bluuebunny/crossref_metadata_2025 huggingface dataset:
Detection of QTL for milk production traits in cattle by application of a specifically developed marker map of BTA6
Authors: Kühn Ch , Freyer G , Weikard R , Goldammer T , Schwerin M
Published: March 2003

Interval mapping was carried out to identify quantitative trait loci (QTL) for milk production traits in five granddaughter design families of the German Holstein population. Fourteen randomly generated markers spanning the whole of BTA6 and six targeted microsatellite markers from BTA6q21–31 were included in the analysis. In one family a QTL with effects on milk fat yield and milk protein yield was mapped to the interval TGLA37‐FBN13 (3 c
m proximal to FBN13, lodscore 3 ·22) in the middle part of the chromosome. Although there are several reports about QTL with effects on milk production traits on BTA6 in the literature, a QTL with effects on milk fat and milk protein yield has not been previously described.

After initial indications of at least two QTL for milk production traits ( Kühn et al. 1996b
) located in the middle of BTA6, microsatellite markers specific for the region of interest were developed (
Weikard et al. 1997
). The addition of five informative markers in the region BM143‐CSN3 decreased the average marker interval from 12 ·5 c
m to 5 ·5 c
m and more than doubled the number of informative geno‐ types.
Characterization and mapping of canine polymorphic markers
Authors: Tiret L , Kessler J L , Bentolila S , Fauré S , Bach J M , Weissenbach J , Panthier J J
Published: March 2003

The nucleotide sequences data reported in this paper were submitted to the EMBL library at the European Bioinformatics Institute (EBI).
Estimations of the efficacy and reliability of paternity assignments from DNA microsatellite analysis of multiple‐sire matings
Authors: Vankan D M , Faddy M J
Published: March 2003

It is important for bovine DNA testing laboratories to provide the cattle industry with accurate estimates of the efficacy and reliability of DNA tests offered so that end users of this technology can adequately assess the cost‐benefits of testing. To address these issues for bovine paternity testing, paternity exclusion probability estimates were obtained from breed panel data and were predictive of the efficacy of the DNA tests used in 39 multiple‐sire mating groups, involving 5960 calves and 505 bulls. Paternity testing of these mating groups has demonstrated that the majority involve a variable proportion of unknown sires and this impacts on the reliability of sire allocation. Mathematical models based on binomial or beta‐binomial probability distributions were used to estimate the reliability of single‐sire allocations from multiple‐sire matings involving unknown sires. Reliability of 98–99% is achieved when the exclusion probability is 0 ·99 or greater, after allowing for up to 20% unknown sires. When the exclusion probability drops below 0 ·90 and there are 20% unknown sires, the reliability is poor, bringing into question the benefits of testing. This highlights the need for DNA testing laboratories to offer paternity tests with an exclusion power of at least 99%.
Extending the chicken‐human comparative map by placing 15 genes on the chicken linkage map
Authors: Groenen M A M , Crooijmans R P M A , Dijkhof R J M , Acar R , Van Der Poel J J
Published: March 2003

To increase the number of type I loci on the chicken linkage map, chicken genes containing microsatellite sequences (TAn, CAn, GAn, An) were selected from the nucleotide sequence database and primers were developed to amplify the repeats. Initially, 40 different microsatellites located within genes were tested on a panel of animals from diverse breeds, and identified 17 polymorphic microsatellites. These polymorphisms allowed us to add 15 new genes to the chicken linkage map. In addition, two genes were added to the chicken map by fluorescent in situ hybridization. As the map position of the human homologues of 13 of these genes is known, these markers extend the comparative map between chicken and man. Our results confirm and refine conserved regions between chicken and man on chicken chromosomes 2 and 7 and on linkage group E29C09W09. Furthermore, an additional conserved region is identified on chromosome 7.
Bovine chromosome 4 workshop: consensus and comprehensive linkage maps
Authors: Casas E , Barendse W , Beever J E , Burns B M , Davis S K , Erhardt G , Förster M , Gomez‐Raya L , Kalm E , Kappes S M , Klungland H , Lewin H A , Lien S , Olsaker I , Reinsch N , Schwerin M , Song Y , Taylor J F , Thomsen H , Våge D I , Wu X , Xu N , Yeh C‐C
Published: March 2003

The report of the bovine chromosome 4 (BTA4) workshop is presented. Six laboratories contributed a total of 30 168 informative meioses from 62 loci. Twenty‐two loci were typed by at least two independent laboratories and were used to construct a consensus linkage map of BTA4. The remaining 40 loci were subsequently incorporated into a comprehensive map. The sex‐averaged consensus map covered 131 ·4 cM. The female map was 124 ·3 cM in length, while the male map was 134 ·3 cM. The comprehensive sex‐averaged map spanned 141 ·6 cM. The length of the female and male comprehensive maps were 123 ·1 cM and 156 ·4 cM, respectively. Average genetic distance between loci was 6 and 2 ·3 cM for the consensus and comprehensive linkage maps, respectively.
Single nucleotide polymorphisms in the equine transferrin gene
Authors: Brandon R B , Giffard J M , Bell K
Published: March 2003

