bluuebunny/crossref_metadata_2025 huggingface dataset:
A simple method for genotyping the bovine growth hormone gene
Authors: Chikuni K , Tanabe R , Muroya S , Fukumoto Y , Ozawa S
Published: December 2003

An allele‐specific polymerase chain reaction (PCR) amplification method was developed to determine the genotypes at the bovine growth hormone locus that result from two nucleotide substitutions in exon 5 of the gene. This method was a multiplex PCR (ASM–PCR) employing a common primer pair and two allele‐specific reverse primers. The common primer pair was designed to amplify a target region containing two substitution points from the three variants of the bovine growth hormone gene. The allele‐specific primers were designed to be mismatched with other genotypes at the 3' end of oligonucleotides. When the common and allele‐specific reverse primers competed with each other, the shorter allele‐specific fragments were amplified preferentially. Consequently, the PCR products of the variant‐specific fragments were 347, 483 and 656 bp for alleles A, B and C, respectively, of the bovine growth hormone gene. Genotypes of the bovine growth hormone gene were easily identified by agarose gel electrophoresis of PCR products. The results suggested that this multiplex PCR method would be useful for identification of genetic variants caused by point mutations.
A partially deficient and atypical equine transferrin variant, TF N
Authors: Niini T , Stratil A , Čížová‐Schröffelová D , Sandberg K
Published: December 2003

A new, partially deficient and phenotypically atypical transferrin variant, TF N, was detected in sera of a number of Finnhorses belonging to one family. The variant was inherited codominantly. In polyacrylamide gel electrophoresis (pH9.0) of sera, variant N appeared as a single weak band migrating slightly faster than the main anodal band of variant M. After immunoblotting or isolation an additional, still weaker, faster band was observed as well as some trace bands. The cathodal component, which is present in other transferrin variants, could not be convincingly proved. The main component of variant N contained four sialic acid residues.
Microsatellite markers in common carp (Cyprinus carpio L.)
Authors: Crooijmans R P M A , Poel J J Van der , Groenen M A M , Bierbooms V A F , Komen J
Published: December 2003

Microsatellite markers of the poly (CA) type in common carp (Cyprinus carpio L.) are described. Clones containing a (CA) repeat were isolated from a common carp genomic library and sequenced. The number of repeats found was high compared to mammals but comparable with other teleost fishes. Classification of the repeats (perfect, imperfect and compound) are compared with the Atlantic cod (Gadus morhua L.), rainbow trout (Oncorhynchus mykiss), and Atlantic salmon (Salmo salar L.). A total of 41 primer sets were designed and tested for polymorphism on a test panel of eight animals (derived from outbred lines, inbred lines and gynogenetic clones). Thirty‐two markers were found to be polymorphic. The heterozygosity in the outbred animals was 60·4%, 51·1% in the inbred animals and 0% in the gynogenetic clones. The average number of alleles among the eight animals was 4·7 per marker. Six markers (18·8%) gave an additional polymorphic amplification product besides the polymorphic amplification product in the expected size range. The possibility that these loci are tetraploid is discussed. The polymorphic loci described for common carp will be valuable as genetic markers for use in population, breeding, and evolutionary studies.
Analysis of genetic diversity of domestic water buffaloes and anoas based on variations in the mitochondrial gene for cytochrome b
Authors: Kikkawa Y , Yonekawa H , Suzuki H , Amano T
Published: December 2003

There are two major groups of domestic water buffaloes in East and Southeast Asia: swamp buffaloes and river buffaloes. Genetic diversity among swamp and river buffaloes was studied by DNA sequence analysis of the mitochondrial gene for cytochrome b. The results showed that each of the two groups has mitochondrial DNA (mtDNA) with a specific cytochrome b haplotype. The pairwise nucleotide sequence divergence was calculated to be 2·67% between swamp and river buffaloes, suggesting that they might have diverged from the ancestral populations of Asiatic domestic water buffaloes, approximately 1 million years ago. In addition, the sequences of the same gene from three subspecies of anoa (lowland, mountain and quarles anoa) were determined and compared with that of a domestic water buffalo. The sequence divergence was 1·2% for mountain anoa vs quarles anoa, 3·6% for mountain anoa vs lowland anoa and 3·3% for quarles anoa vs lowland anoa. Moreover, the sequence divergence between water buffaloes and anoas was found to be approximately 3·33%. Our results provide molecular evidence to support the taxonomic classification, namely, that Asiatic buffaloes may be classified into four lineages, swamp buffalo, river buffalo, lowland anoa and mountain plus quarles anoa. However, the sequence divergence values among these four groups were lower than the sequence divergence values found in the genus and subgenus levels within the subfamily Bovinae. In particular, in contrast to some proposed taxonomic classifications, our results indicated that mtDNA in the water buffaloes and anoas did not diverge at the genus level.
Characterization of CR1 repeat random PCR markers for mapping the chicken genome
Authors: Okimoto R , Dodgson J B , Cheng H H
Published: December 2003

