The Roslin Institute

Genetics and Genomics

Recent Publications

  • The duck genome and transcriptome provide insight into an avian influenza virus reservoir species Yinhua Huang, Dave Burt, Jacqueline Smith, Pete Kaiser and 46 others — 2013 — Nature Genetics Vol: 45 Pages: 776-U797
    Abstract
    The duck (Anas platyrhynchos) is one of the principal natural hosts of influenza A viruses. We present the duck genome sequence and perform deep transcriptome analyses to investigate immune-related genes. Our data indicate that the duck possesses a contractive immune gene repertoire, as in chicken and zebra finch, and this repertoire has been shaped through lineage-specific duplications. We identify genes that are responsive to influenza A viruses using the lung transcriptomes of control ducks and ones that were infected with either a highly pathogenic (A/duck/Hubei/49/05) or a weakly pathogenic (A/goose/Hubei/65/05) H5N1 1 virus. Further, we show how the duck’s defense mechanisms against influenza infection have been optimized through the diversification of its b-defensin and butyrophilin-like repertoires. These analyses, in combination with the genomic and transcriptomic data, provide a resource for characterizing the interaction between host and influenza viruses.
    DOI
    10.1038/ng.2657
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    http://www.research.ed.ac.uk/portal/files/8760798/The_duck_genome_and_transcriptome_provide_insight_into_an_avian_influenza_virus_reservoir_species.pdf
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    http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.2657.html
  • Npas4 is activated by melatonin, and drives the clock gene Cry1 in the ovine pars tuberalis A West, Sm Dupre, L Yu, Bob Paton, K Miedzinska, As McNeilly, Jre Davis, Dw Burt, Asi Loudon — 18 Apr 2013 — Molecular Endocrinology Vol: 27 Pages: 979-989
    Abstract
    Seasonal mammals integrate changes in the duration of nocturnal melatonin secretion to drive annual physiological cycles. Melatonin receptors within the proximal pituitary region, the pars tuberalis (PT), are essential in regulating seasonal neuroendocrine responses. In the ovine PT, melatonin is known to influence acute changes in transcriptional dynamics coupled to the onset (dusk) and offset (dawn) of melatonin secretion, leading to a potential interval-timing mechanism capable of decoding changes in day-length (photoperiod). Melatonin offset at dawn is linked to cAMP accumulation, which directly induces transcription of the clock gene Per1. The rise of melatonin at dusk induces a separate and distinct cohort, including the clock-regulated genes Cry1 and Nampt, but little is known of the up-stream mechanisms involved. Here, we used next generation sequencing of the ovine PT transcriptome at melatonin onset, and identified Npas4 as a rapidly induced bHLH-PAS domain transcription factor. In vivo we show nuclear localisation of NPAS4 protein in presumptive melatonin target cells of the PT (αGSU-expressing cells), while in situ hybridisation studies identified acute and transient expression in the PT of Npas4 in response to melatonin. In vitro, NPAS4 forms functional dimers with bHLH-PAS domain co-factors ARNT, ARNT2 and ARNTL, transactivating both Cry1 and Nampt ovine promoter reporters. Using a combination of 5` deletions and site-directed mutagenesis we show NPAS4:ARNT transactivation to be co-dependent upon two conserved central midline elements (CMEs) within the Cry1 promoter. Our data thus reveal NPAS4 as a candidate immediate early-response gene in the ovine PT, driving molecular responses to melatonin.
    DOI
    10.1210/me.2012-1366
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    http://www.research.ed.ac.uk/portal/files/8373406/979.full.pdf
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  • The chicken talpid3 gene encodes a novel protein essential for Hedgehog signaling Megan G Davey, I Robert Paton, Yili Yin, Maike Schmidt, Fiona K Bangs, David R Morrice, Terence Gordon Smith, Paul Buxton, Despina Stamataki, Mikiko Tanaka, Andrea E Münsterberg, James Briscoe, Cheryll Tickle, Dave W Burt — 2006 — Genes & Development Vol: 20 Pages: 1365-77
    Abstract
    Talpid3 is a classical chicken mutant with abnormal limb patterning and malformations in other regions of the embryo known to depend on Hedgehog signaling. We combined the ease of manipulating chicken embryos with emerging knowledge of the chicken genome to reveal directly the basis of defective Hedgehog signal transduction in talpid3 embryos and to identify the talpid3 gene. We show in several regions of the embryo that the talpid3 phenotype is completely ligand independent and demonstrate for the first time that talpid3 is absolutely required for the function of both Gli repressor and activator in the intracellular Hedgehog pathway. We map the talpid3 locus to chromosome 5 and find a frameshift mutation in a KIAA0586 ortholog (ENSGALG00000012025), a gene not previously attributed with any known function. We show a direct causal link between KIAA0586 and the mutant phenotype by rescue experiments. KIAA0586 encodes a novel protein, apparently specific to vertebrates, that localizes to the cytoplasm. We show that Gli3 processing is abnormal in talpid3 mutant cells but that Gli3 can still translocate to the nucleus. These results suggest that the talpid3 protein operates in the cytoplasm to regulate the activity of both Gli repressor and activator proteins.
    DOI
    10.1101/gad.369106
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    http://www.research.ed.ac.uk/portal/files/10119977/The_chicken_talpid3_gene_encodes_a_novel_protein_essential_for_Hedgehog_signaling.pdf
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  • Development of a high density 600K SNP genotyping array for chicken Andreas Kranis, Almas A Gheyas, Clarissa Boschiero, Frances Turner, Le Yu, Sarah Smith, Richard Talbot, Ali Pirani, Fiona Brew, Pete Kaiser, Paul M Hocking, Mark Fife, Nigel Salmon, Janet Fulton, Tim M Strom, Georg Haberer, Steffen Weigend, Rudolf Preisinger, Mahmood Gholami, Saber Qanbari, Henner Simianer, Kellie A Watson, John A Woolliams, David W Burt — 01 Jan 2013 — BMC Genomics Vol: 14
    Abstract
    BACKGROUND: High density (HD) SNP genotyping arrays are an important tool for genetic analyses of animals and plants. Although the chicken is one of the most important farm animals, no HD array is yet available for high resolution genetic analysis of this species.

    RESULTS: We report here the development of a 600 K Affymetrix(R) Axiom(R) HD genotyping array designed using SNPs segregating in a wide variety of chicken populations. In order to generate a large catalogue of segregating SNPs, we re-sequenced 243 chickens from 24 chicken lines derived from diverse sources (experimental, commercial broiler and layer lines) by pooling 10--15 samples within each line. About 139 million (M) putative SNPs were detected by mapping sequence reads to the new reference genome (Gallus_gallus_4.0) of which ~78 M appeared to be segregating in different lines. Using criteria such as high SNP-quality score, acceptable design scores predicting high conversion performance in the final array and uniformity of distribution across the genome, we selected ~1.8 M SNPs for validation through genotyping on an independent set of samples (n = 282). About 64% of the SNPs were polymorphic with high call rates (>98%), good cluster separation and stable Mendelian inheritance. Polymorphic SNPs were further analysed for their population characteristics and genomic effects. SNPs with extreme breach of Hardy-Weinberg equilibrium (P <0.00001) were excluded from the panel. The final array, designed on the basis of these analyses, consists of 580,954 SNPs and includes 21,534 coding variants. SNPs were selected to achieve an essentially uniform distribution based on genetic map distance for both broiler and layer lines. Due to a lower extent of LD in broilers compared to layers, as reported in previous studies, the ratio of broiler and layer SNPs in the array was kept as 3:2. The final panel was shown to genotype a wide range of samples including broilers and layers with over 100 K to 450 K informative SNPs per line. A principal component analysis was used to demonstrate the ability of the array to detect the expected population structure which is an important pre-investigation step for many genome-wide analyses.

    CONCLUSIONS: This Affymetrix(R) Axiom(R) array is the first SNP genotyping array for chicken that has been made commercially available to the public as a product. This array is expected to find widespread usage both in research and commercial application such as in genomic selection, genome-wide association studies, selection signature analyses, fine mapping of QTLs and detection of copy number variants.
    DOI
    10.1186/1471-2164-14-59
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    http://www.research.ed.ac.uk/portal/files/8357038/Development_of_a_high_density_600K_SNP_genotyping_array_for_chicken.pdf
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    http://www.biomedcentral.com/1471-2164/14/59/abstract
  • Identification of Eya3 and TAC1 as long-day signals in the sheep pituitary S.M. Dupre, K. Miedzinska, C.V. Duval, L. Yu, R.L. Goodman, G.A. Lincoln, J.R.E. Davis, A.S. McNeilly, D.W. Burt, A.S.I. Louden — 2010 — Current Biology Vol: 20 Pages: 829-835
    Abstract
    Seasonally breeding mammals such as sheep use photoperiod, encoded by the nocturnal secretion of the pineal hormone melatonin, as a critical cue to drive hormone rhythms and synchronize reproduction to the most optimal time of year [1, 2]. Melatonin acts directly on the pars tuberalis (PT) of the pituitary, regulating expression of thyrotropin, which then relays messages back to the hypothalamus to control reproductive circuits [3, 4]. In addition, a second local intrapituitary circuit controls seasonal prolactin (PRL) release via one or more currently uncharacterized low-molecular-weight peptides, termed "tuberalins," of PT origin [5-7]. Studies in birds have identified the transcription factor Eya3 as the first molecular response activated by long photoperiod (LP) [8]. Using arrays and in situ hybridization studies, we demonstrate here that Eya3 is the strongest LP-activated gene in sheep, revealing a common photoperiodic molecular response in birds and mammals. We also demonstrate TAC1 (encoding the tachykinins substance P and neurokinin A) to be strongly activated by LP within the sheep PT. We show that these PRL secretagogues act on primary pituitary cells and thus are candidates for the elusive PT-expressed tuberalin seasonal hormone regulator.
    DOI
    10.1016/j.cub.2010.02.066
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    http://www.research.ed.ac.uk/portal/files/8172172/Dupre_et_al_2010.pdf
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    http://dx.doi.org/10.1016/j.cub.2010.02.066
  • Normalized long read RNA sequencing in chicken reveals transcriptome complexity similar to human Richard I Kuo, Elizabeth Tseng, Lel Eory, Ian R Paton, Alan L Archibald, David W Burt — 24 Apr 2017 — BMC Genomics Vol: 18 Pages: 323
    Abstract

    BACKGROUND: Despite the significance of chicken as a model organism, our understanding of the chicken transcriptome is limited compared to human. This issue is common to all non-human vertebrate annotations due to the difficulty in transcript identification from short read RNAseq data. While previous studies have used single molecule long read sequencing for transcript discovery, they did not perform RNA normalization and 5'-cap selection which may have resulted in lower transcriptome coverage and truncated transcript sequences.

    RESULTS: We sequenced normalised chicken brain and embryo RNA libraries with Pacific Bioscience Iso-Seq. 5' cap selection was performed on the embryo library to provide methodological comparison. From these Iso-Seq sequencing projects, we have identified 60 k transcripts and 29 k genes within the chicken transcriptome. Of these, more than 20 k are novel lncRNA transcripts with ~3 k classified as sense exonic overlapping lncRNA, which is a class that is underrepresented in many vertebrate annotations. The relative proportion of alternative transcription events revealed striking similarities between the chicken and human transcriptomes while also providing explanations for previously observed genomic differences.

    CONCLUSIONS: Our results indicate that the chicken transcriptome is similar in complexity compared to human, and provide insights into other vertebrate biology. Our methodology demonstrates the potential of Iso-Seq sequencing to rapidly expand our knowledge of transcriptomics.

    DOI
    10.1186/s12864-017-3691-9
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    http://www.research.ed.ac.uk/portal/files/35206120/art_3A10.1186_2Fs12864_017_3691_9.pdf
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  • A New Chicken Genome Assembly Provides Insight into Avian Genome Structure Andrew S Mason, Richard Kuo, David W Burt and 29 others — 01 Jan 2017 — G3 Vol: 7 Pages: 109-117
    Abstract

    The importance of the Gallus gallus (chicken) as a model organism and agricultural animal merits a continuation of sequence assembly improvement efforts. We present a new version of the chicken genome assembly (Gallus_gallus-5.0; GCA_000002315.3) built from combined long single molecule sequencing technology, finished BACs, and improved physical maps. In overall assembled bases, we see a gain of 183 Mb including 16.4 Mb in placed chromosomes with a corresponding gain in the percentage of intact repeat elements characterized. Of the 1.21 Gb genome, we include three previously missing autosomes, GGA30, 31 and 33 and improve sequence contig length 10-fold over the previous Gallus_gallus-4.0. Despite the significant base representation improvements made, 138 Mb of sequence is not yet located to chromosomes. Gallus_gallus-5.0 when annotated for gene content shows an increase of 4,679 annotated genes, 2,768 non-coding and 1,911 protein-coding, over those in Gallus_gallus-4.0. We also revisited the question of what genes are missing in the avian lineage, as assessed by the highest quality avian genome assembly to date, and found that a large fraction of the original set of missing genes are still absent in sequenced bird species. Finally, our new data support a detailed map of MHC-B encompassing two segments; one with a highly stable gene copy number and another in which the gene copy number is highly variable. The chicken model has been a critical resource for many other fields of study, and this new reference assembly will substantially further these efforts.