Single nucleotide polymorphisms (SNPs) in exons 13, 15 and 16 of equine transferrin for common, rare and mutant variants were investigated. Compared with previous work a further 13 SNPs have been identified, allowing for the two previously identified clades to be subdivided into 11 groups. A combination of one or more of eight SNPs can be used to classify the equine variants into these 11 groups, since most are co‐inherited. Putative sites of glycosylation in exons 13 and 16 showed no polymorphism, suggesting that presence or absence of sugar moieties does not lead to electrophoretic variation between the variants. Using the 26 SNPs currently identified in transferrin it is still not possible to differentiate variants F1 from F2, or D from H2, which represent 75% of the variants occurring in Thoroughbred equine population. This suggests that further SNPs exist in equine transferrin. The significance of the high level of variation in exon 15 is discussed.
A single nucleotide deletion resulting in a premature stop codon is associated with marked reduction of transcripts from a goat β‐casein null allele
Authors: Persuy M‐A , Printz C , Medrano J F , Mercier J‐C
Published: March 2003

A null β‐casein allele (CSN2O) was investigated in Creole and Pyrenean goats producing milk devoid of β‐casein (CSN2). Northern blot analyses of total mammary RNA showed much lower amounts of CSN2 transcripts that were similar in size to the wild‐type counterpart. The amount of CSN2O mRNA was roughly 5% of the amount of mRNA obtained at the same age and stage of lactation from CSN2A/A goats. Comparative sequence analyses of full‐length CSN2O and CSN2A cDNAs showed that both alleles were of similar size, but allele CSN2O had a one‐nucleotide deletion in the 5′ end of exon 7, which introduces a premature stop codon. The open reading frame of allele CSN2O encodes a shortened polypeptide of 72 amino acids, compared to 223 amino acids for caprine preβ‐casein A. Comparative analyses of RT‐PCR products suggested that alleles CSN2O and CSN2A might also differ in the amount and relative ratio of minor deleted CSN2 transcripts. The lower amount of CSN2O mRNA was associated with the occurrence of the premature stop codon which may mediate a rapid decay of CSN2O mRNA and promote skipping of nucleotide stretches containing premature nonsense triplets.
Genetic variation in the bovine myostatin gene in UK beef cattle: Allele frequencies and haplotype analysis in the South Devon
Authors: Smith J A , Lewis A M , Wiener P , Williams J L
Published: March 2003

Work on Belgian Blue cattle revealed that an 11 base pair (bp) deletion within the bovine myostatin gene (GDF8) is associated with the double‐muscled phenotype seen in this breed. Investigations focusing on other European breeds known to show double‐muscling identified several mutations within the coding region of the gene associated with the double‐muscled phenotype in different breeds. The number of mutations found suggest that myostatin is highly variable within beef cattle. Variations that alter the structure of the gene product such that the protein is inactivated are associated with the most pronounced form of double‐muscling as seen in the Belgian Blue. However, other mutations may have a less extreme affect on muscle development. While overt double‐muscling gives rise to a high incidence of dystocia (calving difficulty), it is possible that some variants may give enhanced muscling, but with limited calving problems. We describe sequence analysis of the myostatin gene in ten beef breeds commonly used in the UK and show that the 11‐bp deletion responsible for double‐muscling in the Belgian Blue is also present in the South Devon cattle population. Allele frequencies and haplotypes in the South Devon and a polymerase chain reaction (PCR) based test for the deletion are described. PCR amplification across the deleted region provides a quick and effective test with clear identification of heterozygous individuals. We discuss our results with regard to the effect of genotype on phenotype and differences observed between the Belgian Blue and the South Devon.
Differences in gene density on chicken macrochromosomes and microchromosomes
Authors: Smith J , Bruley C K , Paton I R , Dunn I , Jones C T , Windsor D , Morrice D R , Law A S , Masabanda J , Sazanov A , Waddington D , Fries R , Burt D W
Published: March 2003

The chicken karyotype comprises six pairs of large macrochromosomes and 33 pairs of smaller microchromosomes1. Cytogenetic evidence suggests that microchromosomes may be more gene‐dense than macrochromosomes. In this paper, we compare the gene densities on macrochromosomes and microchromosomes based on sequence sampling of cloned genomic DNA, and from the distribution of genes mapped by genetic linkage and physical mapping. From these different approaches we estimate that microchromosomes are twice as gene‐dense as macrochromosomes and show that sequence sampling is an effective means of gene discovery in the chicken. Using this method we have also detected a conserved linkage between the genes for serotonin 1D receptor (HTR1D) and the platelet‐activating factor receptor protein gene (PTAFR) on chicken chromosome 5 and human chromosome 1p34 ·3. Taken together with its advantages as an experimental animal, and public access to genetic and physical mapping resources, the chicken is a useful model genome for studies on the structure, function and evolution of the vertebrate genome.
Localisation of Xho1 repetitive sequences on autosomes in addition to the W chromosome in chickens and its relevance for sex diagnosis
Authors: Klein S , Ellendorff F
Published: March 2003

Repetitive sequences of the Xho1 family comprise about 70% of the W chromosome in chickens, are considered to be restricted to this sex chromosome and are used in sex diagnosis. This study investigated the reliability of sex diagnosis on small cell numbers. Fluorescent in situ hybridisations (FISH) with the Xho1 repeat sequence were performed on metaphases and signals were detected on the W chromosome and on some autosomes. Differences in signal intensity suggested that the number of repeats ranged from several thousand on the W chromosome to only a few on the autosomes. These results confirm the report from
Clinton (1994) of minor male products in sex specific PCR of the Xho1 repeat. We adopted his PCR protocol to analyse small numbers of cells. FISH on blastomeres and on blood cells from E3 to E11 embryos were compared to PCR results. The FISH procedure as well as the PCR protocol are suitable for sexing. For single cells FISH was slightly more consistent.
Genetic mapping of a locus associated with bovine chronic interstitial nephritis to chromosome 1
Authors: Kobayashi N , Hirano T , Maruyama S , Matsuno H , Mukoujima K , Morimoto H , Noike H , Tomimatsu H , Hara K , Itoh T , Imakawa K , Nakayama H , Nakamaru T , Sugimoto Y
Published: March 2003

