bluuebunny/crossref_metadata_2025_split huggingface dataset:
Organization of the sex‐linked late‐feathering haplotype in chickens
Authors: Iraqi F , Smith E J 
Published: July 2010

SummaryNucleotide sequence analysis of polymerase chain reaction products confirmed that ev21 integrated into one of two large homologous elements on the Z chromosome of late‐feathering (LF) White Leghorn chickens. Southern blots of NotI‐, NaeI‐, KspI‐ and BamHI‐digested DNA from early‐feathering (EF) and LF White Leghorns, that had been hybridized with a probe that flanks ev21, indicated a 180 kb duplication of an unoccupied repeat in the LF genotype of White Leghorns. A KspI fragment that carries ev21 was about 32 kb smaller than the KspI fragment found in EF DNA. In the evolution of LF, retroviral insertion into one of two large repeats and a 32 kb deletion may have generated LF.
Sequence and PCR‐RFLP analysis of 14 novel BoLA‐DRB3 alleles
Authors: Gelhaus A , Schnittger L , Mehlitz D , Horstmann R D , Meyer C G 
Published: July 2010

SummaryThe genetic diversity of the bovine class IIDRB3 locus was investigated by polymerase chain reaction (PCR) amplification and DNA sequencing of the first domain exon. Studying 34 animals of various cattle breeds, 14 previously unrecognized DRB3 alleles were identified. In three alleles, amino acid substitutions were observed that had not been previously found in bovine DRB3, but occurred at the same position in bovine DQB and in the DRB alleles of other mammals. For all newly identified alleles, the restriction fragment length polymorphism (RFLP) patterns of PCR products obtained with the enzymes RsaI, BstYI, and HaeIII were compared with patterns of 38 previously described alleles. Altogether, eleven novel PCR‐RFLP types were defined. Twelve out of the 42 PCR‐RFLP types identified so far were not found to be fully informative because they corresponded to more than one allelic sequence. PCR‐RFLP may therefore be a rapid and useful method for DRB3 typing in cattle families, but for studies on outbred populations, sequencing and hybridization techniques are required.
Probability of random sire exclusion using microsatellite markers for parentage verification
Authors: Usha A. P. , Simpson S. P. , Williams J. L. 
Published: July 2010

SummaryMany microsatellite sequences have been described in the bovine genome. Being highly polymorphic these have been suggested as markers for parentage verification and individual identification in cattle. We have evaluated the use of five highly polymorphic microsatellite markers for parentage verification in 14 breeds of cattle in the UK. Three of the microsatellite loci occur within introns in genes: BoLA DRB3, steroid 21‐hydroxylase, and the beta subunit of the follicle‐stimulating hormone. The other two are anonymous sites ETH131 and HEL6. Results were analysed by a statistical approach that takes in to account deviations from Hardy‐Wienberg equilibrium and linkage disequilibrium for multiple loci. The method of determining the probability of random sire exclusion uses observed genotype frequencies instead of allele frequencies. Independently, the markers used have a probability of between 0.72 and 0.62 of identifying a parentage error, while used together the five markers give, on average across breeds, a probability of 0.99 of excluding an incorrect sire.
Extensive mtDNA diversity in horses revealed by PCR–SSCP analysis
Authors: Marklund S , Chaudhary R , Marklund L , Sandberg K , Andersson L 
Published: July 2010

SummaryThe hypervariable D‐loop region of mitochondrial DNA (mtDNA) was amplified with the polymerase chain reaction using total horse DNA samples. Analysis of single strand conformation polymorphism (SSCP) of denatured amplification products was carried out by native polyacrylamide (8%) gel electrophoresis followed by silver staining. As many as 15 distinct SSCP variants were revealed when screening a total of 78 maternally unrelated horses representing five different breeds. All breeds showed a high degree of polymorphism and the estimated probability (PImt) that two maternally unrelated individuals have, by chance, identical SSCP variants varied between 0.14 and 0.30. We detected no heteroplasmy or deviations from strict and stable maternal inheritance when examining four maternal lineages, each represented by six to eight horses, separated by up to five generations from a common ancestral mare. The study establishes a simple screening method for detecting equine mtDNA types, which can be applied for tracing maternal genealogies and for association studies.
Report of the First Workshop on the Genetic Map of Bovine Chromosome 23
Authors: Beever J. E. , Lewin H. A. , Barendse W. , Andersson L. , Armitage S. M. , Beattie C. W. , Burns B. M. , Davis S. K. , Kappes S. M. , Kirkpatrick B. W. , Ma R. Z. , McGraw R. A. , Stone R. T. , Taylor J. F. 
Published: July 2010