Polymerase chain reaction (PCR) primers complementary to portions of the chicken repetitive element CR1 have been used previously to generate useful markers on the chicken genome linkage map. To understand better the genetic basis for this technique and to convert CR1–PCR loci to markers useful in physical genome mapping, five polymorphic CR1–PCR‐generated DNAs were cloned and partially sequenced. Inverse PCR was then employed to clone the corresponding region of the genomes of both the Jungle Fowl (JF) and White Leghorn (WL) parental DNA templates. Our results demonstrate that some of the CR1–PCR‐generated DNAs arise from priming at an endogenous CR1 element, whereas others are due to chance complementarity between the CR1–PCR primer in use and random annealing sites in the genome, unrelated to a demonstrable CR1 element. In all five instances, it was possible to identify the sequence difference between the JF and WL parental DNAs that gave rise to the initial polymorphism and design allele‐specific PCR primer sets that uniquely detect that polymorphism. In four of the five instances, the polymorphism was a one or two basepair sequence difference within the primer annealing site, but in the fifth case the responsible difference was outside, but very close to, the annealing site. In all instances the allele‐specific PCR for the sequence polymorphism mapped identically with the corresponding CR1–PCR amplification polymorphism. We conclude that CR1–PCR provides an efficient and reliable mechanism for genome mapping in avians that can correlate linkage and physical mapping approaches.
Ovine‐specific Y‐chromosome RAPD–SCAR marker for embryo sexing
Authors: A Gutiérrez‐Adán  , W T Cushwa*  , Anderson G B , Medrano J F
Published: December 2003

An accurate, sensitive, and quick (approximately 3 h) method for determining the sex of ovine embryos was developed using polymerase chain reaction (PCR) primers derived from an ovine‐specific Y‐chromosome random amplified polymorphic DNA marker (UcdO43). The accuracy and sensitivity of the assay were first tested using genomic DNA from 10 males and 10 females of five different sheep breeds, and then tested using serial dilutions of male‐in‐female DNA. The assay was 100% accurate in confirming the sex of the individuals and the ovine male‐specific fragment was detected in dilutions containing as little as 10 pg of male DNA in 50 ng of female DNA. The assay was also confirmed to be specific for the ovine Y‐chromosome as bovine, caprine, porcine, murine, and human DNA did not amplify. The ovine embryo sexing method is a duplex PCR system that also includes ZFY/ZFX primers. ZFY/ZFX provide an internal positive control for amplification as well as a means to confirm the results obtained with the UcdO43 primers. All embryo sexing results (36/36) from our method were in agreement with the ZFY/ZFX assay results. However, while our method requires an internal control to detect PCR failure, it has the advantages of not requiring nested PCR or restriction endonuclease digestion of the PCR product, and concerns about cross‐species contamination are eliminated.
Isolation and molecular characterization of bovine Rhesus‐like transcripts and chromosome mapping of the relevant locus
Authors: Méténier‐Delisse L , Hayes H , Leroux C , Giraud‐Delville C , Levéziel H , Guérin G , Martin P , Grosclaude F
Published: December 2003

The bovine erythrocyte membrane carries Rhesus (Rh)‐like proteins. To obtain a bovine nucleotide probe, a cDNA library of foetal liver was constructed and screened with the human RhCE probe. Three clones (245 bp, 1012 bp and 1400 bp) were isolated and sequenced. They share a high degree of similarity (up to 73%) with Rh‐like cDNAs of primates characterized so far and all of them were shown to contain a polymorphic microsatellite in their 3' untranslated region. Their sequences support the occurrence of different splicing isoforms transcribed from the same RH‐like gene. One of the clones (1400 bp), which has a 134‐nucleotide deletion causing a frameshift, is structurally similar to the human Rh4 cDNA isoform. Synteny mapping and genetic linkage analysis located the bovine RH‐like locus on chromosome BTA2, on which none of the 10 previously mapped blood group systems are found. In situ hybridization mapped the RH‐like locus to BTA2q45. No linkage was detected between the microsatellite and the only unmapped blood group system (locus F). These results strongly suggest that the putative bovine Rh‐like polypeptides do not correspond to any previously described bovine blood group. Comparative studies of human and bovine maps clearly show that the human RH locus, which is located on HSA1p34‐p36, and its bovine counterpart belong to a linkage group highly conserved between both species.
Nomenclature for factors of the BoLA system, 1996: report of the ISAG BoLA Nomenclature Committee
Authors: Davies C J , Andersson L , Mikko S , Ellis S A , Hensen E J , Lewin H A , Muggli‐Cockett N E , Poel J J van der , Russell G C
Published: December 2003

The BoLA (bovine lymphocyte antigen) Nomenclature Committee met during the 1994 and 1996 conferences of the International Society for Animal Genetics to define a sequence‐based nomenclature system for genes of the BoLA system. The rules for acceptance of new sequences are described and names are assigned to the sequenced alleles of the class II genes DRA, DRB1, DRB2, DRB3, DQA, DQB, DYA, DIB, DMA and DMB. The assignment of BoLA class I sequences to loci will be considered at a later workshop when further sequencing/mapping data are available.
Localization of swine PRE‐1 homologues in 13 loci of Phacochoerus aethiopicus and Tayassu tajacu genomes, and their sequence divergence
Authors: Sulandari S , Harumi T , Wada Y , Yasue H , Muladno  , Yanai S
Published: December 2003

