20 Works

Data from: A brief history of bird flu

Samantha J. Lycett, Florian Duchatel & Paul Digard
In 1918, a strain of influenza A virus caused a human pandemic resulting in the deaths of 50 million people. A century later, with the advent of sequencing technology and corresponding phylogenetic methods, we know much more about the origins, evolution and epidemiology of influenza epidemics. Here we review the history of avian influenza viruses through the lens of their genetic makeup: from their relationship to human pandemic viruses, starting with the 1918 H1N1 strain,...

Data from: Genomic analysis offers insights into the evolution of the bovine TRA/TRD locus

Timothy K. Connelley, Kathryn Degnan, Cassandra W. Longhi & W. Ivan Morrison
Background: The TRA/TRD locus contains the genes for V(D)J somatic rearrangement of TRA and TRD chains expressed by αβ and γδ T cells respectively. Previous studies have demonstrated that the bovine TRA/TRD locus contains an exceptionally large number of TRAV/TRDV genes. In this study we combine genomic and transcript analysis to provide insights into the evolutionary development of the bovine TRA/TRD locus and the remarkable TRAV/TRDV gene repertoire. Results: Annotation of the UMD3.1 assembly identified...

Data from: Commercial chicken breeds exhibit highly divergent patterns of linkage disequilibrium

Reuben Pengelly, Almas A Gheyas, Richard Kuo, Enrico Mossotto, Eleanor G Seaby, David W Burt, Sarah Ennis & Andrew Collins
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...

Data from: Genome-wide SNP data unveils the globalization of domesticated pigs

Bin Yang, Leilei Cui, Miguel Perez-Enciso, Aleksei Traspov, Richard P. M. A. Crooijmans, Natalia Zinovieva, Lawrence B. Schook, Alan Archibald, Kesinee Gatphayak, Christophe Knorr, Alex Triantafyllidis, Panoraia Alexandri, Gono Semiadi, Olivier Hanotte, Deodália Dias, Peter Dovč, Pekka Uimari, Laura Iacolina, Massimo Scandura, Martien A. M. Groenen, Lusheng Huang & Hendrik-Jan Megens
Background: Pigs were domesticated independently in Eastern and Western Eurasia early during the agricultural revolution, and have since been transported and traded across the globe. Here, we present a worldwide survey on 60K genome-wide single nucleotide polymorphism (SNP) data for 2093 pigs, including 1839 domestic pigs representing 122 local and commercial breeds, 215 wild boars, and 39 out-group suids, from Asia, Europe, America, Oceania and Africa. The aim of this study was to infer global...

Data from: Genome-wide association and regional heritability mapping to identify loci underlying variation in nematode resistance and body weight in Scottish Blackface lambs

Valentina Riggio, Oswald Matika, Ricardo Pong-Wong, Michael J. Stear & Stephen C. Bishop
The genetic architecture underlying nematode resistance and body weight in Blackface lambs was evaluated comparing genome-wide association (GWA) and regional heritability mapping (RHM) approaches. The traits analysed were faecal egg count (FEC) and immunoglobulin A activity against third-stage larvae from Teladorsagia circumcincta, as indicators of nematode resistance, and body weight in a population of 752 Scottish Blackface lambs, genotyped with the 50k single-nucleotide polymorphism (SNP) chip. FEC for both Nematodirus and Strongyles nematodes (excluding Nematodirus),...

Data from: Genomic diversity and differentiation of a managed island wild boar population

Laura Iacolina, Massimo Scandura, Daniel J. Goedbloed, Panoraia Alexandri, Richard P. M. A. Crooijmans, Greger Larson, Alan Archibald, Marco Apollonio, Lawrence B. Schook, Martien A. Groenen & Hendrik-Jan Megens
The evolution of island populations in natural systems is driven by local adaptation and genetic drift. However, evolutionary pathways may be altered by humans in several ways. The wild boar (WB) (Sus scrofa) is an iconic game species occurring in several islands, where it has been strongly managed since prehistoric times. We examined genomic diversity at 49 803 single-nucleotide polymorphisms in 99 Sardinian WBs and compared them with 196 wild specimens from mainland Europe and...

UK dogs data from: Genome-wide association studies for canine hip dysplasia in single and multiple populations – implications and potential novel risk loci

Juliane Friedrich, Shizhi Wang, Erling Strandberg, Per Arvelius, Dylan N Clements & Pamela Wiener
Background: Association mapping studies of quantitative trait loci (QTL) for canine hip dysplasia (CHD) can contribute to the understanding of the genetic background of this common and debilitating disease and might contribute to its genetic improvement. The power of association studies for CHD is limited by relatively small sample numbers for CHD records within countries, suggesting potential benefits of joining data across countries. However, this is complicated due to the use of different scoring systems...