    DOI
    10.1534/g3.116.035923
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    http://www.research.ed.ac.uk/portal/files/30947212/109.full.pdf
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  • Deciphering chicken fatness trait with integrative genetic and genomic approaches. C. K. Khoo, A. Gheyas, R. Kuo, L. Eory, P. M. Hocking, D. Burt — Sep 2016 — Journal of Animal Science Vol: 94 Pages: 36-37
  • A new look at the LTR retrotransposon content of the chicken genome Andrew S Mason, Janet E Fulton, Paul M Hocking, David W Burt — 30 Aug 2016 — BMC Genomics Vol: 17 Pages: 688
    Abstract

    BACKGROUND: LTR retrotransposons contribute approximately 10 % of the mammalian genome, but it has been previously reported that there is a deficit of these elements in the chicken relative to both mammals and other birds. A novel LTR retrotransposon classification pipeline, LocaTR, was developed and subsequently utilised to re-examine the chicken LTR retrotransposon annotation, and determine if the proposed chicken deficit is biologically accurate or simply a technical artefact.

    RESULTS: Using LocaTR 3.01 % of the chicken galGal4 genome assembly was annotated as LTR retrotransposon-derived elements (nearly double the previous annotation), including 1,073 that were structurally intact. Element distribution is significantly correlated with chromosome size and is non-random within each chromosome. Elements are significantly depleted within coding regions and enriched in gene sparse areas of the genome. Over 40 % of intact elements are found in clusters, unrelated by age or genera, generally in poorly recombining regions. The transcription of most LTR retrotransposons were suppressed or incomplete, but individual domain and full length retroviral transcripts were produced in some cases, although mostly with regularly interspersed stop codons in all reading frames. Furthermore, RNAseq data from 23 diverse tissues enabled greater characterisation of the co-opted endogenous retrovirus Ovex1. This gene was shown to be expressed ubiquitously but at variable levels across different tissues. LTR retrotransposon content was found to be very variable across the avian lineage and did not correlate with either genome size or phylogenetic position. However, the extent of previous, species-specific LTR retrotransposon annotation appears to be a confounding factor.

    CONCLUSIONS: Use of the novel LocaTR pipeline has nearly doubled the annotated LTR retrotransposon content of the chicken genome compared to previous estimates. Further analysis has described element distribution, clustering patterns and degree of expression in a variety of adult tissues, as well as in three embryonic stages. This study also enabled better characterisation of the co-opted gamma retroviral envelope gene Ovex1. Additionally, this work suggests that there is no deficit of LTR retrotransposons within the Galliformes relative to other birds, or to mammalian genomes when scaled for the three-fold difference in genome size.

    DOI
    10.1186/s12864-016-3043-1
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    http://www.research.ed.ac.uk/portal/files/27590662/art_3A10.1186_2Fs12864_016_3043_1.pdf
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  • A strategy to discover new organizers identifies a putative heart organizer Claire Anderson, Mohsin A F Khan, Frances Wong, Tatiana Solovieva, Nidia M M Oliveira, Richard A Baldock, Cheryll Tickle, Dave W Burt, Claudio D Stern — 25 Aug 2016 — Nature Communications Vol: 7 Pages: 12656
    Abstract

    Organizers are regions of the embryo that can both induce new fates and impart pattern on other regions. So far, surprisingly few organizers have been discovered, considering the number of patterned tissue types generated during development. This may be because their discovery has relied on transplantation and ablation experiments. Here we describe a new approach, using chick embryos, to discover organizers based on a common gene expression signature, and use it to uncover the anterior intestinal portal (AIP) endoderm as a putative heart organizer. We show that the AIP can induce cardiac identity from non-cardiac mesoderm and that it can pattern this by specifying ventricular and suppressing atrial regional identity. We also uncover some of the signals responsible. The method holds promise as a tool to discover other novel organizers acting during development.

    DOI
    10.1038/ncomms12656
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    http://www.research.ed.ac.uk/portal/files/27510321/ncomms12656.pdf
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  • Novel insights into chromosome evolution in birds, archosaurs, and reptiles Marta Farre, Jitendra Narayan, Gancho T. Slavov, Joana Damas, Loretta Auvil, Li Cai, Erich D Jarvis, David Burt, Darren K Griffin, Denis M. Larkin — Aug 2016 — Genome Biology and Evolution Vol: 8 Pages: 2442-2451
    Abstract
    Homologous synteny blocks (HSBs) and evolutionary breakpoint regions (EBRs) in mammalian chromosomes are enriched for distinct DNA features, contributing to distinct phenotypes. To reveal HSB and EBR roles in avian evolution, we performed a sequence-based comparison of 21 avian and five outgroup species using recently sequenced genomes across the avian family tree and a newly-developed algorithm. We identified EBRs and HSBs in ancestral bird, archosaurian (bird, crocodile, dinosaur), and reptile chromosomes. Genes involved in the regulation of gene expression and biosynthetic processes were preferably located in HSBs, for example the avian-specific HSBs were enriched for genes involved in limb development. Within birds, some lineage-specific EBRs rearranged genes related to distinct phenotypes, such as forebrain development in parrots. Our findings provide novel evolutionary insights into genome evolution in birds, particularly how chromosome rearrangements likely contributed to the formation of novel phenotypes.
    DOI
    10.1093/gbe/evw166
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    http://www.research.ed.ac.uk/portal/files/27918414/Genome_Biol_Evol_2016_Farr_2442_51.pdf
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  • Commercial chicken breeds exhibit highly divergent patterns of linkage disequilibrium Reuben J. Pengelly, Almas Gheyas, Richard Kuo, Enrico Mossotto, Eleanor G. Seaby, David Burt, Sarah Ennis, Andrew Collins — 06 Jul 2016 — Heredity Vol: 117 Pages: 375-382
    Abstract
    The analysis of linkage disequilibrium (LD) underpins the development of effective genotyping technologies, trait mapping and understanding of biological mechanisms such as those driving recombination and the impact of selection. We apply the Malécot-Morton model of LD to create additive LD maps which describe the high-resolution LD landscape of commercial chickens. We investigated LD in chickens (Gallus gallus) at the highest resolution to date for broiler, white egg and brown egg layer commercial lines. There is minimal concordance between breeds of fine scale LD patterns (correlation coefficient < 0.21), and even between discrete broiler lines. Regions of LD breakdown, which may align with recombination hotspots, are enriched near CpG islands and transcription start sites (p < 2.2x10-16), consistent with recent evidence described in finches, but concordance in hotspot locations between commercial breeds is only marginally greater than random. As in other birds functional elements in the chicken genome are associated with recombination, but, unlike evidence from other bird species, the LD landscape is not stable in the populations studied. The development of optimal genotyping panels for genome-led selection programmes will depend on careful analysis of the LD structure of each line of interest. Further study is required to fully elucidate the mechanisms underlying highly divergent LD patterns found in commercial chickens.
    DOI
    10.1038/hdy.2016.47
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    http://www.research.ed.ac.uk/portal/files/25459679/ChickenLD_paper_19may2016.pdf
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  • Leukocyte protein Trojan, as a candidate for apoptotic regulatory role Petar Petrov, Riikka Syrjanen, Tatsuya Uchida, David Burt, Olli Vainio — May 2016 — Scandinavian Journal of Immunology Vol: 83 Pages: 353-353
  • Quantitative trait loci with sex-specific effects for internal organs weights and hematocrit value in a broiler-layer cross A. S. A. M. T. Moura, M. C. Ledur, C. Boschiero, K. Nones, L. F. B. Pinto, F. R. F. Jaenisch, D. W. Burt, L. L. Coutinho — May 2016 — Journal of applied genetics Vol: 57 Pages: 215-224
  • Animal genomics and infectious disease resistance in poultry J Smith, A Gheyas, D W Burt — 01 Apr 2016 — Revue scientifique et technique-Office international des epizooties Vol: 35 Pages: 105-19
    Abstract

    Avian pathogens are responsible for major costs to society, both in terms of huge economic losses to the poultry industry and their implications for human health. The health and welfare of millions of birds is under continued threat from many infectious diseases, some of which are increasing in virulence and thus becoming harder to control, such as Marek's disease virus and avian influenza viruses. The current era in animal genomics has seen huge developments in both technologies and resources, which means that researchers have never been in a better position to investigate the genetics of disease resistance and determine the underlying genes/mutations which make birds susceptible or resistant to infection. Avian genomics has reached a point where the biological mechanisms of infectious diseases can be investigated and understood in poultry and other avian species. Knowledge of genes conferring disease resistance can be used in selective breeding programmes or to develop vaccines which help to control the effects of these pathogens, which have such a major impact on birds and humans alike.

    DOI
    10.20506/rst.35.1.2421
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    http://www.research.ed.ac.uk/portal/files/25439806/SmithGheyasBurt_back_from_author.doc
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  • Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project The FAANG Consortium — 01 Dec 2015 — Genome Biology Vol: 16
  • Binary Switching of Calendar Cells in the Pituitary Defines the Phase of the Circannual Cycle in Mammals Shona H. Wood, Helen C. Christian, Katarzyna Miedzinska, Ben R.C. Saer, Mark Johnson, Bob Paton, Le Yu, Judith Mcneilly, Julian R.E. Davis, Alan S. McNeilly, Dave Burt, Andrew S.I. Loudon — 19 Oct 2015 — Current Biology Vol: 25 Pages: 2651–2662
    Abstract
    Persistent free-running circannual (approximately year-long) rhythms have evolved in animals to regulate hormone cycles, drive metabolic rhythms (including hibernation), and time annual reproduction. Recent studies have defined the photoperiodic input to this rhythm, wherein melatonin acts on thyrotroph cells of the pituitary pars tuberalis (PT), leading to seasonal changes in the control of thyroid hormone metabolism in the hypothalamus. However, seasonal rhythms persist in constant conditions in many species in the absence of a changing photoperiod signal, leading to the generation of circannual cycles. It is not known which cells, tissues, and pathways generate these remarkable long-term rhythmic processes. We show that individual PT thyrotrophs can be in one of two binary states reflecting either a long (EYA3+) or short (CHGA+) photoperiod, with the relative proportion in each state defining the phase of the circannual cycle. We also show that a morphogenic cycle driven by the PT leads to extensive re-modeling of the PT and hypothalamus over the circannual cycle. We propose that the PT may employ a recapitulated developmental pathway to drive changes in morphology of tissues and cells. Our data are consistent with the hypothesis that the circannual timer may reside within the PT thyrotroph and is encoded by a binary switch timing mechanism, which may regulate the generation of circannual neuroendocrine rhythms, leading to dynamic re-modeling of the hypothalamic interface. In summary, the PT-ventral hypothalamus now appears to be a prime structure involved in long-term rhythm generation.
    DOI
    10.1016/j.cub.2015.09.014
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    http://www.research.ed.ac.uk/portal/files/21937915/Binary_Switching_of_Calendar_Cells_in_the_Pituitary_Defines_the_Phase_of_the_Circannual_Cycle_in_Mammals.pdf
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    http://linkinghub.elsevier.com/retrieve/pii/S0960982215010933
  • Genome-wide analysis reveals the extent of EAV-HP integration in domestic chicken David Wragg, Andrew S Mason, Le Yu, Richard Kuo, Raman A Lawal, Takele Taye Desta, Joram M Mwacharo, Chang-Yeon Cho, Stephen Kemp, David W Burt, Olivier Hanotte — 14 Oct 2015 — BMC Genomics Vol: 16 Pages: 784
    Abstract

    BACKGROUND: EAV-HP is an ancient retrovirus pre-dating Gallus speciation, which continues to circulate in modern chicken populations, and led to the emergence of avian leukosis virus subgroup J causing significant economic losses to the poultry industry. We mapped EAV-HP integration sites in Ethiopian village chickens, a Silkie, Taiwan Country chicken, red junglefowl Gallus gallus and several inbred experimental lines using whole-genome sequence data.

    RESULTS: An average of 75.22 ± 9.52 integration sites per bird were identified, which collectively group into 279 intervals of which 5 % are common to 90 % of the genomes analysed and are suggestive of pre-domestication integration events. More than a third of intervals are specific to individual genomes, supporting active circulation of EAV-HP in modern chickens. Interval density is correlated with chromosome length (P < 2.31(-6)), and 27 % of intervals are located within 5 kb of a transcript. Functional annotation clustering of genes reveals enrichment for immune-related functions (P < 0.05).

    CONCLUSIONS: Our results illustrate a non-random distribution of EAV-HP in the genome, emphasising the importance it may have played in the adaptation of the species, and provide a platform from which to extend investigations on the co-evolutionary significance of endogenous retroviral genera with their hosts.

    DOI
    10.1186/s12864-015-1954-x
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    http://www.research.ed.ac.uk/portal/files/21906137/s12864_015_1954_x.pdf
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    http://www.biomedcentral.com/1471-2164/16/784
  • The early immune response to infection of chickens with Infectious Bronchitis Virus (IBV) in susceptible and resistant birds Jacqueline Smith, Jean-Remy Sadeyen, David Cavanagh, Pete Kaiser, David W Burt — 09 Oct 2015 — BMC Veterinary Research Vol: 11
    Abstract

    BACKGROUND: Infectious Bronchitis is a highly contagious respiratory disease which causes tracheal lesions and also affects the reproductive tract and is responsible for large economic losses to the poultry industry every year. This is due to both mortality (either directly provoked by IBV itself or due to subsequent bacterial infection) and lost egg production. The virus is difficult to control by vaccination, so new methods to curb the impact of the disease need to be sought. Here, we seek to identify genes conferring resistance to this coronavirus, which could help in selective breeding programs to rear chickens which do not succumb to the effects of this disease.

    METHODS: Whole genome gene expression microarrays were used to analyse the gene expression differences, which occur upon infection of birds with Infectious Bronchitis Virus (IBV). Tracheal tissue was examined from control and infected birds at 2, 3 and 4 days post-infection in birds known to be either susceptible or resistant to the virus. The host innate immune response was evaluated over these 3 days and differences between the susceptible and resistant lines examined.