Chronic interstitial nephritis with diffuse zonal fibrosis (CINF) occurs in Japanese Black cattle (Wagyu) as an autosomal recessive disorder leading to death prior to puberty, first six months or a year of life. We performed a genome‐wide scan using microsatellite markers in a Wagyu pedigree segregating for CINF and mapped theCINFlocus to bovine chromosome 1.CINFwas closest to microsatellitesBM9019andINRA49(Z score = 12 ·0;P< 3 ·4 × 10−10).
Characterisation of Iberian pig genotypes using AFLP markers
Authors: Óvilo C , Cervera M T , Castellanos C , Martínez‐Zapater J M
Published: March 2003

The use of the AFLP (amplified fragment length polymorphism) technique for the characterisation of highly inbred Iberian pig breed genotypes and the detection of strain‐specific polymorphisms is demonstrated. Twelve different primer combinations were used on individual DNA samples from animals belonging to two black hairless Iberian pig strains, Guadyerbas and Coronado. These amplification reactions allowed the detection of more than 1700 amplification products of which 26 were identified as strain‐specific markers, present in all individuals of one strain and absent in the other. Comparison of male and female amplification products within one strain also allowed the identification of 8 male‐specific amplified bands. AFLP showed a great power of marker detection due to a high multiplex ratio and high reproducibility. Comparison of similarity and co‐ancestry coefficient matrices also showed the usefulness of AFLP markers to estimate genetic relationships between individuals pigs.
Exclusion of the PDE6A gene for generalised progressive retinal atrophy in 11 breeds of dog
Authors: Dekomien G , Epplen J T
Published: March 2003

The cyclic guanosine monophosphate specific phosphodiesterase (cGMP‐specific PDE) is a key enzyme in the phototransduction cascade of the vertebrate retina. This enzyme consists of two catalytic α and β subunits, two identical inhibitory γ subunits as well as a δ subunit. Mutations in PDE6A and the PDE6B genes lead to autosomal recessive (ar) forms of retinitis pigmentosa (RP) in human and to the homologous disease in dogs, designated generalised progressive retinal atrophy (gPRA). We investigated the PDE6A gene in 13 gPRA‐affected dog breeds including healthy animals, obligate gPRA carriers and gPRA‐affected dogs. In the coding region of PDE6A only a rare sequence variation (G103A; Asp35Asn) was found in exon 1 of two healthy Tibet Terriers and one affected Cocker Spaniel. Using single‐stranded conformation polymorphism (SSCP) analyses we detected several sequence variations in eight of the PDE6A introns in different investigated breeds. Most informative for excluding the PDE6A gene as a cause for gPRA was a polymorphic microsatellite ((GT)10CG(GT)2CG(GT)12) in intron 14 and four sequence variations in intron 18 for almost all breeds investigated. The sequence variations of PDE6A did not segregate together with gPRA in 11 breeds. Since diseased animals were heterozygous for the polymorphisms, the PDE6A gene is unlikely to harbour the critical mutation causing gPRA in the following breeds: Chesapeake Bay Retriever, Entlebucher Sennenhund, Labrador Retriever, Tibet Mastiff, Dachshund (long‐and wire‐haired), Tibetan Terrier, Miniature Poodle, Australian Cattle Dog, Cocker Spaniel, Saarloos/Wolfshound, Sloughi.
Geographic and breed distribution of an Msp I PCR‐RFLP in the bovine growth hormone (bGH) gene
Authors: Lagziel A , DeNise S , Hanotte O , Dhara S , Glazko V , Broadhead A , Davoli R , Russo V , Soller M
Published: March 2003

Information is presented on the frequency of the Msp I (‐) allele in the third intron of the bovine growth hormone gene in a large number of cattle breeds. Consideration of the breed frequencies in relation to their geographic origin shows a low frequency for breeds originating in Northern Europe, moderate frequencies for breeds originating in Eastern Europe or the countries surrounding the Mediterranean basin, and very high frequencies for breeds originating in the Indian subcontinent. Consideration of breed frequencies in relation to breed type, shows low to moderate frequencies for the humpless breeds, high frequencies for the humped breeds. Various explanations for this distribution are discussed, among them the possibility that the Msp I (‐) allele originated in the Bos indicus breeds of the Indian subcontinent, from which it diffused through the humpless Bos taurus breeds of Eastern Europe, the Mediterranean basin, eventually reaching Western, Northern Europe, Western Africa in low frequencies.
Linkage mapping and comparative analysis of bovine expressed sequence tags (ESTs)
Authors: Grosse W M , Kappes S M , McGraw R A
Published: March 2003

Bovine expressed sequence tags (ESTs) containing microsatellites are suitable markers for both linkage and comparative maps. We isolated clones from a bovine fetal thigh skeletal muscle cDNA library that were positive for a (CA)10 probe. Thirty individual clones were isolated and characterised by sequencing. Sequences from the 5′ and 3′ ends of a clone were considered as separate ESTs until a contiguous sequence was identified. A total of 47 ESTs were sequenced from the 5′ and/or 3′ ends and full sequence was obtained for the 30 clones. BLAST nucleotide analysis identified significant homology to known mammalian coding regions for 31 of the bovine ESTs, 30 of which also matched human ESTs or sequence‐tagged sites (STS). The remaining 16 bovine ESTs represented novel transcripts. Microsatellites were isolated in 27 of the ESTs, 11 of which were developed into markers and placed on the MARC bovine linkage map. Human cytogenetic map positions were available for 20 of the 30 human EST orthologs, and a putative bovine map position for 17 of the sequences could be inferred using comparative mapping data. These results demonstrated that mapping bovine ESTs containing microsatellites is a plausible strategy to increase the density of gene markers on the bovine linkage and comparative maps.
Characterisation of gene expression in bovine adipose tissue before and after fattening
Authors: Oishi M , Taniguchi Y , Nishimura K , Yamada T , Sasaki Y
Published: March 2003

It has been reported that fattening causes bovine adipose tissue development associated with an enlargement in adipocyte cell size. As a first study to elucidate mechanisms of bovine adipose tissue development during fattening, our experiment was designed to characterise gene expression in bovine adipose tissue before and after fattening. We randomly isolated a large number of cDNA clones derived from bovine adipose tissue before and after fattening. Sequence analysis of the isolated clones showed that 3 and 10 clones from before and after fattening, respectively, correspond to genes related to adipocyte development and/or function in the adipose tissue. In addition, we isolated cDNA clones that possess negative signal by hybridising the cDNA population from the adipose tissue after fattening with that before fattening as a probe. As a result, we identified five types of transcripts observed in the adipose tissue after fattening but not before fattening. Two of the five are likely to encode bovine orthologs of phospholipase A2 and RNA helicase p68, while the other three represent unknown genes. Further functional investigation of the identified genes might lead to elucidation of mechanisms of bovine adipose tissue development during fattening.
Consensus and comprehensive linkage maps of bovine chromosome 7
Authors: Gu Z , Gomez‐Raya L , Våge D I , Elo K , Barendse W , Davis G , Grosz M , Erhardt G , Kalm E , Reinsch N , Kappes S M. , Stone R T , Davis S K , Taylor J F , Kirkpatrick B W
Published: March 2003

The objective of this project was to integrate the currently available linkage maps for bovine chromosome 7 (BTA7) by combining data sets from eight research groups. A total of 54 unique markers were typed in eight pedigrees. Multilocus linkage analysis with CRI‐MAP produced a bovine chromosome 7 consensus framework map of 27 loci ordered with odds greater than 1000 : 1. Furthermore, we present a bovine chromosome 7 comprehensive map integrating 54 loci. The locus order is in general agreement with the recently published linkage maps except for one discrepancy. The order of loci BM9289, BMS713, and ILSTS001 was reversed in the consensus framework map relative to the published USDA‐MARC bovine chromosome 7 linkage map.
Evaluation of RDS/Peripherin and ROM1 as candidate genes in generalised progressive retinal atrophy and exclusion of digenic inheritance
Authors: Runte M , Dekomien G , Epplen J T
Published: March 2003

Generalised progressive retinal atrophy (gPRA) is a heterogeneous group of hereditary diseases causing degeneration of the retina in dogs and cats. As a combination of mutations in theRDS/Peripherin and the ROM1 genes leads to the phenotype of retinitis pigmentosa in man we first performed mutation analysis to screen these genes for disease causing mutations followed by the investigation of a digenic inheritance in dogs. We cloned the RDS/Peripherin gene and investigated the RDS/Peripherin and ROM1 genes for disease causing mutations in 13 gPRA‐affected dog breeds including healthy animals, obligate gPRA carriers and gPRA‐affected dogs. We screened for mutations using single strand conformation polymorphism (SSCP) analysis. Sequence analysis revealed several sequence variations. In the coding region of the RDS/Peripherin gene three nucleotide exchanges were identified (A277C; C316T; G1255A), one of which leads to an amino acid substitution (Ala339Thr). Various silent sequence variations were found in the coding region of the ROM1 gene (A536G, G1006A, T1018C, T1111C, C1150T, C1195T), as well as an amino acid substitution (G252T; Ala54Ser). By excluding the respective gene as a cause for gPRA several sequence variations in the intronic regions were investigated. None of these sequence variations cosegregated with autosomal recessively (ar) transmitted gPRA in 11 breeds. The candidate geneRDS/Peripherin obviously does not harbour the critical mutation causing the autosomal recessive form of gPRA because diseased individuals show heterozygous genotypes for sequence variations in the Miniature Poodle, Dachshund, Australian Cattle Dog, Cocker Spaniel, Chesapeake Bay Retriever, Entlebucher Sennenhund, Sloughi, Yorkshire Terrier, Tibet Mastiff, Tibet Terrier and Labrador Retriever breeds. In the following breeds the ROM1 gene was also excluded indirectly for gPRA: Miniature Poodle, Dachshund, Australian Cattle Dog, Sloughi, Collie, Tibet Terrier, Labrador Retriever and Saarloos/Wolfhound. Digenic inheritance for gPRA is practically excluded for both these genes in four breeds: Miniature Poodle, Dachshund, Labrador Retriever and Saarloos/Wolfhound.
Genetic variation within the Merino sheep breed: analysis of closely related populations using microsatellites
Authors: Diez‐Tascón C , Littlejohn R P , Almeida P A R , Crawford A M
Published: March 2003

