A L Archibald

The University of Edinburgh, Edinburgh, Scotland, United Kingdom

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Publications (242)715.24 Total impact

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    ABSTRACT: Background Improving meat quality including taste and tenderness is critical to the protection and development of markets for sheep meat. Phenotypic selection for such measures of meat quality is constrained by the fact that these parameters can only be measured post-slaughter. Carcass composition has an impact on meat quality and can be measured on live animals using advanced imaging technologies such as X-ray computed tomography (CT). Since carcass composition traits are heritable, they are potentially amenable to improvement through marker-assisted and genomic selection. We conducted a genome-wide association study (GWAS) on about 600 Scottish Blackface lambs for which detailed carcass composition phenotypes, including bone, fat and muscle components, had been captured using CT and which were genotyped for ~40,000 single nucleotide polymorphisms (SNPs) using the Illumina OvineSNP50 chip. Results We confirmed that the carcass composition traits were heritable with moderate to high (0.19–0.78) heritabilities. The GWAS analyses revealed multiple SNPs and quantitative trait loci (QTL) that were associated with effects on carcass composition traits and were significant at the genome-wide level. In particular, we identified a region on ovine chromosome 6 (OAR6) associated with bone weight and bone area that harboured SNPs with p values of 5.55 × 10−8 and 2.63 × 10−9, respectively. The same region had effects on fat area, fat density, fat weight and muscle density. We identified plausible positional candidate genes for these OAR6 QTL. We also detected a SNP that reached the genome-wide significance threshold with a p value of 7.28 × 10−7 and was associated with muscle density on OAR1. Using a regional heritability mapping approach, we also detected regions on OAR3 and 24 that reached genome-wide significance for bone density. Conclusions We identified QTL on OAR1, 3, 24 and particularly on OAR6 that are associated with effects on muscle, fat and bone traits. Based on available evidence that indicates that these traits are genetically correlated with meat quality traits, these associated SNPs have potential applications in selective breeding for improved meat quality. Further research is required to determine whether the effects associated with the OAR6 QTL are caused by a single gene or several closely-linked genes. Electronic supplementary material The online version of this article (doi:10.1186/s12711-016-0191-3) contains supplementary material, which is available to authorized users.
    No preview · Article · Dec 2016 · Genetics Selection Evolution
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    ABSTRACT: The evolution of island populations in natural systems is driven by local adaptation and genetic drift. However, evolutionary pathways may be altered by humans in several ways. The wild boar (WB) (Sus scrofa) is an iconic game species occurring in several islands, where it has been strongly managed since prehistoric times. We examined genomic diversity at 49 803 single-nucleotide polymorphisms in 99 Sardinian WBs and compared them with 196 wild specimens from mainland Europe and 105 domestic pigs (DP; 11 breeds). High levels of genetic variation were observed in Sardinia (80.9% of the total number of polymorphisms), which can be only in part associated to recent genetic introgression. Both Principal Component Analysis and Bayesian clustering approach revealed that the Sardinian WB population is highly differentiated from the other European populations (F ST = 0.126–0.138), and from DP (F ST = 0.169). Such evidences were mostly unaffected by an uneven sample size, although clustering results in reference populations changed when the number of individuals was standardized. Runs of homozygosity (ROHs) pattern and distribution in Sardinian WB are consistent with a past expansion following a bottleneck (small ROHs) and recent population substructuring (highly homozygous individuals). The observed effect of a non-random selection of Sardinian individuals on diversity, F ST and ROH estimates, stressed the importance of sampling design in the study of structured or introgressed populations. Our results support the heterogeneity and distinctiveness of the Sardinian population and prompt further investigations on its origins and conservation status.
    Full-text · Article · Jan 2016 · Heredity
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    ABSTRACT: Giving access to sequence and annotation data for genome assemblies is important because, while facilitating research, it places both assembly and annotation quality under scrutiny, resulting in improvements to both. Therefore we announce Avianbase, a resource for bird genomics, which provides access to data released by the Avian Phylogenomics Consortium.
    Full-text · Article · Dec 2015 · Genome Biology