    RESULTS: Genes and biological pathways involved in the early host response to IBV infection were determined andgene expression differences between susceptible and resistant birds were identified. Potential candidate genes for resistance to IBV are highlighted.

    CONCLUSIONS: The early host response to IBV is analysed and potential candidate genes for disease resistance are identified. These putative resistance genes can be used as targets for future genetic and functional studies to prove a causative link with resistance to IBV.

    DOI
    10.1186/s12917-015-0575-6
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    http://www.research.ed.ac.uk/portal/files/21807210/s12917_015_0575_6.pdf
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  • Evolution of the avian β-defensin and cathelicidin genes Yuanyuan Cheng, Michael Dennis Prickett, Maria Gutowska, Richard Kuo, Katherine Belov, David W Burt — 15 Sep 2015 — BMC Evolutionary Biology Vol: 15 Pages: 188
    Abstract

    BACKGROUND: β-defensins and cathelicidins are two families of cationic antimicrobial peptides (AMPs) with a broad range of antimicrobial activities that are key components of the innate immune system. Due to their important roles in host defense against rapidly evolving pathogens, the two gene families provide an ideal system for studying adaptive gene evolution. In this study we performed phylogenetic and selection analyses on β-defensins and cathelicidins from 53 avian species representing 32 orders to examine the evolutionary dynamics of these peptides in birds.

    RESULTS AND CONCLUSIONS: Avian β-defensins are found in a gene cluster consisting of 13 subfamiles. Nine of these are conserved as one to one orthologs in all birds, while the others (AvBD1, AvBD3, AvBD7 and AvBD14) are more subject to gene duplication or pseudogenisation events in specific avian lineages. Avian cathelicidins are found in a gene cluster consisting of three subfamilies with species-specific duplications and gene loss. Evidence suggested that the propiece and mature peptide domains of avian cathelicidins are possibly co-evolving in such a way that the cationicity of the mature peptide is partially neutralised by the negative charge of the propiece prior to peptide secretion (further evidence obtained by repeating the analyses on primate cathelicidins). Negative selection (overall mean dN < dS) was detected in most of the gene domains examined, conserving certain amino acid residues that may be functionally crucial for the avian β-defensins and cathelicidins, while episodic positive selection was also involved in driving the diversification of specific codon sites of certain AMPs in avian evolutionary history. These findings have greatly improved our understanding of the molecular evolution of avian AMPs and will be useful to understand their role in the avian innate immune response. Additionally, the large dataset of β-defensin and cathelicidin peptides may also provide a valuable resource for translational research and development of novel antimicrobial agents in the future.

    DOI
    10.1186/s12862-015-0465-3
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    http://www.research.ed.ac.uk/portal/files/22245115/Evolution_of_the_avian_defensin_and_cathelicidin_genes.pdf
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  • Transcriptomic Profiling of Virus-Host Cell Interactions following Chicken Anaemia Virus (CAV) Infection in an In Vivo Model Efstathios S. Giotis, Lisa Rothwell, Alistair Scott, Tuanjun Hu, Richard Talbot, Daniel Todd, David W. Burt, Elizabeth J. Glass, Pete Kaiser — 05 Aug 2015 — PLoS One Vol: 10
    Abstract
    Chicken Anaemia Virus (CAV) is an economically important virus that targets lymphoid and erythroblastoid progenitor cells leading to immunosuppression. This study aimed to investigate the interplay between viral infection and the host’s immune response to better understand the pathways that lead to CAV-induced immunosuppression. To mimic vertical transmission of CAV in the absence of maternally-derived antibody, day-old chicks were infected and their responses measured at various time-points post-infection by qRT-PCR and gene expression microarrays. The kinetics of mRNA expression levels of signature cytokines of innate and adaptive immune responses were determined by qRT-PCR. The global gene expression profiles of mock-infected (control) and CAV-infected chickens at 14 dpi were also compared using a chicken immune-related 5K microarray. Although in the thymus there was evidence of induction of an innate immune response following CAV infection, this was limited in magnitude. There was little evidence of a Th1 adaptive immune response in any lymphoid tissue, as would normally be expected in response to viral infection. Most cytokines associated with Th1, Th2 or Treg subsets were down-regulated, except IL-2, IL-13, IL-10 and IFNγ, which were all up-regulated in thymus and bone marrow. From the microarray studies, genes that exhibited significant (greater than 1.5-fold, false discovery rate <0.05) changes in expression in thymus and bone marrow on CAV infection were mainly associated with T-cell receptor signalling, immune response, transcriptional regulation, intracellular signalling and regulation of apoptosis. Expression levels of a number of adaptor proteins, such as src-like adaptor protein (SLA), a negative regulator of T-cell receptor signalling and the transcription factor Special AT-rich Binding Protein 1 (SATB1), were significantly down-regulated by CAV infection, suggesting potential roles for these genes as regulators of viral infection or cell defence. These results extend our understanding of CAV-induced immunosuppression and suggest a global immune dysregulation following CAV infection.
    DOI
    10.1371/journal.pone.0134866
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    http://www.research.ed.ac.uk/portal/files/21155131/Transcriptomic_Profiling_of_Virus_Host_Cell_Interactions_following_Chicken_Anaemia_Virus_CAV_Infection_in_an_In_Vivo_Model.pdf
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    http://dx.plos.org/10.1371/journal.pone.0134866
  • Third Report on Chicken Genes and Chromosomes 2015 Jacqueline Smith, David W. Burt, Alan L. Archibald, Dirk-jan De Koning, Ian C. Dunn, Lel Eory, Valerie Garceau, Almas A. Gheyas, Alan Hart, David A. Hume, Pete Kaiser, Stephen Kemp, Richard Kuo, Heather A. Mccormack and 90 others — Aug 2015 — Cytogenetic and Genome Research Vol: 145 Pages: 78-179
  • Functional classification of 15 million SNPs detected from diverse chicken populations Almas A Gheyas, Clarissa Boschiero, Lel Eory, Hannah Ralph, Richard Kuo, John A Woolliams, David W Burt — 29 Apr 2015 — DNA Research Vol: 22 Pages: 205-217
    Abstract

    Next-generation sequencing has prompted a surge of discovery of millions of genetic variants from vertebrate genomes. Besides applications in genetic association and linkage studies, a fraction of these variants will have functional consequences. This study describes detection and characterization of 15 million SNPs from chicken genome with the goal to predict variants with potential functional implications (pfVars) from both coding and non-coding regions. The study reports: 183K amino acid-altering SNPs of which 48% predicted as evolutionary intolerant, 13K splicing variants, 51K likely to alter RNA secondary structures, 500K within most conserved elements and 3K from non-coding RNAs. Regions of local fixation within commercial broiler and layer lines were investigated as potential selective sweeps using genome-wide SNP data. Relationships with phenotypes, if any, of the pfVars were explored by overlaying the sweep regions with known QTLs. Based on this, the candidate genes and/or causal mutations for a number of important traits are discussed. Although the fixed variants within sweep regions were enriched with non-coding SNPs, some non-synonymous-intolerant mutations reached fixation, suggesting their possible adaptive advantage. The results presented in this study are expected to have important implications for future genomic research to identify candidate causal mutations and in poultry breeding.

    DOI
    10.1093/dnares/dsv005
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    http://www.research.ed.ac.uk/portal/files/19489768/DNA_Res_2015_Gheyas_dnares_dsv005.pdf
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  • Characterization of the avian trojan gene family reveals contrasting evolutionary constraints Petar Petrov, Riikka Syrjänen, Jacqueline Smith, Maria Weronika Gutowska, Tatsuya Uchida, Olli Vainio, David W Burt — 24 Mar 2015 — PLoS One Vol: 10 Pages: e0121672
    Abstract

    "Trojan" is a leukocyte-specific, cell surface protein originally identified in the chicken. Its molecular function has been hypothesized to be related to anti-apoptosis and the proliferation of immune cells. The Trojan gene has been localized onto the Z sex chromosome. The adjacent two genes also show significant homology to Trojan, suggesting the existence of a novel gene/protein family. Here, we characterize this Trojan family, identify homologues in other species and predict evolutionary constraints on these genes. The two Trojan-related proteins in chicken were predicted as a receptor-type tyrosine phosphatase and a transmembrane protein, bearing a cytoplasmic immuno-receptor tyrosine-based activation motif. We identified the Trojan gene family in ten other bird species and found related genes in three reptiles and a fish species. The phylogenetic analysis of the homologues revealed a gradual diversification among the family members. Evolutionary analyzes of the avian genes predicted that the extracellular regions of the proteins have been subjected to positive selection. Such selection was possibly a response to evolving interacting partners or to pathogen challenges. We also observed an almost complete lack of intracellular positively selected sites, suggesting a conserved signaling mechanism of the molecules. Therefore, the contrasting patterns of selection likely correlate with the interaction and signaling potential of the molecules.

    DOI
    10.1371/journal.pone.0121672
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    http://www.research.ed.ac.uk/portal/files/19508995/Characterization_of_the_avian_trojan_gene_family_reveals_contrasting_evolutionary_constraints.pdf
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    http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0121672
  • Analysis of the crow lung transcriptome in response to infection with highly pathogenic H5N1 avian influenza virus Periyasamy Vijayakumar, Anamika Mishra, Pradip B. Ranaware, Atul P. Kolte, Diwakar D. Kulkarni, David W. Burt, Ashwin Ashok Raut — 15 Mar 2015 — Gene Vol: 559 Pages: 77-85
    Abstract

    The highly pathogenic avian influenza (HPAI) H5N1 virus, currently circulating in Asia, causes severe disease in domestic poultry as well as wild birds like crow. However, the molecular pathogenesis of HPAIV infection in crows and other wild birds is not well known. Thus, as a step to explore it, a comprehensive global gene expression analysis was performed on crow lungs, infected with HPAI H5N1 crow isolate (A/Crow/India/11TI11/2011) using high throughput next generation sequencing (NGS) (GS FLX Titanium XLR70). The reference genome of crow is not available, so RNA seq analysis was performed on the basis of a de novo assembled transcriptome. The RNA seq result shows, 4052 genes were expressed uniquely in noninfected, 6277 genes were expressed uniquely in HPAIV infected sample and of the 6814 genes expressed in both samples, 2279 genes were significantly differentially expressed. Our transcriptome profile data allows for the ability to understand the molecular mechanism behind the recent lethal HPAIV outbreak in crows which was, until recently, thought to cause lethal infections only in gallinaceous birds such as chickens, but not in wild birds. The pattern of differentially expressed genes suggest that this isolate of H5N1 virus evades the host innate immune response by attenuating interferon (IFN)-inducible signalling possibly by down regulating the signalling from type I IFN (IFNAR1 and IFNAR2) and type II IFN receptors, upregulation of the signalling inhibitors suppressor of cytokine signalling 1 (SOCS1) and SOCS3 and altering the expression of toll-like receptors (TLRs). This may be the reason for disease and mortality in crows.

    DOI
    10.1016/j.gene.2015.01.016
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  • Analysis of the early immune response to infection by Infectious Bursal Disease Virus (IBDV) in chickens differing in their resistance to the disease Jacqueline Smith, Jean-Remy Sadeyen, Colin Butter, Pete Kaiser, David W Burt — Mar 2015 — Journal of Virology Vol: 89 Pages: 2469-2482
    Abstract

    Chicken whole genome gene expression arrays were used to analyse the host response to infection by Infectious Bursal Disease Virus (IBDV). Spleen and bursal tissue were examined from control and infected birds at 2, 3 and 4 days post-infection from two lines that differ in their resistance to IBDV infection. The host response was evaluated over this period and differences between susceptible and resistant chicken lines were examined. Anti-viral genes, including IFNA, IFNG, MX1, IFITM1, IFITM3 and IFITM5 were up-regulated in response to infection. Evaluation of this gene expression data has allowed us to predicted several genes as candidates for involvement in resistance to IBDV.

    IMPORTANCE: Infectious bursal disease (IBD) is of economic importance to the poultry industry and thus is also important for food security. Vaccines are available but field strains of the virus are of increasing virulence. There is thus an urgent need to explore new control solutions, one of which would be to breed birds with greater resistance to IBD. A goal which is perhaps uniquely achievable with poultry, of all farm animal species, as the genetics of 85% of the 60 billion chickens produced worldwide each year is under the control of essentially two breeding companies. This is the most comprehensive study to try to identify global transcriptomic differences in the target organ of the virus between chicken lines that differ in resistance, and to predict candidate resistance genes.

    DOI
    10.1128/JVI.02828-14
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    http://www.research.ed.ac.uk/portal/files/18649018/J._Virol._2015_Smith_2469_82.pdf
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    http://jvi.asm.org/content/early/2014/12/04/JVI.02828-14
  • The development and maintenance of the mononuclear phagocyte system of the chick is controlled by signals from the macrophage colony-stimulating factor (CSF1) receptor Valerie Garceau, Adam Balic, Carla Garcia-Morales, Kristin A Sauter, Mike J McGrew, Jacqueline Smith, Lonneke Vervelde, Adrian Sherman, Troy E Fuller, Theodore Oliphant, John A Shelley, Raksha Tiwari, Thomas L Wilson, Cosmin Chintoan-Uta, Dave W Burt, Mark P Stevens, Helen M Sang, David A Hume — 19 Feb 2015 — BMC Biology Vol: 13 Pages: 121
    Abstract

    BACKGROUND: Macrophages have many functions in development and homeostasis as well as innate immunity. Recent studies in mammals suggest that cells arising in the yolk sac give rise to self-renewing macrophage populations that persist in adult tissues. Macrophage proliferation and differentiation is controlled by macrophage colony-stimulating factor (CSF1) and interleukin 34 (IL34), both agonists of the CSF1 receptor (CSF1R). In the current manuscript we describe the origin, function and regulation of macrophages, and the role of CSF1R signalling during embryonic development, using the chick as a model.