In our previous study, PRE‐1 (a swine short interspersed nuclear element, SINE) was found to be present in the genomes of animal species related to swine (Sus scrofa) i.e. warthog (Phacochoerus aethiopicus) and collared peccary (Tayassu tajacu) at almost the same frequency as in Sus scrofa. In the present study, we investigated whether PRE‐1 was present in hippopotamus (Hippopotamus amphibius), which is in the same order but in a different family to Sus scrofa. Hippopotamus amphibius was found to contain no PRE‐1. Then, in order to study the localization of PRE‐1 sequences at locus level and the sequence divergence of the PRE‐1 of individual loci among Sus scrofa, Phacochoerus aethiopicus and Tayassu tajacu, primer sets, which can amplify PRE‐1 sequences at 13 loci of swine genome with the polymerase chain reaction, were prepared to identify any corresponding sequences in Phacochoerus aethiopicus and Tayassu tajacu. Twelve and nine of the 13 primer sets identified fragments in Phacochoerus aethiopicus and Tayassu tajacu respectively. Ten of the 12 Phacochoerus aethiopicus fragments and two of the nine Tayassu tajacu fragments contained PRE‐1 sequences. Based on the divergence between the corresponding PRE‐1 sequences at individual loci and on the mutation rate of the pseudogenes (r=4·6×10–9), Phacochoerus aethiopicus and Tayassu tajacu are currently calculated to have been separated from Sus scrofa later than 1·4million years before present (MYBP) and 16·8 MYBP, respectively.
Marker‐assisted introgression using non‐unique marker alleles I: selection on the presence of linked marker alleles
Authors: Heelsum A M van , Haley C S , Visscher P M
Published: December 2003

This paper investigates marker‐assisted introgression of a major gene into an outbred line, where identification of the introgressed gene is incomplete because marker alleles are not unique to the base populations (the same marker allele can occur in both donor and recipient population). Those markers are used to identify the introgressed allele as well as the background genotype. The effect of using those markers, as if they were completely informative on the retention of the introgressed allele, was examined over five generations of backcrossing by using a single marker or a marker bracket for different starting frequencies of the marker alleles. Results were calculated by using both a deterministic approach, where selection is only for the desired allele, and by a stochastic approach, where selection is also on background genotype. When marker allele frequencies in donor and recipient population diverged from 1 and 0 (using a diallelic marker), the ability to retain the desired allele rapidly declined. Marker brackets performed notably better than single markers. If selection on background marker genotype was applied, the desired allele could be lost even more quickly than expected at random because the chance that the allele, which is common in the donor line, is present on the locus identifying the introgressed allele and is surrounded by alleles common in the recipient line on the background marker loci, will descend from the donor line (double recombination has taken place), is a lot smaller than the chance that this allele will stem from the recipient line (in which the allele occurs in low frequency). Marker brackets again performed better. Preselection against marker homozygotes (producing uninformative gametes) gave a slightly better retention of the introgressed allele.
Marker‐assisted introgression using non‐unique marker alleles II: selection on probability of presence of the introgressed allele
Authors: Heelsum A M van , Haley C S , Visscher P M
Published: December 2003

If marker alleles that identify a gene for introgression are not completely unique to the different base populations, the trait allele can be lost quickly during the process of backcrossing. This study considers ways to deal with incompletely informative markers in order to retain the desired allele. Selection was based on the probability of the presence of the desired (introgressed) trait allele, which was calculated for each marker genotype, using a single marker or a diallelic or triallelic marker bracket. The percentage of individuals retaining the introgressed allele was calculated over five generations of backcrossing, for selected fractions between 0 and 1, for marker alleles that could occur in both base populations. The best results were obtained with a rather large selected fraction, when all individuals, heterozygous and homozygous for the most desirable allele at the marker loci, were selected. Additional selection against marker homozygotes (which might have the highest probability of carrying the desired‐trait allele, but produce uninformative gametes) altered the optimum selected fraction, making the selected fraction more consistently inversely related to a better retention of the desired‐trait allele. A marker bracket was found to give a better retention of the desired‐trait allele than a single marker and triallelic markers were better than diallelic markers, giving a retention of almost 50%. The earlier that preselection of parents (on informativeness) took place the better the overall result; preselection should occur preferably in the base populations. Preselection could make marker alleles unique to alternative base populations and markers would effectively become fully informative. Selection in the base populations might not be possible or not desirable, for example, because of the available number of individuals. This is unlikely to be a problem when parents are paired up to exclude any common marker alleles.
Detection of loci affecting milk production and health traits in an elite US Holstein population using microsatellite markers
Authors: Ashwell M S , Jr C E Rexroad , Miller R H , VanRaden P M , Da Y
Published: December 2003

Quantitative trait loci (QTL) affecting health and milk production traits were studied in seven large half‐sib US Holstein families by using the granddaughter design. Genotyping for 16 markers was completed and marker allele differences within and pooled‐across families were analysed. Potential QTL were identified for somatic cell score (SCS), fat yield, fat percentage, protein yield and protein percentage. Three markers (BM203, BM4505 and BM2078) were associated with significant effects for different traits and, after further analysis, may be useful in marker‐assisted selection in specific families. Comparisons between these data and previously identified QTL support the location of a QTL for milk yield and protein yield on chromosome 21.
A consensus linkage map for swine chromosome 7
Authors: Rohrer G A , Alexander L J , Beattie C W , Wilkie P , Flickinger G H , Schook L B , Paszek A A , Andersson L , Mariani P , Marklund L , Fredholm M , Hoyheim B , Archibald A L , Nielsen V H , Milan D , Groenen M A M
Published: December 2003