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    ABSTRACT: Many applications of high throughput sequencing rely on the availability of an accurate reference genome. Variant calling often produces large data sets that cannot be realistically validated and which may contain large numbers of false-positives. Errors in the reference assembly increase the number of false-positives. While resources are available to aid in the filtering of variants from human data, for other species these do not yet exist and strict filtering techniques must be employed which are more likely to exclude true-positives. This work assesses the accuracy of the pig reference genome (Sscrofa10.2) using whole genome sequencing reads from the Duroc sow whose genome the assembly was based on. Indicators of structural variation including high regional coverage, unexpected insert sizes, improper pairing and homozygous variants were used to identify low quality (LQ) regions of the assembly. Low coverage (LC) regions were also identified and analyzed separately. The LQ regions covered 13.85% of the genome, the LC regions covered 26.6% of the genome and combined (LQLC) they covered 33.07% of the genome. Over half of dbSNP variants were located in the LQLC regions. Of copy number variable regions identified in a previous study, 86.3% were located in the LQLC regions. The regions were also enriched for gene predictions from RNA-seq data with 42.98% falling in the LQLC regions. Excluding variants in the LQ, LC, or LQLC from future analyses will help reduce the number of false-positive variant calls. Researchers using WGS data should be aware that the current pig reference genome does not give an accurate representation of the copy number of alleles in the original Duroc sow’s genome.
    Full-text · Article · Nov 2015 · Frontiers in Genetics
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    ABSTRACT: Background: The FANTOM5 consortium used Cap Analysis of Gene Expression (CAGE) tag sequencing to produce a comprehensive atlas of promoters and enhancers within the human and mouse genomes. We reasoned that the mapping of these regulatory elements to the pig genome could provide useful annotation and evidence to support assignment of orthology. Results: For human transcription start sites (TSS) associated with annotated human-mouse orthologs, 17% mapped to the pig genome but not to the mouse, 10% mapped only to the mouse, and 55% mapped to both pig and mouse. Around 17% did not map to either species. The mapping percentages were lower where there was not clear orthology relationship, but in every case, mapping to pig was greater than to mouse, and the degree of homology was also greater. Combined mapping of mouse and human CAGE-defined promoters identified at least one putative conserved TSS for >16,000 protein-coding genes. About 54% of the predicted locations of regulatory elements in the pig genome were supported by CAGE and/or RNA-Seq analysis from pig macrophages. Conclusions: Comparative mapping of promoters and enhancers from humans and mice can provide useful preliminary annotation of other animal genomes. The data also confirm extensive gain and loss of regulatory elements between species, and the likelihood that pigs provide a better model than mice for human gene regulation and function.
    Preview · Article · Nov 2015 · BMC Genomics
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    ABSTRACT: Genetic selection against boar taint, which is caused by high skatole and androstenone concentrations in fat, is a more acceptable alternative than is the current practice of castration. Genomic predictors offer an opportunity to overcome the limitations of such selection caused by the phenotype being expressed only in males at slaughter, and this study evaluated different approaches to obtain such predictors. Samples from 1000 pigs were included in a design which was dominated by 421 sib pairs, each pair having one animal with high and one with low skatole concentration (≥0.3 μg/g). All samples were measured for both skatole and androstenone and genotyped using the Illumina SNP60 porcine BeadChip for 62 153 single nucleotide polymorphisms. The accuracy of predicting phenotypes was assessed by cross-validation using six different genomic evaluation methods: genomic best linear unbiased prediction (GBLUP) and five Bayesian regression methods. In addition, this was compared to the accuracy of predictions using only QTL that showed genome-wide significance. The range of accuracies obtained by different prediction methods was narrow for androstenone, between 0.29 (Bayes Lasso) and 0.31 (Bayes B), and wider for skatole, between 0.21 (GBLUP) and 0.26 (Bayes SSVS). Relative accuracies, corrected for h(2) , were 0.54-0.56 and 0.75-0.94 for androstenone and skatole respectively. The whole-genome evaluation methods gave greater accuracy than using only the QTL detected in the data. The results demonstrate that GBLUP for androstenone is the simplest genomic technology to implement and was also close to the most accurate method. More specialised models may be preferable for skatole.
    No preview · Article · Oct 2015 · Animal Genetics
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    ABSTRACT: The expression patterns of secreted (MUC2 and MUC5AC) and membrane-tethered (MUC1, MUC4, MUC12 and MUC13) mucins were monitored in healthy pigs and pigs challenged orally with Lawsonia intracellularis. These results showed that the regulation of mucin gene expression is distinctive along the GI tract of the healthy pig, and may reflect an association between the function of the mucin subtypes and different physiological demands at various sites. We identified a specific depletion of secreted MUC2 from goblet cells in infected pigs that correlated with the increased level of intracellular bacteria in crypt cells. We concluded that L. intracellularis may influence MUC2 production, thereby altering the mucus barrier and enabling cellular invasion.
    No preview · Article · Sep 2015 · Veterinary Immunology and Immunopathology
  • Alan Archibald · David Hume