    RESULTS: Based upon RNAseq comparison to bone marrow-derived macrophages (BMDM) grown in CSF1, we show that embryonic macrophages contribute around 2% of the total embryo RNA in day 7 chick embryos, and have similar gene expression profiles to BMDM. To explore the origins of embryonic and adult macrophages, we injected HH16 chick embryos with either yolk-sac derived blood cells, or bone marrow cells from EGFP(+) donors. In both cases, the transferred cells gave rise to large numbers of EGFP(+) tissue macrophages in the embryo. In the case of the yolk sac, these cells were not retained in hatched birds. Conversely, bone marrow EGFP(+) cells gave rise to tissue macrophages in all organs of adult birds, and regenerated CSF1-responsive marrow macrophage progenitors. Surprisingly, they did not contribute to any other hematopoietic lineage. To explore the role of CSF1 further, we injected embryonic or hatchling CSF1R-reporter transgenic birds with a novel chicken CSF1-Fc conjugate. In both cases, the treatment produced a large increase in macrophage numbers in all tissues examined. There were no apparent adverse effects of chCSF1-Fc on embryonic or post-hatch development, but there was an unexpected increase in bone density in the treated hatchlings.

    CONCLUSIONS: The data indicate that the yolk sac is not the major source of macrophages in adult birds, and that there is a macrophage-restricted, self-renewing progenitor cell in bone marrow. CSF1R is demonstrated to be limiting for macrophage development during development in ovo and post hatch. The chicken provides a novel and tractable model to study the development of the mononuclear phagocyte system and CSF1R signalling.

    DOI
    10.1186/s12915-015-0121-9
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    http://www.research.ed.ac.uk/portal/files/20038920/The_development_and_maintenance_of_the_mononuclear_phagocyte_system_of_the_chick_is_controlled_by_signals_from_the_macrophage_colony_stimulating_factor_CSF1_receptor.pdf
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    http://www.biomedcentral.com/1741-7007/13/12
  • SNP and INDEL detection in a QTL region on chicken chromosome 2 associated with muscle deposition T. F. Godoy, G. C M Moreira, C. Boschiero, A. A. Gheyas, G. Gasparin, M. Paduan, S. C S Andrade, H. Montenegro, D. W. Burt, M. C. Ledur, L. L. Coutinho — 18 Feb 2015 — Animal Genetics Vol: 46 Pages: 158–163
    Abstract

    Genetic improvement is important for the poultry industry, contributing to increased efficiency of meat production and quality. Because breast muscle is the most valuable part of the chicken carcass, knowledge of polymorphisms influencing this trait can help breeding programs. Therefore, the complete genome of 18 chickens from two different experimental lines (broiler and layer) from EMBRAPA was sequenced, and SNPs and INDELs were detected in a QTL region for breast muscle deposition on chicken chromosome 2 between microsatellite markers MCW0185 and MCW0264 (105 849-112 649 kb). Initially, 94 674 unique SNPs and 10 448 unique INDELs were identified in the target region. After quality filtration, 77% of the SNPs (85 765) and 60% of the INDELs (7828) were retained. The studied region contains 66 genes, and functional annotation of the filtered variants identified 517 SNPs and three INDELs in exonic regions. Of these, 357 SNPs were classified as synonymous, 153 as non-synonymous, three as stopgain, four INDELs as frameshift and three INDELs as non-frameshift. These exonic mutations were identified in 37 of the 66 genes from the target region, three of which are related to muscle development (DTNA, RB1CC1 and MOS). Fifteen non-tolerated SNPs were detected in several genes (MEP1B, PRKDC, NSMAF, TRAPPC8, SDR16C5, CHD7, ST18 and RB1CC1). These loss-of-function and exonic variants present in genes related to muscle development can be considered candidate variants for further studies in chickens. Further association studies should be performed with these candidate mutations as should validation in commercial populations to allow a better explanation of QTL effects.

    DOI
    10.1111/age.12271
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  • Phylogenomic analyses data of the avian phylogenomics project Erich D Jarvis, Siavash Mirarab, Andre J Aberer, Bo Li, Peter Houde, Cai Li, Simon Y W Ho, Brant C Faircloth, Benoit Nabholz, Jason T Howard, Alexander Suh, Claudia C Weber, Rute R da Fonseca, Alonzo Alfaro-Núñez, Nitish Narula, Liang Liu, Dave Burt, Hans Ellegren, Scott V Edwards, Alexandros Stamatakis, David P Mindell, Joel Cracraft, Edward L Braun, Tandy Warnow, Wang Jun, M Thomas Pius Gilbert, Guojie Zhang, Avian Phylogenomics Consortium — 12 Feb 2015 — GigaScience Vol: 4 Pages: 4
    Abstract

    BACKGROUND: Determining the evolutionary relationships among the major lineages of extant birds has been one of the biggest challenges in systematic biology. To address this challenge, we assembled or collected the genomes of 48 avian species spanning most orders of birds, including all Neognathae and two of the five Palaeognathae orders. We used these genomes to construct a genome-scale avian phylogenetic tree and perform comparative genomic analyses.

    FINDINGS: Here we present the datasets associated with the phylogenomic analyses, which include sequence alignment files consisting of nucleotides, amino acids, indels, and transposable elements, as well as tree files containing gene trees and species trees. Inferring an accurate phylogeny required generating: 1) A well annotated data set across species based on genome synteny; 2) Alignments with unaligned or incorrectly overaligned sequences filtered out; and 3) Diverse data sets, including genes and their inferred trees, indels, and transposable elements. Our total evidence nucleotide tree (TENT) data set (consisting of exons, introns, and UCEs) gave what we consider our most reliable species tree when using the concatenation-based ExaML algorithm or when using statistical binning with the coalescence-based MP-EST algorithm (which we refer to as MP-EST*). Other data sets, such as the coding sequence of some exons, revealed other properties of genome evolution, namely convergence.

    CONCLUSIONS: The Avian Phylogenomics Project is the largest vertebrate phylogenomics project to date that we are aware of. The sequence, alignment, and tree data are expected to accelerate analyses in phylogenomics and other related areas.

    DOI
    10.1186/s13742-014-0038-1
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    http://www.research.ed.ac.uk/portal/files/19993333/Phylogenomic_analyses_data_of_the_avian_phylogenomics_project.pdf
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    http://www.gigasciencejournal.com/content/4/1/4
  • Avianbase: a community resource for bird genomics Lel Eory, M Thomas P Gilbert, Cai Li, Bo Li, Alan Archibald, Bronwen L Aken, Guojie Zhang, Erich Jarvis, Paul Flicek, David W Burt — 29 Jan 2015 — Genome Biology Vol: 16
    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.
    DOI
    10.1186/s13059-015-0588-2
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    http://www.research.ed.ac.uk/portal/files/18503107/s13059_015_0588_2.pdf
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    http://genomebiology.com/2015/16/1/21
  • Cetaceans evolution: insights from the genome sequences of common minke whales Jung Youn Park, Yong-Rock An, Naohisa Kanda, Chul-Min An, Hye Suck An, Jung-Ha Kang, Eun Mi Kim, Du-Hae An, Hojin Jung, Myunghee Joung, Myung Hum Park, Sook Hee Yoon, Bo-Young Lee, Taeheon Lee, Kyu-Won Kim, Won Cheoul Park, Dong Hyun Shin, Young Sub Lee, Jaemin Kim, Woori Kwak, Hyeon Jeong Kim, Young-Jun Kwon, Sunjin Moon, Yuseob Kim, David W. Burt, Seoae Cho, Heebal Kim — 22 Jan 2015 — BMC Genomics Vol: 16
    Abstract

    Background: Whales have captivated the human imagination for millennia. These incredible cetaceans are the only mammals that have adapted to life in the open oceans and have been a source of human food, fuel and tools around the globe. The transition from land to water has led to various aquatic specializations related to hairless skin and ability to regulate their body temperature in cold water.

    Results: We present four common minke whale (Balaenoptera acutorostrata) genomes with depth of x13 similar to x17 coverage and perform resequencing technology without a reference sequence. Our results indicated the time to the most recent common ancestors of common minke whales to be about 2.3574 (95% HPD, 1.1521 - 3.9212) million years ago. Further, we found that genes associated with epilation and tooth-development showed signatures of positive selection, supporting the morphological uniqueness of whales.

    Conclusions: This whole-genome sequencing offers a chance to better understand the evolutionary journey of one of the largest mammals on earth.

    DOI
    10.1186/s12864-015-1213-1
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    http://www.research.ed.ac.uk/portal/files/18949934/Cetaceans_evolution_insights_from_the_genome_sequences_of_common_minke_whales.pdf
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    http://www.biomedcentral.com/1471-2164/16/13
  • Variant discovery in a QTL region on chromosome 3 associated with fatness in chickens G. C M Moreira, T. F. Godoy, C. Boschiero, A. Gheyas, G. Gasparin, S. C S Andrade, M. Paduan, H. Montenegro, D. W. Burt, M. C. Ledur, L. L. Coutinho — Jan 2015 — Animal Genetics Vol: 46 Pages: 141-147
    Abstract

    Abdominal fat content is an economically important trait in commercially bred chickens. Although many quantitative trait loci (QTL) related to fat deposition have been detected, the resolution for these regions is low and functional variants are still unknown. The current study was conducted aiming at increasing resolution for a region previously shown to have a QTL associated with fat deposition, to detect novel variants from this region and to annotate those variants to delineate potentially functional ones as candidates for future studies. To achieve this, 18 chickens from a parental generation used in a reciprocal cross between broiler and layer lines were sequenced using the Illumina next-generation platform with an initial coverage of 18X/chicken. The discovery of genetic variants was performed in a QTL region located on chromosome 3 between microsatellite markers LEI0161 and ADL0371 (33 595 706-42 632 651 bp). A total of 136 054 unique SNPs and 15 496 unique INDELs were detected in this region, and after quality filtering, 123 985 SNPs and 11 298 INDELs were retained. Of these variants, 386 SNPs and 15 INDELs were located in coding regions of genes related to important metabolic pathways. Loss-of-function variants were identified in several genes, and six of those, namely LOC771163, EGLN1, GNPAT, FAM120B, THBS2 and GGPS1, were related to fat deposition. Therefore, these loss-of-function variants are candidate mutations for conducting further studies on this important trait in chickens.

    DOI
    10.1111/age.12263
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  • Detection and characterization of small insertion and deletion genetic variants in modern layer chicken genomes Clarissa Boschiero, Almas A Gheyas, Hannah K Ralph, Lel Eory, Bob Paton, Richard Kuo, Janet Fulton, Rudolf Preisinger, Pete Kaiser, David W Burt — 2015 — BMC Genomics Vol: 16
    Abstract

    BACKGROUND: Small insertions and deletions (InDels) constitute the second most abundant class of genetic variants and have been found to be associated with many traits and diseases. The present study reports on the detection and characterisation of about 883 K high quality InDels from the whole-genome analysis of several modern layer chicken lines from diverse breeds.

    RESULTS: To reduce the error rates seen in InDel detection, this study used the consensus set from two InDel-calling packages: SAMtools and Dindel, as well as stringent post-filtering criteria. By analysing sequence data from 163 chickens from 11 commercial and 5 experimental layer lines, this study detected about 883 K high quality consensus InDels with 93 % validation rate and an average density of 0.78 InDels/kb over the genome. Certain chromosomes, viz, GGAZ, 16, 22 and 25 showed very low densities of InDels whereas the highest rate was observed on GGA6. In spite of the higher recombination rates on microchromosomes, the InDel density on these chromosomes was generally lower relative to macrochromosomes possibly due to their higher gene density. About 43-87 % of the InDels were found to be fixed within each line. The majority of detected InDels (86 %) were 1-5 bases and about 63 % were non-repetitive in nature while the rest were tandem repeats of various motif types. Functional annotation identified 613 frameshift, 465 non-frameshift and 10 stop-gain/loss InDels. Apart from the frameshift and stopgain/loss InDels that are expected to affect the translation of protein sequences and their biological activity, 33 % of the non-frameshift were predicted as evolutionary intolerant with potential impact on protein functions. Moreover, about 2.5 % of the InDels coincided with the most-conserved elements previously mapped on the chicken genome and are likely to define functional elements. InDels potentially affecting protein function were found to be enriched for certain gene-classes e.g. those associated with cell proliferation, chromosome and Golgi organization, spermatogenesis, and muscle contraction.

    CONCLUSIONS: The large catalogue of InDels presented in this study along with their associated information such as functional annotation, estimated allele frequency, etc. are expected to serve as a rich resource for application in future research and breeding in the chicken.

    DOI
    10.1186/s12864-015-1711-1
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    http://www.research.ed.ac.uk/portal/files/21170916/s12864_015_1711_1.pdf
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  • A comparative analysis of host responses to avian influenza infection in ducks and chickens highlights a role for the interferon-induced transmembrane proteins in viral resistance Jacqueline Smith, Nikki Smith, Le Yu, Ian R Paton, Maria Weronika Gutowska, Heather L Forrest, Angela F Danner, J Patrick Seiler, Paul Digard, Robert G Webster, David W Burt — 2015 — BMC Genomics Vol: 16
    Abstract

    BACKGROUND: Chickens are susceptible to infection with a limited number of Influenza A viruses and are a potential source of a human influenza pandemic. In particular, H5 and H7 haemagglutinin subtypes can evolve from low to highly pathogenic strains in gallinaceous poultry. Ducks on the other hand are a natural reservoir for these viruses and are able to withstand most avian influenza strains.