Unravelling selection signatures in a single dog breed suggests recent selection for morphological and behavioural traits

Juliane Friedrich, Andrea Talenti, Per Arvelius, Erling Strandberg, Marie J Haskell & Pam Wiener
Strong selection has resulted in substantial morphological and behavioural diversity across modern dog breeds, which makes dogs interesting model animals to study the underlying genetic architecture of these traits. However, results from between-breed analyses may confound selection signatures for behaviour and morphological features that were co-selected during breed development. In this study, we assess population genetic differences in a unique resource of dogs of the same breed but with systematic behavioural selection in only one...

Data from: Signatures of selection for environmental adaptation and zebu x taurine hybrid fitness in East African Shorthorn Zebu

Hussain Bahbahani, Abdulfatai Tijjani, Christopher Mukasa, David Wragg, Faisal Almathen, Oyekanmi Nash, Gerald N. Akpa, Mary Mbole-Kariuki, Sunir Malla, Mark Woolhouse, Tad Sonstegard, Curtis Van Tassell, Martin Blythe, Heather Huson & Olivier Hanotte
The East African Shorthorn Zebu (EASZ) cattle are ancient hybrid between Asian zebu × African taurine cattle preferred by local farmers due to their adaptability to the African environment. The genetic controls of these adaptabilities are not clearly understood yet. Here, we genotyped 92 EASZ samples from Kenya (KEASZ) with more than 770,000 SNPs and sequenced the genome of a pool of 10 KEASZ. We observe an even admixed autosomal zebu × taurine genomic structure...

Data from: Genomic data illuminates demography, genetic structure and selection of a popular dog breed

Pamela Wiener, Enrique Sánchez-Molano, Dylan N. Clements, John A. Woolliams, Marie J. Haskell & Sarah C. Blott
Background: Genomic methods have proved to be important tools in the analysis of genetic diversity across the range of species and can be used to reveal processes underlying both short- and long-term evolutionary change. This study applied genomic methods to investigate population structure and inbreeding in a common UK dog breed, the Labrador Retriever. Results: We found substantial within-breed genetic differentiation, which was associated with the role of the dog (i.e. working, pet, show) and...

Data from: Genome-wide association study identifies novel loci associated with resistance to bovine tuberculosis

Mairead L. Bermingham, Stephen C. Bishop, John A. Woolliams, Ricardo Pong-Wong, Adrian R. Allen, Stewart H. McBride, Stanley W. J. McDowell, Robin A. Skuce, Jon J. Ryder, David M. Wright & Elizabeth J. Glass
Tuberculosis caused by Mycobacterium bovis is a re- emerging disease of livestock which is of major economic importance world-wide, as well as being a zoonotic risk. There is significant heritability for host resistance to bovine tuberculosis (bTB) in dairy cattle. To identify resistance loci for bTB, we undertook a genome-wide association study in female Holstein-Friesian cattle with 592 cases and 559 age-matched controls from case herds. Cases and controls were categorised into distinct phenotypes: skin...

Data from: Health trajectories reveal the dynamic contributions of host genetic resistance and tolerance to infection outcome

Graham Lough, Ilias Kyriazakis, Andreas Lengeling, Silke Bergmann & Andrea B. Doeschl-Wilson
Resistance and tolerance are two alternative strategies hosts can adopt to survive infections. Both strategies may be genetically controlled. To date, the relative contribution of resistance and tolerance to infection outcome is poorly understood. A bioluminescent Listeria monocytogenes (Lm) infection challenge model on four genetically diverse mouse strains was used to study the genetic determination and dynamic contributions of host resistance and tolerance to listeriosis, a serious food-borne infectious disease in humans. Conventional statistical analyses...

Data from: Synchronous diversification of Sulawesi's iconic artiodactyls driven by recent geological events

Laurent A. F. Frantz, Anna Rudzinski, Abang Mansyursyah Surya Nugraha, Allowen Evin, James Burton, Ardern Hulme-Beaman, Anna Linderholm, Ross Barnett, Rodrigo Vega, Evan K. Irving-Pease, James Haile, Richard Allen, Kristin Leus, Jill Shephard, Mia Hillyer, Sarah Gillemot, Jeroen Van Den Hurk, Sharron Ogle, Cristina Atofanei, Mark G. Thomas, Friederike Johansson, Abdul Haris Mustari, John Williams, Kusdiantoro Mohamad, Chandramaya Siska Damayanti … & Greger Larson
The high degree of endemism on Sulawesi has previously been suggested to have vicariant origins, dating back 40 Myr ago. Recent studies, however, suggest that much of Sulawesi’s fauna assembled over the last 15 Myr. Here, we test the hypothesis that more recent uplift of previously submerged portions of land on Sulawesi promoted diversification, and that much of its faunal assemblage is much younger than the island itself. To do so, we combined palaeogeographical reconstructions...

