Animals with the PL‐resistance associated DRB3.2*11 allele had significantly fewer BLV‐infected B cells than did age‐ and seroconversion‐matched cows with DRB3 alleles associated with susceptibility to PL. Our results demonstrate that DRB3 or a closely linked gene may play a direct role in controlling the number of BLV‐infected peripheral B cells in vivo. Association of MHC class II alleles with resistance to disease progression in cattle naturally infected with BLV provides a unique immunogenetic model for the study of host resistance to human and other animal retroviral infections.
Genetic structure of seven European cattle breeds assessed using 20 microsatellite markers
Authors: MacHugh D. E. , Loftus R. T. , Cunningham P. , Bradley D. G.
Published: March 2003

Genotype data from 20 microsatellites typed in 253 animals is used here to assess the genetic structure of seven European pedigree cattle breeds. Estimation of genetic subdivision using classical drift‐based measures shows that the average proportion of genetic variation among breeds varies between 10 and 11% of the total, depending on the estimator used. We demonstrate that a simple allele‐sharing genetic distance parameter can be used to construct a dendrogram of relationships among animals. This phylogenetic tree displays a remarkable degree of breed clustering and reflects an extensive underlying kinship structure, particularly for the Swiss Simmental breed and four breeds originating from the British Isles. Condensation of allele frequencies and individual genotypic compositions using principal component analysis is also used to investigate genetic structure among breeds and individual animals. In addition, the underlying genetic demarcation of European cattle breeds is emphasized in simulations of breed assignment using allele frequency distributions from samples of microsatellite loci. Correct breed designation can be inferred with accuracies approaching 100% using data from a panel of 10 microsatellite loci.
Allelic variation of ovine MHC class II DQA1 and DQA2 genes
Authors: Snibson K. J. , Maddox J. F. , Fabb S. A. , Brandon M. R.
Published: March 2003

In the present study we characterize allelic variation of polymorphic OLA‐DQA1 and OLA‐DQA2 genes in sheep. To achieve this, PCR primers were designed to independently amplify the second exons of OLA‐DQA1 and OLA‐DQA2 genes. Single strand conformation polymorphism (SSCP) gel analyses reveals that there are at least 12 distinct OLA‐DQA2 sequences, 10 of which have been characterized by sequencing. Six distinct OLA‐DQA1 alleles have been sequenced in sheep and we can detect at least seven DQA1 alleles, including a null allele, by SSCP analysis. The second exon of the OLA‐DQA2 gene is more polymorphic than the equivalent region of the OLA‐DQA1 gene. Thirty‐two per cent of nucleotide and 49% of amino acid sites showed variation at the DQA2 locus, compared to 20% of nucleotide and 33% of amino acid sites for DQA1. Phylogenetic analysis of DQA sequences from a number of species show that sheep DQA1 sequences group together and are more similar to bovine DQA1 sequences than to sheep DQA2 alleles. The majority of OLA‐DQA2 sequences are on the same main branch of the phylogenetic tree as bovine DQA2 sequences. However, three sheep DQA2 sequences have a tendency to group with putative bovine DQA3 sequences rather than to other ovine DQA2 alleles. A variety of SSCP gel conditions were tried in order to develop a typing system for the OLA‐DQA2 gene. We describe a set of PCR and SSCP conditions which distinguish between all known OLA‐DQA2 alleles.
Fitting genetic mapping functions based on sperm typing: results for three chromosomal segments in cattle
Authors: Windemuth C. , Simianer H. , Lien S.
Published: March 2003