The First International Workshop on Swine Chromosome 7 (SSC7) was held in Minnesuing, Wisconsin, USA on 21–24 September 1995. The objective was to develop a comprehensive linkage map for porcine chromosome 7 by combining genotypic data from four swine reference populations. Contributions of genotypic data were made from the US Meat Animal Research Center, the University of Minnesota, the PiGMaP consortium and the Scandinavian consortium. Primers for selected sequence tagged site markers, to be genotyped across the reference populations, were exchanged to integrate individual maps of SSC7. Eighty‐six loci were genotyped; these loci represented microsatellite, minisatellite, single‐strand conformation polymorphism, restriction fragment length polymorphism, erythrocyte antigen and protein polymorphisms. Eighteen genes were mapped, including 12 markers within class I, class II and class III regions (four markers in each class) of the swine major histocompatibility complex. Forty‐two markers were either genotyped on more than one population or were included in a haplotype system and used to develop skeletal linkage maps that spanned 147·6, 212·7 and 179·5 cM for the male, female and sex‐average maps, respectively. A comprehensive linkage map was developed incorporating those markers with more than 30 informative meioses. The comprehensive map was slightly longer than the skeletal map, at 153·3, 215·3 and 183·8 cM, respectively, with only three intervals greater than 10 cM. These results significantly improve the genetic resolution of the porcine chromosome 7 map and represent an accurate approach for the merging of genetic maps produced in different reference populations.
Genetic mapping of bovine T‐cell receptor complex loci
Authors: Agaba M , Teale A , S J Kemp  , Barendse W
Published: December 2003

Thymic‐derived lymphocytes (T cells) recognize and respond to antigens through the mediation of the T‐cell receptor complex. Here we report polymorphism at each of the five loci that encode the different components of the T‐cell receptor complex in cattle. These genes were mapped on the bovine genome by genetic linkage analysis in the International Bovine Reference Panel (IBRP). These mapping data provide additional type I markers for linking the bovine genetic map with the human and mouse maps and also permit investigation of the effect of T‐cell receptor polymorphism on immune responsiveness and disease susceptibility.
Validation of microsatellite markers for routine horse parentage testing
Authors: Bowling A T , Eggleston‐Stott M L , Byrns G , Clark R S , Dileanis S , Wictum E
Published: December 2003

A parallel testing of 4803 routine Quarter Horse parentage cases, using 15 loci of blood group and protein polymorphisms (blood typing) and 11 loci of dinucleotide repeat microsatellites (DNA typing), validated DNA markers for horse pedigree verification. For the 26 loci, taken together, the theoretical effectiveness of detecting incorrect parentage was 99·999%, making it extremely unlikely that false parentage would fail to be recognized. The tests identified incorrect parentage assignment for 95 offspring (2% of cases). Despite fewer loci, DNA typing was as effective as blood typing and, in parentage exclusion cases, provided more systems to substantiate the genetic incompatibility. Five offspring presented potential genetic incompatibilities with their parents in only a single microsatellite system, but the parentage exclusions could not be confirmed with discordant results at additional loci. Two of these five incompatibilities could be explained as consequences of a null allele and three as fragment size increases or decreases (putative mutations). Provided that an exclusion assignment was based on at least two systems of genetic incompatibility, such rare genetic events did not lead to false exclusions. Notwithstanding the near 100% effectiveness estimations for either typing panel alone to identify incorrect parentage, this validation test showed an actual effectiveness of 97·3% for blood typing and 98·2% for DNA typing. The DNA‐based test, however, may feasibly achieve higher efficacy than reported here by adding selected systems to the parentage test panel.
Random amplified polymorphic DNA markers in crosses between inbred lines of Rhode Island Red and White Leghorn chickens
Authors: Wei R , Bitgood J J , Dentine M R
Published: December 2003

Reciprocal crosses and backcrosses were conducted between inbred Rhode Island Red and White Leghorn chickens differentiated for egg production and egg quality traits. Random amplified polymorphic DNA (RAPD) markers distinguishing inbred lines were detected. Twenty‐two polymorphic bands were found from screening 120 single 10‐mer random primers of which two were consistent with sex‐linked markers. Of 90 pairwise two‐point linkage analyses completed for the autosomal markers, four close linkages (8·2 cM to 14·9 cM) were significantly different from zero.
Genetic mapping of five human chromosome 4 orthologues to bovine chromosomes 6 and 17
Authors: Fisher S R , Beever J E , Lewin H A
Published: December 2003

Five loci that map to human chromosome 4 (HSA4) were selected to expand the bovine comparative linkage map. Loci included b‐casein (CSN2), basic fibroblast growth factor (FGF2), immunoglobulin J chain (IGJ), interleukin 2 (IL2) and microsomal triglyceride transfer protein (MTTP). Polymorphisms for each locus were identified by either polymerase chain reaction‐restriction fragment length polymorphism (PCR–RFLP) or single‐strand conformational polymorphism (SSCP) analysis. The bovine genes for CSN2, IGJ and MTTP were mapped by linkage analysis to chromosome 6; FGF2 and IL2 mapped to chromosome 17. These data refine a position of chromosomal evolution to a small region between FGF2 and the previously mapped complement I factor (IF).
Polymorphic microsatellite loci in the European rabbit (Oryctolagus cuniculus) are also amplified in other lagomorph species
Authors: Surridge A K , Bell D J , Rico C , Hewitt G M
Published: December 2003

Six polymorphic microsatellite markers developed for the European wild rabbit (Oryctolagus cuniculus) were amplified with 20 other species of lagomorphs, representing both commercially important species and species important from a conservation perspective. Successful amplification of a number of these loci has provided an important set of new molecular markers for this mammalian order.
Characterization of the erythrocyte superoxide dismutase allozymes in the deer Cervus elaphus
Authors: He K , Murphy M P , Tate M L , Wilton S D
Published: December 2003