    RESULTS: Transcriptomic sequencing of lung and ileum tissue samples from birds infected with high (H5N1) and low (H5N2) pathogenic influenza viruses has allowed us to compare the early host response to these infections in both these species. Chickens (but not ducks) lack the intracellular receptor for viral ssRNA, RIG-I and the gene for an important RIG-I binding protein, RNF135. These differences in gene content partly explain the differences in host responses to low pathogenic and highly pathogenic avian influenza virus in chicken and ducks. We reveal very different patterns of expression of members of the interferon-induced transmembrane protein (IFITM) gene family in ducks and chickens. In ducks, IFITM1, 2 and 3 are strongly up regulated in response to highly pathogenic avian influenza, where little response is seen in chickens. Clustering of gene expression profiles suggests IFITM1 and 2 have an anti-viral response and IFITM3 may restrict avian influenza virus through cell membrane fusion. We also show, through molecular phylogenetic analyses, that avian IFITM1 and IFITM3 genes have been subject to both episodic and pervasive positive selection at specific codons. In particular, avian IFITM1 showed evidence of positive selection in the duck lineage at sites known to restrict influenza virus infection.

    CONCLUSIONS: Taken together these results support a model where the IFITM123 protein family and RIG-I all play a crucial role in the tolerance of ducks to highly pathogenic and low pathogenic strains of avian influenza viruses when compared to the chicken.

    DOI
    10.1186/s12864-015-1778-8
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    http://www.research.ed.ac.uk/portal/files/21169923/s12864_015_1778_8.pdf
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  • Two Antarctic penguin genomes reveal insights into their evolutionary history and molecular changes related to the Antarctic environment David W Burt, Chris P Ponting and 39 others — 12 Dec 2014 — GigaScience Vol: 3 Pages: 27
    Abstract

    BACKGROUND: Penguins are flightless aquatic birds widely distributed in the Southern Hemisphere. The distinctive morphological and physiological features of penguins allow them to live an aquatic life, and some of them have successfully adapted to the hostile environments in Antarctica. To study the phylogenetic and population history of penguins and the molecular basis of their adaptations to Antarctica, we sequenced the genomes of the two Antarctic dwelling penguin species, the Adélie penguin [Pygoscelis adeliae] and emperor penguin [Aptenodytes forsteri].

    RESULTS: Phylogenetic dating suggests that early penguins arose ~60 million years ago, coinciding with a period of global warming. Analysis of effective population sizes reveals that the two penguin species experienced population expansions from ~1 million years ago to ~100 thousand years ago, but responded differently to the climatic cooling of the last glacial period. Comparative genomic analyses with other available avian genomes identified molecular changes in genes related to epidermal structure, phototransduction, lipid metabolism, and forelimb morphology.

    CONCLUSIONS: Our sequencing and initial analyses of the first two penguin genomes provide insights into the timing of penguin origin, fluctuations in effective population sizes of the two penguin species over the past 10 million years, and the potential associations between these biological patterns and global climate change. The molecular changes compared with other avian genomes reflect both shared and diverse adaptations of the two penguin species to the Antarctic environment.

    DOI
    10.1186/2047-217X-3-27
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    http://www.research.ed.ac.uk/portal/files/23446888/2047_217X_3_27.pdf
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  • Whole-genome analyses resolve early branches in the tree of life of modern birds Yinhua Huang, Dave Burt and 103 others — 12 Dec 2014 — Science Vol: 346 Pages: 1320-1331
    Abstract

    To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.

    DOI
    10.1126/science.1253451
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    http://www.sciencemag.org/content/346/6215/1320
  • Comparative genomics reveals insights into avian genome evolution and adaptation David W Burt, Jacqueline Smith and 105 others — 12 Dec 2014 — Science Vol: 346 Pages: 1311-20
    Abstract

    Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.

    DOI
    10.1126/science.1251385
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    http://www.sciencemag.org/content/346/6215/1311
  • Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor Michael N. Romanov, Marta Farre, Pamela E. Lithgow, Katie E. Fowler, Benjamin M. Skinner, Rebecca O'Connor, Gothami Fonseka, Niclas Backstrom, Yoichi Matsuda, Chizuko Nishida, Peter Houde, Erich D. Jarvis, Hans Ellegren, David W. Burt, Denis M. Larkin, Darren K. Griffin — 11 Dec 2014 — BMC Genomics Vol: 15
    Abstract

    Background: The availability of multiple avian genome sequence assemblies greatly improves our ability to define overall genome organization and reconstruct evolutionary changes. In birds, this has previously been impeded by a near intractable karyotype and relied almost exclusively on comparative molecular cytogenetics of only the largest chromosomes. Here, novel whole genome sequence information from 21 avian genome sequences (most newly assembled) made available on an interactive browser (Evolution Highway) was analyzed.

    Results: Focusing on the six best-assembled genomes allowed us to assemble a putative karyotype of the dinosaur ancestor for each chromosome. Reconstructing evolutionary events that led to each species' genome organization, we determined that the fastest rate of change occurred in the zebra finch and budgerigar, consistent with rapid speciation events in the Passeriformes and Psittaciformes. Intra-and interchromosomal changes were explained most parsimoniously by a series of inversions and translocations respectively, with breakpoint reuse being commonplace. Analyzing chicken and zebra finch, we found little evidence to support the hypothesis of an association of evolutionary breakpoint regions with recombination hotspots but some evidence to support the hypothesis that microchromosomes largely represent conserved blocks of synteny in the majority of the 21 species analyzed. All but one species showed the expected number of microchromosomal rearrangements predicted by the haploid chromosome count. Ostrich, however, appeared to retain an overall karyotype structure of 2n = 80 despite undergoing a large number (26) of hitherto un-described interchromosomal changes.

    Conclusions: Results suggest that mechanisms exist to preserve a static overall avian karyotype/genomic structure, including the microchromosomes, with widespread interchromosomal change occurring rarely (e.g., in ostrich and budgerigar lineages). Of the species analyzed, the chicken lineage appeared to have undergone the fewest changes compared to the dinosaur ancestor.

    DOI
    10.1186/1471-2164-15-1060
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    http://www.research.ed.ac.uk/portal/files/18985588/Reconstruction_of_gross_avian_genome_structure_organization_and_evolution_suggests_that_the_chicken_lineage_most_closely_resembles_the_dinosaur_avian_ancestor.pdf
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    http://www.biomedcentral.com/1471-2164/15/1060
  • Major transcriptome re-organisation and abrupt changes in signalling, cell cycle and chromatin regulation at neural differentiation in vivo Isabel Olivera-Martinez, Nick Schurch, Roman A Li, Junfang Song, Pamela A Halley, Raman M Das, Dave W Burt, Geoffrey J Barton, Kate G Storey — Aug 2014 — Development Vol: 141 Pages: 3266-76
    Abstract

    Here, we exploit the spatial separation of temporal events of neural differentiation in the elongating chick body axis to provide the first analysis of transcriptome change in progressively more differentiated neural cell populations in vivo. Microarray data, validated against direct RNA sequencing, identified: (1) a gene cohort characteristic of the multi-potent stem zone epiblast, which contains neuro-mesodermal progenitors that progressively generate the spinal cord; (2) a major transcriptome re-organisation as cells then adopt a neural fate; and (3) increasing diversity as neural patterning and neuron production begin. Focussing on the transition from multi-potent to neural state cells, we capture changes in major signalling pathways, uncover novel Wnt and Notch signalling dynamics, and implicate new pathways (mevalonate pathway/steroid biogenesis and TGFβ). This analysis further predicts changes in cellular processes, cell cycle, RNA-processing and protein turnover as cells acquire neural fate. We show that these changes are conserved across species and provide biological evidence for reduced proteasome efficiency and a novel lengthening of S phase. This latter step may provide time for epigenetic events to mediate large-scale transcriptome re-organisation; consistent with this, we uncover simultaneous downregulation of major chromatin modifiers as the neural programme is established. We further demonstrate that transcription of one such gene, HDAC1, is dependent on FGF signalling, making a novel link between signals that control neural differentiation and transcription of a core regulator of chromatin organisation. Our work implicates new signalling pathways and dynamics, cellular processes and epigenetic modifiers in neural differentiation in vivo, identifying multiple new potential cellular and molecular mechanisms that direct differentiation.

    DOI
    10.1242/dev.112623
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    http://www.research.ed.ac.uk/portal/files/16673426/Major_transcriptome_re_organisation_and_abrupt_changes_in_signalling_cell_cycle_and_chromatin_regulation_at_neural_differentiation_in_vivo.pdf
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    http://dev.biologists.org/content/141/16/3266
  • Trojan, a Possible Regulator of Apoptosis, Belongs to a Novel Protein Family P. Petrov, D. Burt, R. Syrjanen, T. Uchida, O. Vainio — 2014 — Scandinavian Journal of Immunology Vol: 79 Pages: 436
  • All creatures great and small: 10 years on Darren Griffen, Dave Burt — 2014 — Chromosome Research Vol: 22 Pages: 1-6
  • Visualisation of chicken macrophages using transgenic reporter genes: insights into the development of the avian macrophage lineage Adam Balic, Carla Garcia-Morales, Lonneke Vervelde, Hazel Gilhooley, Adrian Sherman, Valerie Garceau, Maria Gutowska, Dave Burt, Pete Kaiser, David Hume, Helen Sang — 2014 — Development Vol: 141 Pages: 3255-3265
    Abstract
    We have generated the first transgenic chickens in which reporter genes are expressed in a specific immune cell lineage, based upon control elements of the colony stimulating factor 1 receptor (CSF1R) locus. The Fms intronic regulatory element (FIRE) within CSF1R is shown to be highly conserved in amniotes and absolutely required for myeloid-restricted expression of fluorescent reporter genes. As in mammals, CSF1R-reporter genes were specifically expressed at high levels in cells of the macrophage lineage and at a much lower level in granulocytes. The cell lineage specificity of reporter gene expression was confirmed by demonstration of coincident expression with the endogenous CSF1R protein. In transgenic birds, expression of the reporter gene provided a defined marker for macrophage-lineage cells, identifying the earliest stages in the yolk sac, throughout embryonic development and in all adult tissues. The reporter genes permit detailed and dynamic visualisation of embryonic chicken macrophages. Chicken embryonic macrophages are not recruited to incisional wounds, but are able to recognise and phagocytose microbial antigens.
    DOI
    10.1242/dev.105593
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    http://www.research.ed.ac.uk/portal/files/16556876/Development_2014_Balic_dev.105593.pdf
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    http://dev.biologists.org/content/141/16/3255
  • Peeling Back the Evolutionary Layers of Molecular Mechanisms Responsive to Exercise-Stress in the Skeletal Muscle of the Racing Horse Hyeongmin Kim, Taeheon Lee, WonCheoul Park, Jin Woo Lee, Jaemin Kim, Bo-Young Lee, Hyeonju Ahn, Sunjin Moon, Seoae Cho, Kyoung-Tag Do, Heui-Soo Kim, Hak-Kyo Lee, Chang-Kyu Lee, Hong-Sik Kong, Young-Mok Yang, Jongsun Park, Hak-Min Kim, Byung Chul Kim, Seungwoo Hwang, Jong Bhak, Dave Burt, Kyoung-Do Park, Byung-Wook Cho, Heebal Kim — Jun 2013 — DNA Research Vol: 20 Pages: 287-298
    Abstract

    The modern horse (Equus caballus) is the product of over 50 million yrs of evolution. The athletic abilities of the horse have been enhanced during the past 6000 yrs under domestication. Therefore, the horse serves as a valuable model to understand the physiology and molecular mechanisms of adaptive responses to exercise. The structure and function of skeletal muscle show remarkable plasticity to the physical and metabolic challenges following exercise. Here, we reveal an evolutionary layer of responsiveness to exercise-stress in the skeletal muscle of the racing horse. We analysed differentially expressed genes and their co-expression networks in a large-scale RNA-sequence dataset comparing expression before and after exercise. By estimating genome-wide d(N)/d(S) ratios using six mammalian genomes, and F-ST and iHS using re-sequencing data derived from 20 horses, we were able to peel back the evolutionary layers of adaptations to exercise-stress in the horse. We found that the oldest and thickest layer (d(N)/d(S)) consists of system-wide tissue and organ adaptations. We further find that, during the period of horse domestication, the older layer (F-ST) is mainly responsible for adaptations to inflammation and energy metabolism, and the most recent layer (iHS) for neurological system process, cell adhesion, and proteolysis.