Genetic mapping functions translate the observed recombination rate between two loci into the corresponding map distance in Morgan units. Different mapping functions give different weights to multiple crossing overs and therefore lead to different results. This points out that not every function is best suited to fit a data set. The data used in this study originated from 2214 sperm from 37 Norwegian bulls, which were genotyped for 11 markers. The optimal functions for the chromosomes 6, 23 and the sex chromosome of cattle were derived using the maximum likelihood method, the likelihood ratio test and empirical discriminant analysis. It became apparent that for each chromosome a different function fitted the data best. These were the function of Rao et al. (Human Heredity 1977, 27, 99–104) with p = 0·63 for chromosome 6, the function of Goldgar & Fain (American Journal of Human Genetics 1988, 43, 38–45) with c0 = 0·42, c1 = 0·47, c2 = 0·07 and c3 = 0·04 for chromosome 23 and the function of Felsenstein (Genetics 1979, 91, 769–75) with K = 0·23 for the sex chromosome. The well known functions of Haldane (Journal of Genetics 1919, 8, 299–309) and Kosambi (Annals of Eugenics 1944, 12, 172–5) were shown to be suboptimal in most cases. A function is said to be multilocus feasible if the evaluation of the probability of all possible recombination events does not lead to negative values. The optimal function for chromosome 23 turned out to be multilocus feasible, whereas the functions for chromosome 6 and the sex chromosome were not. The choice of the correct mapping function is shown to have a considerable impact in mapping studies, when double recombinations have to be taken into account. Since there is no unique best mapping function, it is argued that it might be useful to use a simple parametric mapping function (like the one of Felsenstein 1979) and to estimate the respective parameter specifically for a given data set.
Genetic relationships among Spanish sheep using microsatellites
Authors: Arranz J. J. , Bayón Y. , Primitivo F. San
Published: March 2003

Five indigenous Spanish breeds of sheep, Churra, Latxa, Manchega, Rasa–Aragonesa and Merino, with Awassi sheep as a reference breed were genotyped for 19 DNA microsatellites. Allele frequencies and mean heterozygosities revealed the greatest genetic variation in Merino sheep and the lowest in Awassis. Differences in variability were not great in the other breeds studied. The dendrograms obtained based on genetic distances showed a large differentiation between Awassi sheep and the Spanish breeds, as was to be expected from their distinct genetic origin. Merinos appeared separated from the other four breeds, of which, according to a classification based on the fleece characteristics, Churra and Latxa belong to the churro type and Manchega and Rasa–Aragonesa to the so called entrefino type, though no clear separation was evident between the two types. These results suggest that morphological data alone are insufficient for determining relationships between breeds and that studies involving genetic markers may be of great assistance.
Targeting of marker loci to chicken chromosome 16 by representational difference analysis
Authors: Wain H. M. , Toye A. A. , Hughes S. , Bumstead N.
Published: March 2003

Representational difference analysis (RDA) was initially used to identify differences between two inbred lines of chickens, line N and line 15I, on which the Compton mapping reference population is based. RDA was subsequently used to identify marker loci targeted specifically to chicken chromosome 16. Chromosome 16 contains the major histocompatibility complex (MHC), nucleolar organiser region (NOR) and Rfp‐Y complex. To generate markers specific for this chromosome a bird was selected from the Compton mapping reference population which had inherited N line alleles for the MHC, NOR and Rfp‐Y regions on this chromosome. DNA from this bird was compared with pooled DNA from 16 of its siblings, all of which had inherited line 15I alleles for the MHC, NOR and Rfp‐Y regions. Initially amplicons were derived from BamHI digested samples, RDA products were cloned after the first round of hybridisation and 113 clones were investigated: 45 of these identified BamHI polymorphisms in this population. Of the 45 polymorphic clones, 17 have been mapped in the reference population so far, and these have identified seven new loci on chromosome 16. Interestingly a group of 16 other loci were linked on chromosome 4. The same birds were also compared by RDA following digestion with TaqI. Again large numbers of clones were generated of which 65 were investigated. Of these 17 clones were polymorphic and of five clones mapped so far three lie on chromosome 16. Two of the loci mapped to chromosome 16 have been used to identify yeast artificial chromosome (YAC) clones (GenBank accession numbers: AF057302, AF057303, AF057304, AF063218, AF06347, AF06348, AF06349, AF06350, AF063#51, AF06353, AF06354, AF06355, AF06356).
Mitochondrial control region and 12S rRNA variation in Przewalski’s horse (Equus przewalskii)
Authors: Oakenfull E. A. , Ryder O. A.
Published: March 2003

