bluuebunny/crossref_metadata_2025 huggingface dataset:
Polymorphism analysis of the prion gene in BSE‐affected and unaffected cattle
Authors: Neibergs H. L. , Ryan A. M. , Womack J. E. , Spooner R. L. , Williams J. L.
Published: July 2010

Polymerase chain reaction (PCR) primers designed to amplify the octapeptide repeat region of the bovine prion gene were used to test the association of genotypes with bovine spongiform encephalitis (BSE) in 56 BSE‐affected and 177 unaffected animals. Three alleles (A, B, C) were detected as single‐strand conformation polymorphisms (SSCPs) and two alleles (1,2 representing six or five copies of the octapeptide repeat respectively) were detected as amplified double‐strand fragment length polymorphisms (AMFLPs). Observed genotypes of SSCPs and AMFLPs were analysed by x‐square. The SSCP genotypes of nuclear family members of animals with BSE and BSE‐affected animals were different (P < 0.001, P < 0.01) from unrelated animals of the same breed without BSE. No genotypic differences were found between the BSE‐affected animals and their relatives (P > 0.469). No AMFLP genotypic differences were detected between BSE‐affected animals, their relatives, unrelated animals of the same breed or animals of different breeds (P > 0.05). These data suggest that BSE‐affected animals and their relatives are more likely to have the AA SSCP genotype than unrelated animals of the same breed or animals of different breeds.
A rapid protocol for sexing chick embryos (Gallus g. domesticus)
Authors: Clinton M.
Published: July 2010

A method for establishing the sex of chick embryos before the appearance or morphological differences between males and females has been developed. DNA was isolated from 5–7‐day‐old embryos by proteinase K digestion and subjected to polymerase chain reaction (PCR) amplification with W‐chromosome specific primers. Sexing can be achieved within 1 day using as little as 1 ng template DNA.
A new buffer system for acid PAGE typing of equine protease inhibitor
Authors: Henney P. J. , Johnson E. L. , Cothran E. G.
Published: July 2010

A new buffer system for acid PAGE typing of protease inhibitor (Pi) is described. This buffer system replaces pyridine and cacodylic acid with L‐histidine and MES, making the buffer less toxic and less expensive than the acid PAGE system commonly used but with no loss of resolution.
The cardinal principle of like attracting like generates many ubiquitous oligopeptides shared by divergent proteins
Authors: Ohno S
Published: July 2010

Actual protein amino acid sequences are very different from random assemblages of 20 varieties of amino acids. The separate survey of 20 unrelated proteins in two steps that included eight of the 18 discussed in this paper, revealed that at the level of 5000 total residues, one out of every 32 tetrapeptides appeared in two or more identical copies, whereas at the level of 10 000 total residues, the frequency was elevated to one out of every 29. It would thus appear that only 60 000 or so, out of the possible 160 000 (204) varieties of tetrapeptides, are regularly used by all proteins. These shall be defined as ubiquitous tetrapeptides. Those tetrapeptides occasionally found to be stray which did not belong to the above group of 60 000 must have been generated by new mutations. Thus, they are expected to return to the group by subsequent mutations.

The above ubiquity is due to the cardinal principle of protein construction which is like attracting like. On the average, 28% of each residue is devoted to the formation of homodipeptides such as Leu‐Leu, Asn‐Asn and Trp‐Trp. Consequently, homo‐oligopeptides, pentapeptidic and longer, are readily found in two or more proteins unrelated to each other. The next in line among the ubiquitous oligopeptides are those made of similar residues. They usually contain palindromic cores such as Leu‐Val‐Leu, Ala‐Gly‐Ala and Lys‐Arg‐Lys. For example, the hexapeptide Ala‐Gly‐Ala‐Asp‐Ala‐Ala is shared between human phosphofructokinase and bacterial cytochrome C. Provided that they are longer than 60 residues, all proteins contain repeating oligopeptides, tetrapeptidic to heptapeptidic in length. The above principle of like attracting like is the very reason that hydropathic profiles of most proteins readily yield alternating stretches of hydrophilic and hydrophobic segments.
The effectiveness of using co‐dominant polymorphic allelic series for (1) checking pedigrees and (2) distinguishing full‐sib pair members
Authors: Jamieson A
Published: July 2010

Formulae express the effectiveness of parentage exclusion tests and differences separating full‐sib pairs by compounding genotypic information on discrete examples of co‐dominant alleles segregating at gene loci on different autosomes. Such polymorphisms occur among structural genes and polymorphic DNA sequences. Two general formulae state the theoretical effectiveness of using co‐dominant alleles for (1) testing parentage and (2) distinguishing sibs. The formula for parentage exclusion tates the probability (PE) that a given series of co‐dominant alleles of known frequency should detect a falsely recorded father (or mother). The other formula describes how genetic polymorphism can distinguished closely related individuals. It states the probability (PS) that alleles distinguish the members of full‐sib pairs, dizygotic twins and tissue chimeras. To derive the two general formulae, particular formulae were calculated for n = 2,3 and 4 co‐dominant alleles. By increasing the numbers of alleles, the formulae were seen to contain recurrent patterns which were then expressed in the two general formulae for n alleles. Some examples demonstrate applications of the two formulae in problems concerning parentage and sibship.
Aspermatogenic effect of the bull seminal ribonuclease (BS RNase) in the presence of anti‐BS RNase antibodies in mice
Authors: Matous̆ek J
Published: July 2010