Genetic relationships among six populations of Merino sheep were investigated using microsatellites. The history of the six populations is relatively well documented, with all being derived from the Spanish Merino breed within the last 400 years. Genetic variation was highest amongst the Spanish and Portuguese populations, although the preservation of genetic diversity within the other populations was high. By a variety of different statistical tests the French Mutton, German Mutton and New Zealand Merino populations could be differentiated from each other and the Iberian Merinos, indicating that microsatellites are able to track relatively recent changes in the population structure of sheep breeds. The dendrograms constructed on the basis of microsatellite allelic frequencies showed that populations that have shared selection criteria (meat vs. wool) tend to cluster together.
Are DNA profiles breed‐specific? A pilot study in pigs
Authors: Signer E N , Jeffreys A J , Dubrova Y E
Published: March 2003

In this study, DNA fingerprints from 32 unrelated domestic pigs were analysed and screened for breed‐specificity. Three breed groups were analysed: Chinese Meishan, Large White and a collection of other European breeds. Ninety‐three distinct and variable bands were used to estimate genetic distances between the animals. Between the groups these individual genetic distances substantially exceeded those within a group. Linear discriminant analysis showed that the 23 most common DNA fragments revealed sufficient breed‐specificity as to assign each pig correctly to its breed or breed group. These findings, although based on a small sample, indicate that selective use of minisatellite variation in pigs appears to be a valuable novel approach toward the development of breed DNA profiles and the resolution of breed relationships.
Single nucleotide polymorphisms (SNPs) within Bov‐A2 SINE in the second intron of bovine and buffalo k‐casein (CSN3) gene
Authors: Damiani G , Florio S , Budelli E , Bolla P , Caroli A
Published: March 2003

The genetic polymorphism of an entire Bov‐A2 element located in the second intron of the buffalo and bovine k‐casein (CSN3) gene was investigated by amplification and sequencing of PCR products. Single nucleotide polymorphisms were detected. A PCR‐RFLP method was developed to detect an A or G mutation at position 605 of bovine Bov‐A2 element which creates a BfaI polymorphic site. The frequencies of the B allele, with the BfaI site, were for 0·275, 0·775, 0·750, 0·975, respectively, for Italian Holstein Friesian, Grey Alpine, Friuli Red Pied and Reggio bovine breeds. The mutation rate (substitutions and deletions/insertions per nucleotide site per year) was 2·5 × 10−9 for Bov‐A2 sequences in the second intron of CSN3. The comparison with other Bov‐A2 elements suggests that this retroelement might be an important source of single nucleotide polymorphism for analysis of Bovidae genomes.
A 12 000 rad whole genome radiation hybrid panel for high resolution mapping in cattle: characterization of the centromeric end of chromosome 1
Authors: Rexroad Iii C E , Owens E K , Johnson J S , Womack J E
Published: March 2003

We have constructed a 12 000 rad bovine whole‐genome radiation hybrid panel (BovR12) to complement the 5000 rad panel (BovR5) currently available to the bovine genomics research community. Initial characterization with markers from chromosome 1 reveals a higher frequency of breakage between adjacent markers and subsequently a larger number of ‘linkage’ groups on this chromosome. For this set of markers, the retention frequency is also higher than in BovR5.
Mapping of the CYP1A1, SSTR1 and TTF1 genes to pig chromosome 7q refines the porcine–human comparative map
Authors: Marklund S , K Tuggle C , Rothschild Mf
Published: March 2003

The cytochrome P‐450, subfamily I, polypeptide 1 (CYP1A1), somatostatin receptor 1 (SSTR1) and transcription termination factor 1 (TTF1) genes, predicted to reside on SSC7q based on chromosome painting studies, were selected for genetic mapping in the pig. Porcine sequence tagged sites (STSs) spanning 0.9–1.5 kb genomic DNA sequences were generated and all genes were physically assigned to SSC7q12‐q23, q26 using a pig–rodent somatic cell hybrid panel. Direct sequencing of PCR products from four different breeds revealed single nucleotide polymorphisms (SNPs) in all genes. SNPs in the SSTR1 and CYP1A1 genes allowed simple genotyping using PCR‐restriction fragment length polymorphism (RFLP) analysis and linkage mapping with the PiGMaP reference families. SSTR1 was found to be closely linked to CYP1A1 (0·0 cm; LOD=11·1) and ANPEP (0·0 cm; LOD=9·0). This refined the localization of a previously identified breakpoint in the linkage map between regions with orthology to human chromosome 15q (represented by CYP1A1 and ANPEP) and 14q (represented by SSTR1). Moreover, multipoint linkage data suggest inverted segments of orthology between HSA14q11‐q13 and SSC7q. The TTF1 SNP was confirmed by allele‐specific PCR but was not informative in any of the families used for linkage analysis.
Genetic structure of the Iberian pig breed using microsatellites
Authors: Martınez A M , Delgado J V , Rodero A , Vega‐Pla J L
Published: March 2003

An analysis of 25 microsatellite loci in 210 animals has been used to define the genetic structure of the Iberian pig, traditionally classified into several varieties. In addition, a sample of 20 Duroc pigs was used as an outgroup for topology trees. Inter‐variety genetic variation was estimated by unbiased average heterozygosity and the number of alleles observed. Significant deviations from the Hardy–Weinberg equilibrium (HWE) were shown for 19 loci across the whole population. By contrast, equilibrium deviation within varieties was much lower. Genetic variation measures, genetic distance values and a neighbour‐joining tree were used to estimate subdivision. In addition, an individual tree was constructed to contrast the assignation of animals into varieties. Despite the low bootstrap values obtained in the varieties neighbour‐joining tree, the degree of genetic variation found was sufficient to support the division of the Iberian pig into varieties, although in some cases the traditional classification cannot be accepted. These results have shown the value of this marker panel in the study of intra‐breed genetic structures.
Analysis of diversity and genetic relationships between four Chinese indigenous pig breeds and one AustraliaN commercial pig breed
Authors: Li K , Fan B , Zhao S , Peng Z , Li K , Chen Y , Moran C
Published: March 2003

The genetic diversities and relationships of four Chinese indigenous pig breeds and one Australian commercial pig breed have been evaluated using 27 microsatellites recommended by the International Society of Animal Genetics (ISAG) and the Food and Agriculture Organization (FAO). The allele frequencies, effective numbers of alleles and the polymorphic information content have been calculated. Nei's standard genetic distances have been used to construct a UPGMA dendrogram, which has been evaluated by the Bootstrap test. The utility of microsatellites for evaluating genetic diversity of pigs is discussed.
Relationships between the endangered Pustertaler–Sprinzen and three related European cattle breeds as analysed with 20 microsatellite loci
Authors: Edwards C J , Loftus R T , Bradley D G , Dolf G , Looft C
Published: March 2003

We estimated the genetic relationships between the endangered German Pustertaler–Sprinzen cattle breed and the Pinzgauer, Vosges and Simmental breeds – decided upon after consultation of the available historical literature. Within‐breed diversity of the four breeds was also assessed. Twenty microsatellite markers were amplified in 27–50 unrelated individuals from populations of each breed. Within‐breed variation was estimated from average heterozygosity values and mean number of alleles. Breed relationships were evaluated by genetic distance and a neighbour‐joining tree was calculated from these estimates. Bootstrap resampling of loci tested the robustness of the tree topology obtained. A tree was also constructed from distance matrices using individual animals as operational taxonomic units. From both the average heterozygosity values and mean number of alleles calculated, the Pustertaler breed appears to be no more genetically impoverished than the other breeds analysed. The breed tree showed an 85% support for the Pustertaler–Pinzgauer grouping, and this result is echoed in the genetic distance values and allele‐sharing individual tree.
Assessment of the population structure of five Finnish dog breeds with microsatellites
Authors: Koskinen M T , Bredbacka P
Published: March 2003

Genetic variabilities within and between Finnish populations of Golden Retrievers, German Shepherds, Wirehaired Dachshunds, Pembroke Welsh Corgis and Bedlington Terriers were quantified with microsatellite allele numbers, observed heterozygosities, expected heterozygosities, FIS estimates, FST estimates and DS distances. In a sample of 50 individuals from each breed and ten polymorphic loci, the highest genetic diversity was exhibited in the Wirehaired Dachsunds and lowest in the Bedlington Terriers. Although statistically significant deviations from the Hardy–Weinberg (H–W) equilibrium were observed, they occurred at an unexpectedly low frequency. Most strikingly, the extremely small Bedlington Terrier population displayed genotypes in H–W proportions in all investigated loci. The H–W deviations always occurred with positive FIS estimates, which, on average, were not larger than values reported for free‐living canids. Genetic differentiation between the breeds was very large. As a comparison, present estimates were, on average, over two times higher than previously observed between breeds of sheep, and over two times higher than the highest estimates reported between human populations. Moreover, the highest DS distances were only slightly lower than the lowest values inferred between humans and chimpanzees. Severe bottlenecks in the recent past of the examined breeds were not statistically supported. The presented data imply genetic isolation and intense artificial selection in the history of these breeds of dogs.
Convenient genotyping of six myostatin mutations causing double‐muscling in cattle using a multiplex oligonucleotide ligation assay
Authors: Karim L , Coppieters W , Grobet L , Georges M , Valentini A
Published: March 2003

We herein describe a procedure that allows for simultaneous genotyping of six loss‐of‐function mutations in the bovine myostatin gene associated with the double‐muscling phenotype. The proposed method relies on a multiplex oligonucleotide ligation assay and detection of the fluorescently labelled products using automatic sequencers.
Validation of 15 microsatellites for parentage testing in North American bison, Bison bison and domestic cattle
Authors: Schnabel R D , Ward T J , Derr J N
Published: March 2003

Fifteen bovine microsatellites were evaluated for use in parentage testing in 725 bison from 14 public populations, 178 bison from two private ranches and 107 domestic cattle from five different breeds. The number of alleles per locus ranged from five to 16 in bison and from five to 13 in cattle. On average, expected heterozygosity, polymorphism information content (PIC) and probability of exclusion values were slightly lower in bison than in cattle. A core set of 12 loci was further refined to produce a set of multiplexed markers suitable for routine parentage testing. Assuming one known parent, the core set of markers provides exclusion probabilities in bison of 0·9955 and in cattle of 0·9995 averaged across all populations or breeds tested. Tests of Hardy‐Weinberg and linkage equilibrium showed only minor deviations. This core set of 12 loci represent a powerful and efficient method for determining parentage in North American bison and domestic cattle.
Mapping of 14 expressed sequence tags (ESTs) from porcine skeletal muscle by somatic cell hybrid analysis
Authors: Davoli R , Bigi D , Fontanesi L , Zambonelli P , Yerle M , Zijlstra C , Bosma A A , Robic A , Russo V
Published: March 2003

Chromosomal assignments are reported for fourteen porcine expressed sequence tags (ESTs) —CALM1, CRYAB, MYH7, MYL1, PDK4, PGAM2, PYGM, REV3L, RFC1, SLN, SPTBN1, SRM160, TPM1 and YWHAG. The ESTs were derived from our porcine skeletal muscle cDNA library. The ESTs sequences selected for mapping included the presence of the 3′‐untranslated region. The assignments were performed using two independent somatic cell hybrid panels providing the possibility of confirmation of the results obtained. The observed localizations are compared with the locations predicted from heterologous (human–pig, pig–human) chromosome painting data and knowledge of the map locations of the human homologues. These results add new information to the porcine genome transcript map.
Testing for the presence of previously identified QTL for milk production traits in new populations
Authors: Wiener P , Maclean I , Williams J L , Woolliams J A
Published: March 2003

Five chromosomal regions previously associated with milk production traits were tested in 16 families of Black and White cattle from the UK. The traits were also linearly transformed into genetically and phenotypically independent variables normalized by phenotypic variances (‘canonical traits’). Significant associations with the untransformed and canonical traits were found for bovine chromosome 6. There was also evidence that chromosome 9 influenced these traits. The linear transformation clarified the effects of chromosomal regions; regions with effects on all three untransformed traits (milk, fat and protein yields) were generally condensed into an effect on a single canonical trait. Comparison of our results with those reported previously for American Holstein cattle suggested that the QTL may not be the same.
Quantitative trait loci (QTL) analysis in a Meishan×Göttingen cross population
Authors: Wada Y , Akita T , Awata T , Furukawa T , Sugai N , Ishii K , Ito Y , Kobayashi E , Mikawa S , Yasue H , Sugai N , Inage Y , Kusumoto H , Matsumoto T , Miyake M , Murase A , Shimanuki S , Sugiyama T , Uchida Y , Yanai S
Published: March 2003

In order to locate the genetic regions in the swine genome that are responsible for economically important traits, a resource population has been constructed by mating two female Meishan pigs with a male Göttingen miniature pig. In subsequent generations, 265 F2 offspring were produced from two F1 males and 19 F1 females. The F2 offspring were scored for eight traits including growth rate, teat number, vertebra number and backfat thickness, and genotyped for 318 genetic markers spanning the swine genome. Least‐square analysis revealed quantitative trait loci (QTL) effects for vertebra number on chromosomes 1 and 2; for teat number on chromosomes 1 and 7; for birth weight on chromosome 1; for average daily gain between 4 and 13 weeks of age on chromosomes 9 and 10; for backfat thickness on chromosome 7; and for backskin thickness on chromosome 3.
Chicken microsatellite primers are not efficient markers for Japanese quail
Authors: Inoue‐Murayama M. , Kayang B. B. , Kimura K. , Ide H. , Nomura A. , Takahashi H. , Nagamine Y. , Takeda T. , Hanada H. , Tatsuda K. , Tsudzuki M. , Matsuda Y. , Mizutani M. , Murayama Y. , Ito S.
Published: March 2003

Domestic fowl or chicken (Gallus gallus) and Japanese quail (Coturnix japonica) belong to the family Phasianidae. The exchange of marker information between chicken and quail is an important step towards the construction of a high‐resolution comparative genetic map in Phasianidae, which includes several poultry species of agricultural importance. We tested chicken microsatellite markers to see if they would be suitable as genetic linkage markers in Japanese quail. Twenty‐six per cent (31/120) of chicken primers amplified individual loci in Japanese quail and 65% (20/31) of the amplified loci were found to be polymorphic. Eleven of the polymorphic loci were excluded as uninformative because of the lack of amplification in some individuals or high frequency of nonspecific amplification. The sequence information of the remaining nine loci revealed six of them to contain microsatellites that were nearly identical with those of the orthologous regions in chicken. For these six loci, allele frequencies were estimated in 50 unrelated quails. Although the very few chicken markers that do work well in quail could be used as anchor points for a comparative mapping, most chicken markers are not useful for studies in quail. Therefore, more effort should be committed to developing quail‐specific markers rather than attempting to adapt chicken markers for work in quail.
Analysis of expressed sequence tags from a cDNA library of somatic nuclear transfer‐derived cloned bovine whole foetus
Authors: Taniguchi Y. , Lejukole H. Y. , Yamada T. , Akagi S. , Takahashi S. , Shimizu M. , Yasue H. , Sasaki Y.
Published: March 2003

The expression profile of genes in specific tissues is studied through analysing expressed sequence tags (ESTs) and provides useful information for characterizing gene function and tissue physiology. Analysis of ESTs is achieved by partial sequencing and characterization of clones isolated randomly from cDNA libraries. In the present study, we analysed the genes expressed in the somatic nuclear transfer‐derived cloned bovine foetus in the early period of foetal development. To this aim, we constructed a directionally cloned cDNA library from somatic nuclear transfer‐derived cloned 60 day‐old whole foetus of cattle and sequenced 3′ end of 510 randomly isolated clones. By BLASTN analysis, we identified 403 unique clones: 186 showed homology to previously identified genes, 123 matched uncharacterized ESTs and 94 showed no significant matches to sequences already present in DNA databases. Analysis of these cDNA clones revealed that this library contained a variety of functional genes, while foetuin, insulin‐like growth factor 2, collagen type I αI and maternal G10 transcript genes were the most abundant transcripts. Our study allowed the establishment of a first list of genes expressed in bovine whole foetus. In future, the list of genes might help facilitate the understanding of physiology of foetal development in somatic nuclear transfer‐derived cloned bovine foetus.
The canine homeobox gene MSX2: sequence, chromosome assignment and genetic analysis in dogs of different breeds
Authors: Haworth K. , Breen M. , Binns M. , Hopkinson D. A. , Edwards Y. H.
Published: March 2003

The MSX2 gene encodes a homeodomain transcription factor important for normal head and face morphogenesis. MSX2 is expressed in key craniofacial structures during development and mutations in the human gene give rise to various craniofacial abnormalities. We are interested in the genetic basis of non‐pathogenic variation in skull and face shape. As part of this study we have analysed DNA from a panel of different dog breeds, selected for the differences they show in these traits and investigated MSX2 as a candidate gene. In this paper we describe the cloning of the canine homologue of MSX2, the determination of its structure, sequence and localization of the gene to dog chromosome 4q23. The DNAs from 11 individual domestic dogs belonging to 10 different breeds were sequenced in a search for genetic variation. Our studies show that variation in MSX2 does not contribute to the diversity of face shape observed in these domestic dogs and that the MSX2 sequence is strongly conserved between different dog breeds. The proximal promoter shows a high level of interspecies sequence conservation and several conserved transcription factor binding motifs have been identified and their significance discussed.
Breed demarcation and potential for breed allocation of horses assessed by microsatellite markers
Authors: Bjørnstad G. , Røed K. H.
Published: March 2003

Population demarcation of eight horse breeds was investigated using genotype information of 306 horses from 26 microsatellite loci. The breeds include the indigenous Norwegian breeds Fjord Horse, Nordland/Lyngen Horse, Døle Horse and Coldblooded Trotter together with Icelandic Horse, Shetland Pony, Standardbred and Thoroughbred. Both phylogenetic analysis and a maximum likelihood method were applied to examine the potential for breed allocation of individual animals. The phylogenetic analysis utilizing simple allele sharing statistics revealed clear demarcation among the breeds; 95% of the individuals clustered together with animals of the same breed in the phylogenetic tree. Even breeds with a short history of divergence like Døle Horse and Coldblooded Trotter formed distinct clusters. Implementing the maximum likelihood method allocated 96% of the individuals to their source population, applying an assignment stringency of a log of the odds ratio larger than 2. Lower allocation stringency assigned nearly all the horses. Only three individuals were wrongly allocated a breed by both methods. In conclusion, the study demonstrates clear distinction among horse breeds, and by combining the two assignment methods breed allocation could be determined for more than 99% of the individuals.
An allele associated with a non‐detectable amount of αs2 casein in goat milk
Authors: Ramunno L. , Longobardi E. , Pappalardo M. , Rando A. , Di Gregorio P. , Cosenza G. , Mariani P. , Pastore N. , Masina P.
Published: March 2003

The goat CSN1S2 locus is characterized by the presence of three alleles, A, B and C, all associated with about 2.5 g/l of protein per allele. The SDS–PAGE analysis of 441 individual milk samples obtained from goats belonging to a population reared in Southern Italy showed that the milk produced by three goats did not apparently contain αs2‐casein, whereas milk produced by 37 goats showed a less intense electrophoretic band of this casein fraction (about 50%). These results can be explained by hypothesizing the presence of another allele at this locus, CSN1S20, associated with a ‘null’ content of αs2‐casein. Southern blot, PCR and PCR–RFLP analyses of the DNA region containing the CSN1S2 gene of individuals producing milk with and without αs2‐casein did not show differences between the two groups. As a consequence, goats producing milk without αs2‐casein carry an apparently intact gene. The first results obtained by sequencing part of the CSN1S20 allele revealed a G→A transition at nucleotide 80 of the 11th exon which creates a stop codon and could be responsible for the absence of the αs2‐casein in goat milk. This mutation eliminates a NcoI restriction site. A test based on this polymorphism has been established in order to identify carriers of the CSN1S20 allele.
Physical anchorage and orientation of equine linkage groups by FISH mapping BAC clones containing microsatellite markers
Authors: Lindgren G. , Swinburne J. E. , Breen M. , Mariat D. , Sandberg K. , Guérin G. , Ellegren H. , Binns M. M.
Published: March 2003

A horse bacterial artificial chromosome (BAC) library was screened for 19 microsatellite markers from unassigned or non‐oriented linkage groups. Clones containing 11 (AHT20, EB2E8, HMS45, LEX005, LEX014, LEX023, LEX044, TKY111, UCDEQ425, UCDEQ464 and VIASH21) of these were found, which were from eight different linkage groups. The BAC clones were used as probes in dual colour FISH to identify their precise chromosomal origin. The microsatellite markers are located on nine different horse chromosomes, four of which (ECA6, ECA25, ECA27 and ECA28) had no previously in situ assigned markers.
Polymorphism of bovine major histocompatibility complex (MHC) class I genes revealed by polymerase chain reaction (PCR) and restriction enzyme analysis
Authors: Sawhney S. M. S. , Taylor D. W. , Russell G. C.
Published: March 2003

The polymorphic exon 2–exon 3 region of bovine major histocompatibility complex (MHC) class I genes was amplified by polymerase chain reaction (PCR) from genomic DNA samples with characterized class I polymorphism. The primers for amplification were designed in conserved regions at the borders of exons 2 and 3, based on all available cDNA sequences. The primers should, therefore, amplify most expressed class I genes, but may also amplify non‐expressed class I genes. The PCR amplified class I gene fragments of 700 bp were characterized on the basis of restriction fragment length polymorphism (RFLP). The PCR–RFLP analysis of class I genes showed that the bands in each digestion could be classified as non‐polymorphic, as shared between several bovine lymphocyte antigen (BoLA)‐A types, or as specific to a single BoLA‐A type. The same primers were then used for amplification of class I gene fragments from eight Sahiwal animals, a breed which originated in the Indian subcontinent. These studies showed that BoLA class I PCR–RFLP could be used to study class I polymorphism in family groups.