Variation in the control region and the 12S rRNA gene of all surviving mitochondrial lineages of Przewalski’s horse was investigated. Variation is low despite the present day population being descended from 13 individuals probably representing animals from three different regions of its range. Phylogenetic comparison of these sequences, with sequences for the domestic horse, does not resolve the ancestral status of either horse.
DNA sequence of SSCP haplotypes at the bovine growth hormone (bGH) gene
Authors: Lagziel A , Soller M
Published: March 2003

Previous studies using SSCP and PCR‐RFLP methodologies uncovered nine polymorphic sites within the bGH gene, defining eight intragenic haplotypes falling into two main groups. In the present study we report the DNA sequence of these eight haplotypes. A total of 1494 bp were sequenced uncovering a total of 12 sequence variants. Haplotypes within groups differed among themselves at one or two sites; compared across groups, haplotypes of the two groups differed consistently at six sites, each of which was monomorphic within the respective groups. This comes to 4 differentiating sites per kb, suggesting that the two haplotype groups began to diverge about 400 000 years ago. This corresponds approximately to the estimated time of divergence of the Bos taurus and Bos indicus lineages, raising the possibility, supported by other evidence, that the two haplotype classes represent taurine and indicine haplotypes, respectively. Nucleotide sequence divergence of taurine and indicine genomes of this magnitude has far reaching implications with respect to QTL mapping and marker assisted selection in breeds derived from taurine × indicine crosses.
A radiation hybrid map of bovine chromosome one
Authors: Rexroad C E , Schlapfer J S , Yang Y , Harlizius B , Womack J E
Published: March 2003

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.
Bovine UCP2 and UCP3 map to BTA15
Authors: Stone R T , Rexroad C E , Smith T P L
Published: March 2003

Two recently described uncoupling proteins, &itUCP2 and UCP3, may have important roles in determining feed conversion and/or maintenance energy requirements in livestock. Sequence was determined for the entire coding region and four of the six introns for bovine UCP3. A partial cDNA sequence was obtained for bovine UCP2. Radiation hybrid mapping was used to place UCP3 on BTA15, a chromosome previously shown to harbor a locus influencing meat tenderness. In order to place UCP3 in the existing linkage map, five single nucleotide polymorphisms (SNPs) were developed. Linkage analysis using one of five SNPs was used to place UCP3 between 53 ·1 and 53 ·5 c
m. No recombination was detected between UCP3 and IDVGA10, IDVGA32, and INRA145. The sequence of PCR products from a single BAC amplified with primers specific for either UCP2 or UCP3 indicate that UCP2 and UCP3 are separated by < 200 kb.
Report of the International Equine Gene Mapping Workshop: male linkage map
Authors: Guérin G , Bailey E , Bernoco D , Anderson I , Antczak D F , Bell K , Binns M M , Bowling A T , Brandon R , Cholewinski G , Cothran E G , Ellegren H , Förster M , Godard S , Horin P , Ketchum M , Lindgren G , McPartlan H , Mériaux J ‐C , Mickelson J R , Millon L V , Murray J , Neau A , Røed K , Sandberg K , Shiue Y‐L , Skow L C , Stott M , Swinburne J , Valberg S J , Van Haeringen H , Van Haeringen W A , Ziegle J
Published: March 2003

The goal of the First International Equine Gene Mapping Workshop, held in 1995, was the construction of a low density, male linkage map for the horse. For this purpose, the International Horse Reference Family Panel (IHRFP) was established, consisting of 12 paternal half‐sib families with 448 half‐sib offspring provided by 10 laboratories. Blood samples were collected and DNA extracted in each laboratory and sent to the Lexington laboratory (KY, USA) for dispatch in aliquots to 14 typing laboratories. In total, 161 markers (144 microsatellites, seven blood groups and 10 proteins) were tested for all families for which the sire was heterozygous. Genealogies and typing data were sent for analysis to the INRA laboratory (Jouy‐en‐Josas, France) according to a specific format and entered into a database with input verification and output processes. Linkage analysis was performed with the CRIMAP program. Significant linkage was detected for 124 loci, of which 95 were unambiguously ordered using a multipoint analysis with an average spacing of 14 ·2 c m. These loci were distributed among 29 linkage groups. A more comprehensive analysis including synteny group data and FISH data suggested that 26 autosomes out of 31 are covered. The complete map spans 936 c
m.
Molecular cloning and mapping of the bovine and ovine skeletal muscle‐specific calpains1
Authors: Nonneman D , Koohmaraie M
Published: March 2003

