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Reference Families (reference + family)
Selected AbstractsLinkage mapping of gene-associated SNPs to pig chromosome 11ANIMAL GENETICS, Issue 3 2006M. Sawera Summary Single nucleotide polymorphisms (SNPs) were discovered in porcine expressed sequence tags (ESTs) orthologous to genes from human chromosome 13 (HSA13) and predicted to be located on pig chromosome 11 (SSC11). The SNPs were identified as sequence variants in clusters of EST sequences from pig cDNA libraries constructed in the Sino,Danish pig genome project. In total, 312 human gene sequences from HSA13 were used for similarity searches in our pig EST database. Pig ESTs showing significant similarity with HSA13 genes were clustered and candidate SNPs were identified. Allele frequencies for 26 SNPs were estimated in a group of 80 unrelated pigs from Danish commercial pig breeds: Duroc, Hampshire, Landrace and Large White. Eighteen of the 26 SNPs genotyped in the PiGMaP Reference Families were mapped by linkage analysis to SSC11. The EST-based SNPs published here are new genetic markers useful for linkage and association studies in commercial and experimental pig populations. This study represents the first gene-associated SNP linkage map of pig chromosome 11 and adds new comparative mapping information between SSC11 and HSA13. Furthermore, our data facilitate future studies aimed at the identification of interesting regions on pig chromosome 11, positional cloning and fine mapping of quantitative trait loci in pig. [source] A canine linkage map: 39 linkage groupsJOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 1 2001F. Lingaas A low resolution canine marker map is an important tool in the further advancements in genetic analysis of dog breeds and the control and reduction of the frequency of inherited diseases. This study presents a genetic linkage analysis with 39 linkage groups using 222 polymorphic canine markers based on typing in the International DogMap reference families, consisting of 129 Beagle and German Shepherd dogs. Of these 39 linkage groups, 14 have been assigned to canine chromosomes by fluorescence in-situ hybridization (FISH). These results are a further refinement on the first linkage groups from the International DogMap collaboration and represent a continuing collaboration. Eine Markerkarte des Hundes mit 39 Kopplungsgruppen Schwach auflösende Markerkarten des Genoms stellen wichtige Hilfsmittel für die genetische Charakterisierung von Hunderassen dar. Sie können für die Kontrolle und Eindämmung von Erbkrankheiten verwendet werden. Die Resultate der vorgestellten Studie basieren auf der genetischen Typisierung von Hundefamilien des Internationalen DogMap Konsortiums. Die Familien bestehen aus 129 Beagle und Deutschen Schäferhunden. Die Studie stellt eine Kopplungsanalyse mit 39 Kopplungsgruppen vor, die insgesamt 1216 cM des Hundegenoms abdecken. Die Markerkarte enthält 222 polymorphe Hundemarker von denen 18 Gene sind. Fünfundachtzig Marker sind in keiner anderen Markerkarte publiziert. Vierzehn Kopplungsgruppen konnten mittels FISH chromosomal zugewiesen werden. Unsere Resultate stellen eine weitere Verfeinerung der ersten Markerkarte des DogMap Projektes dar und sind Ausdruck einer kontinuierlichen internationalen Zusammenarbeit. [source] A male bovine linkage map for the ADR granddaughter designJOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 5 2000H. Thomsen Summary The aim of this paper is to present the construction of a male genetic linkage map as a result of the bovine genome mapping project, which is a common effort of the German cattle breeding federation (ADR), four animal breeding institutes, three blood group laboratories and two animal data and breeding value evaluation centres. In total 20 grandsires with 1074 sires were provided from the German cattle population as reference families, 16 of these paternal half-sib groups are German Holstein families (DH), three are German Simmental (ST) families, and one is a Brown Swiss family (BS). Of 265 markers included in the linkage map, 248 were microsatellite markers, five were bovine blood group systems, eight SSCP markers and four proteins and enzymes. More than 239 000 genotypes resulted from typing the offspring for the respective markers and these were used for the construction of the map. On average 478 informative meioses were provided from each marker of the map. The summarized map length over all chromosomes was 3135.1 cM with an average interval size of 13.34 cM. About 17, 35.7 and 79.1% of the map intervals showed a maximum genetic distance between the adjacent markers of 5, 10 and 20 cM, respectively. The number of loci ranged from two (pseudoautosomal region of the sex chromosome, BTAY) to 15 (BTA23) with an average of 8.8 markers per chromosome. Comparing the length of the chromosomes shows variation from 49.6 cM for BTA26 to 190.5 cM for BTA1 with a mean of 107.7 cM for all autosomes of the genetic linkage map. It was possible to identify chromosomal discrepancies in locus order and map intervals by comparison with other published maps. The map provided sufficient marker density to serve as a useful tool for a scan of segregating quantitative trait loci. Zusammenfassung Im vorliegenden Artikel wird die Erstellung der genetischen Markerkarten für das Rindergenom im Rahmen des Genomanalyseprojektes der Arbeitsgemeinschaft Deutscher Rinderzüchter (ADR) vorgestellt. Auf der Basis des ,Granddaughter Designs' wurde ein Familienmaterial bestehend aus 20 väterlichen Halbgeschwistergruppen mit 1074 Söhnen für die Typisierung mit genetischen Markern bereitgestellt. Insgesamt 16 dieser paternalen Halbgeschwisterfamilien lassen sich der Rasse Deutsche Holsteins zuordnen, drei Familien entstammen der Rasse Deutsches Fleckvieh, und eine Familie gehört der Rasse Deutsches Braunvieh an. Dabei variiert die Anzahl der Söhne von 19,128 pro Vater. Für die Typisierung wurden 248 Mikrosatellitenmarker aus bereits publizierten Karten ausgewählt. Zusätzlich konnten 8 SSCP-und RFLP Marker, 5 Blutgruppensysteme und 4 Proteinmarker zur Entwicklung der genetischen Karte herangezogen werden. Die Anzahl der Marker variierte von 2 (pseudoautosomaler Bereich des Geschlechtschromosoms) bis 15 (Chromosom 23), wobei durchschnittlich 8.8 genetische Marker pro Chromosom typisiert wurden. Im Durchschnitt lieferten die genetischen Marker 478 informative Meiosen pro Marker. Alle Typisierungsergebnisse wurden in die Kieler Markerdatenbank übertragen und auf etwaige Fehler geprüft. Als Ergebnis konnten die genetischen Karten für alle 29 Autosomen und den pseudoautosomalen Bereich des Geschlechtschromosoms erstellt werden. Dabei wurde ein Bereich von 3135.1 cM des Rindergenoms abgedeckt, wobei die Länge des durchschnittlichen Markerintervalls 13.34 cM beträgt. Die Längen der Chromosomen zeigten eine Variation von 49.6 cM für Chromosom 26 bis zu 190.5 cM für Chromosom 1. Aufgrund der Anzahl informativer Meiosen und der Markerdichte bildet diese genetische Markerkarte in gutes Instrument für eine genomweite Suche nach segregierenden Genorten, die für die Variation von quantitativen Merkmalen verantwortlich sind. [source] Localizing the X-linked orange colour phenotype using feline resource familiesANIMAL GENETICS, Issue 1 2005R. A. Grahn Summary Many genes influencing mammalian coat colours are well conserved. While genes responsible for pelage phenotypes in one species provide strong evidence for a candidate gene in a different species, the X-linked orange phenotype of the domestic cat is unique within mammals. The orange locus (O) undergoes X-inactivation, producing females that express both wildtype black (wt) and orange (variant) phenotypes when heterozygous (tortoiseshell). The orange locus has not yet been localized on the X chromosome. Tortoiseshell male cats have been identified but have been shown to be sex chromosome trisomies (XXY). To localize the cat orange locus, 10 feline-derived X-linked microsatellites were analysed in two extended cat pedigrees consisting of 79 and 55 individuals, respectively, segregating for the orange phenotype. Linkage analyses excluded close association of orange in the vicinity of the nine informative X-linked microsatellites. One marker was not polymorphic within either family. Several markers suggested exclusion (Z < ,2.0) at distances of 7.5,33 cM. Exclusion analyses suggested a possible location for orange a 14 cM region near Xcen. Recombination distances of markers in the segregating feline pedigrees were reduced as compared with the feline interspecies backcross family. Thus, the presented pedigrees may be useful as reference families for the domestic cat because more accurate recombination rates for domestic cats can be determined. [source] Trends in affordability of the Illawarra Healthy Food Basket 2000,2007NUTRITION & DIETETICS, Issue 1 2009Peter WILLIAMS Abstract Aims:, The Illawarra Healthy Food Basket was developed as one measure to monitor the affordability of healthy eating in Australia. It consists of 57 items selected to meet the nutritional requirements of a reference family of five. The basket was first costed in the Illawarra region of Australia in 2000 and again in 2001 and 2003. The present study aimed to repeat the costing of the basket in 2005 and 2007 and to assess the trends in affordability since 2000. Methods:, Costing was carried out in the same five suburbs as previous surveys, using a large supermarket, greengrocer and butcher from each. Comparison data included: welfare entitlements obtained from Centrelink, average weekly earnings and the consumer price index for food. Main outcome measures:, The average weekly cost of the Illawarra Healthy Food Basket in 2005 and 2007, and trends in the costs compared with changes in average weekly earning and welfare benefits for the reference family. Results:, The total cost of the Illawarra Healthy Food Basket in 2007 was $242.49, an increase of 20.4% since 2000, with the greatest increases in the prices of vegetables (55.7%) and fruit (46.7%). Fruits, vegetables and meat were cheaper at independent grocers and butchers than in supermarkets. The percentage of average weekly earning or welfare payments required to purchase the Illawarra Healthy Food Basket remained stable at slightly below 30%. Conclusion:, These results indicate that the affordability of healthy eating has remained relatively constant from 2000 to 2007, but the significant increases in fruit and vegetable prices might be making healthy food choices more difficult. [source] Characterization of the porcine melanocortin 2 receptor gene (MC2R,)ANIMAL GENETICS, Issue 6 2002K. Jacobs A porcine bacterial artificial chromosome (BAC) clone, containing the melanocortin 2 receptor gene (MC2R) was isolated. The complete coding sequence of the MC2R gene, contained in 1 exon, was determined. Polymerase chain reaction-single stranded conformational polymorphism (PCR-SSCP) was performed on a 241-bp coding fragment. An AluI polymorphism, detecting a silent mutation, was found and typed on unrelated animals of five different pig breeds. The Meishan, Piétrain and Large White breeds differ significantly in allele frequencies from the Landrace and Czech Meat Pig breeds. The melanocortin 5 receptor gene (MC5R) was detected by PCR in the same BAC clone, as could be expected from the human and porcine mapping data. PCR-SSCP was performed on a 200-bp coding of MC5R, but no polymorphisms were detected. The BAC clone was mapped to Sscr6q27 by fluorescent in situ hybridization (FISH). A (CA)n microsatellite (SGU0002), isolated from the BAC, was localized on chromosome 6 by RH mapping near marker SW1473 and by linkage mapping on the MARC reference family at the same position as the marker SW2173 (97 cM). Allele frequencies, heterozygosity and polymorphism information contents (PIC) values were calculated for the five different pig breeds examined. The transcription of both genes in porcine liver, heart, kidney, fat, brain, pancreas, stomach, bladder, ovaries, lung, spleen, skin, adrenal gland and muscle tissues was examined by reverse transcriptase-polymerase chain reaction. Transcription was detected in skin and adrenal gland tissues for MC2R, while a positive signal was detected for MC5R in kidney, fat, pancreas, skin, adrenal gland and spleen tissues. [source] Single nucleotide polymorphism (SNP) discovery in porcine expressed genesANIMAL GENETICS, Issue 3 2002S. C. Fahrenkrug High-throughput genotyping of swine populations is a potentially efficient method for establishing animal lineage and identification of loci important to animal health and efficient pork production. Markers were developed based upon single nucleotide polymorphisms (SNPs), which are abundant and amenable to automated genotyping platforms. The focus of this research was SNP discovery in expressed porcine genes providing markers to develop the porcine/human comparative map. Locus specific amplification (LSA) and comparative sequencing were used to generate PCR products and allelic information from parents of a swine reference family. Discovery of 1650 SNPs in 403 amplicons and strategies for optimizing LSA-based SNP discovery using alternative methods of PCR primer design, data analysis, and germplasm selection that are applicable to other populations and species are described. These data were the first large-scale assessment of frequency and distribution of porcine SNPs. [source] | ||||||||||