bluuebunny/crossref_metadata_2025 huggingface dataset:
Comprehensive linkage map of bovine chromosome 27
Authors: Casas E. , Sonstegard T. S. , Barendse W. , Bennett G. L. , Bottema C. D. K. , Crawford A. , Grosz M. D. , Kalm E. , Kappes S. M. , Kister A. , Li Y. , 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 for Animal Genetics (ISAG) Bovine Chromosome 27 Workshop are presented. Eight laboratories contributed 23 261 informative meioses from 44 loci. Eighteen loci were typed by at least two laboratories and were used to construct a consensus linkage map. Twenty‐one loci were subsequently incorporated into a comprehensive map. The sex‐averaged consensus map covered 66·9 cM. The sex‐averaged comprehensive map was 75·5 cM, while the female and male maps were 73·1 and 63·7 cM, respectively. Five loci were excluded from the analysis because of ambiguous position in the linkage group and a low LOD score (less than 2·0). Average distance between loci in the comprehensive map was 1·98 cM.
Chromosome assignment of six dog genes by FISH, and correlation with dog–human Zoo‐FISH data
Authors: Thomas R. , Breen M. , Binns M. M.
Published: March 2003

Cross‐species chromosome painting analyses have recently demonstrated the presence of regions of conserved synteny between the human and domestic dog genomes, aiding the search for candidate genes for inherited traits. Concerted efforts to subchromosomally assign substantial numbers of dog gene sequences are now needed in order to refine these comparative data, both in terms of marker density and resolution. We have developed novel PCR markers representing three dog genes (ALB, FOS, HNRPA2B1) for which no sequence or mapping data were previously available, to our knowledge. These, in addition to three gene markers previously described (ALDOA, RPE65, VCAM1), were used to isolate and chromosomally assign corresponding large insert genomic clones by fluorescence in situ hybridization (FISH). Chromosome assignments for these six dog genes are discussed in terms of those of the human orthologues, and correlated with existing comparative mapping information, identifying one apparent exception to existing Zoo‐FISH data, and aiding refinement of the boundaries of conserved chromosome segments in both genomes.
The assignment by linkage mapping of four genes from human chromosome 22 to bovine chromosome 5 and 17
Authors: Ariza F. , Harrison B. , Drinkwater R. D.
Published: March 2003

Polymerase chain reaction oligonucleotides were designed to amplify bovine specific sequences for four genes that are located on human chromosome 22 (HSA22): crystallin β A4 (CRY B A4), parvalbumin (PVALB), tissue inhibitor of metalloproteinase 3 (TIMP3) and matrix metalloproteinase 11 (MMP11). Single strand conformation analysis of these bovine gene fragments defined polymorphisms within a population of three large half‐sib families of three F1 Charolais × Brahman sires and a composite herd comprising an equal proportion of Africander, Brahman, Hereford and Shorthorn breeds (CSIRO pedigree). The DNA marker genotypes were used to define linkage associations to other DNA markers already placed on the CSIRO linkage map. The genes TIMP3 and PVALB were assigned to BTA5 and CRYβA4 and MMP11 to BTA17.
Polymorphism identification within 50 equine gene‐specific sequence tagged sites
Authors: Shubitowski D. M. , Venta P. J. , Douglass C. L. , Zhou R.‐X. , Ewart S. L.
Published: March 2003

The continued discovery of polymorphisms in the equine genome will be important for future studies using genomic screens and fine mapping for the identification of disease genes. Segments of 50 equine genes were examined for variability in 10 different horse breeds using a pool‐and‐sequence method. We identified 11 single nucleotide polymorphisms (SNPs) in 9380 bp of sequenced exon, and 25 SNPs, six microsatellites, and one insertion/deletion in 16961 bp of sequenced intron. Of all genes studied 52% contained at least one polymorphism, and polymorphisms were found at an overall rate of 1/613 bp. Several of the putative SNPs were tested and verified by restriction enzyme analysis using natural restriction sites or ones created by primer mutagenesis. The lowest allele frequency for a SNP detected in pooled samples was 10%. Three of the SNPs verified in the diverse horse pool were further tested in six breed‐specific horse pools and were found to be reasonably variable within breeds. The pool‐and‐sequence method allows identification of polymorphisms in horse populations and will be a valuable tool for future disease gene and comparative mapping in horses.
Mapping of expressed sequence tags from a porcine early embryonic cDNA library
Authors: Smith T. P. L. , Fahrenkrug S. C. , Rohrer G. A. , Simmen F. A. , Rexroad C. E. , Keele J. W.
Published: March 2003

The goal of this study was to identify and map genes expressed during the elongation phase of embryogenesis in swine. Expressed sequence tags were analysed from a previously described porcine cDNA library prepared from elongating swine embryos. Average insert length of randomly selected clones was approximately 600 bp, with a range from <100 to >2500 bp. Single‐pass, coding strand sequences from 1132 independent clones were compared with the GenBank non‐redundant (nr) database via BLASTN analysis to identify potential porcine homologous of known genes. Among these sequences, 781 (69%) showed significant (score >300) homology to non‐ mitochondrial sequences previously deposited in GenBank. Sequences matching interleucin 1 β and thymosin β 10 were most frequently observed (24 and 18 clones, respectively), in addition to matches with 310 other distinct genes. No significant match in the GenBank nr database was obtained for 303 sequences. Analysis demonstrated that 151 (50%) had open reading frames (ORF) extending at least 50 codons from the first base of the clone insert. Genetic markers were developed and used to map a subset of 17 genes, selected on the basis of function or of the ability to design primers that successfully amplified porcine genomic DNA, to 10 different porcine chromosomes, providing a set of mapped markers corresponding to genes expressed during conceptus elongation.
Development and mapping of microsatellites from a microdissected BTA 11‐specific DNA library
Authors: Ambady S. , Kappes S. M. , Park C. , Ma R. Z. , Beever J. E. , Lewin H. A. , Smith T. P. L. , Beattie C. W. , Basrur P. K. , De León F. Abel Ponce
Published: March 2003