The cDNA sequences for Cu,Zn superoxide dismutase from two Cervus elaphus subspecies, North American wapiti and European red deer, were determined. The derived amino acid sequences showed two differences: residue 8 was Leu in wapiti and Met in red deer and residue 25 was His in wapiti and Asn in red deer. The extra positive charge at position 25 in the wapiti isoform accounted for its greater mobility towards the cathode during non‐denaturing electrophoresis, a procedure widely used in the genetic analysis of deer. There was no difference in specific activity between the two Cu,Zn superoxide dismutase isoforms, but the wapiti isoform was slightly more susceptible to heat denaturation.
Cloning and characterization of microsatellite loci in channel catfish, Ictalurus punctatus
Authors: Waldbieser G C , Bosworth B G
Published: December 2003

Short tandem repeat (microsatellite) loci were cloned from the channel catfish, Ictalurus punctatus, genome for use as molecular markers for genetic improvement of this important agricultural species. Plasmid clones containing catfish genomic DNA inserts were identified, by hybridization with tandem repeat DNA probes, and sequenced using automated laser fluorescence. A feral population of catfish displayed levels of heterozygosity greater than 0·7 for 13 of 22 loci and heterozygosity greater than 0·5 for 20 of 22 loci. Allelic polymorphism ranged from three to 17 alleles per locus in the feral population. Populations of domestic, farm‐raised catfish and a research strain displayed levels of heterozygosity similar to the feral population. Non‐invasive tissue sampling provided abundant material for the polymerase chain reaction‐based genotype assay. The microsatellite loci will be useful in the molecular characterization and genetic improvement of channel catfish populations.
Molecular characterization of major histocompatibility complex (B) haplotypes in broiler chickens
Authors: Li L , Johnson L W , Ewald S J
Published: December 2003

In Leghorn (laying) chickens, susceptibility to a number of infectious diseases is strongly associated with the major histocompatibility (B) complex. Nucleotide sequence data have been published for six class I (B‐F) alleles and for class II (B‐Lβ) alleles or isotypes from 17 Leghorn haplotypes. It is not known if classical B‐L or B‐F alleles in broilers are identical, at the sequence level, to any Leghorn alleles. This report describes molecular and immunogenetic characterization of two haplotypes from commercial broiler breeder chickens that were originally identified by serology as a single haplotype, but were differentiated serologically in the present work. The two haplotypes, designated BA4 and BA4variant, shared identical B‐G restriction fragment length polymorphism patterns, but differed in one B‐Lβ fragment that cosegregated with the serological B haplotype. Furthermore, the nucleotide sequences of the highly variable exons of an expressed B‐LβII family gene and B‐F gene from the two haplotypes were markedly different from each other. Both the B‐LβII family and B‐F gene sequences from the BA4 haplotype were identical to the sequences obtained from the reference B21 haplotype in Leghorns; however, in the BA4 haplotype the B‐Lβ21 and B‐F21 alleles were in linkage with B‐G alleles that were not G21. The nucleotide sequences from BA4variant were unique among the reported chicken B‐LβII family and B‐F alleles.
Genetic relationship between equine apolipoproteins A4 and A1
Authors: Kakoi H , Gawahara H
Published: December 2003

Genetic polymorphism of equine apolipoprotein (APO) A4 was investigated using two‐dimensional electrophoresis in four horse breeds, including Japanese native horses. A linkage relationship between the equine APOA4 and APOA1 structural loci was assumed from the segregation data of these loci in one family line of the Japanese Hokkaido native breed.
Linkage of the gene for equine combined immunodeficiency disease to microsatellite markers HTG8 and HTG4; synteny and FISH mapping to ECA9
Authors: Bailey E , Reid R C , Lear T L , Skow L C , Mathiason K , McGuire T C
Published: December 2003

Equine combined immunodeficiency disease (CID) is caused by homozygosity for an autosomal recessive gene. To identify linked markers for the disease, we studied a family segregating for the equine CID gene. A stallion and 19 of his CID‐affected offspring were tested for marker segregation at 23 microsatellite DNA loci. His CID‐affected offspring inherited only one of his two alleles at the HTG8 and HTG4 loci, namely HTG8–186 and HTG4–124, respectively. Lod scores for linkage to the CID gene using a Θ of 0·01were 5·34 for HTG8 and 2·37 for HTG4. The apparent genotypes also suggested linkage disequilibrium between the HTG8–186 allele and the gene for CID. The gene for the DNA protein kinase catalytic subunit (DNA‐PK) was recently suggested as a candidate gene for equine CID. A defect of this gene causes a disease in mice that is similar to equine CID. Therefore, we investigated whether this gene might be associated with the microsatellite markers. Analysis of a somatic cell hybrid panel demonstrated synteny of DNA‐PK with HTG4 and HTG8 (Kentucky Synteny Group 3). Fluorescence in situ hybridization (FISH) studies demonstrated that DNA‐PK is located on horse chromosome ECA9p12. This work supports the hypothesis of DNA‐PK as the probable cause of equine CID.
Extensive genomic conservation of cattle microsatellite heterozygosity in sheep
Authors: Gortari M J de , Freking B A , Kappes S M , Leymaster K A , Stone R T , Beattie C W , Crawford A M
Published: December 2003