    No preview · Article · Aug 2015 · The Journal of Agricultural Science
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    ABSTRACT: Contents 79 The Chicken Leads the Way in Avian Genomics. Prepared by J. Smith. 80 The Chicken Genome: Current Status of Genome Assembly and Annotations. Prepared by D.W. Burt, L. Eöry, A.L. Archibald, B.L. Aken, P. Flicek, K. Howe, W. Chow, M. Dunn, J.M.D. Wood, R. Nag, and W.C. Warren. 83 The Avian RNAseq Consortium: A Community Effort to Annotate the Chicken Genome. Prepared by J. Smith, D.W. Burt, and the Avian RNAseq Consortium. 89 Noncoding RNAs in the Chicken Genome. Prepared by J. Hertel, M. Fasold, A. Nitsche, I. Erb, P. Prieto, D. Kedra, C. Notredame, T.E. Steeves, P.P. Gardner, and P.F. Stadler. 91 Genome Sequencing in Birds and Evolutionary Inferences from Avian Genome Sequences. Prepared by H. Ellegren. 94 The Use of Avian BAC Libraries and Clones. Prepared by M.N. Romanov and D.K. Griffin. 96 Comparative Genomics. Prepared by D.M. Larkin, M. Farré, and J. Damas. 100 Avian Cytogenetics Goes Functional. Prepared by D.K. Griffin, M.N. Romanov, R. O’Connor, K.E. Fowler, and D.M. Larkin. 105 Hypermethylated Chromosome Regions in Chicken and Other Birds. Prepared by M. Schmid, C. Steinlein, A.-S. Schneider, I. Nanda, and T. Haaf. 109 An Overview of Avian Evolution. Prepared by S.B. Hedges. 114 An Update on Chicken Sex Determination and Gonadal Sex Differentiation. Prepared by C.A. Smith. 119 Avian Epigenetics. Prepared by H. Zhou. 122 Structural Variation and Copy Number Variation in Poultry. Prepared by R.P.M.A. Crooijmans and M.A.M. Groenen. 124 SNPs and InDels – The Most Abundant Sources of Genetic Variations. Prepared by A.A. Gheyas, C. Boschiero, and D.W. Burt. 130 Genetic Diversity of Village Chickens. Prepared by T.T. Desta, R.A. Lawal, and O. Hanotte. 133 Mendelian Traits. Prepared by D. Wragg. 137 Treasure the Exceptions: Utilizing Chicken Mutant Lines and Advanced Genetic Technologies to Uncover Genes Involved in Developmental Processes. Prepared by E.A. O’Hare and M.E. Delany. 141 Genomic Landscape of the Chicken DT40 Cell Line. Prepared by A. Motegi and M. Takata. 145 RNA-seq: Primary Cells, Cell Lines and Heat Stress. Prepared by C.J. Schmidt, E.M. Pritchett, L. Sun, R.V.N. Davis, A. Hubbard, K.E. Kniel, S.M. Markland, Q. Wang, C. Ashwell, M. Persia, M.F. Rothschild, and S.J. Lamont. 148 Host-Viral Genome Interactions in Marek’s Disease. Prepared by M.C. McPherson, C.M. Robinson, and M.E. Delany. 154 Transcriptome Variation in Response to Marek’s Disease Virus Acute Infection. Prepared by L. Preeyanon, C.T. Brown, and H.H. Cheng. 163 The National Avian Research Facility. Prepared by A. Hart, R. Kuo, L. Eöry, P. Kaiser, and D.W. Burt.
    Full-text · Article · Jul 2015 · Cytogenetic and Genome Research
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    ABSTRACT: The falling cost of DNA sequencing has made the technology affordable to many research groups, enabling researchers to link genomic variants to observed phenotypes in a range of species. This review focusses on whole exome sequencing and its applications in humans and other species. The exome has traditionally been defined to consist of only the protein coding portion of the genome; a region where mutations are likely to affect protein structure and function. There are several commercial kits available for exome sequencing in a number of species and, owing to the highly conserved nature of exons, many of these can be applied to other closely related species. The data set produced from exome sequencing is many times smaller than that of whole genome sequencing, making it more easily manageable and the analysis less complex. Exome sequencing for disease gene discovery in humans is well established and has been used successfully to identify mutations that are causative of complex and rare diseases. Exome sequencing has also been used in a number of domesticated and companion species. The successful application of exome sequencing to crops has yielded results that may be used in selective breeding to improve production in these species, and there is potential for exome sequencing to provide similar advances in livestock species that have not yet been realized. Copyright © 2015 Author et al.
    Full-text · Article · Jul 2015 · G3-Genes Genomes Genetics
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    ABSTRACT: Whipworms (Trichuris spp.) infect a variety of hosts, including domestic animals and humans. Of considerable interest is the porcine whipworm, T. suis, which is particularly prevalent in outdoor production systems. High infection levels may cause growth retardation, anaemia and haemorrhagic diarrhoea. A significant proportion of the variation in Trichuris faecal egg count (FEC) has been attributed to the host's genetic make-up. The aim of the present study was to identify genetic loci associated with resistance to T. suis in pigs. We used single nucleotide polymorphism (SNP) markers to perform a whole-genome scan of an F1 resource population (n=195) trickle-infected with T. suis. A measured genotype analysis revealed a putative quantitative trait locus (QTL) for T. suis FEC on chromosome 13 covering ∼4.5Mbp, although none of the SNPs reached genome-wide significance. We tested the hypothesis that this region of SSC13 harboured genes with effects on T. suis burden by genotyping three SNPs within the putative QTL in unrelated pigs exposed to either experimental or natural T. suis infections and from which we had FEC (n=113) or worm counts (n=178). In these studies, two of the SNPs (rs55618716, ST) were associated with FEC (P<0.01), thus confirming our initial findings. However, we did not find any of the SNPs to be associated with T. suis worm burden. In conclusion, our study demonstrates that genetic markers for resistance to T. suis as indicated by low FEC can be identified in pigs.