    DOI
    10.1093/dnares/dst010
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    http://www.research.ed.ac.uk/portal/files/8760778/Peeling_Back_the_Evolutionary_Layers_of_Molecular_Mechanisms_Responsive_to_Exercise_Stress_in_the_Skeletal_Muscle_of_the_Racing_Horse.pdf
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    http://dnaresearch.oxfordjournals.org/content/20/3/287
  • Chick genomics David W. Burt, Peter G. Farlie — May 2013 — Genesis Vol: 51 Pages: 295-295
  • Decreased expression of the satiety signal receptor CCKAR is responsible for increased growth and body weight during the domestication of chickens Ian C Dunn, Simone Meddle, Peter Wilson, Chloe A Wardle, Andy Law, Valerie Bishop, Camilla Hindar, Graeme W Robertson, Dave W Burt, Stephanie Jl Ellison, David M Morrice, Paul M Hocking — May 2013 — American Journal of Physiology - Endocrinology and Metabolism Vol: 304 Pages: E909-E921
    Abstract
    Animal domestication has resulted in changes in growth and size. It has been suggested this may have involved selection for differences in appetite. Divergent growth between chickens selected for egg laying or meat production is one such example. The neurons expressing AGRP and POMC in the basal hypothalamus are important components of appetite regulation as are the satiety feedback pathways which carry information from the intestine including CCK and its receptor CCKAR (CCK1 receptor). Using 16 generations of a cross between fast and a relatively slow growing strain of chicken has identified a region on chromosome 4, downstream of the CCKAR gene, responsible for up to a 19% difference in body weight at 12 weeks of age. Animals possessing the high growth haplotype at the locus have lower expression of mRNA and immunoreactive CCKAR in the brain, intestine and exocrine organs which is correlated with increased levels of orexigenic AGRP in the hypothalamus. Animals with the high growth haplotype are resistant to the anorectic effect of exogenously administered CCK suggesting their satiety set point has been altered. Comparison with traditional breeds shows the high growth haplotype has been present in the founders of modern meat type strains and may have been selected early in domestication. This is the first dissection of the physiological consequences of a genetic loci for a quantitative trait which alters appetite and gives us an insight into the domestication of animals. This will allow elucidation of how differences in appetite occur in birds but also mammals.
    DOI
    10.1152/ajpendo.00580.2012
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    http://ajpendo.physiology.org/content/304/9/E909
  • Npas4 is activated by melatonin, and drives the clock gene Cry1 in the ovine pars tuberalis A West, Sm Dupre, L Yu, Bob Paton, K Miedzinska, As McNeilly, Jre Davis, Dw Burt, Asi Loudon — 18 Apr 2013 — Molecular Endocrinology Vol: 27 Pages: 979-989
    Abstract
    Seasonal mammals integrate changes in the duration of nocturnal melatonin secretion to drive annual physiological cycles. Melatonin receptors within the proximal pituitary region, the pars tuberalis (PT), are essential in regulating seasonal neuroendocrine responses. In the ovine PT, melatonin is known to influence acute changes in transcriptional dynamics coupled to the onset (dusk) and offset (dawn) of melatonin secretion, leading to a potential interval-timing mechanism capable of decoding changes in day-length (photoperiod). Melatonin offset at dawn is linked to cAMP accumulation, which directly induces transcription of the clock gene Per1. The rise of melatonin at dusk induces a separate and distinct cohort, including the clock-regulated genes Cry1 and Nampt, but little is known of the up-stream mechanisms involved. Here, we used next generation sequencing of the ovine PT transcriptome at melatonin onset, and identified Npas4 as a rapidly induced bHLH-PAS domain transcription factor. In vivo we show nuclear localisation of NPAS4 protein in presumptive melatonin target cells of the PT (αGSU-expressing cells), while in situ hybridisation studies identified acute and transient expression in the PT of Npas4 in response to melatonin. In vitro, NPAS4 forms functional dimers with bHLH-PAS domain co-factors ARNT, ARNT2 and ARNTL, transactivating both Cry1 and Nampt ovine promoter reporters. Using a combination of 5` deletions and site-directed mutagenesis we show NPAS4:ARNT transactivation to be co-dependent upon two conserved central midline elements (CMEs) within the Cry1 promoter. Our data thus reveal NPAS4 as a candidate immediate early-response gene in the ovine PT, driving molecular responses to melatonin.
    DOI
    10.1210/me.2012-1366
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    http://www.research.ed.ac.uk/portal/files/8373406/979.full.pdf
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  • Comparative analysis of quantitative trait loci for body weight, growth rate and growth curve parameters from 3 to 72 weeks of age in female chickens of a broiler-layer cross Baitsi K. Podisi, Sara A. Knott, David W. Burt, Paul M. Hocking — 13 Mar 2013 — BMC Genetics Vol: 14
    Abstract

    Background: Comparisons of quantitative trait loci (QTL) for growth and parameters of growth curves assist in understanding the genetics and ultimately the physiology of growth. Records of body weight at 3, 6, 12, 24, 48 and 72 weeks of age and growth rate between successive age intervals of about 500 F-2 female chickens of the Roslin broiler-layer cross were available for analysis. These data were analysed to detect and compare QTL for body weight, growth rate and parameters of the Gompertz growth function.

    Results: Over 50 QTL were identified for body weight at specific ages and most were also detected in the nearest preceding and/or subsequent growth stage. The sum of the significant and suggestive additive effects for bodyweight at specific ages accounted for 23-43% of the phenotypic variation. A single QTL for body weight on chromosome 4 at 48 weeks of age had the largest additive effect (550.4 +/- 68.0 g, 11.5% of the phenotypic variation) and a QTL at a similar position accounted 14.5% of the phenotypic variation at 12 weeks of age. Age specific QTL for growth rate were detected suggesting that there are specific genes that affect developmental processes during the different stages of growth. Relatively few QTL influencing Gompertz growth curve parameters were detected and overlapped with loci affecting growth rate. Dominance effects were generally not significant but from 12 weeks of age they exceeded the additive effect in a few cases. No evidence for epistatic QTL pairs was found.

    Conclusions: The results confirm the location for body weight and body weight gain during growth that were identified in previous studies and were consistent with QTL for the parameters of the Gompertz growth function. Chromosome 4 explained a relatively large proportion of the observed growth variation across the different ages, and also harboured most of the detected QTL for Gompertz parameters, confirming its importance in controlling growth. Very few QTL were detected for body weight or gain at 48 and 72 weeks of age, probably reflecting the effect of differences in reproduction and random environmental effects.

    DOI
    10.1186/1471-2156-14-22
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    http://www.research.ed.ac.uk/portal/files/8169067/BMC_2013_Knott_S.pdf
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    http://www.biomedcentral.com/1471-2156/14/22
  • Microarray resources for genetic and genomic studies in chicken: a review Almas A Gheyas, David W Burt — Mar 2013 — Genesis Vol: 51 Pages: 337-356
    Abstract
    Advent of microarray technologies revolutionized the nature and scope of genetic and genomic research in human and other species by allowing massively parallel analysis of thousands of genomic sites. They have been used for diverse purposes such as for transcriptome analysis, CNV detection, SNP and CNV genotyping, studying DNA-protein interaction, and detection of genome methylation. Microarrays have also made invaluable contributions to research in chicken which is an important model organism for studying embryology, immunology, oncology, virology, evolution, genetics, and genomics and also for other avian species. Despite their huge contributions in life science research, the future of microarrays is now being questioned with the advent of massively parallel next generation sequencing (NGS) technologies, which promise to overcome some of the limitations of microarray platforms. In this article we review the various microarray resources developed for chicken and their past and potential future applications. We also discuss about the future of microarrays in the NGS era particularly in the context of livestock genetics. We argue that even though NGS promises some major advantages-in particular, offers the opportunity to discover novel elements in the genome-microarrays will continue to be major tools for research and practice in the field of livestock genetics/genomics due to their affordability, high throughput nature, mature established technologies and ease of application. Moreover, with advent of new microarray technologies like capture arrays, the NGS and microarrays are expected to complement each other in future research in life science. genesis 00:1-20. © 2013 Wiley Periodicals, Inc.
    DOI
    10.1002/dvg.22387
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    http://www.research.ed.ac.uk/portal/files/8760793/Microarray_resources_for_genetic_and_genomic_studies_in_chicken_a_review.pdf
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    http://onlinelibrary.wiley.com/doi/10.1002/dvg.22387/abstract;jsessionid=F8FADDA162E6C7723B8F35E2386C8968.d03t02
  • Association of IGF1 and KDM5A polymorphisms with performance, fatness and carcass traits in chickens Clarissa Boschiero, Erika C Jorge, Kerli Ninov, Kátia Nones, Millor Fernandes do Rosário, Luiz Lehmann Coutinho, Mônica Corrêa Ledur, David W Burt, Ana Silvia A M T Moura — Feb 2013 — Journal of applied genetics Vol: 54 Pages: 103-112
    Abstract
    Two functional and positional candidate genes were selected in a region of chicken chromosome 1 (GGA1), based on their biological roles, and also where several quantitative trait loci (QTL) have been mapped and associated with performance, fatness and carcass traits in chickens. The insulin-like growth factor 1 (IGF1) gene has been associated with several physiological functions related to growth. The lysine (K)-specific demethylase 5A (KDM5A) gene participates in the epigenetic regulation of genes involved with the cell cycle. Our objective was to find associations of selected single-nucleotide polymorphisms (SNPs) in these genes with performance, fatness and carcass traits in 165 F(2) chickens from a resource population. In the IGF1 gene, 17 SNPs were detected, and in the KDM5A gene, nine SNPs were detected. IGF1 SNP c.47673G > A was associated with body weight and haematocrit percentage, and also with feed intake and percentages of abdominal fat and gizzard genotype × sex interactions. KDM5A SNP c.34208C > T genotype × sex interaction affected body weight, feed intake, percentages of abdominal fat (p = 0.0001), carcass, gizzard and haematocrit. A strong association of the diplotype × sex interaction (p 
    DOI
    10.1007/s13353-012-0129-6
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    http://www.research.ed.ac.uk/portal/files/11804876/Association_of_IGF1_and_KDM5A_polymorphisms_with_performance_fatness_and_carcass_traits_in_chickens.pdf
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    http://link.springer.com/article/10.1007%2Fs13353-012-0129-6
  • Development of a high density 600K SNP genotyping array for chicken Andreas Kranis, Almas A Gheyas, Clarissa Boschiero, Frances Turner, Le Yu, Sarah Smith, Richard Talbot, Ali Pirani, Fiona Brew, Pete Kaiser, Paul M Hocking, Mark Fife, Nigel Salmon, Janet Fulton, Tim M Strom, Georg Haberer, Steffen Weigend, Rudolf Preisinger, Mahmood Gholami, Saber Qanbari, Henner Simianer, Kellie A Watson, John A Woolliams, David W Burt — 01 Jan 2013 — BMC Genomics Vol: 14
    Abstract
    BACKGROUND: High density (HD) SNP genotyping arrays are an important tool for genetic analyses of animals and plants. Although the chicken is one of the most important farm animals, no HD array is yet available for high resolution genetic analysis of this species.

    RESULTS: We report here the development of a 600 K Affymetrix(R) Axiom(R) HD genotyping array designed using SNPs segregating in a wide variety of chicken populations. In order to generate a large catalogue of segregating SNPs, we re-sequenced 243 chickens from 24 chicken lines derived from diverse sources (experimental, commercial broiler and layer lines) by pooling 10--15 samples within each line. About 139 million (M) putative SNPs were detected by mapping sequence reads to the new reference genome (Gallus_gallus_4.0) of which ~78 M appeared to be segregating in different lines. Using criteria such as high SNP-quality score, acceptable design scores predicting high conversion performance in the final array and uniformity of distribution across the genome, we selected ~1.8 M SNPs for validation through genotyping on an independent set of samples (n = 282). About 64% of the SNPs were polymorphic with high call rates (>98%), good cluster separation and stable Mendelian inheritance. Polymorphic SNPs were further analysed for their population characteristics and genomic effects. SNPs with extreme breach of Hardy-Weinberg equilibrium (P <0.00001) were excluded from the panel. The final array, designed on the basis of these analyses, consists of 580,954 SNPs and includes 21,534 coding variants. SNPs were selected to achieve an essentially uniform distribution based on genetic map distance for both broiler and layer lines. Due to a lower extent of LD in broilers compared to layers, as reported in previous studies, the ratio of broiler and layer SNPs in the array was kept as 3:2. The final panel was shown to genotype a wide range of samples including broilers and layers with over 100 K to 450 K informative SNPs per line. A principal component analysis was used to demonstrate the ability of the array to detect the expected population structure which is an important pre-investigation step for many genome-wide analyses.

    CONCLUSIONS: This Affymetrix(R) Axiom(R) array is the first SNP genotyping array for chicken that has been made commercially available to the public as a product. This array is expected to find widespread usage both in research and commercial application such as in genomic selection, genome-wide association studies, selection signature analyses, fine mapping of QTLs and detection of copy number variants.
    DOI
    10.1186/1471-2164-14-59
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    http://www.research.ed.ac.uk/portal/files/8357038/Development_of_a_high_density_600K_SNP_genotyping_array_for_chicken.pdf
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    http://www.biomedcentral.com/1471-2164/14/59/abstract
  • Identification of Differentially Evolved Genes: An Alternative Approach to Detection of Accelerated Molecular Evolution from Genome-Wide Comparative Data Kyu-Won Kim, David W. Burt, Heebal Kim, Seoae Cho — 2013 — Evolutionary bioinformatics Vol: 9 Pages: 285-293
    Abstract

    One of the most important measures for detecting molecular adaptations between species/lineages at the gene level is the comparison of relative fixation rates of synonymous (dS) and non-synonymous (dN) mutations. This study shows that the branch model is sensitive to tree topology and proposes an alternative approach, devogs, which does not require phylogenetic topology for analysis. We compared devogs with a branch model method using virtual data and a varying omega ratio, in which parameters were obtained from real data. The positive predictive value, sensitivity, and specificity of the branch model were affected by the phylogenic tree topology. Devogs showed greater positive predictive value, whereas the branch model method had greater sensitivity. In a working example using devogs, a group of human RNA polymerase II-related genes, which are important in mediating alternative splicing, were significantly accelerated compared to four other mammals.