The coding regions of the bovine and sheep skeletal muscle‐specific calpains (CANP3 or p94) were cloned and sequenced by RT‐PCR. Direct sequencing confirmed open reading frames of 2466 bp for both species, and bovine and sheep CANP3 shared 98 ·5% identity in their amino acid code. These sequences were greater than 88% identical to human, pig, rat and mouse CANP3 nucleotide sequences, and greater than 93% identical for the amino acid code. Single nucleotide polymorphisms were used to map the bovine and sheep CANP3 genes in two steps. The genes were placed into linkage groups based on two‐point LOD scores (≥ 3 ·0) and the best order was determined with multipoint linkage analysis (CRI‐MAP vs. 2 ·4). Bovine CANP3 mapped to bovine chromosome 10, relative position 33 ·9 c
m with linkage to nine markers; LOD scores ranged from 4 ·89 to 8 ·61 (order, BMS2349‐BL1035‐RME25‐CANP3‐BM6305‐BMS861‐ILSTS053‐BMS2742‐CA090‐BMS529). Ovine CANP3 mapped to chromosome 7, relative position 58 c
m, with linkage to only one marker, BMS861 (a bovine microsatellite that has been used in sheep), with no recombination and a LOD score of 5 ·72. The observed heterozygosity was 50% for both CANP3 markers in bovine and sheep pedigrees.
Chediak‐Higashi syndrome mutation and genetic testing in Japanese black cattle (Wagyu)
Authors: Yamakuchi H , Agaba M , Hirano T , Hara K , Todoroki J , Mizoshita K , Kubota C , Tabara N , Sugimoto Y
Published: March 2003

Chediak‐Higashi Syndrome (CHS) is an autosomal recessive disorder that affects several species including mice, humans, and cattle. Evidence based on clinical characteristics and somatic cell genetics suggests that mutations in a common gene cause CHS in the three species. The CHS locus on human chromosome 1 and mouse chromosome 13 encodes a lysosomal trafficking regulator formerly known asLYST, now known asCHS1, and is defective in CHS patients andbeigemice, respectively. We have mapped theCHSlocus to the proximal region of bovine chromosome 28 by linkage analysis using microsatellite markers previously mapped to this chromosome. Furthermore, we have identified a missense A:T→G:C mutation that results in replacement of a histidine with an arginine residue at codon 2015 of theCHS1gene. This mutation is the most likely cause of CHS in Wagyu cattle. In addition, we describe quick, inexpensive, PCR based tests that will permit elimination of theCHSmutation from Wagyu breeding herds.
Construction and evaluation of a porcine bacterial artificial chromosome library
Authors: Suzuki K , Asakawa S , Iida M , Shimanuki S , Fujishima N , Hiraiwa H , Murakami Y , Shimizu N , Yasue H
Published: March 2003

A porcine bacterial artificial chromosome (BAC) library consisting of 103 488 clones has been constructed. The average insert size in the BAC vector was calculated to be 133 kb based on the examination of 189 randomly selected clones, indicating that the library contained 4.4 genome equivalents. The library can be screened by two‐step PCR. The first screening step is performed on 22 superpools, each containing 4704 clones (49×96 well plates). In the second screening step, 49 plates comprising a superpool are arrayed in a 7×7 matrix and 4D‐PCR is performed. Screening of the library superpools by PCR for 125 marker sequences selected from different regions of swine genome revealed 123 sequences, indicating that the library is not biased. Subsequent screenings (4D‐PCR) were successfully applied for identification of clones containing each marker sequence. This porcine BAC library and the PCR screening system are useful for isolation of genomic DNA fragments containing desired sequences.
Development and characterization of expressed sequence tags for the turkey (Meleagris gallopavo) genome and comparative sequence analysis with other birds
Authors: Smith E , Shi L , Drummond P , Rodriguez L , Hamilton R , Powell E , Nahashon S , Ramlal S , Smith G , Foster J
Published: March 2003