Injection of mouse scrotum with the bull seminal ribonuclease (BS RNase) isolated from bull seminal vesicle fluid inhibited spermatogenesis and caused a decrease in the weight of the testes. Long‐term injection of BS RNase evoked the production of antibodies which reached the titre 524448. These antibodies did not prevent the aspermatogenic action of BS RNase in vivo when a twofold higher amount of this enzyme was injected into mouse scrotum. Aspermatogenesis was reversible in both the first and second part of the experiment. During the period of aspermatogenesis the males were sterile. Increasing the amount of BS RNase injections in the second part of experiments caused aspermatogenesis around 3 months. No malformations were observed among offspring of males recovered from the first stage of aspermatogenesis. The antigen—antibody complex prepared in vitro and injected into testes of mice evoked the same degree of aspermatogenesis as the enzyme itself.
Black‐ear gene and blood polymorphism in four southern Chinese cattle groups
Authors: Chen Y , Wang Y , Cao H , Pang Z , Yang G
Published: July 2010

The gene for black‐ear coat colour pattern, commonly found among cattle of tropical origin, was observed in 809 animals of four breeds of local cattle in southern China. Gene frequencies for Tf, Hb and Alb demonstrated that these groups of cattle were quite divergent from Bos taurus. These breeds of cattle are thought to be descended from ancient Chinese cattle. At the same time certain influences observed in coat colour may be derived from Bali cattle.
Comparison of Thoroughbred and Arabian horses using RAPD markers
Authors: Bailey E , Lear T L
Published: July 2010

We compared pools of DNA from 10 Thoroughbred horses and 10 Arabian horses for the presence of randomly amplified polymorphic DNA (RAPD) markers which might be useful in distinguishing between the breeds. Using 212 decamer oligonucleotides and our polymerase chain reaction (PCR) conditions, 173 of the primers produced scoreable bands. The number of bands ranged from 0 to 9 with an average of 3·6. In family studies using 11 arbitrarily selected primers, five of the 11 primers produced polymorphic bands which exhibited Mendelian inheritance as dominant markers. When comparing the pooled DNA from Thoroughbred and Arabian horses we found 10 primers which identified markers present in the pooled DNA from one breed but absent in the pool from the other breed. Testing individual horses revealed that only two markers were wholly absent for one group while being present among members of the other. Primer UBC‐85 (5′‐GTGCTCGTGC‐3′) detected a pair of markers absent in Thoroughbred horses but present among 11 of 31 Arabian horses. These markers were 1500 and 1700 base pairs (bp) long and designated UBC‐85C and UBC‐85D, respectively. Primer UBC‐126 (5′‐CTTTCGTGCT‐3′) detected a 1000 bp marker (designated UBC‐126C) absent in 20 of 20 Thoroughbred horses but present in 31 of 31 Arabian horses. UBC‐126C would be particularly effective for breed comparisons, especially if the DNA band were cloned, sequenced and an allelic marker present in Thoroughbred horses but rare or absent among Arabian horses was identified. The distribution of such markers among other horse breeds might be useful to infer relationships among breeds. These kinds of markers may also be useful in detecting unwanted crossbreeding between two horse breeds.
Parentage testing and linkage analysis in the horse using a set of highly polymorphic microsatellites
Authors: Marklund S. , Ellegren H. , Eriksson S. , Sandberg K. , Andersson L.
Published: July 2010

Ten (TG)n positive clones, isolated from an equine genomic library and sequenced, contained 12–19 uninterrupted TG repeats. Primers for polymerase chain reaction (PCR) were synthesized and nine of these (TG)n loci (HTG7‐15) were successfully amplified and utilized in this study together with five previously reported equine microsatellite loci (HTG2‐6). The PCR products were analysed by polyacrylamide gel electrophoresis followed by automated laser fluorescence detection or autoradiography. All microsatellites showed polymorphism and stable Mendelian inheritance. Differences in microsatellite variability between horse breeds were detected. A linkage analysis comprising HTG2‐15, one coat colour gene and 16 genetic blood markers enabled addition of HTG2 to linkage group U2 and a new linkage group (U6) was established comprising the loci HTG7 and HTG12. Close linkage was excluded within a set of eight microsatellites. The estimated probability of exclusion in four breeds for a parentage test based on these eight loci varied between 0.96 and 0.99.
A new phenogroup in the horse D system of red cell alloantigens found in the Caspian pony
Authors: Cothran E Gus , Long Y. G.
Published: July 2010

A new D blood group phenogroup consisting of the specificities adeo was observed in a stallion family of Caspian ponies from Iran. An additional six undescribed genetic variants were seen in a total of 82 Iranian horses. This result suggests extensive new genetic variation may be present in domestic horses from geographic regions that have not yet received scientific attention.
Minisatellite DNA markers in the chicken genome
Authors: Bruford M W , Burke T
Published: July 2010

This paper reports the detailed characterization of multilocus minisatellite DNA fingerprints in the chicken. Results are presented of DNA fingerprint segregation analyses carried out in three chicken pedigrees, calculating the number of detected loci, testing for Mendelian inheritance, and cosegregation among fingerprint bands. Two pedigrees (families 1 and 2) were analysed using the Jeffreys probes 33.6 and 33.15 only, and one pedigree (family 3) was analysed using 33.6, 33.15. 3′α‐globin HVR and M13 protein III gene repeat. Mean band transmission frequencies in families 1 and 2 were near to the Mendelian expectation of 0.5 and no mutations were observed. Family 3 showed transmission frequencies slightly exceeding 0.5. Linkage among bands was higher than observed in some other avian species, with each allele represented by a mean of 1.48 HaeIII fragments. Cosegregation of heterozygous parental fragments representing distinguishable loci followed the expected binomial distribution. The number of minisatellites detectable by the four probes was estimated to be 217. The pattern of cosegregation among those minisatellite loci was tested against that expected for different levels of recombination through the use of a simulation model. We conclude that most minisatellites are unlinked and probably widely dispersed in the chicken genome.
Characterization and evolution of ovine MHC class II DQB sequence polymorphism
Authors: van Oorschot R A H , Maddox J F , Adams L A , Fabb S A
Published: July 2010