SummaryA report of the first workshop on the genetic map of bovine chromosome 23 (BTA23) is given. Five laboratories contributed data from 29 loci, including a total 11586 informative genotypes. The combined pedigrees represented 1930 potentially informative meioses. Eighteen of the 29 loci were common to two or more data sets and were used to construct a framework linkage map of BTA23. Twelve of the 18 could be ordered on the linkage map with a likelihood ratio of greater than 1000:1. Thus, a low resolution consensus map was constructed with a high level of support for order. The sex‐averaged, female and male maps span 54.5, 52.7 and 55.8 cM, respectively. Sex‐specific differences in recombination frequency were identified for eight pairs of framework loci. Average genetic distance between framework loci on the sex‐averaged map is 5.0 cM.
Development and mapping of polymorphic microsatellite markers derived from a chicken brain cDNA library
Authors: Ruyter‐Spira C. P. , Crooijmans RPMA , Dijkhof R. J. M. , van Oers P. A. M. , Strijk J. A. , van der Poel J. J. , Groenen M. A. M. 
Published: July 2010

SummaryUntil now the genetic linkage map in chicken has been based mainly on random genomic markers. The addition of expressed sequence tags (ESTs) to the genetic linkage maps is becoming more important because ESTs can form the basis for comparative mapping studies. This may be helpful for the detection of candidate genes for quantitative trait loci (QTLs).In our study we used a (TG)13repeat as probe for the detection of microsatellites in a chicken brain cDNA library. After hybridization 0.15% of the cDNA clones gave a positive signal. The cDNA complexity of the library was high; of the 90 cDNA clones that were sequenced 60 occurred only once. For 29 clones primer sets for the polymerase chain reaction could be developed. Twenty‐one microsatellites were polymorphic on one or more of the test panels and 15 markers could be mapped on either or both of the international reference families. Because sequence homology between chicken and mammalian cDNAs is sometimes low it was difficult to assess the level of sequence homology that indicated a true homologous transcript. In our study seven cDNA clones, of which three could be mapped, showed a relatively high percentage of sequence homology with sequences found in other species. Because sequencing and mapping of expressed sequence tags in human and mouse is progressing very rapidly, it is predicted that further information will soon be readily available. Therefore, increasing the number of expressed sequences on the chicken genetic linkage map will be of value for comparative mapping studies in the near future.
Mapping economic trait loci for somatic cell score in Holstein cattle using microsatellite markers and selective genotyping
Authors: Ashwell M. S. , Rexroad C. E. , Miller R. H. , Van Raden P. M. 
Published: July 2010

SummaryMarker‐assisted selection (MAS) uses genetic marker genotypes to predict an animal's production potential and will provide additional selection information for progeny testing. With the discovery of highly polymorphic microsatellite markers, the tools now exist to begin the search for economic trait loci (ETL), which is the first step toward MAS. The objective of this study was to identify ETL for somatic cell score in an existing Holstein population. Using the granddaughter design, sons from seven grandsire families were genotyped with 20 autosomal microsatellites from five chromosomes (4, 8, 13, 17, 23), with an emphasis on chromosome 23, which is the location of the bovine major histocompatibility complex (BoLA). Selective genotyping was used to reduce the number of genotypes required, in which the 10 highest and 10 lowest sons from the phenotypic distribution curve were tested (140 sons in seven families). One marker (513), located near BoLA, showed evidence of an ETL in three of five polymorphic families. Additional sons were genotyped from the five families to estimate the effect and to compare selective and ‘complete’ genotyping. Both methods detected an ETL at marker 513, but in different families. This study provides evidence of the usefulness of microsatellite markers and the granddaughter design in the detection of ETL; however, additional markers need to be evaluated to determine the usefulness of selective genotyping. Based on the results from the 20 studied markers, the most likely position of a somatic cell score ETL lies near marker 513, located on chromosome 23.
Evidence for a single pedigree source of the hyperkalemic periodic paralysis susceptibility gene in Quarter Horses
Authors: Bowling A. T. , Byrns G. , Spier S. 
Published: July 2010