A chromosome‐specific library was developed for Bos taurus autosome 11 by chromosome microdissection and microcloning using a bovine primary fibroblast culture, obtained from a t(X;23) heifer, that spontaneously developed a translocation chromosome involving bovine chromosome 11. The library was screened using (AC)12 oligos, positive clones selected, sequenced and primers developed to generate bovine chromosome 11‐specific microsatellite markers. This study suggests that chromosome‐specific libraries have great potential for development of microsatellite markers for the construction of marker‐saturated linkage maps for each chromosome.
DNA cloning and sequence analysis of chicken AFLP
Authors: Knorr C. , Cheng H. H. , Dodgson J. B.
Published: March 2003

Amplified fragment length polymorphisms (AFLP) have been shown to be useful for linkage mapping in chickens and other domestic animals. It is often desirable to convert AFLP bands to sequence‐tagged site (STS) markers, in particular, so that AFLP‐based linkage information can be integrated with recombinant DNA clone‐based maps. Sixteen chicken AFLP bands were excised from gels, re‐amplified, cloned and analysed. All inserts proved to be EcoRI‐TaqI fragments, which suggests that unlabelled TaqI‐TaqI AFLP fragments do not amplify well, and therefore do not significantly contaminate AFLP bands. For eight of the AFLP, the cloned fragment was used to probe blots of AFLP reaction fingerprints, confirming that the predominant DNA clone indeed contained the polymorphic fragment. Flanking regions of selected AFLP fragments were isolated using Vectorette cloning. The results obtained suggest that the these chicken AFLP most commonly arise from sequence polymorphism at or near the TaqI site.
Multi‐primer target PCR for rapid identification of bovine DRB3 alleles
Authors: Ledwidge S. A. , Mallard B. A. , Gibson J. P. , Jansen G. B. , Jiang Z. H.
Published: March 2003

Multi‐primer target polymerase chain reaction (MPT‐PCR) is a rapid method for the identification of specific BoLA‐DRB3 alleles. In a single PCR reaction, the presence of two alleles associated with increased risk, DRB3.2*23 (DRB3*2701–2703, 2705–2707) and decreased risk, DRB3.2*16 (DRB3*1501, 1502), of mastitis in Canadian Holstein can be detected. Two outer primers amplify exon 2 of DRB3. Simultaneously, two inner, allele‐specific primers amplify individual alleles. Initially, 40 cows previously typed by PCR‐restriction fragment length polymorphism (PCR‐RFLP) were genotyped using the multi‐primer approach. An additional 30 cows were first genotyped by multi‐primer target PCR, then by PCR‐RFLP. All animals were correctly identified and there were no false positives. This technique can readily be modified to identify other BoLA alleles of interest.
Construction and characterization of BAC libraries for three fish species; rainbow trout, carp and tilapia
Authors: Katagiri T. , Asakawa S. , Minagawa S. , Shimizu N. , Hirono I. , Aoki T.
Published: March 2003

Bacterial artificial chromosome (BAC) libraries are important tools for genomic research. We have constructed seven genomic BAC libraries from three fish species, rainbow trout (Oncorhynchus mykiss), carp (Cyprinus carpio) and tilapia (Oreochromis niloticus). The two rainbow trout BAC libraries have average insert sizes of 58 and 110 kb. The average size of inserts in the carp BAC library is 160 kb. The average insert sizes of the four tilapia BAC libraries are 65, 105, 145 and 194 kb, respectively. These libraries represent good coverage of each genome (2–64 × coverage). The libraries can be screened by conventional colony hybridization and provide a starting point for the construction of high‐density filtres or polymerase chain reaction (PCR) screening approaches. These BAC libraries will facilitate the positional cloning of quantitative trait loci (QTLs) for a variety of economically important traits in these species.
Genetic polymorphism of goat κ‐casein (CSN3) in different breeds and characterization at DNA level
Authors: Caroli A. , Jann O. , Budelli E. , Bolla P. , Jäger S. , Erhardt G.
Published: March 2003

Data on genetic differences at CSN3 in goat breeds including a DNA based typing method and the mutations responsible for variation on protein and DNA level are presented here. Isoelectric focusing (IEF) in ultrathin polyacrylamide gels with carrier ampholytes was used to demonstrate CSN3 polymorphism in milk samples of Italian (Orobica n=88; Ionica n=68) and German goat breeds (Bunte Deutsche Edelziege n=244; Weisse Deutsche Edelziege n=134; Toggenburger n=25; Thüringer Waldziege n=70). A further CSN3 band was found presenting a more cathodic migration than CSN A. After chymosin action, the genetic polymorphism was also observed in the para‐κ‐casein fraction. The new allele CSN3B was spread mainly in Orobica (37%), Bunte Deutsche Edelziege (11%) and Ionica (10%). CSN3B occurred in low frequency (<3%) in Thüringer Waldziege and in Weisse Deutsche Edelziege, and could not be demonstrated in milk samples of Toggenburger. The populations were in Hardy–Weinberg equilibrium at CSN3. The codominant genetic control of CSN3B was confirmed by genetic studies. Discrimination of CSN3 alleles A and B was also obtained by DNA SSCP analysis. Sequencing of CSN3B revealed four transitions at position 247, 309, 471, and 591 compared with CSN3A. From these transitions, the following amino acid substitutions are deduced: 44 Gln → Arg, 65 Val → Ile, 119 Val → Ile, and 159 Ser → Pro. Among the four mutations, only the 44 Gln → Arg can be revealed by milk protein IEF analysis while at DNA level three further genetic variants should exist in addition to CSN3A and CSN3B.
A genetic analysis of the London strain of rainbow trout
Authors: Gregg R. E. , Rhodes O. E. , Armstrong G.
Published: March 2003