The second exons of OLA‐DQB genes from 13 merino sheep were sequenced following amplification by the polymerase chain reaction or isolation from a cDNA library. Ten distinct exon 2 sequences, coding for 10 novel amino acid sequences, were characterized in these sheep. The single‐strand conformation polymorphism technique was shown to be capable of discriminating between all sequences. This brings the total number of different OLA‐DQB exon 2 sequences (nucleotide and amino acid) which have been characterized to 12, and demonstrates that the OLA‐DQB region is highly polymorphic with 29% of nucleotide and 46% of amino acid sites showing variation. Evidence is presented that the OLA‐DQB sequences belong to at least two lineages of DQB genes. Some ovine DQB sequences are more like bovine DQB counterparts than other ovine DQB sequences suggesting that the artiodactyl DQB gene and allele lineages predate the separation of the ovine and bovine species 20 million years ago.
Pig microsatellites isolated from cosmids revealing polymorphism and localized on chromosomes
Authors: Robic A , Parrou J‐L , Yerle M , Goureau A , Dalens M , Milan D , Gellin J
Published: July 2010

One of the most widely studied simple sequences in the mammalian genome is the (TG)n dinucleotide sequence. Because these microsatellites are highly polymorphic, we chose to study microsatellites from cosmids to provide genetic markers for the porcine genome. After screening a porcine cosmid library with a (CA)10 probe, 20 cosmids containing microsatellites were subcloned and 17 microsatellites identified by sequencing. Oligonucleotide primers flanking the repeat were designed for seven (TG)n microsatellites with n > 14. These seven microsatellites revealed polymorphism and were regionally assigned to chromosomes by fluorescent in situ hybridization of initial cosmids. These seven loci will be useful for both the construction of the genetic map and as landmark loci on the physical map of the porcine genome.
Microsatellite‐based parentage control in cattle
Authors: Glowatzki‐Mullis M‐L , Gaillard C , Wigger G , Fries R
Published: July 2010

As a new approach to parentage control we developed two multiplex coamplification polymerase chain reaction (PCR) systems containing a total of six different short tandem repeat (STR) loci; the microsatellite polymorphisms were visualized by automated fluorescence detection on the Applied Biosystems 373 DNA Sequencer with 672 Genescan Analysis software. Allele frequency data were determined from 238 animals. Thirty‐five bovine parentage control cases not solvable by conventional blood typing could be solved.
Features of the DNA fingerprinting probe pITZ1
Authors: Huebscher K J , Dolf G , Frey J , Stranzinger G , Gaillard C
Published: July 2010

Stringently controlled plasmids generate DNA fingerprint patterns in mammals when used at low hybridization temperatures. In order to develop a probe for use in paternity testing in cattle we screened a bovine, partial genomic plasmid library with the PCR‐amplified ori region of plasmid P1. Of eight isolated clones one generated strong band patterns at high stringency in various mammalian species (data not shown). Sequence analysis revealed an imperfect, compound dinucleotide repeat region, which was PCR‐amplified and cloned into the plasmid vector pUC19. Fingerprint results generated by this probe (termed pITZ1) in cattle are compared with the results generated by VNTR‐probe pV47, which itself was developed by screening a human chromosome 16 library with tandem repeats of bacteriophage M13. Probe pITZ1 is useful in conjunction with other VNTR‐probes for DNA fingerprinting in cattle and donkey populations. The dinucleotide repeat region responsible for the band patterns generated with pITZ1 is close to an Alu‐like sequence, which may be involved in eukaryotic replication mechanisms.
Mapping of the genes for rat endothelin receptor type A (ETAR) and type B (ETBR) to chromosomes 19 and 15 respectively
Authors: Cai Y , Yamada T , Xin X , Agui T , Matsumoto K
Published: July 2010

Chromosomal assignments of the genes for rat endothelin receptor type A (ETAR) and type B (ETBR) were performed by analysing somatic cell hybrid DNAs with the polymerase chain reaction (PCR) using primers specific for rat ETAR and ETBR genes. The genes for ETAR and ETBR were assigned to rat chromosomes 19 and 15 respectively.
Mutations in the sequence flanking the microsatellite at the KAP8 locus prevent the amplification of some alleles
Authors: Ede A J , Crawford A M
Published: July 2010

The microsatellite described for the glycine‐ and tyrosine‐rich keratin locus (KAP8) in sheep was used to type nine large three‐generation families comprising the AgResearch International Mapping Flock. The apparent non‐Mendelian inheritance in these families suggested that some of the microsatellite alleles were not being amplified. Sequence analysis showed that a deletion within one of the published primer sites was the likely cause of the ‘null’ alleles. By redesigning the primer all alleles could be amplified.
Functional genes mapped on the chicken genome
Authors: Crooijmans R P M A , van der Poel J J , Groenen M A M
Published: July 2010