We report the evaluation of 1036 bovine microsatellite primer pairs for their suitability as linkage markers in sheep. Approximately 58% (605/1036) of bovine primer pairs amplified a locus in sheep. Sixty‐seven per cent (409/605) of amplified loci were detected as polymorphic. Marker heterozygosity, allele number and range of allele sizes were significantly lower in sheep than cattle sampled in this study. However, median fragment size was similar. These data suggest that high‐resolution comparative linkage maps between closely related species can be constructed relatively efficiently.
Polymorphic sequence of Korean Native goat lactoferrin exhibiting greater antibacterial activity
Authors: Lee T H , Yu S L , Nam M S , Kim S J , Lee K K , Yu D Y , Shimazaki K
Published: December 2003

Lactoferrin, which exhibits antibacterial activity to protect infants from infectious disease, is a major component of colostrum and milk. Lactoferrin was purified from the colostrum of Korean Native goat, and the cDNA from the mammary gland mRNA of the animal was cloned and sequenced. The nucleotide sequence of the lactoferrin gene of Korean Native goat was found to differ in 15 sites from that of the goat lactoferrin gene reported earlier. This difference in nucleotide sequence resulted in six amino acid substitutions: five in the N‐lobe and one in the C‐lobe. The antibacterial activity of Korean Native goat lactoferrin was found to be greater than that of Sannen goat lactoferrin.
Aldolase C polymorphism in the laboratory opossum, Monodelphis domestica
Authors: Sokolova O V , Oorschot R A H van , VandeBerg J L
Published: December 2003

A two‐allele polymorphism in aldolase C was identified in brain extracts of grey short‐tailed opposums, Monodelphis domestica, by electrophoresis in starch or cellulose acetate gels. Pedigree data were consistent with autosomal codominant inheritance. The polymorphism was present in two of the six genetically distinct laboratory populations that have been established for this species.
Isolation of microsatellites from a bovine YAC clone harbouring the SOD1 gene
Authors: Band M , Ron M , Eggen A , Bishop M D
Published: December 2003

A bovine yeast artificial chromosome (YAC) clone containing the superoxide dismutase 1 (SOD1) gene was used as a template for polymerase chain reaction (PCR) amplification using a conserved short interspersed nuclear element (SINE) primer. Two highly polymorphic microsatellites with nine and eight alleles were isolated and mapped by linkage analysis to the centromeric region of BTA1. These microsatellites will be used in the construction of a genetic and physical map of the SOD1 region towards positional cloning of the polled gene.
Isolation, characterization and chromosomal localization of the porcine ciliary neurotrophic factor (CNTF) gene
Authors: Piedrahita J A , Weaks R L , Ramsoondar J J , Nogues C , Gallagher, Jr. D S
Published: December 2003

In the mouse, ciliary neurotrophic factor (CNTF) maintains embryonic stem cells in an undifferentiated state; yet, the heterologous protein has no similar effects on porcine embryonic stem (ES) cells. Consequently, we cloned and sequenced the porcine CNTF gene and assigned it to chromosome 2. The CNTF gene was found to contain two exons, which encoded a deduced polypeptide of 200 amino acids in length with 83%, 82%, 82% and 81% amino acid similarity when compared to known sequences in the rabbit, rat, human and mouse, respectively. Eight non‐conservative amino acid changes were identified in the porcine protein when compared with other species. Comparison of the 5' region of the porcine CNTF and other mammalian cytokines indicated the presence of several conserved transcription‐factor binding motifs, suggesting their importance for controlling the specific expression of these proteins. In addition, CNTF was localized to porcine chromosomes by fluorescence in situ hybridization (FISH). Chromosome arm length ratios were calculated for 40 early metaphase chromosomes and 32 (80%) indicated that the pig CNTF gene is located on chromosome 2p1.6. This was confirmed by aligning R‐banded FISH‐labelled chromosomes to the standard porcine ideogram.
Isolation and mapping of two chicken POU family genes and the identification of a syntenic group with human and mouse
Authors: Heltemes L M , Tuggle C K , Lamont S J
Published: December 2003

Two partial chicken POU domain genes were isolated by genomic library screening and reverse transcriptase–polymerase chain reaction (RT–PCR). A cDNA clone encoding the POU domain of Brn‐3a, which showed near identity to the human Brn‐3a sequence (100% amino acid identity), was isolated and mapped to chicken linkage group E48. A Skn‐1/Epoc‐1/Oct‐11 genomic clone was identified and mapped to chicken linkage group E49. This mapping identified a syntenic group in chicken linkage group E49 that was conserved with human chromosome 11q23 and mouse chromosome 9.
Mapping 28 erythrocyte antigen, plasma protein and enzyme polymorphisms using an efficient genomic scan of the porcine genome
Authors: Rohrer G A , Alexander L J , Beattie C W , Vögeli P , Stranzinger G
Published: December 2003

One hundred and fifty‐four microsatellite markers were selected for genomic scanning of the porcine genome and were grouped into amplification sets to reduce the cost and labour required. Thirty amplification sets had two markers (duplex), 20 sets had three markers (triplex) and five sets had four markers (quadruplex) while 14 markers were analysed separately. The selection criteria for microsatellites were: ease of scoring, level of polymorphism, genetic location and ability to be genotyped in a multiplexed polymerase chain reaction (PCR). The selected microsatellites were chosen to span the entire genome flanked by the porcine linkage map with intervals between adjacent markers of 15–20 cM where possible. The utility of this set of markers was demonstrated by linkage analyses with loci controlling blood plasma protein and red cell enzyme polymorphisms (n = 13), erythrocyte antigens (n = 15), the S blood group, coat colour and ryanodine receptor from 174 backcross Meishan‐White Composite pigs. These loci displayed various forms of inheritance and most (24 loci) have been placed in linkage groups. Significant two‐point linkages (lod > 3·0) were detected for each polymorphic marker. These results provide the first linkage assignments for phosphoglucomutase (PGM2) and erythrocyte antigen F (EAF) to SSC8; and serum amylase (AMY) and erythrocyte antigen I (EAI) to SSC18. All of the remaining polymorphic loci (n = 24) mapped to previously identified regions confirming earlier results. Most of the markers used in this study should be useful in resource populations of various breed crosses as the number of alleles detected in a multibreed reference population was one of the selection criteria.
Mapping of growth hormone releasing hormone receptor to swine chromosome 18
Authors: Sun H S , Taylor C , Wang L , Rothschild M F , Tuggle C K , Robic A
Published: December 2003