The London strain of rainbow trout (Oncorhynchus mykiss) was created by interbreeding three other strains of rainbow trout and therefore was expected to have higher levels of genetic variation than other strains of rainbow trout. We examined 129 London strain rainbow trout from Indiana by allozyme electrophoresis to assess levels of genetic variation and to examine the relationship between the London strain and other hatchery strains. When using the same loci to compare with other hatchery strains the London strain showed levels of genetic variation within the range of other hatchery strains: mean heterozygosity of 0.053 (0.031–0.099), 1.27 (1.20–1.60) alleles per locus and 20.0% (20.0–40.0%) of the loci were polymorphic. The London strain is somewhat distinct from other hatchery strains (D=0.009–0.072), in part because of the high frequency of the sIDHP*40 allele.
Characterization of swine leptin (LEP) polymorphisms and their association with production traits
Authors: Kennes Y. M. , Murphy B. D. , Pothier F. , Palin M.‐F.
Published: March 2003

Four polymorphisms in the swine leptin (LEP) gene were characterized and evaluated for association with economically important production traits in Yorkshire, Landrace and Duroc pigs. Our results show that these polymorphisms are generally of low frequency or are absent in pig populations. Two polymorphisms (A2845T and T3469C) may be associated (P < 0.0078) with feed intake and growth rate traits in Landrace pigs.
Differential expression of the GTL2 gene within the callipyge region of ovine chromosome 18
Authors: Bidwell C. A. , Shay T. L. , Georges M. , Beever J. E. , Berghmans S. , Cockett N. E.
Published: March 2003

The inheritance pattern of the skeletal muscle hypertrophy phenotype caused by the callipyge gene has been characterized as polar overdominance. We hypothesized that this trait may be caused by a gain or loss of gene expression because of the reversible nature of the phenotype in paternal vs. maternal inheritance. Suppression subtraction cDNA probes were made from skeletal muscle mRNA of normal (NN) and callipyge (CPatNMat) animals and hybridized to Southern blots containing bacterial artificial chromosomes (BACs) that comprise a physical contig of the callipyge region. The CN–NN probes hybridized to two ovine and seven bovine BACs. Sequence analysis of fragments within those BACs indicated short regions of similarity to mouse gene trap locus (gtl2). Northern blots analysis of RNA from hypertrophy‐responsive muscles show a population of GTL2 mRNA centred around 2.4 kb that were abundantly expressed in 14‐day prenatal NN and CPatNMat lambs but were down‐regulated in day 14 and day 56 postnatal NN lambs. The expression of GTL2 remained elevated in 14‐ and 56‐day‐old CPatNMat lambs as well as in 56‐day‐old NPatCMat and CC lambs. Expression of GTL2 in the supraspinatus, which does not undergo hypertrophy, was very low for all genotypes and ages. Isolation of cDNA sequences show extensive alternative splicing and a lack of codon bias suggesting that GTL2 does not encode a protein. The mutation of the callipyge allele has altered postnatal expression of GTL2 in muscles that undergo hypertrophy and will help identify mechanisms involved in growth, genomic imprinting and polar overdominance.
Isolation of expressed sequence tags of skeletal muscle of neonatal healthy and splay leg piglets and mapping by somatic cell hybrid analysis
Authors: Maak S. , Jaesert S. , Neumann K. , Yerle M. , Von Lengerken G.
Published: March 2003

We have isolated 14 differentially displayed and 10 further expressed sequence tags (ESTs) from Musculus biceps femoris of newborn healthy and splay leg piglets. By comparison with EMBL/GenBank data we could identify nine porcine homologues to human genes (TATA box binding protein associated factor B TAF1B; B‐cell CLL/lymphoma 7B BCL7B; pyruvate dehydrogenase kinase, isoenzyme 4 PDK4; ribosomal protein S10 RPS10; SPARC‐like 1 SPARCL1; epithelial protein lost in neoplasm β EPLIN; N‐myc downstream‐regulated gene 2 NDRG2; pleiomorphic adenoma gene like 2 PLAGL and, BCL‐2 associated transcription factor short form BTFS). Eight fragments correspond to uncharacterized ESTs and 7 ESTs had no significant match with database sequences. These data provide the first expression profiles in skeletal muscle of neonatal piglets and are a basis for candidate gene investigations for congenital splay leg in piglets. Eleven ESTs were physically mapped to porcine chromosomes 1, 3, 4, 5, 7, 8, 9 and 10 and contribute to the comparative map of humans and pigs.
Genetic variation of the second exon of ELA‐DRB genes in Argentine Creole horses*
Authors: Díaz S. , Giovambattista G. , Dulout F. N. , Peral‐García P.
Published: March 2003

Genetic variation in the equine leucocyte antigen‐DRB (ELA‐DRB) second exon was investigated using polymerase chain reaction (PCR) amplification, restriction fragment length polymorphism (RFLP) of PCR products (PCR‐RFLP) and deoxyribonucleic acid (DNA) sequencing. Eight distinct PCR‐RFLP patterns could be identified in the studied Argentine Creole (AC) horses. The number of observed patterns per individual ranged from four to six, thus confirming the presence of multiple DRB copies in AC horses. Three PCR‐RFLP alleles and three new sequences were identified. The estimated rates of synonymous and non‐synonymous substitutions among ELA‐DRB exon 2 sequences were higher within the antigen recognition site (ABS) than on the non‐ABS. Phylogenetic analysis showed that the nucleotide sequences clustered in two main groups, while some sequences were not included in either group. Finally, the identification of the number of alleles per animal, the phylogenetic and segregation analyses allowed us to explain the number of ELA‐DRB loci. However, it was not possible to identify specific alleles with specific loci.
Characterization of two new alleles at the goat CSN1S2 locus
Authors: Ramunno L. , Cosenza G. , Pappalardo M. , Longobardi E. , Gallo D. , Pastore N. , Di Gregorio P. , Rando A.
Published: March 2003

Two novel alleles at the goat CSN1S2 locus have been identified: CSN1S2F and CSN1S2D. Sequence analyses revealed that the CSN1S2F allele is characterized by a G → A transition at the 13th nucleotide in exon 3 changing the seventh amino acid of the mature protein from Val to Ile. The CSN1S2D allele, apparently associated with a decreased synthesis of αs2‐casein, is characterized by a 106‐bp deletion, involving the last 11 bp of the exon 11 and the first 95 bp of the following intron. Methods (PCR–RFLP and PCR) for identification of carriers of these alleles have been developed.
Improving the comparative map of SSC2p‐q13 by sample sequencing of BAC clones
Authors: Rattink A. P. , Jungerius B. J. , Faivre M. , Chardon P. , Harlizius B. , Groenen M. A. M.
Published: March 2003

To improve the comparative map for pig chromosome 2 and increase the gene density on this chromosome, a porcine bacterial artificial chromosome (BAC) library was screened with 17 microsatellite markers and 18 genes previously assigned to pig chromosome 2. Fifty‐one BAC clones located in the region of a maternally imprinted quantitative trait locus for backfat thickness (BFT) were identified. From these BACs 372 kb were sample sequenced. The average read length of a subclone was 442 basepair (bp). Contig assembly analysis showed that every bp was sequenced 1.28 times. Subsequently, sequences were compared with sequences in the nucleotide databases to identify homology with other mammalian sequences. Sequence identity was observed with sequences derived from 35 BACs. The average percentage identity with human sequences was 87.6%, with an average length of 143 bp. In total, sample sequencing of all BACs resulted in sequence identity with 29 human genes, 13 human expressed sequence tags (ESTs), 17 human genomic clones, one rat gene, one porcine gene and nine porcine ESTs. Eighteen genes located on human chromosome 11 and 19, and seven genes from other human locations, one rat gene and one porcine gene were assigned to pig chromosome 2 for the first time. The new genes were added to the radiation hybrid map at the same position as the locus from which the BAC that was sequenced was derived. In total 57 genes were placed on the radiation hybrid map of SSC2p‐q13.
Mapping of 12 bovine ribosomal protein genes using a bovine radiation hybrid panel
Authors: Wang Y.‐H. , McWilliam S. M. , Barendse W. , Kata S. R. , Womack J. E. , Moore S. S. , Lehnert S. A.
Published: March 2003

Twelve bovine ribosomal protein genes, for which sequence data had been acquired from complementary deoxyribonucleic acid (cDNA) clones isolated from a cattle skin cDNA library, were mapped. As ribosomal protein genes are a group of highly conserved house keeping genes, specific primers were designed to span the intron–exon splice sites and to amplify intronic sequences, in order to obtain bovine‐specific polymerase chain reaction (PCR) products. Two of 12 ribosomal protein genes were genotyped in this way and the remaining 10 were mapped using additional primers designed from within the intron. Eleven previously unmapped ribosomal protein genes were localized and one previously reported ribosomal protein gene localization was confirmed. The 12 ribosomal protein genes mapped in this study are spread over 10 chromosomes, including the X chromosome. The locations show conservation of comparative map position in cattle and human.
Predictors of marker‐informativeness for an outbred F2 design
Authors: Rocha J. L. , Pomp D. , Vleck L. D. Van , Nielsen M. K.
Published: March 2003

Generalization of the polymorphism information content (PIC) index to represent marker informativeness (MI) for a three‐generation F2 design requires that two additional sources of non‐informativeness be added to the PIC formula: the probability of matings between like‐heterozygous F1 individuals, of which one is non‐informative; and that of matings between like‐heterozygous F1 individuals, which are both fully informative but where line of origin of the same alleles is reciprocal. Given the dense marker‐maps currently available for some species, this F2 informativeness parameter constitutes the natural criterion for marker selection in F2 designs, and two computer programs to predict MI from grandparental marker‐genotypes were developed for an F2 population originating from two divergent selection lines of outbred mice (F ∼ 0.2). A total of 403 markers had been genotyped for the F0 grandparents (n=31), and 14 markers had also been genotyped in the complete pedigree including 559 F2 individuals. One program was based on assumptions of random‐mating (RM), while the other (PED) accounted for the pedigreed mating structure. For the 403 markers, the correlation between MI from RM and from PED was 0.95, and the average deviation between the two predictions was 0.005 MI units (MI ranged from 0 to 1). Correlations between predicted and realized MI for the 14 fully genotyped markers were 0.97 for PED and 0.94 for RM, while the corresponding average of deviations between predicted and actual values were 0.01 and 0.04, respectively. Absolute deviations from realized MI never exceeded 0.09 and 0.16 for PED and RM, respectively. Simulated optimization of the mating system to maximize average MI of 28 markers on one chromosome led to improvements in the range of 15–20% average MI (0.07–0.09 MI units). The degree of relative advantage conferred by the F2 generalization of the PIC index over the traditional index was found to be of minor significance.
The cream dilution gene, responsible for the palomino and buckskin coat colours, maps to horse chromosome 21
Authors: Locke M. M. , Ruth L. S. , Millon L. V. , Penedo M. C. T. , Murray J. D. , Bowling A. T.
Published: March 2003

The colour locus historically referred to as C in the horse is linked to microsatellites markers on horse chromosome 21. Preliminary results demonstrated linkage of Ccr, thought to be the cream dilution variant of the C locus, to HTG10. An analysis of horse chromosome 21 using additional families confirmed and established a group of markers linked to Ccr. This work also improved the resolution of previously reported linkage maps for this chromosome. Linkage analysis unambiguously produced the map order: SGCV16‐(19.1 cM)‐HTG10‐(3.8 cM)‐LEX60/COR73‐(1.3 cM)‐COR68‐(4.5 cM)‐ Ccr‐(11.9 cM)‐LEX31. Comparative and synteny data suggested that the horse C locus is not tyrosinase (TYR).
Approaches to interval mapping of QTL in a multigeneration pedigree: the example of porcine chromosome 4
Authors: Knott S. A. , Nyström P. E. , Andersson‐Eklund L. , Stern S. , Marklund L. , Andersson L. , Haley C. S.
Published: March 2003

Quantitative trait loci (QTLs) have been mapped in many studies of F2 populations derived from crosses between diverse lines. One approach to confirming these effects and improving the mapping resolution is genetic chromosome dissection through a backcrossing programme. Analysis by interval mapping of the data generated is likely to provide additional power and resolution compared with treating data marker by marker. However, interval mapping approaches for such a programme are not well developed, especially where the founder lines were outbred. We explore alternative approaches to analysis using, as an example, data from chromosome 4 in an intercross between wild boar and Large White pigs where QTLs have been previously identified. A least squares interval mapping procedure was used to study growth rate and carcass traits in a subsequent second backcross generation (BC2). This procedure requires the probability of inheriting a wild boar allele for each BC2 animal for locations throughout the chromosome. Two methods for obtaining these probabilities were compared: stochastic or deterministic. The two methods gave similar probabilities for inheriting wild boar alleles and, hence, gave very similar results from the QTL analysis. The deterministic approach has the advantage of being much faster to run but requires specialized software. A QTL for fatness and for growth were confirmed and, in addition, a QTL for piglet growth from weaning at 5 weeks up to 7 weeks of age and another for carcass length were detected.
Development of microsatellite markers and comparative mapping for bovine chromosome 19
Authors: Kirkpatrick B. W. , Byla B. , Kurar E. , Warren W. C.
Published: March 2003

Previous research has mapped an ovulation rate quantitative trait locus (QTL) to bovine chromosome 19. In an effort to enhance comparative mapping information and develop additional markers for refined QTL mapping, microsatellite markers were developed in a targeted approach. A bovine bacterial artificial chromosome (BAC) library was screened for loci with either known or predicted locations on bovine chromosome 19. An average of 6.4 positive BAC were identified per screened locus. A total of 10 microsatellite markers were developed for five targeted loci with heterozygosity of 7–83% in a sample of reference family parents. The newly developed markers were typed on reference families along with four previously mapped marker loci and used to create a linkage map. Comparison of locus order between human and cattle provides support for previously observed rearrangement. One of the mapped loci myotubularin related protein 4 (MTMR4) potentially extends the proximal boundary of a conserved linkage group.
Lack of association of GH1 and POU1F1 gene variants with meat production traits in Piemontese cattle
Authors: Di Stasio L. , Sartore S. , Albera A.
Published: March 2003

Growth hormone (GH) and the Pit‐1 transcription factor have been shown to be involved in the physiological mechanisms related to growth. The present study was carried out to investigate the possible association of the polymorphism at GH1 and POU1F1 loci with meat production traits in Piemontese cattle. Fourteen traits were considered, expressing growth (weight at 5, 7 and 11 months, daily gain), size [withers height (WH), trunk length (TL), chest girth (CG) at 12 months] and meat conformation [withers width (WW), shoulder muscularity (SM), loin width (LW), loin thickness (LT), thigh muscularity (TM), thigh profile (TP), bone thinness (BT)]. Data were analysed with a mixed model procedure to estimate the allele substitution and the dominance effects. The results did not provide evidence of association of GH1 and POU1F1 polymorphisms with the evaluated traits.
Assignment of porcine cyclin‐dependent kinase 4 (CDK4) and oncogene c‐mos (MOS) by nonradioactive nonfluorescence in situ hybridization
Authors: Musilová P. , Kubícková S. , Rubeš J.
Published: March 2003

Two pig genes, cyclin‐dependent kinase 4 (CDK4) and the oncogene c‐mos (MOS) were mapped by means of nonradioactive nonfluorescence in situ hybridization. Our approach was based on the detection of hybridized biotinylated probe by peroxidase conjugated extravidin and the reaction of peroxidase with its substrate diaminobenzidine (DAB) resulting in a dark precipitate. To increase the sensitivity of the method in single‐copy gene mapping, two amplifications of the peroxidase signal were used: immunological amplification by biotinylated antiavidin, and peroxidase‐catalysed deposition of biotinylated tyramide. Using this method, two 2‐kb‐long probes for the porcine genes CDK4 and MOS were mapped to pig chromosomes 5p12 and 4q14–15, respectively. Non‐radioactive nonfluorescence in situ hybridization described here is a method of choice for gene mapping of short probes.
A set of cattle microsatellite DNA markers for genome analysis of riverine buffalo (Bubalus bubalis)
Authors: Navani N. , Jain P. K. , Gupta S. , Sisodia B. S. , Kumar S.
Published: March 2003

One hundred and eight microsatellite primer pairs, originally identified from cattle, were evaluated for their applicability in buffalo. Eighty‐one primer pairs (75%) amplified discrete products, and of these, 61 pairs (56%) gave polymorphic band patterns on a panel of 25 buffaloes. The mean number of alleles per polymorphic marker was 4.50 ± 0.20, and the mean heterozygosity per polymorphic marker was 0.66 ± 0.02. Successful genotyping of buffaloes using cattle specific primers suggests that the latter can be a valuable resource for genome analysis in bubaline species.
Melanocortin‐4 receptor (MC4R) genotypes have no major effect on fatness in a Large White × Wild Boar intercross
Authors: Park H. B. , Carlborg Ö. , Marklund S. , Andersson L.
Published: March 2003

The melanocortin‐4 receptor (MC4R), a G‐protein coupled receptor, is implicated in mediating the effect of leptin on food intake and energy balance. A previous candidate gene study reported an association between an MC4R missense mutation (Asp298Asn) and fatness, growth and feed intake in pigs. To assess this association further, we analysed the segregation of this missense mutation in relation to variation in fatness traits using a Wild Boar × Large White intercross. The Wild Boar and Large White founders were homozygous for different MC4R alleles. The MC4R was assigned to the expected region on pig chromosome 1. The statistical evaluation did not reveal any indication of a significant effect on fatness related traits in this pedigree.
Characterization of the porcine sperm adhesion molecule gene SPAM1– expression analysis, genomic structure, and chromosomal mapping
Authors: Day A. E. , Quilter C. R. , Sargent C. A. , Mileham A. J.
Published: March 2003

Sequence analysis of cDNA products, derived from adult porcine testis mRNA, gave overlapping nucleotide sequence correlating to 1952 bp of the sperm adhesion molecule 1 (SPAM1) gene. This sequence was shown to be homologous to SPAM1 genes known in other mammalian species and contained an open reading frame encoding a 493‐amino acid protein. Fluorescence in situ hybridization (FISH), using a bacterial artificial chromosome (BAC) clone from the PigE BAC library, was used to map SPAM1 to chromosome 18 of the pig. This finding is consistent with comparative mapping experiments performed between pig and human chromosomes. Polymerase chain reaction (PCR) analysis of genomic DNA has shown that the 1952 bp of cDNA sequence spans approximately 9 kb of genomic DNA and comprises of at least four exons, with its size and structure being relatively conserved between mouse, human and pig. Reverse transcriptase (RT)‐PCR analysis of mRNA from nine porcine tissues has also suggested that expression of SPAM1 is limited to the testis.
Investigation of candidate genes for meat quality in dry‐cured ham production: the porcine cathepsin B (CTSB) and cystatin B (CSTB) genes
Authors: Russo V. , Fontanesi L. , Davoli R. , Nanni Costa L. , Cagnazzo M. , Buttazzoni L. , Virgili R. , Yerle M.
Published: March 2003

Excessive softness is a serious defect of dry cured hams which seems related to high activity of lysosomal cysteine proteinases, such as cathepsin B, in fresh pork muscles a few days after slaughtering. As it has been shown that cathepsin B activity has a moderate heritability in Italian Large White pigs we started a candidate gene approach to identify the gene(s) that affect(s) this parameter. Here, we studied two candidate genes: cathepsin B (CTSB) and cystatin B (CSTB). We amplified and sequenced porcine DNA fragments for these two genes that were used to identify polymorphisms by SSCP and polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) analysis. Four and two alleles were detected at the CTSB and CSTB loci, respectively. Sequencing of the CSTB alleles showed a missense mutation that changes a codon for aspartic acid into a codon for asparagine in exon 3 of the gene. Allele frequencies for the two loci differed among the pig breeds studied (Large White, Landrace, Duroc, Belgian Landrace, Hampshire, Piétrain, Meishan, Cinta Senese, Casertana, Calabrese and Nero di Sicilia). Linkage, somatic cell hybrid panel and radiation hybrid panel analyses assigned CTSB to porcine chromosome (Sscr) 14 and CSTB to Sscr 13. The markers identified at the CTSB and CSTB loci were used in association studies with several traits of economic importance including parameters that may indicate the suitability of pig meat to produce dry‐cured hams. Significant associations were observed between CTSB and back‐fat thickness and between CSTB and average daily gain. In this study, cathepsin B activity was not associated with the polymorphisms identified at the CTSB and CSTB loci.
MHC‐DRB exon 2 allele polymorphism in Indian river buffalo (Bubalus bubalis)
Authors: De S. , Singh R. K. , Butchaiah G.
Published: March 2003

The polymorphism of the major histocompatibility complex (MHC) class II DRB gene of riverine buffalo (Bubalus bubalis) was studied. Second exon sequences from the buffalo DRB locus, homologous to the cattle DRB3 gene, were amplified and characterized. A combination of single strand conformation polymorphism (SSCP) and heteroduplex analysis (HA) in a non‐denaturing gel was used to identify new DRB second exon sequences. SSCP, HA and finally sequencing allowed the identification of 22 MHC‐DRB exon 2 alleles from 25 unrelated Indian river buffalo. These are the first river buffalo DRB second exon sequences reported. A high degree of polymorphism in the sequences encoding the peptide binding regions was observed and some amino acid substitutions were found unique to the river buffalo.
A new deletion mutation in bovine Claudin‐16 (CL‐16) deficiency and diagnosis
Authors: Hirano T. , Hirotsune S. , Sasaki S. , Kikuchi T. , Sugimoto Y.
Published: March 2003

Bovine claudin‐16/paracellin‐1 (CL‐16/PCLN‐1) deficiency is an autosomal recessive disorder caused by a 37‐kb deletion mutation containing the first four exons of theCL‐16gene, which leads to the absence of theCL‐16transcript (type‐1 mutation). A PCR‐based DNA test for theCL‐16mutation (type‐1) was used to screen a herd of Wagyu cattle. A recent report suggested that affected cattle can be bred by dams diagnosed as normal, suggesting the presence of a new mutation in theCL‐16locus. We identified the new mutation as a 56‐kb deletion containing exon‐1 to ‐4 and 21‐bp of exon‐5 ofCL‐16, and refer to this as a type‐2 mutation. A DNA test for specific for this mutation was then established.
Genetic diversity of north‐east Asian cattle based on microsatellite data
Authors: Kim K. S. , Yeo J. S. , Choi C. B.
Published: March 2003

In order to assess the genetic variability and population structure of north‐east Asian cattle, 13 microsatellite loci were analysed for a total of 200 individuals including Korean, Chinese, Japanese Black and European Holstein cattle. Observed and expected heterozygosity, two estimators (FST and GST) of gene differentiation, and Nei's DA distance were evaluated. Based on expected mean heterozygosity, the lowest genetic diversity was exhibited in Japanese Black cattle (HE=0.471), and the highest in Chinese cattle (HE=0.744). Korean cattle revealed a relatively high degree of genetic diversity (HE=0.728). Average proportion of genetic variation because of interpopulation subdivision among north‐east Asian cattle varied between 10.9 and 9.9%, depending on the estimator used. N‐J tree based on Nei's DA genetic distance showed that Korean and Chinese cattle are closely related, whereas Japanese Black cattle are clearly distinct from the other two populations, forming a north‐east Asian outgroup.
A PCR‐RFLP for KIT associated with tobiano spotting pattern in horses
Authors: Brooks S. A. , Terry R. B. , Bailey E.
Published: March 2003

An MspI polymorphism was identified in intron 13 of the equine homologue of proto‐oncogene c‐kit (KIT) by comparing DNA sequences from horses with solid coat colour and horses homozygous for the tobiano spotting (To) gene. The allele associated with solid coat colour was designated KM0, while the allele associated with the tobiano pattern created an additional MspI restriction site and was designated KM1. Polymerase chain reaction‐restriction fragment length polymorphism (PCR‐RFLP) studies using DNA from hair follicles demonstrated that all 129 of 129 tobiano patterned horses possessed the KM1 allele. However, three of 104 solid‐coloured thoroughbred horses also possessed the KM1 allele. Therefore, while KM1 is strongly associated with the gene for To, the association is not absolute. However, this test appears more efficacious to identify putative homozygotes for To than current biochemical testing methods using albumin (Alb) and vitamin D binding protein (Gc) haplotypes.
A comparative map of chicken chromosome 24 and human chromosome 11
Authors: Jennen D. G. J. , Crooijmans R. P. M. A. , Kamps B. , Açar R. , Veenendaal A. , Van Der Poel J. J. , Groenen M. A. M.
Published: March 2003

To improve the physical and comparative map of chicken chromosome 24 (GGA24; former linkage group E49C20W21) bacterial artificial chromosome (BAC) contigs were constructed around loci previously mapped on this chromosome by linkage analysis. The BAC clones were used for both sample sequencing and BAC end sequencing. Sequence tagged site (STS) markers derived from the BAC end sequences were used for chromosome walking. In total 191 BAC clones were isolated, covering almost 30% of GGA24, and 76 STS were developed (65 STS derived from BAC end sequences and 11 STS derived within genes). The partial sequences of the chicken BAC clones were compared with sequences present in the EMBL/GenBank databases, and revealed matches to 19 genes, expressed sequence tags (ESTs) and genomic clones located on human chromosome 11q22‐q24 and mouse chromosome 9. Furthermore, 11 chicken orthologues of human genes located on HSA11q22‐q24 were directly mapped within BAC contigs of GGA24. These results provide a better alignment of GGA24 with the corresponding regions in human and mouse and identify several intrachromosomal rearrangements between chicken and mammals.
Amplification of multiple copies of mitochondrial Cytochrome b gene fragments in the Australian freshwater crayfish, Cherax destructor Clark (Parastacidae: Decapoda)
Authors: Nguyen T. T. T. , Murphy N. P. , Austin C. M.
Published: March 2003