    DOI
    10.4137/EBO.S12166
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    http://www.research.ed.ac.uk/portal/files/9286806/Identification_of_differentially_evolved_genes_an_alternative_approach_to_detection_of_accelerated_molecular_evolution_from_genome_wide_comparative_data.pdf
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    http://www.la-press.com/identification-of-differentially-evolved-genes-an-alternative-approach-article-a3793
  • The duck genome and transcriptome provide insight into an avian influenza virus reservoir species Yinhua Huang, Dave Burt, Jacqueline Smith, Pete Kaiser and 46 others — 2013 — Nature Genetics Vol: 45 Pages: 776-U797
    Abstract
    The duck (Anas platyrhynchos) is one of the principal natural hosts of influenza A viruses. We present the duck genome sequence and perform deep transcriptome analyses to investigate immune-related genes. Our data indicate that the duck possesses a contractive immune gene repertoire, as in chicken and zebra finch, and this repertoire has been shaped through lineage-specific duplications. We identify genes that are responsive to influenza A viruses using the lung transcriptomes of control ducks and ones that were infected with either a highly pathogenic (A/duck/Hubei/49/05) or a weakly pathogenic (A/goose/Hubei/65/05) H5N1 1 virus. Further, we show how the duck’s defense mechanisms against influenza infection have been optimized through the diversification of its b-defensin and butyrophilin-like repertoires. These analyses, in combination with the genomic and transcriptomic data, provide a resource for characterizing the interaction between host and influenza viruses.
    DOI
    10.1038/ng.2657
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    http://www.research.ed.ac.uk/portal/files/8760798/The_duck_genome_and_transcriptome_provide_insight_into_an_avian_influenza_virus_reservoir_species.pdf
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    http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.2657.html
  • eChickAtlas: An introduction to the database Frances Wong, Monique C M Welten, Claire Anderson, Andrew A Bain, Jiahui Liu, Mike Wicks, Gordana Pavlovska, Megan G Davey, Paula Murphy, Duncan Davidson, Cheryll A Tickle, Claudio D Stern, Richard A Baldock, Dave W Burt — 2013 — Genesis Vol: 51 Pages: 365-371
    Abstract
    The precise control of gene expression is critical in embryonic development. Quantitative assays, such as microarrays and RNA sequencing, provide gene expression levels for a large number of genes, but do not contain spatial information. In contrast, in situ methods, such as in situ hybridisation and immunohistochemistry, provide spatial resolution, but poor quantification and can only reveal the expression of one, or very few genes at a time. Furthermore, the usual methods of documenting the results, by photographing whole mounts or sections, makes it very difficult to assess the three-dimensional (3D) relationships between expressing and non-expressing cells. Optical projection tomography (OPT) can capture the full 3D expression pattern in a whole embryo at a reasonable level of resolution and at moderately high throughput. A large database containing spatio-temporal patterns of expression for the mouse (e-Mouse Atlas Project, EMAP, www.emouseatlas.org) has been created, incorporating 3D information. Like the mouse, the chick is an important model in developmental biology and translational studies. To facilitate comparisons between these important model organisms, we have created a 3D anatomical atlas, accompanied by an anatomical ontology of the chick embryo and a database of gene expression patterns during chick development. This database is publicly available (www.echickatlas.org).
    DOI
    10.1002/dvg.22374
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    http://onlinelibrary.wiley.com/doi/10.1002/dvg.22374/abstract
  • Many quantitative trait loci for feather growth in an F broiler × layer cross collocate with body weight loci P M Hocking, D M Morrice, A S Law, D W Burt — 01 Apr 2012 — British Poultry Science Vol: 53 Pages: 162-167
    Abstract
    1. A genome-wide scan of 467 F(2) progeny of a broiler x layer cross was conducted to identify quantitative trait loci (QTL) affecting the rate of growth of the tail, wing and back feathers, and the width of the breast feather tract, at three weeks of age. 2. Correlations between the traits ranged from 0·36 to 0·61. Males had longer tail and wing feathers and shorter back feathers than females. Breast feather tract width was greater in females than males. 3. QTL effects were generally additive and accounted for 11 to 45% of sex average feather lengths of the breeds, and 100% of the breast feather tract width. Positive and negative alleles were inherited from both lines, whereas the layer allele was larger than the broiler allele after adjusting for body weight. 4. A total of 4 genome-significant and 4 suggestive QTL were detected. At three or 6 weeks of age, 5 of the QTL were located in similar regions as QTL for body weight. 5. Analysis of a model with body weight at three weeks as a covariate identified 5 genome significant and 6 suggestive QTL, of which only two were coincident with body weight QTL. One QTL for feather length at 148 cM on GGA1 was identified at a similar location in the unadjusted analysis. 6. The results suggest that the rate of feather growth is largely controlled by body weight QTL, and that QTL specific for feather growth also exist.
    DOI
    10.1080/00071668.2012.668613
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    http://www.research.ed.ac.uk/portal/files/11806109/Many_quantitative_trait_loci_for_feather_growth_in_an_F2_broiler_X_layer_cross_collocate_with_body_weight_loci.pdf
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  • Bone mineral density QTL at sexual maturity and end of lay B K Podisi, S A Knott, I C Dunn, D W Burt, P M Hocking — 2012 — British Poultry Science Vol: 53 Pages: 763-9
    Abstract
    1. An F(2) cross of a broiler male line and a White Leghorn layer line was used to identify quantitative trait loci (QTL) for bone density at the onset of lay and at the end of the laying period. A total of 686 measures of humeral bone density were available for analysis. 2. There was no evidence for epistasis. 3. Genome-wide significant QTL for bone density at the onset of lay were identified on chromosomes 1 (311 cM) and 8 (2 cM) and on chromosomes 1 (311 cM), 3 (57 cM) and 8 (2 cM) with a covariate for the number of yellow follicles (a proxy for the concentration of circulating oestrogen). 4. Evidence for only 4 chromosome-wide suggestive QTL were detected at the end of lay (72 weeks). 5. Analysis of the combined data confirmed two genome-wide suggestive QTL on chromosome 1 (137 and 266 cM) and on chromosomes 8 (2 cM) and 9 (10 cM) in analyses with or without the covariate. 6. Positive QTL alleles came from the broiler line with the exception of 2 suggestive QTL at the onset of lay on chromosomes 3 and 5 in an analysis with the covariate. 7. In general, QTL acted additively, except that dominant effects were identified for three suggestive QTL at the onset of lay on chromosomes 3 (57 and 187 cM) and 5 (9 cM). 8. The significant QTL in this study were at similar locations to QTL identified in a range of crosses in other publications, suggesting that they are prime candidates for the search for genes and mutations that could be used as selection criteria to improve bone strength and decrease fractures in commercial laying hens.
    DOI
    10.1080/00071668.2012.747674
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    http://www.research.ed.ac.uk/portal/files/11823493/Bone_mineral_density_QTL_at_sexual_maturity_and_end_of_lay.pdf
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    http://www.tandfonline.com/doi/abs/10.1080/00071668.2012.747674
  • A high resolution genome-wide scan for significant selective sweeps: an application to pooled sequence data in laying chickens Saber Qanbari, Tim M Strom, Georg Haberer, Steffen Weigend, Almas A Gheyas, Frances Turner, David W Burt, Rudolf Preisinger, Daniel Gianola, Henner Simianer — 2012 — PLoS One Vol: 7
    Abstract
    In most studies aimed at localizing footprints of past selection, outliers at tails of the empirical distribution of a given test statistic are assumed to reflect locus-specific selective forces. Significance cutoffs are subjectively determined, rather than being related to a clear set of hypotheses. Here, we define an empirical p-value for the summary statistic by means of a permutation method that uses the observed SNP structure in the real data. To illustrate the methodology, we applied our approach to a panel of 2.9 million autosomal SNPs identified from re-sequencing a pool of 15 individuals from a brown egg layer line. We scanned the genome for local reductions in heterozygosity, suggestive of selective sweeps. We also employed a modified sliding window approach that accounts for gaps in the sequence and increases scanning resolution by moving the overlapping windows by steps of one SNP only, and suggest to call this a "creeping window" strategy. The approach confirmed selective sweeps in the region of previously described candidate genes, i.e. TSHR, PRL, PRLHR, INSR, LEPR, IGF1, and NRAMP1 when used as positive controls. The genome scan revealed 82 distinct regions with strong evidence of selection (genome-wide p-value
    DOI
    10.1371/journal.pone.0049525
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    http://www.research.ed.ac.uk/portal/files/7837369/A_high_resolution_genome_wide_scan_for_significant_selective_sweeps_an_application_to_pooled_sequence_data_in_laying_chickens.pdf
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    http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0049525
  • Quantitative trait loci associated with chemical composition of the chicken carcass K Nones, M C Ledur, E L Zanella, C Klein, L F B Pinto, A S A M T Moura, D C Ruy, E E Baron, M Ambo, R L R Campos, C Boschiero, D W Burt, L L Coutinho — 2012 — Animal Genetics Vol: 43 Pages: 570-6
    Abstract
    Major objectives of the poultry industry are to increase meat production and to reduce carcass fatness, mainly abdominal fat. Information on growth performance and carcass composition are important for the selection of leaner meat chickens. To enhance our understanding of the genetic architecture underlying the chemical composition of chicken carcasses, an F(2) population developed from a broiler × layer cross was used to map quantitative trait loci (QTL) affecting protein, fat, water and ash contents in chicken carcasses. Two genetic models were applied in the QTL analysis: the line-cross and the half-sib models, both using the regression interval mapping method. Six significant and five suggestive QTL were mapped in the line-cross analysis, and four significant and six suggestive QTL were mapped in the half-sib analysis. A total of eleven QTL were mapped for fat (ether extract), five for protein, four for ash and one for water contents in the carcass using both analyses. No study to date has reported QTL for carcass chemical composition in chickens. Some QTL mapped here for carcass fat content match, as expected, QTL regions previously associated with abdominal fat in the same or in different populations, and novel QTL for protein, ash and water contents in the carcass are presented here. The results described here also reinforce the need for fine mapping and to perform multi-trait analyses to better understand the genetic architecture of these traits.
    DOI
    10.1111/j.1365-2052.2012.02321.x
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    http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2052.2012.02321.x/abstract;jsessionid=AA84A674CBD46953D8D72D4949BB83CB.d03t04
  • Complex traits analysis of chicken growth using targeted genetical genomics C P Cabrera, I C Dunn, M Fell, P W Wilson, D W Burt, D Waddington, R Talbot, P M Hocking, A Law, S Knott, C S Haley, D J de Koning — 2012 — Animal Genetics Vol: 43 Pages: 163-71
    Abstract
    Dissecting the genetic control of complex trait variation remains very challenging, despite many advances in technology. The aim of this study was to use a major growth quantitative trait locus (QTL) in chickens mapped to chromosome 4 as a model for a targeted approach to dissect the QTL. We applied a variant of the genetical genomics approach to investigate genome-wide gene expression differences between two contrasting genotypes of a marked QTL. This targeted approach allows the direct quantification of the link between the genotypes and the genetic responses, thus narrowing the QTL-phenotype gap using fewer samples (i.e. microarrays) compared with the genome-wide genetical genomics studies. Four differentially expressed genes were localized under the region of the QTL. One of these genes is a potential positional candidate gene (AADAT) that affects lysine and tryptophan metabolism and has alternative splicing variants between the two genotypes. In addition, the lysine and glycolysis metabolism pathways were significantly enriched for differentially expressed genes across the genome. The targeted approach provided a complementary route to fine mapping of QTL by characterizing the local and the global downstream effects of the QTL and thus generating further hypotheses about the action of that QTL.
    DOI
    10.1111/j.1365-2052.2011.02223.x
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    http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2052.2011.02223.x/abstract
  • Systemic virus distribution and host responses in brain and intestine of chickens infected with low pathogenic or high pathogenic avian influenza virus Jacob Post, Dave W Burt, Jan B W J Cornelissen, Venice Broks, Diana van Zoelen, Ben Peeters, Johanna M J Rebel — 2012 — Virology Journal Vol: 9 Pages: -
    Abstract
    ABSTRACT: BACKGROUND: Avian influenza virus (AIV) is classified into two pathotypes, low pathogenic (LP) and high pathogenic (HP), based on virulence in chickens. Differences in pathogenicity between HPAIV and LPAIV might eventually be related to specific characteristics of strains, tissue tropism and host responses. METHODS: To study differences in disease development between HPAIV and LPAIV, we examined the first appearance and eventual load of viral RNA in multiple organs as well as host responses in brain and intestine of chickens infected with two closely related H7N1 HPAIV or LPAIV strains. RESULTS: Both H7N1 HPAIV and LPAIV spread systemically in chickens after a combined intranasal/intratracheal inoculation. In brain, large differences in viral RNA load and host gene expression were found between H7N1 HPAIV and LPAIV infected chickens. Chicken embryo brain cell culture studies revealed that both HPAIV and LPAIV could infect cultivated embryonic brain cells, but in accordance with the absence of the necessary proteases, replication of LPAIV was limited. Furthermore, TUNEL assay indicated apoptosis in brain of HPAIV infected chickens only. In intestine, where endoproteases that cleave HA of LPAIV are available, we found minimal differences in the amount of viral RNA and a large overlap in the transcriptional responses between HPAIV and LPAIV infected chickens. Interestingly, brain and ileum differed clearly in the cellular pathways that were regulated upon an AI infection. CONCLUSIONS: Although both H7N1 HPAIV and LPAIV RNA was detected in a broad range of tissues beyond the respiratory and gastrointestinal tract, our observations indicate that differences in pathogenicity and mortality between HPAIV and LPAIV could originate from differences in virus replication and the resulting host responses in vital organs like the brain.
    DOI
    10.1186/1743-422X-9-61
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    http://www.research.ed.ac.uk/portal/files/7837892/Systemic_virus_distribution_and_host_responses_in_brain_and_intestine_of_chickens_infected_with_low_pathogenic_or_high_pathogenic_avian_influenza_virus.pdf
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    http://www.virologyj.com/content/9/1/61/abstract
  • Systems analysis of immune responses in Marek's disease virus-infected chickens identifies a gene involved in susceptibility and highlights a possible novel pathogenicity mechanism J. Smith, J.-R. Sadeyen, I.R. Paton, P.M. Hocking, N. Salmon, M. Fife, V. Nair, D.W. Burt, P. Kaiser — Nov 2011 — Journal of Virology Vol: 85 Pages: 11146-11158
    Abstract
    Marek's disease virus (MDV) is a highly contagious oncogenic alphaherpesvirus that causes disease that is both a cancer model and a continuing threat to the world's poultry industry. This comprehensive gene expression study analyzes the host response to infection in both resistant and susceptible lines of chickens and inherent expression differences between the two lines following the infection of the host. A novel pathogenicity mechanism, involving the downregulation of genes containing HIC1 transcription factor binding sites as early as 4 days postinfection, was suggested from this analysis. HIC1 drives antitumor mechanisms, suggesting that MDV infection switches off genes involved in antitumor regulation several days before the expression of the MDV oncogene meq. The comparison of the gene expression data to previous QTL data identified several genes as candidates for involvement in resistance to MD. One of these genes, IRG1, was confirmed by single nucleotide polymorphism analysis to be involved in susceptibility. Its precise mechanism remains to be elucidated, although the analysis of gene expression data suggests it has a role in apoptosis. Understanding which genes are involved in susceptibility/resistance to MD and defining the pathological mechanisms of the disease gives us a much greater ability to try to reduce the incidence of this virus, which is costly to the poultry industry in terms of both animal welfare and economics.
    DOI
    10.1128/JVI.05499-11
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    http://www.research.ed.ac.uk/portal/files/8340990/Systems_analysis_of_immune_responses_in_Marek_s_disease_virus_infected_chickens_identifies_a_gene_involved_in_susceptibility_and_highlights_a_possible_novel_pathogenicity_mechanism.pdf
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    http://jvi.asm.org/content/85/21/11146
  • QTL for percentage of carcass and carcass parts in a broiler x layer cross E. E. Baron, A. S. A. M. T. Moura, M. C. Ledur, L. F. B. Pinto, C. Boschiero, D. C. Ruy, K. Nones, E. L. Zanella, M. F. Rosario, D. W. Burt, L. L. Coutinho — Apr 2011 — Animal Genetics Vol: 42 Pages: 117-124
    Abstract