The growth hormone releasing hormone receptor (GHRHR) was mapped in the pig for study as a potential candidate gene in controlling pig quantitative growth and carcass characteristics. Primers were designed from the pig GHRHR sequence to amplify a 1·65‐kb intronic fragment between exons 6 and 7. By using a pig–rodent somatic cell hybrid panel, GHRHR was mapped to pig chromosome 18 (SSC18) with 100% concordance, and the regional assignment was SSC18q24 with 89% concordance. The polymerase chain reaction–restriction fragment length polymorphisms (PCR–RFLPs) with MseI and TaqI were developed to confirm this assignment with linkage analysis by using the European Pig Gene Mapping Project (PiGMaP) reference families. Pig GHRHR was mapped with strong linkage to SSC18 markers S0062 and S0120 (lod > 8). The GHRHR and IGFBP3 were found to map near to each other on human chromosome 7 (HSA7), and the pig IGFBP3 gene has been mapped to SSC18 by others. Our mapping of pig GHRHR increases the comparative information available on the SSC18 maps and further confirms the synteny conservation between HSA7 and SSC18.
Analysis of genetic relationships between 10 cattle breeds with 17 microsatellites
Authors: Moazami‐Goudarzi K , Furet J P , Grosclaude F , Laloë D
Published: December 2003

To guide genetic conservation programmes with objective criteria, general genetic variability has to be taken into account. This study was conducted to determine the genetic variation between 10 cattle breeds by using 17 microsatellite loci and 13 biochemical markers (11 blood groups, the transferrin and β‐casein loci). Microsatellite loci were amplified in 31–50 unrelated individuals from 10 cattle breeds: Charolais, Limousin, Breton Black Pied, Parthenais, Montbéliard, Vosgien, Maine‐Anjou, Normande, Jersey and Holstein. Neighbor‐joining trees were calculated from genetic distance estimates. The robustness of tree topology was obtained by bootstrap resampling of loci. A total of 210 alleles of the 17 microsatellites were detected in this study and average heterozygosities ranged from 0·53 in the Jersey breed to 0·66 in the Parthenais breed. In general, low bootstrap values were obtained: with the 17 microsatellites, the highest bootstrap values concerned the Holstein/Maine‐Anjou grouping with an occurrence of 74%; with the biochemical markers, this node had an occurrence of 79% and the Charolais/Limousin grouping appeared with an occurrence of 74%; when microsatellites and biochemical polymorphism were analysed together, the occurrence of the Holstein/Maine‐Anjou grouping was 90% and that of the Charolais/Limousin grouping was 42%. These results suggest that 30 microsatellites, a number currently considered as sufficient to distinguish closely related breeds is, in fact, probably insufficient.
A medium density microsatellite map of BTA10: reassignment of INRA69
Authors: Taylor J F , Lutaaya E , Sanders J O , Turner J W , Davis S K
Published: December 2003

We have developed a genetic map of BTA10 based on 8952 informative meioses for 13 microsatellite markers and the erythrocyte antigen Z. With the exception of OarAE64, the support for the order of all loci in the map exceeded a LOD > 3·0. The length of the BTA10 genetic map was 87·0 centimorgans (cM). The 14‐marker, sex‐average map in Kosambi cM was: CSSM38–8·9‐BM1237–5·2‐HH8A–2·6‐INRA69–10·6‐TGLA378–0·8‐BM6305–17·2‐TGLA102–17·9‐INRA96–0·3‐CSRM60–9·2‐DIK20–3·0‐EAZ–6·7‐CSSM46–3·7‐SRCRSP3–1·0‐OarAE64 with an average interval of 6·70 cM. The microsatellite INRA69 was recently assigned to the pseudoautosomal region of the bovine X chromosome by linkage analysis. However, we found that twopoint support for linkage between INRA69 and 15 X‐linked bovine microsatellites was LOD < 0·50 in 529 reciprocal backcross and F2 fullsib progeny. We performed twopoint analyses of INRA69 against 275 markers distributed throughout the bovine genome and found significant associations with a LOD > 3·0 only between INRA69 and eight BTA10 microsatellite loci. Consequently, we excluded INRA69 from the genetic map of the X chromosome and reassign this microsatellite to BTA10.
Non‐association between Rfp‐Y major histocompatibility complex‐like genes and susceptibility to Marek’s disease virus‐induced tumours in 63× 72 F2 intercross chickens
Authors: Vallejo R L , Liu H C , Cheng H H , Witter R L , Bacon L D , Pharr G T
Published: December 2003