Twenty‐one randomly selected clones from a turkey (Meleagris gallopavo) pituitary complementary DNA (cDNA) library were sequenced to develop expressed sequence tags (ESTs) for this economically important avian species whose genome is among the least understood. Primers specific for the ESTs were used to produce amplicons from the genomic DNA of turkey, chicken (Gallus gallus), guinea fowl (Numidia meleagris), pigeon (Columba domestica), and quail (Corturnix japonica). The amplicons were sequenced and analyzed for sequence variation within‐and similarity among‐species and with GenBank database sequences. The proportion of shared bases between the turkey sequence and the consensus sequence from each of the other species ranged from 72% to 93% between turkey and pigeon and quail and between turkey and chicken, respectively. The total number of single nucleotide polymorphisms (SNPs) observed ranged from 3 in quail to 18 in chicken out of 4898 and 5265 bases analyzed, respectively. The most frequent nucleotide variation observed was a C→T transition. Linkage analysis of one such SNP in the backcross progeny of the East Lansing reference DNA panel, localized TUS0005, the chicken sequence derived from primers specific for turkey TUT2E EST, to chromosome 4. The ESTs reported, as well as the SNPs may provide a useful resource for on‐going efforts to develop high utility genome maps for the turkey and chicken. The primers described can also be used as a tool in future investigations directed at further understanding the biology of the guinea fowl, pigeon and quail and their relatedness to the turkey.
Chromosomal assignment of canine TSC2, PKD1 and CLN3 genes by radiation hybrid‐ and linkage analyses
Authors: Jónasdóttir T J , Mellersh C S , Moe L , Vignaux F , Ostrander E A , Lingaas F
Published: March 2003

The canine tuberous sclerosis 2 (TSC2) gene has been mapped to canine chromosome 6 using a canine whole genome radiation hybrid panel. There is close linkage between canine TSC2 and the polycystic kidney disease 1 gene (PKD1), as has been observed in humans and other mammalian species. The gene responsible for the human juvenile form of neuronal ceroid lipofuscinosis (CLN3), maps close to TSC2 and PKD1 in humans, and is also syntenic in the dog. We further demonstrate linkage to a group of polymorphic markers assigned to canine chromosome 6 (CFA6).
Y‐specific microsatellite polymorphisms in a range of bovid species
Authors: Edwards C J , Gaillard C , Bradley D G , MacHugh D E
Published: March 2003

At least five dinucleotide (CA)n microsatellite repeat arrays have been assigned to the bovine Y‐chromosome, with one marker (INRA124) shown to be polymorphic. We describe here the assessment of a panel of four Y‐specific microsatellite markers for polymorphism in a range of cattle and related species. It was possible to amplify all the markers in the animals sampled and all showed variation. Three of the microsatellite loci (INRA124, INRA189 and BM861) displayed putative taurine‐ and zebu‐specific alleles which can be useful indicators of male‐mediated gene flow in hybrid populations. In the future these microsatellites, in combination with other Y‐specific markers should provide a high‐resolution Y haplotype system for evolutionary studies in both domesticated cattle and other related species.
Resolution of conflicting assignments for the bovine casein kinase IIα (CSNK2A2) gene
Authors: Aasland M , Våge D I , Lien S , Klungland H
Published: March 2003

The casein kinase IIα′ gene (CSNK2A2), which physically maps to human chromosome 16 (HSA16), has previously been mapped to bovine chromosome 5 (BTA5). Based on these results, a new segment of homology between the human and bovine genomes was suggested. In this paper we demonstrate linkage between CSNK2A2 and several markers on BTA18. Our result is supported by the extensive conservation of synteny between HSA16q and BTA18. Bovine chromosome 18 markers used in this study included several microsatellites, as well as the MC1R gene previously mapped to HSA16q24 ·3. Sequencing of the PCR‐fragment mapped to BTA5 reveals that a CSNK‐like retroposon was responsible for the conflicting assignments. The present results further extend the observed conservation of synteny between HSA16q and BTA18.
Microsatellite marker based genetic linkage maps of Oreochromis aureus and O. niloticus (Cichlidae): extensive linkage group segment homologies revealed
Authors: McConnell  , Beynon  , Leamon  , Skibinski
Published: March 2003