Microsatellite polymorphisms are finding increasing use in genetics. In addition to the random isolation of microsatellite markers, such markers can also be developed from sequences already present in public domain databases. An advantage of public domain databases is that these microsatellites are known to be located within or close to identified functional genes. In this study the GenBank and EMBL databases were screened for microsatellite markers and primers were defined for amplification. Subsequently, these markers were tested on a panel of five different birds from layer and broiler stocks and on the international reference families: the East Lansing reference family and the Compton reference family. Of the 33 loci tested, 25 were polymorphic on the test panel and from these 25, 14 were polymorphic in one or both reference families. Twelve of the 14 loci that could be mapped fell into previously defined linkage groups. The other two markers were not linked. Because three of the loci had previously been mapped to specific chromosomes by in situ hybridization, linkage groups E6 and C3 could be assigned to chromosome 6, E5 and C17 to chromosome 4 and E21 to one of the microchromosomes.
Analysis of the fine specificities of sheep major histocompatibility complex class II‐specific monoclonal antibodies using mouse L‐cell transfectants
Authors: Ballingall K T , Dutia B M , Hopkins J , Wright H
Published: July 2010

The fine specificities of two panels of monoclonal antibodies (mAbs) for sheep major histocompatibility complex (MHC) class II molecules were determined using five mouse L‐cell transfectaents, each expressing a defined sheep DQ or DR MHC class II A/B gene pair. Using the transfectants in an indirect fluorescence antibody assay, previous immunochemical characterization of the mAbs was confirmed for 16 of 23 mAbs tested. The MHC class II subtype specificity (DQ or DR) of each mAb was assigned without interference from the products of other expressed class II loci. This allowed the identification of both cross‐locus specificities as well as defining fine specificities of mAbs previously only partially characterized by immunochemical techniques.
Discrimination between major histocompatibility complex class II DQ and DR locus products in cattle
Authors: Dutia B M , MacCarthy‐Morrogh L , Glass E J , Knowles G , Spooner R L , Hopkins J
Published: July 2010

We have used a panel of anti‐major histocompatibility complex (MHC) class II monoclonal antibodies (mAbs) and have assessed their specificity for the products of the individual bovine MHC (BoLA) class II subregions. The mAbs identified two distinct class II molecules by affinity purification and ELISA. Two‐dimensional immunoblotting confirmed these data and NH2‐terminal sequencing of the purified class II α chains of one member of each group identified the subregion specificity of the mAbs. The mAbs VPM36, TH22A and TH81A are specific for BoLA DQ, whereas VPM54, TH14B and J11 are specific for BoLA DR. SW73.2 reacts with both MHC subgroups of all cattle tested.
Number and distribution of silver‐stained nucleolar organizer regions and evolutionary relationships in domestic pigs
Authors: Liu W S , Lu X Z , Qiu H
Published: July 2010

Variation in the numbers of silver‐stained nucleolar organizer regions (Ag‐NORS) were examined in 36 breeds of domestic pig of different geographic origins and five subspecies of wild boar. The relationship between Ag‐NORs and evolution of domestic pigs was investigated. In all pigs observed, Ag‐NORs were localized on the secondary constriction of chromosomes 10 and 8. The mean Ag‐NOR numbers varied from 2.0–4.0, and decreased gradually with the different geographical distribution from south to north in China and from east to west in Europe. This regular change was caused mainly by the differences of frequency in chromosome 8 Ag‐NOR type and was closely related to the evolution of domestic pig breeds.
A panel of polymorphic bovine, ovine and caprine microsatellite markers
Authors: Kemp S J , Hishida O , Wambugu J , Rink A , Teale A J , Longeri M L , Ma R Z , Da Y , Lewin H A , Barendse W , Teale A J
Published: July 2010

A panel of 81 new polymorphic bovine microsatellite markers is described, together with further information on a previously reported group of 16 markers. The mean polymorphism information content of the 97 markers determined in 20 cattle was 0.66. Seventythree of these markers have been assigned to chromosomes by either linkage analysis or use of hybrid cell panels. Thirty‐nine of the markers were polymorphic in sheep, and 32 were polymorphic in goat. This study identified a set of 18 robust markers that were polymorphic in all three species and that covered 14 bovine chromosomes. This provides a single group of markers, which would be suited to genetic distance analysis and parentage control in cattle, sheep and goat.
Biochemical identification of the bovine blood group M‘ antigen as a major histocompatibility complex class I‐like molecule
Authors: Hønberg L S , Larsen B , Koch C , østergård H , Skjødt K
Published: July 2010

Absorption and elution experiments showed that it was impossible to separate antibodies against blood group factor M' from antibodies against bovine lymphocyte antigen (BoLA) A16 in an antiserum showing haemolytic activity against M' as well as lymphocytotoxic activity against BoLA‐A16. To elucidate the structural relationship between BoLA‐A16 and blood group antigen M', immunoprecipitation experiments on red and white cell lysates isolated from M'‐A16 positive and negative cattle were carried out. These results showed that Mr 44 000 and Mr 12000 polypeptides can be precipitated from both red and white cells isolated from M'‐A16 positive animals, whereas no bands were seen in M'‐A16 negative animals in precipitations with the same antibody. Precipitation with a crossreacting human β2‐microglobulin (β2‐m) specific antibody confirmed a class‐I‐like structure associated with β2‐m on M' positive red cells and the absence of such a structure on M' negative red cells. Sequential precipitations gave analogous results. Proteolytic degradation by papain and V8 protease did not reveal any substantial difference between red and white M'‐A16 positive cells, but a slight difference in the pI of the immunoprecipitable components of red and white cells was observed. All together, this indicates that either the blood group antigen M' is the BoLA‐A16 class I antigen or M' and BoLA‐A16 are two different class I polypeptides with the same relative mass, sharing identical epitopes and both associated with β2‐m. Comparable results were obtained with M1 and BoLA‐A24.
Genotyping of Bison bonasus K‐casein gene following DNA sequence amplification
Authors: Burzynska B , Topczewski J
Published: July 2010