Marek’s disease (MD) is a lymphoproliferative disease caused by a member of the herpesvirus family, and the best understood genetic resistance to MD involves the chicken major histocompatibility complex (MHC) B‐complex. Preliminary observations have suggested that MHC‐like Rfp‐Y genes might also influence the incidence of MD. This study describes the differentiation and definition of unique Rfp‐Y genes in inbred lines 63 and 72, lines that possess identical B‐complex genes, but that are resistant or susceptible to MD, respectively. To assess if Rfp‐Y genes affect susceptibility to MD, 265 63× 72 F2 chickens were challenged with the JM strain of MD virus at 1 week of age and were evaluated for MD lesions at up to 10 weeks of age. Genotyping of the F2 chickens for Rfp‐Y haplotypes was performed by restriction fragment length polymorphism analysis of genomic DNA using TaqI and a B‐FIV probe. Analysis of variance and interval mapping procedures were used to determine association between the Rfp‐Y haplotypes and the phenotypic MD values of the F2 chickens. The cosegregation analysis of 265 F2 chickens indicated that there was no association between Rfp‐Y haplotypes and MD susceptibility. Furthermore, the fact that the Rfp‐Y haplotypes fit the 1:2:1 segregation ratio and the Rfp‐Y allele frequencies did not differ significantly from 0·5 in the full population or in selected subpopulations (of either 40 MD‐resistant or 39 MD‐susceptible chickens) also indicated that Rfp‐Y haplotypes do not significantly influence MD susceptibility. We conclude that Rfp‐Y haplotypes do not play a major role in determining the genetic susceptibility to MD in 63× 72 F2 White Leghorn chickens.
Chicken microsatellite markers isolated from libraries enriched for simple tandem repeats
Authors: Gibbs M , Dawson D A , McCamley C , Wardle A F , Burke T , Armour J A L
Published: December 2003

The total number of microsatellite loci is considered to be at least 10‐fold lower in avian species than in mammalian species. Therefore, efficient large‐scale cloning of chicken microsatellites, as required for the construction of a high‐resolution linkage map, is facilitated by the construction of libraries using an enrichment strategy. In this study, a plasmid library enriched for tandem repeats was constructed from chicken genomic DNA by hybridization selection. Using this technique the proportion of recombinant clones that cross‐hybridized to probes containing simple tandem repeats was raised to 16%, compared with < 0·1% in a non‐enriched library. Primers were designed from 121 different sequences. Polymerase chain reaction (PCR) analysis of two chicken reference pedigrees enabled 72 loci to be localized within the collaborative chicken genetic map, and at least 30 of the remaining loci have been shown to be informative in these or other crosses.
Cloning of canine rom‐1 and its investigation as a candidate gene for generalized progressive retinal atrophies in dogs
Authors: Gould D J , Petersen‐Jones S M , Lin C T , Sargan D R
Published: December 2003

Generalized progressive retinal atrophy (gPRA) represents a genetically heterogenous group of retinal degenerations affecting pedigree dogs. Currently, we are using a candidate gene approach in an attempt to identify mutations causing gPRA in dogs. Here we report the cloning, sequencing and analysis of canine rom‐1, a structural gene of the rod photoreceptor. Single‐stranded conformation polymorphism (SSCP) analysis was used to look for polymorphisms segregating with gPRA in the English cocker spaniel, Labrador retriever, miniature poodle, miniature long‐haired dachshund, Tibetan terrier, miniature schnauzer, Cardigan Welsh corgi and Irish wolfhound. Further investigation involved DNA sequencing and restriction fragment length polymorphism (RFLP) analysis. Our studies revealed the presence of three polymorphisms, none of which segregated with disease phenotype. Haplotype analysis identified four rom‐1 alleles. Our results indicate that rom‐1 is unlikely to be a cause of gPRA in the breeds of dog examined.
Comparisons of three probability formulae for parentage exclusion
Authors: Jamieson A , C S Taylor St.
Published: December 2003

Three general formulae calibrate the average capability of marker systems to dispute falsely reported pedigree records in uniparous species. The most familiar exclusion formula applies to paternity, although the same formula applies equally to maternity. Another formula faults the relationship of a single offspring with its putative parent; for example, where the genotype of the other parent is not available. The remaining formula excludes both of the falsely recorded parents of a substituted offspring. Simplified forms of the three general formulae facilitate the calculation of maximal average exclusion values over a range of hypothetical markers. Allele frequency data on eight marker systems in horses provide practical examples. The exclusion values of the three formulae are compared.
A single base transversion in the flanking region of an equine microsatellite locus affects amplification of one allele
Authors: Eggleston‐Stott M L , Delvalle A , Dileanis S , Wictum E , Bowling A T
Published: December 2003

The equine dinucleotide microsatellite HMS7 is part of a microsatellite panel utilized in a parentage verification programme at the Veterinary Genetics Laboratory (Davis, California, USA). Apparent non‐Mendelian inheritance was noted when a Quarter Horse mare was excluded as the parent of two offspring based on analysis of the HMS7 locus. The mare’s DNA type qualified her as a parent of the offspring at an additional 20 microsatellite loci. The three animals appeared homozygous for HMS7 with each possessing an allele different from that of the other two animals. Polymerase chain reaction primers designed to bind outside the published primer‐binding sites amplified an additional shared allele in all three horses, which qualified the mare as the dam of the two offspring. Sequencing of this newly detected allele revealed a C to A transversion in one of the published primer‐binding regions. Apparent non‐Mendelian inheritance at the HMS7 locus has been encountered in an additional 26 Quarter Horse parentage cases. In all instances, the lack of amplification and resultant ‘null’ allele was shown to be caused by the same transversion.