Partial genetic linkage maps, based on microsatellite markers, were constructed for two tilapia species, Oreochromis aureus and Oreochromis niloticus using an interspecific backcross population. The linkage map for O. aureus comprised 28 markers on 10 linkage groups and covered 212·8 c
M. Nine markers were mapped to four linkage groups on an O. niloticus female linkage map covering 40·6 c
M. Results revealed a high degree of conservation of synteny between the linkage groups defined inO. aureus and the previously published genetic linkage map of O. niloticus.
Construction and characterization of a gridded cattle BAC library
Authors: Buitkamp J , Kollers S , Durstewitz G , Fries R , Welzel K , Schäfer K , Kellermann A , Lehrach H
Published: March 2003

A bovine genomic large‐insert bacterial artificial chromosome (BAC) library has been constructed from leukocytes of a Holstein‐Friesian male. Size fractionated DpnII‐digested genomic DNA was ligated to the dephosphorylated BamH1 ends of a pBACe3·6 vector. Approximately 8·3×104 individual BAC clones were picked into 384‐well plates. Two‐hundred and sixty‐seven randomly chosen clones were characterized by pulsed‐field gel electrophoresis (PFGE). The average insert size was 104 kb with a frequency of clones without inserts of 5·5%. Thirty‐four BAC clones were mapped by fluorescence in situ hybridization (FISH) to cattle chromosomes. Three showed signals at more than one location, one of them on the centromeric regions of all autosomes, indicating that the clone contains centromeric repeats. A subset of these BAC clones was used for the development of sequence tagged sites. Both subcloning and direct sequencing of the BACs were used for generating sequence tagged site information. The clones from the library were gridded onto high‐density membranes, and PCR superpools were produced from the same set of clones. Membranes and superpools are available through the Resource Centre of the German Human Genome Project in Berlin (http://www.rzpd.de).
Characterization and chromosomal localization of the chicken avidin gene family
Authors: Ahlroth M K , Kola E H , Kulomaa M S , Ewald D , Masabanda J , Sazanov A , Fries R
Published: March 2003

Chicken avidin is a biotin‐binding protein expressed under inflammation in several chicken tissues and in the oviduct after progesterone induction. The gene encoding avidin belongs to a family that has been shown to include multiple genes homologous to each other. The screening and chromosomal localization studies performed to reveal the structure and organization of the complete avidin gene family is described. The avidin gene family is arranged in a single cluster within a 27‐kb genomic region. The cluster is located on the sex chromosome Z on band q21. The organization of the genes was determined and two novel avidin‐related genes, AVR6 and AVR7, were cloned and sequenced.
Comparative mapping of chicken anchor loci orthologous to genes on human chromosomes 1, 4 and 9
Authors: Suchyta S. P. , Cheng H. H. , Burnside J. , Dodgson J. B.
Published: March 2003

Comparative mapping of chicken and human genomes is described, primarily of regions corresponding to human chromosomes 1, 4 and 9. Segments of chicken orthologues of selected human genes were amplified from parental DNA of the East Lansing backcross reference mapping population, and the two parental alleles were sequenced. In about 80% of the genes tested, sequence polymorphism was identified between reference population parental DNAs. The polymorphism was used to design allele‐specific primers with which to genotype the backcross panel and place genes on the chicken linkage map. Thirty‐seven genes were mapped which confirmed the surprisingly high level of conserved synteny between orthologous chicken and human genes. In several cases the order of genes in conserved syntenic groups differs between the two genomes, suggesting that there may have been more frequent intrachromosomal inversions as compared with interchromosomal translocations during the separate evolution of avian and mammalian genomes.
Comprehensive linkage map of bovine chromosome 11
Authors: Casas E. , Bennett G. L. , Bottema C. D. K. , Crawford A. , Kalm E. , Kappes S. M. , Kister A. , Lewin H. A. , Lien S. , Morris C. A. , Olsaker I. , Pitchford W. S. , Schmutz S. M. , Thomsen H. , Xu N.
Published: March 2003