SummaryThe pedigree origin of a base pair substitution in the horse muscle sodium channel gene that confers susceptibility to the muscle disease hyperkalemic periodic paralysis (HYPP) was investigated with a set of 978 Quarter Horses. The horses were chosen at random, based on a collection of blood samples taken between 1989 and 1991 to meet parentage testing requirements, primarily but not exclusively from breeding stallions. The frequency of Quarter Horses positive for the base pair substitution, all heterozygotes, was 4‐4%, which corresponds to an allelic frequency of 0.02. All horses positive for the gene traced to a single previously identified stallion as first, second or third generation descendants. A higher frequency of the HYPP susceptibility trait than expected by random occurrence was found among his descendants in this study.
Comparison of protein markers and microsatellites in differentiation of cattle populations
Authors: Arranz J J , Bayón Y , Primitivo F San 
Published: July 2010

SummaryFive cattle populations, representing four breeds, were analysed for 14 protein markers and five microsatellite loci. The breeds studied were Brown Swiss and three autochthonous Spanish cattle: Avileña‐Negra Ibérica (A‐NI), two populations (A‐NI 1 and A‐NI 2) from different, reproductively isolated, locations; Sayaguesa; and Morucha. A total of 752 animals were examined for biochemical polymorphisms, of which 488 were also DNA typed. Genetic parameters and phylogenetic trees were obtained separately for each group of markers and results were compared. Estimates of heterozygosity and genetic distances from microsatellites were greater than those obtained using protein markers. The overall topology of the two dendrograms was similar. A‐NI 1 and A‐NI 2 populations were grouped together, related to Morucha, and the three of them related to Sayaguesa. Brown Swiss appeared in a separate branch from Spanish cattle. These results support the usefulness of microsatellites in the study of genetic relationships among closely related populations and breeds.
Introgression of the avian naked neck gene assisted by DNA fingerprints
Authors: Yancovich A , Levin I , Cahaner A , Hillel J 
Published: July 2010

SummaryTheoretical predictions suggest that DNA markers can be useful tools for genomic selection in gene introgression programmes. An experiment was carried out to evaluate the efficiency of using multi‐locus DNA markers in an introgression programme designed to transfer the naked neck gene from a donor to a recipient chicken line. The donor line was a commercial egg layer chicken stock heterozygous at the naked neck locus (Na/na+), while the recipients were from a Cornish broiler line. These two lines differ markedly in their average body weight, a quantitative trait that can also represent the comprehensive differences between the genomes of the two lines involved. Three groups of naked neck BC1 individuals were selected according to the following criteria: (i) low band‐sharing with their donor grandsires evaluated by multi‐locus DNA markers, (ii) high body weight at six weeks of age, and (iii) selection at random as a control group. Birds from each of these groups were mated at random to individuals from the heavier Cornish line to produce three groups of BC2 individuals whose body weights were recorded weekly from three to seven weeks of age. Results indicated that BC2 birds obtained from BC1 parents selected for band‐sharing levels and those selected for body weight, performed equally well at 4–7 weeks of age; both were 3.1–3.9% heavier than birds from the randomly selected group. The additional genome recovery of the heavier broiler line, obtained by DNA markers, was found to be in agreement with theoretically predicted values.
A search for quantitative trait loci for ovulation rate in cattle
Authors: Blattman A N , Kirkpatrick B W , Gregory K E 
Published: July 2010

SummarySeventy‐seven polymorphic microsatellites were analysed in offspring of three elite sires that were part of the foundation of an experimental population selected for twinning rate at the US Meat Animal Research Center, Clay Center, Nebraska. All females were assessed for ovulation rate by rectal palpation of corpora lutea over 8–10 consecutive oestrous cycles from approximately 12 to 18 months of age, and associations between ovulation rate and sire allele were examined in each of the three sire groups. A preliminary analysis was performed using selectively genotyped daughters of each sire. Markers found significant or approaching significance were also genotyped in all daughters, sons and granddaughters of these sires. A test of marker associations limited to the granddaughter data provided an independent confirmation of marker effect and significance relative to the initial test with daughter data. Putative ovulation rate quantitative trait loci were detected on chromosomes 7 and 23. Marker UWCA20 on chromosome 7 was associated with an effect in excess of one phenotypic standard deviation and accounted for approximately 10% of phenotypic variation ovulation rate. Marker CYP21 (steroid 21‐hydroxylase) on chromosome 23 was associated with an effect of slightly less than half a phenotypic standard deviation and accounted for approximately 4% of phenotypic variation.
Integration of the PiGMaP and USD A maps for porcine chromosome 14
Authors: Kapke P , Wang L , Helm J , Rothschild M F 
Published: July 2010

SummaryIn order to align two previously published genetic linkage maps, a set of four of the United States Department of Agriculture (USDA) microsatellite linkage markers was mapped in the International Pig Gene Mapping Project (PiGMaP) reference families. Two‐point linkage analysis was used between these USDA markers and the set of genes and markers previously mapped on the PiGMaP chromosome 14 map‐Markers with threshold lod scores of three or greater were used for multipoint map construction. The USDA and PigGMaP linkage maps of chromosome 14 were aligned using the four USDA microsatellite markers along with three markers that are common to both maps. The PiGMaP genetic linkage map order for chromosome 14 was confirmed and the map was expanded to 193 cM with addition of the new markers.
Linkage between the loci for serum albumin and vitamin D binding protein (GC) in the Japanese quail
Authors: Shibata T , Abe T 
Published: July 2010

SummaryVitamin D binding protein (GC) and serum protease inhibitor (PI) have been added to genetic markers in the Japanese quail. Both loci were controlled by autosomal codominant alleles named GCA, GCB and PIA, PIB, PIC, respectively. Close linkage between the loci for serum albumin (ALB) and GC protein is reported. Two recombinants were observed in 145 informative offspring of 14 families. The recombination frequency between the loci was estimated as 0.014±0.006. Thus, GC was assigned to linkage group II in the Japanese quail. No signs of linkage were observed among the loci for the ALB‐GC complex, PI. serum prealbumin 2 (PA2), phosphoglucose isomerase (PG1), 6‐phosphogluconate dehydrogenase (PGD) and esterase‐D (ESD).
Simultaneous analysis of bovine K‐casein and BLAD alleles by multiplex PCR followed by parallel digestion with two restriction enzymes
Authors: Zsolnai A , Fésüs L 
Published: July 2010

SummaryAn improved and simplified method allowing simultaneous genetic typing of K‐casein and CD 18 (bovine leucocyte adhesion deficiency; BLAD) loci has been developed. The method is based on the simultaneous amplification of fragments of the two groups of alleles by multiplex PCR, and on a concurrent, parallel digestion of the products by two restriction enzymes (PstI andHaeIII) in the same incubation buffer. Digestion withPstI distinguishes K‐casein A and B alleles and does not cut within any of the BLAD alleles, while digestion withHaeIII allows the differentiation between normal and mutant allele variants of theCD28locus. All combinations of the known mutants of the two alleles, characterized to the regions amplified and resulting in phenotypic effect, could be detected by electrophoretic separation performed on the same agarose gel owing to the vast differences in the length of the restriction fragments.
Molecular genetic characterization of new bovine kappa‐casein alleles CSN3F and CSN3G and genotyping by PCR‐RFLP
Authors: Prinzenberg E‐M , Hiendleder S , Ikonen T , Erhardt G , Prinzenberg E‐M , Hiendleder S , Erhardt G , Ikonen T 
Published: July 2010

SummaryIn order to characterize the two new kappa‐casein variants F and G (CSN3F and CSN3G) recently detected in Ayrshire and Pinzgauer cattle, exon IV of CSN3 from heterozygous animals was amplified by polymerase chain reaction (PCR), cloned and sequenced. The sequencing data revealed single point mutations at nucleotide positions 10530 (G→A) for CSN3F and 10790 (C→T) for CSN3G, corresponding to amino acid exchanges in positions 10 (Arg→His) and 97 (Arg→Cys) respectively. These mutations alter recognition sites for the restriction enzymes HhaI and MaeII, which were subsequently used to confirm these polymorphisms in cattle carrying CSN3F or CSN3G. A PCR‐restriction fragment length polymorphism (RFLP) genotyping procedure for all currently known CSN3 alleles (CSN3A, CSN3B, CSN3C, CSNJE, CSNF, CSN3G) was developed.
Characterization of 42 highly polymorphic bovine microsatellite markers
Authors: Hirano T , Nakane S , Mizoshitat K , Yamakuchit H , Inoue‐Murayama M , Watanabe T , Sugimoto Y , Barendse W 
Published: July 2010

SummaryWe have isolated 42 highly polymorphic microsatellite (GT/CA)n markers from Japanese black cattle Wagyu (Bos taurus). Forty‐one of the markers were assigned to bovine autosomes with lod scores > 6, through linkage analyses performed on the International Bovine Reference Family Panel (IBRP). The remaining marker showed X‐linked inheritance. These markers exhibited an average heterozygosity value of 0.67 with between four and 17 alleles on the IBRP.
Polymerase chain reaction‐based polymorphisms in the porcine cholecystokinin (CCK) gene and assignment to chromosome 13
Authors: Clutter A C , Sasaski S , Pomp D 
Published: July 2010

SummaryPolymorphisms were identified in the porcine cholecystokinin (CCK) gene by digestion of products from polymerase chain reaction (PCR) with the restriction enzyme DpnII. Individuals from the European pig gene mapping project (PiGMaP) consortium reference families (eight full‐sib families, 91 total progeny) were genotype to determine linkage relationships between the CCK gene and previously mapped loci. Linkage analysis revealed that the CCK gene is located on porcine chromosome 13.
Genetic markers linked to quantitative traits in poultry
Authors: Lamont S. J. , Lakshmanan N. , Plotsky Y. , Kaiser M. G. , Kuhn M. , Arthur J. A. , Beck N. J. , O'Sullivan N. P. 
Published: July 2010

SummaryThis study utilized DNA fingerprints and crosses of two genetically distinct lines of layer‐type chickens to identify genetic markers linked to quantitative trait loci (QTL). In phase I, back‐cross (BC1) hens were separately ranked for each of eight traits and then blood pools were produced in groups along each phenotypic distribution. The DNA was isolated from the blood pools and used in a gradient analysis to screen for DNA fingerprint bands that exhibited intensity gradients associated with the phenotypic traits. To identify linkage of bands with QTL and to estimate band effects, F2 progeny were produced in phase II from the phase I BC, population. A single‐trait animal model was used for analysis of associations of all individual DNA fingerprint bands of sires and their progeny phenotypic performance. Twenty fingerprint bands, only two of which had shown trait‐associated gradients in phase I, were identified by the animal model analysis of the progeny test as QTL linked (P≤005) to specific traits of growth, reproduction and egg quality. These 20 bands warrant further study as potentially valuable molecular markers for QTL.
Efficient resolution of parentage in dogs by amplification of microsatellites
Authors: Fredholm M. , Winterø A. K. 
Published: July 2010

SummaryParentage control has been performed for 15 litters from 12 different dog breeds by amplification of microsatellites. As it was possible to include all putative parents in all cases, they were solved by exclusion. Discrimination between parents/non‐parents was made after genotyping of 6–9 microsatellite loci. In 12 of the cases all but one of the alleged fathers were excluded while in three cases it was unambiguously shown that superfecundation had taken place. Furthermore, one inclusion case concerning disputed maternity has been investigated. Maternity indices were calculated for 12 loci and probability of maternity was estimated to be 99‐99%. These results testify that microsatellites can be applied very efficiently for resolution of parentage in dogs.
Isolation and characterization of 45 polymorphic microsatellites from the bovine genome
Authors: Ma R. Z. , Russ I. , Park C. , Heyen D. W. , Beever J. E. , Green C. A. , Lewin H. A. 
Published: July 2010

SummaryA small‐insert bovine genomic library was constructed in pBluescript II SK(+) and enriched for microsatellites by selective rescue of single‐stranded pBluescript DNA carrying (CA)n/(TG) n tandem repeats. Approximately 50% of the clones in the enriched library contained (CA) nrepeats or CA‐rich sequences. Sequencing of clones selected for (CA) n repeats resulted in the identification and characterization of 45 (CA) npolymorphic microsatellites. Genotyping in 9 large paternal half‐sib families indicated that 40 of these microsatellite markers exhibit autosomal Mendelian inheritance. The numbers of alleles range from 2 to 18, with an average of 6‐3 per locus. The polymorphic microsatellite markers we have identified and characterized will contribute to the construction of a high‐resolution linkage map of bovine genome.