    No preview · Article · Jun 2015 · Veterinary Parasitology
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    ABSTRACT: We report here the complete genome of the pathogenic eastern European subtype 3 porcine reproductive and respiratory syndrome virus (PRRSV) strain SU1-Bel, sequenced directly from a pig lymph node. While sharing substantial sequence similarity with other subtype 3 strains, SU1-Bel is found to harbor unique indels and contain putative novel subgenomic RNAs. FOOTNOTES Address correspondence to Tahar Ait-Ali, tahar.aitali{at}roslin.ed.ac.uk. Citation Lu ZH, Wilson AD, Wang X, Frossard J-P, Stadejek T, Archibald AL, Ait-Ali T. 2015. Complete genome sequence of a pathogenic genotype 1 subtype 3 porcine reproductive and respiratory syndrome virus (strain SU1-Bel) from pig primary tissue. Genome Announc 3(3):e00340-15. doi:10.1128/genomeA.00340-15. Received 9 March 2015. Accepted 17 April 2015. Published 21 May 2015. Copyright © 2015 Lu et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.
    Full-text · Article · May 2015 · Genome Announcements
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    ABSTRACT: We describe the organization of a nascent international effort, the Functional Annotation of Animal Genomes (FAANG) project, whose aim is to produce comprehensive maps of functional elements in the genomes of domesticated animal species. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0622-4) contains supplementary material, which is available to authorized users.
    Full-text · Article · Mar 2015 · Genome biology
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    ABSTRACT: The evolution of island populations in natural systems is driven by local adaptation and genetic drift. However, evolutionary pathways may be altered by humans in several ways. The wild boar (WB) (Sus scrofa) is an iconic game species occurring in several islands, where it has been strongly managed since prehistoric times. We examined genomic diversity at 49 803 single-nucleotide polymorphisms in 99 Sardinian WBs and compared them with 196 wild specimens from mainland Europe and 105 domestic pigs (DP; 11 breeds). High levels of genetic variation were observed in Sardinia (80.9% of the total number of polymorphisms), which can be only in part associated to recent genetic introgression. Both Principal Component Analysis and Bayesian clustering approach revealed that the Sardinian WB population is highly differentiated from the other European populations (F ST = 0.126–0.138), and from DP (F ST = 0.169). Such evidences were mostly unaffected by an uneven sample size, although clustering results in reference populations changed when the number of individuals was standardized. Runs of homozygosity (ROHs) pattern and distribution in Sardinian WB are consistent with a past expansion following a bottleneck (small ROHs) and recent population substructuring (highly homozygous individuals). The observed effect of a non-random selection of Sardinian individuals on diversity, F ST and ROH estimates, stressed the importance of sampling design in the study of structured or introgressed populations. Our results support the heterogeneity and distinctiveness of the Sardinian population and prompt further investigations on its origins and conservation status.
    Full-text · Article · Jan 2015 · Heredity
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    Zen H. Lu · Alan L. Archibald · Tahar Ait-Ali
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    ABSTRACT: The highly heterogeneous porcine reproductive and respiratory syndrome virus (PRRSV) is the causative agent responsible for an economically important pig disease with the characteristic symptoms of reproductive losses in breeding sows and respiratory illnesses in young piglets. The virus can be broadly divided into the European and North American-like genotype 1 and 2 respectively. In addition to this intra-strains variability, the impact of coexisting viral quasispecies on disease development has recently gained much attention; owing very much to the advent of the next-generation sequencing (NGS) technologies. Genomic data produced from the massive sequencing capacities of NGS have enabled the study of PRRSV at an unprecedented rate and details. Unlike conventional sequencing methods which require knowledge of conserved regions, NGS allows de novo assembly of the full viral genomes. Evolutionary variations gained from different genotypic strains provide valuable insights into functionally important regions of the virus. Together with the advancement of sophisticated bioinformatics tools, ultra-deep NGS technologies make the detection of low frequency co-evolving quasispecies possible. This short review gives an overview, including a proposed workflow, on the use of NGS to explore the genetic diversity of PRRSV at both macro- and micro-evolutionary levels.
    Full-text · Article · Oct 2014 · Virus Research
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    Dataset: cp98agab