The results of genotypic data contributed to the International Society of Animal Genetics (ISAG) Bovine Chromosome 11 (BTA11) Workshop are presented. Six laboratories contributed a total of 26 199 informative meioses from 80 loci. Thirty‐six loci were typed by at least two independent laboratories and were used to construct a consensus linkage map of the chromosome. The remaining loci were subsequently incorporated into a comprehensive map. The sex‐averaged consensus map covered 128.9 cM. The female consensus map was 101.2 cM, while the male consensus map was 129.8 cM. The comprehensive sex‐averaged map was 134.2 cM and the average genetic distance between loci was 1.72 cM.
Physical mapping of CSF2RA, ANT3 and STS on the pseudoautosomal region of bovine chromosome X
Authors: Moore S. S. , Byrne K. , Johnson S. E. , Kata S. , Womack J. E.
Published: March 2003

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.
Isolation of a porcine UDP‐GalNAc transferase cDNA mapping to the region of the blood group EAA locus on pig chromosome 1
Authors: Meijerink E. , Neuenschwander S. , Dinter A. , Yerle M. , Stranzinger G. , Vögeli P.
Published: March 2003

In our studies of the genes constituting the porcine A0 blood group system, we have characterized a cDNA, encoding an α(1,3)N‐acetylgalactosaminyltransferase, that putatively represents the blood group A transferase gene. The cDNA has a 1095‐bp open reading frame and shares 76.9% nucleotide and 66.7% amino acid identity with the human ABO gene. Using a somatic cell hybrid panel, the cDNA was assigned to the q arm of pig chromosome 1, in the region of the erythrocyte antigen A locus (EAA), which represents the porcine blood group A transferase gene. The RNA corresponding to our cDNA was expressed in the small intestinal mucosae of pigs possessing EAA activity, whereas expression was absent in animals lacking this blood group antigen. The UDP‐N‐acetylgalactosamine (UDP‐GalNAc) transferase activity of the gene product, expressed in Chinese hamster ovary (CHO) cells, was specific for the acceptor fucosyl‐α(1,2)galactopyranoside; the enzyme did not use phenyl‐β‐D‐galactopyranoside (phenyl‐β‐D‐Gal) as an acceptor. Because the α(1,3)GalNAc transferase gene product requires an α(1,2)fucosylated acceptor for UDP‐GalNAc transferase activity, the α(1,2)fucosyltransferase gene product is necessary for the functioning of the α(1,3)GalNAc transferase gene product. This mechanism underlies the epistatic effect of the porcine S locus on expression of the blood group A antigen.

Abbreviations: CDS: coding sequence; CHO: Chinese Hamster Ovary; EAA: erythrocyte antigen A; FCS: foetal calf serum; Fucα(1,2)Gal: fucosyl‐α(1,2)galactopyranoside; Gal: galactopyranoside; GGTA1: Galα(1,3)Gal transferase; PCR: polymerase chain reaction; phenyl‐β‐D‐Gal: phenyl‐β‐D‐galactopyranoside; R: Galβ1‐4Glcβ1‐1Cer; UDP‐GalNAc: uridine diphosphate N‐acetylgalactosamine
Genetic relationship amongst the major non‐coding regions of mitochondrial DNAs in wild boars and several breeds of domesticated pigs
Authors: Okumura N. , Kurosawa Y. , Kobayashi E. , Watanobe T. , Ishiguro N. , Yasue H. , Mitsuhashi T.
Published: March 2003

We completed phylogenetic analysis of the major non‐coding region of the mitochondrial DNA (mtDNA) from 159 animals of eight Euro‐American and six East Asian domesticated pig breeds and 164 Japanese and five European wild boars. A total of 62 mtDNA haplotypes were detected. Alignment of these regions revealed nucleotide variations (including gaps) at 73 positions, including 58 sites with transition nucleotide substitutions, and two transversion substitutions. Phylogenetic analysis of the sequences could not organize domestic pig breeds into discrete clusters. In addition, many of the haplotypes found in members of diverged clustering groups were found primarily in Euro‐American pig breeds, indicating extensive introgression of Asian domestic pigs into European breeds. Furthermore, phylogenetic analysis allocated the DNA sequences of non‐coding regions into two different groups, and the deepest branchpoint of this porcine phylogeny corresponded to 86 000–136 000 years before present. This time of divergence would predate the historical period when the pig is thought to have been domesticated from the wild boar.
Indigenous domestic breeds as reservoirs of genetic diversity: the Argentinean Creole cattle
Authors: Giovambattista G. , Ripoli M. V. , Peral‐Garcia P. , Bouzat J. L.
Published: March 2003