DNA isolated from 30 Bison bonasus blood samples was used for amplification of a kappacasein gene fragment to detect possible polymorphism. Bovine K‐caseins exist in A, B and E variants. In the European bison from Poland, we have found only BB genotypes. Sequencing of the polymerase chain reaction product revealed further polymorphisms typical for B. bonasus.
Expression of multiple DQB genes in Bos indicus cattle
Authors: Marello K L , Gallagher A , McKeever D J , Spooner R L , Russel G C
Published: July 2010

Polymorphism of expressed bovine major histo‐compatibility complex (MHC) class II DQB genes was investigated in a group of nine MHC‐homozygous Kenya Boran cattle (Bos indicus). DQB second exon fragments were amplified by reverse transcription‐polymerase chain reaction of total mononuclear cell RNA, cloned and sequenced. While a single DQB sequence was obtained from some animals, two DQB exon 2 sequences were found in others, implying expression of duplicated DQB genes. Two pairs of duplicated DQB genes were found in this group of homozygotes, and sequence analysis showed that both pairs contained distinct DQB alleles. One DQB duplication was observed in two related animals with the same MHC haplo‐type (F100 and F188), while the second was detected in three animals (F187, G166 and G277) that expressed the same class II DRB3 and DQB alleles but had different class I (BoLA‐A) types, suggesting that this DR/DQ haplotype may be widespread in Boran cattle.
First International Workshop on Porcine Chromosome 6
Authors: Paszek A A , Schook LB , Louis C F , Mickelson JR , Flickinger G H , Murtaugh J , Mendiola J R , Janzen M A , Beattie C W , Rohrer G A , Alexander L J , Andersson L , Ellegren H , Johansson M , Mariani P , Marklund L , Høyheim B , Davies W , Fredholm M , Archibald A L , Haley C S
Published: July 2010

Recent advances in the use of microsatellite markers and the development of comparative gene mapping techniques have made the construction of high resolution genetic maps of livestock species possible. Framework and comprehensive genetic linkage maps of porcine chromosome 6 have resulted from the first international effort to integrate genetic maps from multiple laboratories. Eleven highly polymorphic genetic markers were exchanged and mapped by four independent laboratories on a total of 583 animals derived from four reference populations. The chromosome 6 framework map consists of 10 markers ordered with high local support. The average marker interval of the framework map is 15.1 cM (sex averaged). The framework map is 135, 175 and 109 cM in length (for sex averaged, female and male maps, respectively). The comprehensive map includes a total of 48 type I and type II markers with a sex averaged interval of 3.5 cM and is 166, 196 and 126 cM (for sex averaged, female and male maps, respectively). Additional markers within framework map marker intervals can thus be selected from the comprehensive map for further analysis of quantitive trait loci (QTL) located on chromosome 6. The resulting maps of swine chromosome 6 provide a valuable tool for analysing and locating QTL.
Survey on swine SINEs (PRE‐1) as candidates for SSCP markers in genetic linkage analysis
Authors: Harumi T , Kimura M , Yasue H
Published: July 2010

Of 310 random cosmid clones, 216 were positive for PRE‐1 sequences by Southern hybridization. Thirty nine sub‐fragments positive for the PRE‐1 sequences were cloned from independent cosmid clones, and sequenced, with 17 complete PRE‐1 elements found. Seven PRE‐1 loci were amplified by polymerase chain reaction using genomic DNA of 12 unrelated pigs as template. The amplified fragments were then subjected to an analysis of single strand conformation polymorphism, with all the loci being polymorphic.
Relations between genetic distance of parental pig breeds and heterozygosity of their F1 crosses measured by genetic markers
Authors: Čepica S , Wolf J , Hojný J , Vacková I , Schröffel J
Published: July 2010

The aim of this paper is to examine the extent to which increment of heterozygosity in F1 crosses can be predicted from genetic distance of parental breeds. For this purpose, 38 polymorphic marker loci (blood groups, allotypes, polymorphic proteins and enzymes) were tested in 1115 purebred animals (Duroc, Hampshire and Czech Meat Pig as sire breeds; Landrace, Large White and Black Pied Přeštice as dam breeds) and in 1428 crossbred animals of the resulting nine crossbred groups. The number of animals in each genetic group ranged from 75 to 230. On the basis of the allele frequencies of the scored loci, three measures of genetic diversity (heterozygosity, standardized heterozygosity, effective number of alleles) were calculated in all 15 genetic groups. Furthermore, two measures of genetic distance (Nei's standard genetic distance and Gregorius' absolute genetic distance) were calculated between the parental populations. High correlations (Pearson product‐moment correlation 0.62 to 0.73; Spearman rank correlation 0.58 to 0.85) were found between the increment of heterozygosity in the crosses (in relation to the mean of the heterozygosities of parental populations) and the genetic distance between the parental populations.
Genetic characterization of highly inbred chicken lines by two DNA methods: DNA fingerprinting and polymerase chain reaction using arbitrary primers
Authors: Plotsky Y. , Kaiser M. G. , Lamont S. J.
Published: July 2010