Salmonella enterica serovar Enteritidis EN1660 proteome spectral data

Tzu-Chiao Chao, Stephen Fitzgerald, Stefani C Kary, Keith D MacKenzie, Daniel M Stoebel, Ebtihal Y Alshabib & Andrew DS Cameron
H-NS is a nucleoid structuring protein and global repressor of virulence and horizontally-acquired genes in bacteria. H-NS can interact with itself or with homologous proteins, but protein family diversity and regulatory network overlap remain poorly defined. Here we present a comprehensive phylogenetic analysis that revealed deep-branching clades, dispelling the presumption that H-NS is the progenitor of varied molecular backups. With few exceptions, clades are either entirely chromosomal or entirely plasmid-encoded proteins. On chromosomes, StpA and...

A single genomic region involving a putative chromosome rearrangement in flat oyster (Ostrea edulis) is associated with differential host resilience to the parasite Bonamia ostreae

Paulino Martínez Portela, Inés Sambade, Adrian Casanova, Andrés Blanco, Manu Gundappa, Tim Bean, Daniel L. Macqueen, Ross D. Houston, Antonio Villalba, Pauline Kamermans & Manuel Vera
European flat oyster (Ostrea edulis) is an ecologically and economically important marine bivalve, that has been severely affected by the intracellular parasite Bonamia ostreae. In this study, a flat oyster SNP array (~14,000 SNPs) was used to validate previously reported outlier loci for divergent selection associated with B. ostreae exposure in the Northeast Atlantic Area. A total of 134 wild and hatchery individuals from the North Sea, collected in naïve (NV) and long-term affected (LTA)...

Quantification of selected antimicrobial resistance genes in pig faeces on a British commercial pig farm during a typical production cycle

J. Pollock, A. Corbishley, M.R. Hutchings & D.L. Gally
The data presented are quantitative polymerase chain reaction (qPCR) read outs from antimicrobial resistance gene (AMRG) assays and associated metadata from this project. In this dataset, the mean gene copy numbers per microlitre of DNA extract are shown. The data were collected from faecal and environmental samples which were obtained from a single British commercial pig unit. The former were collected from the sow housing barn, pig growing houses and slurry tanks within the farm...

Data from: Regional heritability mapping method helps explain missing heritability of blood lipid traits in isolated populations

Masoud Shirali, Ricardo Pong-Wong, Pau Navarro, Sara Knott, Caroline Hayward, Veronique Vitart, Igor Rudan, Harry Campbell, Nicholas Hastie, Alan Wright & Christopher Haley
Single single-nucleotide polymorphism (SNP) genome-wide association studies (SSGWAS) may fail to identify loci with modest effects on a trait. The recently developed regional heritability mapping (RHM) method can potentially identify such loci. In this study, RHM was compared with the SSGWAS for blood lipid traits (high-density lipoprotein (HDL), low-density lipoprotein (LDL), plasma concentrations of total cholesterol (TC) and triglycerides (TG)). Data comprised 2246 adults from isolated populations genotyped using ~300 000 SNP arrays. The results...

Data from: Mapping and validation of a major QTL affecting resistance to pancreas disease (salmonid alphavirus) in Atlantic salmon (Salmo salar)

Serap Gonen, Matthew Baranski, Ingunn Thorland, Ashie Norris, Harald Grove, Petter Arnesen, Håvard Bakke, Sigbjørn Lien, Stephen C. Bishop & Ross D. Houston
Pancreas disease (PD), caused by a salmonid alphavirus (SAV), has a large negative economic and animal welfare impact on Atlantic salmon aquaculture. Evidence for genetic variation in host resistance to this disease has been reported, suggesting that selective breeding may potentially form an important component of disease control. The aim of this study was to explore the genetic architecture of resistance to PD, using survival data collected from two unrelated populations of Atlantic salmon; one...

Data from: Genetic dissection of complex behaviour traits in German Shepherd dogs

Juliane Friedrich, Erling Strandberg, Per Arvelius, