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A L Archibald

Publications and source records attributed to A L Archibald.

At least 19 recordsLinked to original sources
PubMed2006

A polymorphism in the 5'-untranslated region of the porcine cholecystokinin type a receptor gene affects feed intake and growth.

The location and utilization of quantitative trait loci (QTL) and candidate genes with significant effects on economically important traits are becoming increasingly important in livestock breeding programs. The porcine cholecystokinin type A receptor (CCKAR) is a candidate gene for performance traits, due to its known role in the physiological control of feed intake, satiety, and obesity. We investigated the association of CCKAR polymorphisms with feeding, growth, and efficiency traits in an F2 population derived from a cross between Meishan and Large White founder animals and in lines of Large White pigs that had been divergently selected on the basis of lean growth efficiency traits. In the F2 population, CCKAR genotype was significantly associated with daily feed intake and average daily gain. The effects of the polymorphisms were then assessed in a larger-scale analysis of segregating commercial lines. A newly discovered single-nucleotide polymorphism (SNP) within the 5'-untranslated region (5'-UTR) had highly significant effects on feed intake, average daily gain, and days to 110 kg, which were not seen for a previously reported SNP within the CCKAR gene. Furthermore, we provide evidence that the novel SNP disrupts the binding of the YY1 transcription factor, which raises the possibility that it is the causal variant. The 5'-UTR SNP could be utilized as a molecular genetic test for increased feed intake, faster lean growth, and reduced days to market weight in segregating commercial lines.

5' Untranslated Regions↗
PubMed2006

Genetic diversity within and between European pig breeds using microsatellite markers.

An important prerequisite for a conservation programme is a comprehensive description of genetic diversity. The aim of this study was to use anonymous genetic markers to assess the between- and the within-population components of genetic diversity for European pig breeds at the scale of the whole continent using microsatellites. Fifty-eight European pig breeds and lines were analysed including local breeds, national varieties of international breeds and commercial lines. A sample of the Chinese Meishan breed was also included. Eleven additional breeds from a previous project were added for some analyses. Approximately 50 individuals per breed were genotyped for a maximum of 50 microsatellite loci. Substantial within-breed variability was observed, with the average expected heterozygosity and observed number of alleles per locus being 0.56 [range 0.43-0.68] and 4.5 respectively. Genotypic frequencies departed from Hardy-Weinberg expectations (P < 0.01) in 15 European populations, with an excess of homozygotes in 12 of them. The European breeds were on average genetically very distinct, with a Wright F(ST) index value of 0.21. The Neighbour-Joining tree drawn from the Reynolds distances among the breeds showed that the national varieties of major breeds and the commercial lines were mostly clustered around their breeds of reference (Duroc, Hampshire, Landrace, Large White and Piétrain). In contrast, local breeds, with the exception of the Iberian breeds, exhibited a star-like topology. The results are discussed in the light of various forces, which may have driven the recent evolution of European pig breeds. This study has consequences for the interpretation of biodiversity results and will be of importance for future conservation programmes.

Alleles↗
PubMed2005

Detection of quantitative trait loci for androstenone, skatole and boar taint in a cross between Large White and Meishan pigs.

'Boar taint' is a strong perspiration-like, urine-like unpleasant odour given off upon heating or cooking of meat from some intact (uncastrated) male pigs. Data from the F(2) generation of a Large White (LW) x Meishan (MS) crossbred population were analysed to detect quantitative trait loci (QTL) for traits associated with boar taint. Fat samples from 178 intact male pigs slaughtered at 85 +/- 5 kg were analysed for the major contributors to boar taint (androstenone, indole and skatole). Fat and lean samples from cooked meat were scored for boar, abnormal and pork flavour and odour by a trained sensory panel (SP). A scan with 117 markers covering the whole genome was performed in the F(2) individuals, together with their F(1) parents and purebred grandparents. At the 5% chromosomal significance threshold (approximately equal to the genome-wide suggestive significance threshold), QTL were detected for the laboratory estimate of androstenone on chromosomes 2, 4, 6, 7 and 9. However, only on chromosome 6 were there QTL for boar flavour (BF) traits in the same or adjacent marker intervals as a QTL for the laboratory estimate of androstenone. On chromosome 14, QTL were detected for the laboratory estimates of indole and skatole, the SP score for skatole and the scores for BF in lean and BF in fat. In all five cases, the MS allele generally increased the estimate or score, compared with the LW allele, but it appeared that desirable and undesirable alleles were present in both breeds. This locus on chromosome 14 has considerable potential for use to reduce the incidence of boar taint, especially if further research can identify the causative polymorphism or strongly associated markers.

Androsterone↗
PubMed2005

Cloning and mapping of the porcine cytochrome-p450 2E1 gene and its association with skatole levels in the domestic pig.

The porcine cytochrome-p450 2E1 (CYP2E1) gene was isolated by screening a pig BAC library and partially sequenced. This sequence information was used to identify six single nucleotide polymorphisms (SNPs) within the CYP2E1 gene and its promoter. In addition, a microsatellite marker tightly linked to the CYP2E1 gene was subcloned from the BAC. One of these markers was used to map the CYP2E1 gene distal of SWC27 on SSC14, well outside reported quantitative trait loci on SSC14 for skatole, indole and taste test measures of boar taint. However, in a population of commercial pigs scored for backfat skatole levels, there was evidence of association between a SNP in the CYP2E1 promoter and skatole deposition, although there was no significant association between this SNP and skatole levels in the experimental cross.

Adipose Tissue↗
PubMed2003

Linkage and comparative mapping of the locus controlling susceptibility towards E. COLI F4ab/ac diarrhoea in pigs.

In 1995, Edfors-Lilja and coworkers mapped the locus for the E. COLI K88ab (F4ab) and K88ac (F4ac) intestinal receptor to pig chromosome 13 (SSC13). Using the same family material we have refined the map position to a region between the microsatellite markers Sw207 and Sw225. Primers from these markers were used to screen a pig BAC library and the positive clones were used for fluorescent in situ hybridization (FISH) analysis. The results of the FISH analysis helped to propose a candidate gene region in the SSC13q41-->q44 interval. Shotgun sequencing of the FISH-mapped BAC clones revealed that the candidate region contains an evolutionary breakpoint between human and pig. In order to further characterise the rearrangements between SSC13 and human chromosome 3 (HSA3), detailed gene mapping of SSC13 was carried out. Based on this mapping data we have constructed a detailed comparative map between SSC13 and HSA3. Two candidate regions on human chromosome 3 have been identified that are likely to harbour the human homologue of the gene responsible for susceptibility towards E. COLI F4ab/ac diarrhoea in pigs.

Animals↗
PubMed2002

No detectable association of the ESR PvuII mutation with sow productivity in a Meishan x Large White F2 population.

The polymorphism at the PvuII recognition site in the ESR gene showed no statistically significant association with sow productivity traits in a Meishan x Large White F2 population. Estimates of the effect on litter size were, however, in the opposite direction and statistically different from previously published estimates. Taken together with results from other publications, results here indicate that this PvuII polymorphism displays different degrees of linkage disequilibrium with a gene or genes controlling litter size in different populations.

Animals↗
PubMed2001

The ARKdb: genome databases for farmed and other animals.

The ARKdb genome databases provide comprehensive public repositories for genome mapping data from farmed species and other animals (http://www.thearkdb.org) providing a resource similar in function to that offered by GDB or MGD for human or mouse genome mapping data, respectively. Because we have attempted to build a generic mapping database, the system has wide utility, particularly for those species for which development of a specific resource would be prohibitive. The ARKdb genome database model has been implemented for 10 species to date. These are pig, chicken, sheep, cattle, horse, deer, tilapia, cat, turkey and salmon. Access to the ARKdb databases is effected via the World Wide Web using the ARKdb browser and Anubis map viewer. The information stored includes details of loci, maps, experimental methods and the source references. Links to other information sources such as PubMed and EMBL/GenBank are provided. Responsibility for data entry and curation is shared amongst scientists active in genome research in the species of interest. Mirror sites in the United States are maintained in addition to the central genome server at Roslin.

Animals↗
PubMed2001

Molecular and quantitative characterisation of the porcine embryonic myosin heavy chain gene.

The porcine embryonic myosin heavy chain (MyHC) is a major isoform in foetal skeletal muscle, and is the last remaining major porcine skeletal MyHC gene to be isolated and characterised. We report here on its cDNA and genomic isolation, molecular characterisation, quantification and expression. Unlike all other porcine and mammalian skeletal MyHC genes reported to date, the deduced translated start site of the porcine embryonic gene was located in exon 2, instead of exon 3. Its promoter conferred differentiation-specific expression. We found, by quantitative real-time RT-PCR, that for much of gestation the embryonic MyHC was by far the most transcriptionally active gene compared with the slow/I and perinatal MyHC isoforms, and it was consistently more highly expressed than the perinatal isoform throughout gestation. The embryonic MyHC isoform was, however, rapidly down-regulated at around birth. By contrast, 22 weeks after birth, the porcine perinatal isoform remained detectable by PCR. Additionally, we discovered the presence of differential splicing at the 3'-end of the embryonic MyHC gene that resulted in an in-frame deletion, with the consequential loss of 93 amino acids close to the ACD domain, a region that is important for the assembly of myosin filaments. The detection of this truncated variant points to a possible major post-transcriptional mechanism of embryonic MyHC regulation that may be linked to myosin filament formation or turnover.

Alternative Splicing↗
PubMed2001

The porcine gonadotropin-releasing hormone receptor gene (GNRHR): genomic organization, polymorphisms, and association with the number of corpora lutea.

The interaction of gonadotropin-releasing hormone (GNRH) and its receptor (GNRHR) is critical in the endocrine regulation of reproduction. The gene (GNRHR) encoding the receptor has been mapped to porcine chromosome 8. There is evidence for three quantitative trait loci (QTL) influencing ovulation rate on this chromosome. We obtained an almost complete sequence (3993 bp, excluding intron 1) of the porcine GNRHR gene using PCR-based comparative genomic walking and inverse genomic walking approaches. Twelve polymorphisms were detected by sequencing of pooled DNA of Chinese Taihu and European Large White pigs, including 7 base substitutions and 5 insertions-deletions (indels). A F2 population of Meishan x European Large White pigs was genotyped for a TG indel in the promoter region, and a C/G substitution in the 3' UTR (untranslated region). A significant association of the C/G substitution with number of corpora lutea at first parity was observed.

3' Untranslated Regions↗
PubMed2001

Genetic and physical mapping, expression analysis and partial sequence of porcine PER1.

The porcine PER1 gene was mapped to chromosome 12q1.4-->q1.5 using fluorescence in situ hybridisation. A polymorphic microsatellite marker (S0601) was isolated from a BAC clone shown to contain the PER1 gene. Linkage analysis assigned S0601 distal to ALOX12 on SSC12, providing further evidence for the conservation of synteny between HSA17 and SSC12. RT-PCR analysis demonstrated the expression of PER1 in all 11 tissues tested, consistent with the data from other mammalian species. Part of the PER1 gene was sequenced, homologous to exons 2-14 of the human gene and encoding the N-terminus of porcine PER1. The predicted amino acid sequence of the partial pig PER1 protein shares over 96% identity with its human orthologue.

Animals↗
PubMed2001

Non-coordinate expression of closely linked mouse casein genes.

Expression levels of five mouse casein genes were analysed in the mammary gland of virgin, pregnant and lactating mice. We have already shown that the five murine casein genes are arranged in the order, alpha-beta-gamma-epsilon-kappa in a tandem array, very close to each other in a 250 kb DNA fragment of mouse genome. Northern blot analysis showed that, of the calcium-sensitive casein genes, the epsilon casein gene is expressed only during lactation unlike the alpha, beta and gamma casein genes which are expressed during pregnancy and lactation. Even though the alpha, beta and gamma genes exhibited a co-ordinated expression pattern from mid to the later stages of pregnancy, the mRNA levels varied considerably (60, 90 and 100% respectively) by the onset of lactation. The mRNA level of the calcium-insensitive kappa casein gene increased from mid-pregnancy but at a lower rate and reached approximately 60% by the first day of lactation. Considering the locations and closeness of the casein genes, a non-coordinate expression profile is exhibited by the mouse casein genes, particularly the epsilon casein gene.

Animals↗
PubMed2000

Farm animal genome databases.

The requirements for bioinformatics resources to support genome research in farm animals is reviewed. The resources developed to meet these needs are described. Resource databases and associated tools have been developed to handle experimental data. Several of these systems serve the needs of multinational collaborations. Genome databases have been established to provide contemporary summaries of the status of genome maps in a range of farm and domestic animals along with experimental details and citations. New resources and tools will be required to address the informatics needs of emerging technologies such as microarrays. However, continued investment is also required to maintain the currency and utility of the current systems, especially the genome databases.

Animals↗
PubMed2000

Combined analyses of data from quantitative trait loci mapping studies. Chromosome 4 effects on porcine growth and fatness.

For many species several similar QTL mapping populations have been produced and analyzed independently. Joint analysis of such data could be used to increase power to detect QTL and evaluate population differences. In this study, data were collated on almost 3000 pigs from seven different F(2) crosses between Western commercial breeds and either the European wild boar or the Chinese Meishan breed. Genotypes were available for 31 markers on chromosome 4 (on average 8.3 markers per population). Data from three traits common to all populations (birth weight, mean backfat depth at slaughter or end of test, and growth rate from birth to slaughter or end of test) were analyzed for individual populations and jointly. A QTL influencing birth weight was detected in one individual population and in the combined data, with no significant interaction of the QTL effect with population. A QTL affecting backfat that had a significantly greater effect in wild boar than in Meishan crosses was detected. Some evidence for a QTL affecting growth rate was detected in all populations, with no significant differences between populations. This study is the largest F(2) QTL analysis achieved in a livestock species and demonstrates the potential of joint analysis.

Adipose Tissue↗