Thirteen highly inbred chicken lines were analysed at the DNA level by DNA fingerprinting (DFP) and by polymerase chain reaction (PCR) using random primers. In general, the DFP patterns of individuals within a line were identical. The DFP band‐sharing (BS) values among lines from different breeds (Leghorn, Fayoumi, Spanish) ranged from 0.10 to 0.20. The DFP BS values among Leghorn lines from different genetic backgrounds ranged from 0.42 to 0.79. The DFP BS values among lines selected for different major histocompatibility complex serotypes from a common genetic background ranged from 0.70 to 0.95. Some randomly amplified polymorphic DNA (RAPD) PCR products were specific to a single line, some to all lines from the same genetic base, and some to all lines from the same breed. The RAPD‐PCR band‐sharing values ranged from 0.66 to 0.99 for all between‐line comparisons. Thus, the ability to detect biodiversity at the DNA level was greater in this study for DFP than for RAPD‐PCR. The possible origin of line‐specific bands, relative advantages of detecting biodiversity by using different molecular screening techniques and uses of highly inbred chicken lines in molecular analysis are discussed.
Synteny‐mapping horse microsatellite markers using a heterohybridoma panel
Authors: Bailey E , Graves K. T. , Cothran E. G. , Reid R. , Lear T. L. , Ennis R. B.
Published: July 2010

A panel of horse‐mouse heterohybridoma cells was tested for genetic markers using biochemical and polymerase chain reaction‐(PCR‐) based tests. Biochemical markers included phospho‐glucomutase (PGM), glucose phosphate isomerase (GPI) and 6‐phosphogluconate dehydrogenase (PGD). Markers detected using PCR‐based tests included microsatellite markersHTG2–15, HMS 1–3, 5–8, VHL20, ECA2and genes for equine major histocompatibility geneELA‐DRA, tumour necrosis factor alpha (TNFA) and transferrin. The results were analysed for correlation and concordance. Based on the results, five synteny groups were identified, specifically betweenELA‐DRA, TNFA, HMS5andHTG5; betweenHTG3andHTG13; betweenHTG4, HTG8andHMS3; betweenHTG6andHMS1; and betweenHTG7, HTG9andHMS6.Evidence was also found for synteny betweenHTG12, HMS7andECA2, however, confirmation requires further testing. Cytogenetic evaluation of the cell lines making up the panel indicated that large metacentric chromosomes were preferentially lost or tended to break at the centromere. Consequently, the results from this analysis can be used to identify synteny, but not to exclude synteny.
Long‐range mapping of the calcium release channel and glucosephosphate isomerase loci using pulsed‐field gel electrophoresis
Authors: Frengen E , Davies W
Published: July 2010

Long range restriction maps of the calcium release channel (CRC) and glucosephosphate isomerase (GPI) loci have been constructed using pulsed field electrophoresis, Southern blotting and CRC‐ and GPI‐specific probes. The maps, deduced from the restriction fragments detected by the probes, covered 1.1 and 0.3 Mb respectively and no overlap between the maps of these closely linked loci was detected. The minimal distance between the GPI and CRC loci was estimated to be at least 500 kb.
Comparative mapping of sheep inhibin subunit βb to chromosome 2 in sheep and cattle by fluorescence in situ hybridization
Authors: Goldammer T , Brunner R. M. , Hiendleder S , Schwerin M
Published: July 2010

A cosmid clone containing the complete sheep inhibin subunit βB gene (INHBB) was assigned to sheep and cattle homologous chromosome bands 2q31‐q33 by fluorescence in situ hybridization. The assignment of INHBB in sheep excludes another candidate gene as the site of the FecB mutation.
Genetic relationships between Marico barb (Barbus motebensis, Steindacher 1894), Redtail barb (B. gurneyi, Günther 1868) and Amatola barb (B. amatolicus, Skelton 1990)
Authors: Engelbrecht J. S. , van der Bank F. H.
Published: July 2010

Starch gel‐electrophoresis was used to assess genetic differences between two populations of Barbus motebensis and two other taxonomic related and morphologically similar barb species. Ten of the 29 protein coding loci studied were polymorphic. In spite of the small bio‐metric and meristic differences between the species studied, the extent of genetic differences suggests four distinct species. The evidence in support of a new barb species in the Ohrigstad River further adds to the current conservation importance of the rivers of the eastern Transvaal escarpment as a ‘hotspot’ for endemic fish species.
Denaturing gradient gel electrophoresis detection of polymorphism in a PCR fragment of sheep epidermal growth factor gene
Authors: Lanneluc I. , Mulsant P. , Harrison B. , Drinkwater R. D.
Published: July 2010

The ovine map is not yet well‐developed, which represents a problem when looking for markers of a region of interest in sheep. A means of circumventing this is to use comparative mapping. In this study primers were determined using consensus sequences for the epidermal growth factor gene of humans, rats and mice, and an ovine epidermal growth factor gene fragment was amplified by polymerase chain reaction (PCR). A new set of specific ovine primers was chosen to study the polymorphism of this DNA fragment by denaturing gradient gel electrophoresis. Eighty‐four individuals belonging to seven sheep breeds were studied with this technique and four alleles were detected. The heterozygosity rate was 0.57. Family analysis showed mendelian inheritance of the alleles. Usually, genetic analysis of type‐I loci used in the comparative mapping is based on the detection of restriction fragment length polymorphisms in sheep DNA using cDNA probes from other species. Our work shows that another method, based on PCR and denaturing gradient gel electrophoresis techniques, can be efficiently used.
A new DNA marker, U15557, is linked to protease inhibitor and adenylate kinase‐1 in the laboratory opossum, Monodelphis domestica
Authors: Perelygin A. A. , Samollow P. B. , Perelygina L. M. , Cherry L. M. , Mahaney S. M. , VandeBerg J. L.
Published: July 2010

A 323‐bp DNA fragment (U15557) was isolated, cloned, and sequenced after polymerase chain reaction (PCR) amplification from Monodelphis domestica genomic DNA. AHindIII restriction fragment length polymorphism was identified in this species using the U15557 PCR. fragment as a hybridization probe. DNA samples exhibited either a 6.4kb band, a 7.2 kb band, or both bands simultaneously. Behaviour of these two variants in family studies was consistent with codominant autosomal inheritance. Linkage between this marker and the loci encoding protease inhibitor (PI) and adenylate kinase 1 (AK1) was found in M. domestica.
Genetic variation in Australian Merino sheep
Authors: Parsons Y. M. , Cooper D. W. , Piper L. R. , Parsons Y. M. , Cooper D. W.
Published: July 2010