    P>An F-2 experimental population, developed from a broiler layer cross, was used in a genome scan of QTL for percentage of carcass, carcass parts, shank and head. Up to 649 F-2 chickens from four paternal half-sib families were genotyped with 128 genetic markers covering 22 linkage groups. Total map length was 2630 cM, covering approximately 63% of the genome. QTL interval mapping using regression methods was applied to line-cross and half-sib models. Under the line-cross model, 12 genome-wide significant QTL and 17 suggestive linkages for percentages of carcass parts, shank and head were mapped to 13 linkage groups (GGA1, 2, 3, 4, 5, 7, 8, 9, 11, 12, 14, 18 and 27). Under the paternal half-sib model, six genome-wide significant QTL and 18 suggestive linkages for percentages of carcass parts, shank and head were detected on nine chicken linkage groups (GGA1, 2, 3, 4, 5, 12, 14, 15 and 27), seven of which seemed to corroborate positions revealed by the previous model. Overall, three novel QTL of importance to the broiler industry were mapped (one significant for shank% on GGA3 and two suggestive for carcass and breast percentages on GGA14 and drums and thighs percentage on GGA15). One novel QTL for wings% was mapped to GGA3, six novel QTL (GGA1, 3, 7, 8, 9 and 27) and suggestive linkages (GGA2, 4, and 5) were mapped for head%, and suggestive linkages were identified for back% on GGA2, 11 and 12. In addition, many of the QTL mapped in this study confirmed QTL previously reported in other populations.

    DOI
    10.1111/j.1365-2052.2010.02105.x
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    http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2052.2010.02105.x/abstract
  • Cryptic patterning of avian skin confers a developmental facility for loss of neck feathering Chunyan Mou, Frederique Pitel, David Gourichon, Florence Vignoles, Athanasia Tzika, Patricia Tato, Le Yu, Dave W Burt, Bertrand Bed'hom, Michele Tixier-Boichard, Kevin J Painter, Denis J Headon — Mar 2011 — PLoS Biology Vol: 9
    Abstract
    Vertebrate skin is characterized by its patterned array of appendages, whether feathers, hairs, or scales. In avian skin the distribution of feathers occurs on two distinct spatial levels. Grouping of feathers within discrete tracts, with bare skin lying between the tracts, is termed the macropattern, while the smaller scale periodic spacing between individual feathers is referred to as the micropattern. The degree of integration between the patterning mechanisms that operate on these two scales during development and the mechanisms underlying the remarkable evolvability of skin macropatterns are unknown. A striking example of macropattern variation is the convergent loss of neck feathering in multiple species, a trait associated with heat tolerance in both wild and domestic birds. In chicken, a mutation called Naked neck is characterized by a reduction of body feathering and completely bare neck. Here we perform genetic fine mapping of the causative region and identify a large insertion associated with the Naked neck trait. A strong candidate gene in the critical interval, BMP12/GDF7, displays markedly elevated expression in Naked neck embryonic skin due to a cis-regulatory effect of the causative mutation. BMP family members inhibit embryonic feather formation by acting in a reaction-diffusion mechanism, and we find that selective production of retinoic acid by neck skin potentiates BMP signaling, making neck skin more sensitive than body skin to suppression of feather development. This selective production of retinoic acid by neck skin constitutes a cryptic pattern as its effects on feathering are not revealed until gross BMP levels are altered. This developmental modularity of neck and body skin allows simple quantitative changes in BMP levels to produce a sparsely feathered or bare neck while maintaining robust feather patterning on the body.
    DOI
    10.1371/journal.pbio.1001028
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    http://www.research.ed.ac.uk/portal/files/7869129/Cryptic_patterning_of_avian_skin_confers_a_developmental_facility_for_loss_of_neck_feathering.pdf
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    http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001028
  • Mpdz null allele in an avian model of retinal degeneration and mutations in human leber congenital amaurosis and retinitis pigmentosa Manir Ali, Paul M Hocking, Martin McKibbin, Sorcha Finnegan, Mike Shires, James A Poulter, Katrina Prescott, Adam Booth, Yasmin Raashid, Hussain Jafri, Jonathan B Ruddle, David A Mackey, Samuel G Jacobson, Carmel Toomes, Douglas H Lester, David W Burt, William J Curry, Chris F Inglehearn — 2011 — Investigative Ophthalmology & Visual Science Vol: 52 Pages: 7432-7440
    Abstract
    Purpose. To identify the defective gene in the sex-linked, recessively inherited retinal dysplasia and degeneration (rdd) chicken and to search for the human equivalent disease. Methods. Microsatellites from chicken chromosome Z were genotyped in 77 progeny of a carrier male (rdd/+) and an affected female (rdd/W), and candidate genes were sequenced. Retinal cross-sections from rdd and wild-type birds were analyzed by immunohistology. The human orthologous gene was screened in a panel of archival DNAs from 276 patients with retinitis pigmentosa (RP) or Leber congenital amaurosis (LCA) using melting curve analysis and DNA sequencing. Results. The rdd locus was refined to an approximately 3-Mb region on chromosome Z. Sequence analysis identified a C-->T change in the mpdz gene that created a premature stop codon (c.1372C-->T, p.R458X), which segregated with the disease phenotype. As expected, the full-length mpdz protein was absent in rdd retinas, but in wild-type birds, it localized to the retinal outer limiting membrane, where it may have a role in the interactions between photoreceptors and Muller glia cells. The screen to identify the human equivalent disease found 10 heterozygous variants in the orthologous gene in patients with RP (three missense and two null alleles) and LCA (four missense and one null allele). Conclusions. These findings reveal that MPDZ is essential for normal development of the retina and may have a role in maintaining photoreceptor integrity. The identification of human mutations suggests that MPDZ plays a role in human retinal disease, but the precise nature of this role remains to be determined.
    DOI
    10.1167/iovs.11-7872
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    http://www.iovs.org/content/52/10/7432
  • Molecular evolution of the vertebrate TLR1 gene family - a complex history of gene duplication, gene conversion, positive selection and co-evolution Y.H. Huang, N.D. Temperley, L.M. Ren, Jacqueline Smith, N. Li, D.W. Burt — 2011 — BMC Evolutionary Biology Vol: 11 Pages: 1-17
    Abstract
    Background: The Toll-like receptors represent a large superfamily of type I transmembrane glycoproteins, some common to a wide range of species and others are more restricted in their distribution. Most members of the Toll-like receptor superfamily have few paralogues; the exception is the TLR1 gene family with four closely related genes in mammals TLR1, TLR2, TLR6 and TLR10, and four in birds TLR1A, TLR1B, TLR2A and TLR2B. These genes were previously thought to have arisen by a series of independent gene duplications. To understand the evolutionary pattern of the TLR1 gene family in vertebrates further, we cloned the sequences of TLR1A, TLR1B, TLR2A and TLR2B in duck and turkey, constructed phylogenetic trees, predicted codons under positive selection and identified co-evolutionary amino acid pairs within the TLR1 gene family using sequences from 4 birds, 28 mammals, an amphibian and a fish. Results: This detailed phylogenetic analysis not only clarifies the gene gains and losses within the TLR1 gene family of birds and mammals, but also defines orthologues between these vertebrates. In mammals, we predict amino acid sites under positive selection in TLR1, TLR2 and TLR6 but not TLR10. We detect co-evolution between amino acid residues in TLR2 and the other members of this gene family predicted to maintain their ability to form functional heterodimers. In birds, we predict positive selection in the TLR2A and TLR2B genes at functionally significant amino acid residues. We demonstrate that the TLR1 gene family has mostly been subject to purifying selection but has also responded to directional selection at a few sites, possibly in response to pathogen challenge. Conclusions: Our phylogenetic and structural analyses of the vertebrate TLR1 family have clarified their evolutionary origins and predict amino acid residues likely to be important in the host's defense against invading pathogens.
    DOI
    10.1186/1471-2148-11-149
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    http://www.research.ed.ac.uk/portal/files/7881892/Molecular_evolution_of_the_vertebrate_TLR1_gene_family_a_complex_history_of_gene_duplication_gene_conversion_positive_selection_and_co_evolution.pdf
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    http://www.biomedcentral.com/1471-2148/11/149
  • The chicken polydactyly (Po) locus causes allelic imbalance and ectopic expression of Shh during limb development Ian C Dunn, I Robert Paton, Allyson K Clelland, Sujith Sebastian, Edward J Johnson, Lynn McTeir, Dawn Windsor, Adrian Sherman, Helen Sang, Dave W Burt, Cheryll Tickle, Megan G Davey — 2011 — Developmental Dynamics Vol: 240 Pages: 1163-72
    Abstract
    Point mutations in the intronic ZRS region of Lmbr1, a limb specific cis-regulatory element of Sonic hedgehog (Shh), are associated with polydactyly in humans, cats, and mice. We and others have recently mapped the dominant preaxial polydactyly (Po) locus in Silkie chickens to a single nucleotide polymorphism (SNP) in the ZRS region. Using polymorphisms in the chicken Shh sequence, we confirm that the ZRS region directly regulates Shh expression in the developing limb causing ectopic Shh expression in the anterior leg, prolonged Shh expression in the posterior limb, and allelic imbalance between wt and Slk Shh alleles in heterozygote limbs. Using Silkie legs, we have explored the consequences of increased Shh expression in the posterior leg on the patterning of the toes, and the induction of preaxial polydactyly. Developmental Dynamics, 2011. (c) 2011 Wiley-Liss, Inc.
    DOI
    10.1002/dvdy.22623
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  • Overlap of quantitative trait loci for early growth rate, and for body weight and age at onset of sexual maturity in chickens B K Podisi, S A Knott, I C Dunn, A S Law, D W Burt, P M Hocking — 2011 — Reproduction Vol: 141 Pages: 381-389
    Abstract
    Critical age, weight and body composition have been suggested as necessary correlates of sexual maturity. A genome scan to identify quantitative trait loci (QTL) for age and body weight at first egg (AFE and WFE) was conducted on 912 birds from an F2 broiler–layer cross using 106 microsatellite markers. Without a covariate, QTL for body WFE were detected on chromosomes 2, 4, 8, 27 and Z and a single QTL for AFE was detected on chromosome 2. With AFE as a covariate, additional QTL for body WFE were found on chromosomes 1 and 13, with abdominal fat pad as covariate a QTL for body WFE was found on chromosome 1. With body WFE as covariate, additional QTL for AFE were found on chromosomes 1, 3, 4, 13 and 27. The QTL generally acted additively and there was no evidence for epistasis. Consistent with the original line differences, broiler alleles had positive effects on body WFE and negative effects on AFE, whereas the phenotypic correlation between the two traits was positive. The mapped QTL for body WFE cumulatively accounted for almost half the body weight difference between the chicken lines at puberty. Overlapping QTL for body WFE and body weight to 9 weeks of age indicate that most QTL affecting growth rate also affect body WFE. The co-localisation of QTL for body weight, growth and sexual maturity suggests that body weight and growth rate are closely related to the attainment of sexual maturity and that the genetic determination of growth rate has correlated effects on puberty.
    DOI
    10.1530/REP-10-0276
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    http://www.reproduction-online.org/content/141/3/381.full