    Full-text · Dataset · Sep 2014
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    Full-text · Dataset · Sep 2014
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    Full-text · Dataset · Sep 2014
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    ABSTRACT: Abstract Text: Porcine Reproductive and Respiratory Syndrome (PRRS) is an important disease of pigs. Sow farrowing and service data were obtained from two commercial pig multiplication units which experienced several confirmed PRRS outbreaks. Genomic regions associated with reproductive failure during PRRS outbreaks were investigated using a regional heritability mapping (RHM) approach combining the two datasets. Covariates were explored both fitting and ignoring the shape of the epidemic. Heritability (h2) of farrowing mortality (FMOR, proportion of dead piglets per litter) was 0.084 ignoring the epidemic shape and 0.059 fitting it. The additive genetic variance was non-estimable for the FMOR trait during non-epidemic phase. Two regions were significantly associated with FMOR at the genome-wide level, on Sus scrofa chromosomes (SSCs) 4 and 7, with several other regions approaching significance. A single SNP on SSC4 was significantly associated (P<0.001) with FMOR. Keywords: Pig PRRS Regional Heritability Mapping
    No preview · Conference Paper · Aug 2014

  • No preview · Presentation · Jul 2014

Publication Stats

5k Citations
715.24 Total Impact Points

Institutions

  • 1999-2015
    • The University of Edinburgh
      • • Division of Genetics and Genomics
      • • Royal (Dick) School of Veterinary Studies
      • • Roslin Institute
      Edinburgh, Scotland, United Kingdom
  • 1994-2013
    • The Roslin Institute
      Edinburgh, Scotland, United Kingdom
  • 2006
    • University of Aberdeen
      Aberdeen, Scotland, United Kingdom
    • Universidade de Trás-os-Montes e Alto Douro
      • Departamento de Zootecnia
      Vila Real, Vila Real, Portugal
    • University of Milan
      Milano, Lombardy, Italy
  • 2000
    • Swedish University of Agricultural Sciences
      • Department of Animal Breeding and Genetics
      Uppsala, Uppsala, Sweden