Variation at 22 gene loci was investigated in a flock of Australian Merino sheep using restriction fragment length polymorphism (RFLP) analysis. Polymorphism was observed at 20 loci, including loci for wool keratin, hormone and immunoglobulin light chain genes. Eleven loci yielded unambiguous genotypes suitable for population data analysis. Average heterozygosity, determined from these and two monomorphic loci, was estimated as 0.107 (SE = 0.024). Average heterozygosity excluding all monomorphic data was estimated as 0–377 (SE = 0.031), which is comparable with human RFLP heterozygosities for loci chosen in the same way that we selected sheep loci.
Creation of a SINE enriched library for the isolation of polymorphic (AGC)n microsatellite markers in the bovine genome
Authors: Band M. , Ron M.
Published: July 2010

Trinucleotide (AGC)n microsatellites are found as 3′ tails of the artiodactyl short interspersed nuclear element (SINE) A‐dimer. We describe a polymerase chain reaction (PCR)‐based method for the construction of a plasmid library enriched for SINE (AGC)n microsatellites. By amplifying Sau3AI inserts with a conserved SINE primer and a flanking vector primer, a 35‐fold enrichment of (AGC)n microsatellites over a conventional genomic library was obtained. The SINE primer was used for both sequencing of AGC‐containing inserts and analysis of polymorphism. Twenty‐three unique reverse primers were synthesized and used on bovine genomic DNA, 21 producing PCR products of expected size. Five polymorphic (AGC)n microsatellites with 2–4 alleles each were characterized. Allele sizes differed by a 3 bp motif and lacked the stutter bands associated with dinucleotide repeats. A tendency of increased polymorphism for longer AGC repeat arrays was observed. High stringency selection for positive clones containing eight or more AGC repeats can thus facilitate the isolation of polymorphic (AGC)n microsatellites, Enrichment for (AGC), microsatellites by SINE‐vector PCR can be applied to other bovidae species, such as sheep or goat, containing the artiodactyl SINE elements.
Physical mapping confirms that sheep chromosome 10 has extensive conserved synteny with cattle chromosome 12 and human chromosome 13
Authors: Broad T. E. , Lambeth M. , Burkin D. J. , Burkin D. J. , Jones C. , Pearce P. D. , Maher D. W. , Ansari H. A.
Published: July 2010

The following loci, on human chromosome 13, have been newly assigned to sheep chromosome 10 using chromosomally characterized sheep‐hamster cell hybrids: gap junction protein, beta 2, 26 kDa (connexin 26) (GJB2); gap junction protein, alpha 3, 46 kDa (connexin 46) (GJA3), and esterase D/formylglutathione hydrolase (ESD). This assignment of ESD is consistent with comparative mapping evidence, but not with an earlier report of it on sheep chromosome 3p26‐p24. Cell hybrid analysis confirmed the location of another human chromosome 13 locus, retinoblastoma 1 (including osteosar‐coma) (RBI), and the anonymous ovine genomic sequence RP11 on sheep chromosome 10. Isotopic in situ hybridization was used to regionally localize RP11 on to sheep 10q15‐q22. The location of microsatellites AGLA226, OarDB3, OarHH41, OarVH58, and TGLA441, previously assigned to sheep chromosome 10 by linkage analysis, was confirmed by polymerase chain reaction using the cell hybrid panel. These mapping data provide further evidence that sheep chromosome 10 is the equivalent of cattle chromosome 12, and that these chromosomes show extensive conserved synteny with human chromosome 13.
A comprehensive linkage map of the pig based on a wild pig ‐ Large White intercross
Authors: Marklund L. , Moller M Johansson , Juneja R. K. , Mariani P. , Ellegren H. , Andersson L. , Høyheim B. , Davies W. , Fredholm M. , Coppieters W.
Published: July 2010

A comprehensive linkage map, including 236 linked markers with a total sex‐average map length of about 2300 cM, covering nearly all parts of the pig genome has been established. Linkage groups were assigned to all 18 autosomes, the X chromosome and the X/Y pseudoautosomal region. Several new gene assignments were made including the assignment of linkage group U1 (EAK‐HPX) to chromosome 9. The linkage map includes 77 type I loci informative for comparative mapping and 72in situmapped markers physically anchoring the linkage groups on chromosomes. A highly significant heterogeneity in recombination rates between sexes was observed with a general tendency towards an excess of female recombination. The average ratio of female to male recombination was estimated at 1–4:1 but this parameter varied between chromosomes as well as between regions within chromosomes. An intriguing finding was that blood group loci were overrepresented at the distal ends of linkage groups.
Detection of a common BOLA‐DRB3 deletion by sequence‐specific oligonucleotide typing
Authors: Sitte K. , Jazwinska E. C. , East I. J.
Published: July 2010

The bovine MHC class II BoLA‐DRB3*2A has an amino acid deletion of unknown function at codon 65 in the second exon, which codes for the antigen‐binding site. Sequence‐specific oligonucleotides were designed based on published nucleotide sequences on BoLA‐DRB3 alleles, and used to detect this deletion in 51 Hereford cattle. Probes 65+ and 65‐ detect the presence or absence of codon 65 respectively. Oligonucleotide probes were labelled with Digoxigenin (DIG), hybridized to dot blots of BOLA‐DRB3 exon 2 polymerase chain reaction (PCR) product, and detected by chemiluminescence. Of the 51 animals screened, two were homozygous and 11 were heterozygous for the deletion at codon 65. The methodology described here provides the necessary tools to screen rapidly for this deletion in a large number of animals in order to study its effect on antigen binding and immune response.
Partial characterization of porcine obesity gene (OBS) and its localization to chromosome 18 by somatic cell hybrids
Authors: Neuenschwander S. , Rettenberger G. , Meijerink E. , Jörg H. , Stranzinger G.
Published: July 2010

Degenerate primers based on human and mouse obesity gene (OBS) sequencing data were used in the reverse transcriptase‐polymerase chain reaction (RT‐PCR) of total RNA from pig white adipose tissue. Both strands of the resultant pig‐ specific 325 bp DNA fragment were sequenced. Comparison of the obtained sequence with known sequences revealed an 86% identity with the human and 84% identity with the mouse OBS cDNA. The OBS gene was physically mapped to pig chromosome 18 by PCR analysis of somatic cell hybrids, using pig‐specific primers. This result is consistent with the recent assignment of the human OBS gene to chromosome 7 and the observation made by comparative mapping that by using a human chromosome 7 specific library two segments of conserved synteny were detected on porcine chromosomes 9 and 18. We conclude the border of conserved synteny to be in the 7q31‐7q32 region of the human chromosome.
Characterization of rabbit DNA micros extracted from the EMBL nucleotide sequence database
Authors: VAN Lith H A , VAN Zutphen L F M
Published: July 2010

Microsatellite polymorphisms are invaluable for mapping vertebrate genomes. In order to estimate the occurrence of microsatellites in the rabbit genome and to assess their feasibility as markers in rabbit genetics, a survey on the presence of all types of mononucleotide, dinucleotide, trinucleotide and tetranucleotide repeats, with a length of about 20 bp or more, was conducted by searching the published rabbit DNA sequences in the EMBL nucleotide database (version 32). A total of 181 rabbit microsatellites could be extracted from the present database. The estimated frequency of microsatellites in the rabbit genome was one microsatellite for every 2–3 kb of DNA. Dinucleotide repeats constituted the prevailing class of microsatellites, followed by trinucleotide, mononucleotide and tetranucleotide repeats, respectively. The average length of the microsatellites, as found in the database, was 26, 23, 23 and 22 bp for mono‐, di‐, tri‐ and tetranucleotide repeats, respectively. The most common repeat motif was AG, followed by A, AC, AGG and CCG. This group comprised about 70% of all extracted rabbit microsatellites. About 61% of the microsatellites were found in non‐coding regions of genes, whereas 15% resided in (protein) coding regions. A significant fraction of rabbit microsatellites (about 22%) was found within interspersed repetitive DNA sequences.
Lack of association of bovine MHC class I alleles with carcass and reproductive traits
Authors: Arriëns M A , Hofer A , Obexer‐Ruff G , Lazary S
Published: July 2010

The present study was carried out to examine whether a relationship between bovine major histocompatibility complex (BoLA) class I alleles and carcass traits or reproductive performance exists in Braunvieh and Fleckvieh A1 (artificial insemination) bulls. The influence of BoLA class I (BOLA‐A) alleles on deregressed breeding values for net growth rate, carcass index and thigh volume was assessed in Braunvieh crosses and Fleckvieh bulls with a gene substitution model. The reproductive traits: non‐return rate and interval between first and last insemination of daughters (female fertility), as well as non‐return rate of inseminated cows (male fertility), were only investigated in Fleckvieh animals. No influence of the BOLA‐A region on the traits evaluated could be demonstrated. An improper, i.e. less restrictive analysis would have led to spurious results.
Assignment of markers by using polymerase chain reaction on pools of swine flow‐sorted chromosomes
Authors: Riquet J , Schmitz A , Cruzel J , Mulsant P , Milan D , Gellin J
Published: July 2010

Gene chromosomal assignment can be realized not only by somatic hybrid panels but also by spot‐blot hybridization or polymerase chain reaction (PCR) of flow‐sorted chromosomes. We propose a swine chromosome assignment strategy by PCR amplification on pooled chromosomal DNA, which allows assignment despite possible chromosomal contamination during sorting. Each pool contains three different chromosomes, each chromosome being present in one or two pools. We present concordant results obtained for eight markers already mapped to different swine chromosomes and we assign the somatostatin gene to chromosome 13, a new marker in the pig genome.
Assessment of genomic variability through DNA fingerprinting within and between chicken lines divergently selected for residual food consumption
Authors: Tixier‐Boichard M , Kritchmann N , Morisson M , Bordas A , Hillel J
Published: July 2010

DNA fingerprints obtained by multi‐locus probes have been shown to be convenient tools to assess genetic variability and genetic distances in animal populations. This method has been applied in the present study to two Rhode Island Red lines of chickens divergently selected for residual food consumption (RFC) for 16 generations (R‐: low RFC; R+: high RFC). Within each line, individuals were sampled from each tail of the phenotypic distribution of RFC for males and for females. The three probes used were two minisatellite probes, R18‐1 and 33‐6, and the endogenous avian retroviral element probe. Altogether, 101 bands were scored. Band‐sharing levels obtained from analysis of pooled DNA were extremely high within‐Line (> 0.9) and still high between the lines (0.82 to 0.86). When band frequencies were compared, correlation coefficients were lower between lines than between extreme groups within lines regardless of the performance level. Although the selected lines differed widely in the selected trait RFC and a few correlated traits, it was concluded that they are probably different by only a low proportion of their genome.