Non‐coding copies of fragments of the mitochondrial genome translocated to the nucleus or pseudogenes are being found with increasing frequency in a diversity of organisms. As part of a study to evaluate the utility of a range of mitochondrial gene regions for population genetic and systematic studies of the Australian freshwater crayfish, Cherax destructor (the yabby), we report the first detection of Cytochrome b (Cyt b) pseudogenes in crustaceans. We amplified and sequenced fragments of the mitochondrial Cyt b gene from 14 individuals of C. destructor using polymerase chain reaction (PCR) with primers designed from conserved regions of Penaeus monodon and Drosophila melanogaster mitochondrial genomes. The phylogenetic tree produced from the amplified fragments using these primers showed a very different topology to the trees obtained from sequences from three other mitochondrial genes, suggesting one or more nuclear pseudogenes have been amplified. Supporting this conclusion, two highly divergent sequences were isolated from each of two single individuals, and a 2 base pair (bp) deletion in one sequence was observed. There was no evidence to support inadvertent amplification of parasite DNA or contamination of samples from other sources. These results add to other recent observations of pseudogenes suggesting the frequent transfer of mitochondrial DNA (mtDNA) genes to the nucleus and reinforces the necessity of great care in interpreting PCR‐generated Cyt b sequences used in population or evolutionary studies in freshwater crayfish and crustaceans more generally.
Evaluation of factors affecting individual assignment precision using microsatellite data from horse breeds and simulated breed crosses
Authors: Bjørnstad G. , Røed K. H.
Published: March 2003

Assignment tests have been utilized to investigate population classification, measure genetic diversity and to solve forensic questions. Using microsatellite data from 26 loci genotyped in eight horse breeds we examined how population differentiation, number of scored loci, number of scored animals per breed and loci variability affected individual assignment precision applying log likelihood methods. We found that both genetic differentiation and number of scored loci were highly important for recognizing the breed of origin. When comparing two and two breeds, a proportion of 95% of the most differentiated breeds (0.200 ≤ FST ≤ 0.259) could be identified scoring only three loci, while the corresponding number was six for the least differentiated breeds (0.080 ≤ FST ≤ 0.139). An identical proportion of simulated breed crosses, differentiated from their parental breeds by FST estimates in the range 0.050–0.069, was identified when scoring 12 loci. This level of source identification was not obtained for the less differentiated breed crosses. The current data further suggested that population sample size and locus variability were not critical for the assignment precision as long as moderately large sample sizes (≥ 20 animals per population) and fairly variable loci were used.
Efficiency of semi‐automated fluorescent multiplex PCRs with 11 microsatellite markers for genetic studies of deer populations
Authors: Bonnet A. , Thévenon S. , Maudet F. , Maillard J. C.
Published: March 2003

Thirty bovine and eight ovine microsatellite primer pairs were tested on four tropical deer species: Eld's and Swamp deer (highly threatened) and Rusa and Vietnamese Sika deer (economically important). Thirty markers gave an amplified product in all four species (78.9%). The number of polymorphic microsatellite markers varied among the species from 14 in Eld's deer (47%) to 20 in Swamp deer (67%). Among them, 11 microsatellite loci were multiplexed in three polymerase chain reactions (PCRs) and labelled with three different fluorochromes that can be loaded in one gel‐lane. To test the efficiency of the multiplex, primary genetic studies (mean number of alleles, expected heterozygosities and Fis values) were carried out on four deer populations. Parentage exclusion probability and probability of identity were computed and discussed on a Swamp deer population. These multiplexes PCRs were also tested on several other deer species and subspecies. The aim of this study is to establish a tool useful for genetic studies of population structure and diversity in four tropical deer species which with few modifications can be applied to other species of the genus Cervus.
The bovine fibroblast growth factor receptor 3 (FGFR3) gene is not the locus responsible for bovine chondrodysplastic dwarfism in Japanese brown cattle
Authors: Takami M. , Yoneda K. , Kobayashi Y. , Moritomo Y. , Kata S. R. , Womack J. E. , Kunieda T.
Published: March 2003

Fibroblast growth factor receptor 3 (FGFR3) is one of the four distinct membrane‐spanning tyrosine kinase receptors for fibroblast growth factors. The FGFR3 is a negative regulator of endochondral ossification and mutations in the FGFR3 gene have been found in patients of human hereditary diseases with chondrodysplastic phenotypes. Recently, we mapped the locus responsible for hereditary chondrodysplastic dwarfism in Japanese brown cattle to the distal region of bovine chromosome 6 close to the FGFR3 gene, suggesting that FGFR3 was a positional candidate gene for this disorder. In the present study, we isolated complementary DNA (cDNA) clones containing the entire coding region of the bovine FGFR3 gene. Comparison of the nucleotide sequence between affected and normal animals revealed no disease‐specific differences in the deduced amino acid sequences. We further refined the localization of FGFR3 by radiation hybrid mapping, which is distinct from that of the disease locus. Therefore we conclude that bovine chondrodysplastic dwarfism in Japanese brown cattle is not caused by mutation in the FGFR3 gene.
Sib‐parentage testing using molecular markers when parents are unknown
Authors: García D. , Carleos C. , Parra D. , Cañón J.
Published: March 2003

The formulae for computing the so‐called Sib Index using codominant alleles for (1) full‐sib and (2) half‐sib parentage are given. Hypothesis testing is based on the distribution of conditional likelihood ratio or Bayes' factor. Thresholds for rejecting the null hypothesis and P‐values were obtained in function of the number of alleles and their frequency distributions. Simulations showed that a relatively low number of marker systems (e.g. 20) are enough to accept the hypothesis of sib parentage with a reasonable power for usual significance levels, but that a higher number would be necessary if full‐sib against half‐sib parentage is the contrast to be carried out. The effect of sampling variation on the allele frequencies on power calculations is also analysed.