Contrary to highly selected commercial breeds, indigenous domestic breeds are composed of semi‐wild or feral populations subjected to reduced levels of artificial selection. As a consequence, many of these breeds have become locally adapted to a wide range of environments, showing high levels of phenotypic variability and increased fitness under natural conditions. Genetic analyses of three loci associated with milk production (αS1‐casein, κ‐casein and prolactin) and the locus BoLA‐DRB3 of the major histocompatibility complex indicated that the Argentinean Creole cattle (ACC), an indigenous breed from South America, maintains high levels of genetic diversity and population structure. In contrast to the commercial Holstein breed, the ACC showed considerable variation in heterozygosity (He) and allelic diversity (A) across populations. As expected, bi‐allelic markers showed extensive variation in He whereas the highly polymorphic BoLA‐DRB3 showed substantial variation in A, with individual populations having 39–74% of the total number of alleles characterized for the breed. An analysis of molecular variance (AMOVA) of nine populations throughout the distribution range of the ACC revealed that 91.9–94.7% of the total observed variance was explained by differences within populations whereas 5.3–8.1% was the result of differences among populations. In addition, the ACC breed consistently showed higher levels of genetic differentiation among populations than Holstein. Results from this study emphasize the importance of population genetic structure within domestic breeds as an essential component of genetic diversity and suggest that indigenous breeds may be considered important reservoirs of genetic diversity for commercial domestic species.
An updated linkage and comparative map of porcine chromosome 18
Authors: Campbell E. M. G. , Fahrenkrug S. C. , Vallet J. L. , Smith T. P. L. , Rohrer G. A.
Published: March 2003

Swine chromosome 18 (SSC18) has the poorest marker density in the USDA‐MARC porcine linkage map. In order to increase the marker density, seven genes from human chromosome 7 (HSA7) expected to map to SSC18 were selected for marker development. The genes selected were: growth hormone releasing hormone receptor (GHRHR), GLI‐Kruppel family member (GLI3), leptin (LEP), capping protein muscle Z‐line α 2 subunit (CAPZA2), β A inhibin (INHBA), T‐cell receptor β (TCRB) and T‐cell receptor γ (TCRG). Large‐insert clones (YACs, BACs and cosmids) that contained these genes, as well as two previously mapped microsatellite markers (SW1808 and SW1984), were identified and screened for microsatellites. New microsatellite markers were developed from these clones and mapped. Selected clones were also physically assigned by fluorescence in situ hybridization (FISH). Fifteen new microsatellite markers were added to the SSC18 linkage map resulting in a map of 28 markers. Six genes have been included into the genetic map improving the resolution of the SSC18 and HSA7 comparative map. Assignment of TCRG to SSC9 has identified a break in conserved synteny between SSC18 and HSA7.
Comparative porcine gene mapping relative to human chromosomes 9, 10, 20 and 22
Authors: Lee J. H. , Zhang W. , Moran C.
Published: March 2003

Comparative anchor tagged sequence (CATS) consensus primers from loci mapped to human chromosomes 9, 10, 20, and 22 have been used to amplify homologous loci in pigs. Of 53, CATS primers tested in pigs, only 23 yielded products homologous to the human locus (42% success). Ten loci were physically mapped (43% success rate for verified products, but only 19% for primers tested). Due to lack of polymorphism, linkage mapping was possible only for AMBP. Map locations were consistent with human/pig ZOO‐FISH, except for ADRA1A, whose position is still equivocal in humans. These CATS primers have made very limited contributions to pig/human comparative gene mapping because of low efficiency of amplification of orthologous porcine product, frequent amplification from rodent template in a somatic hybrid panel and low level of polymorphism.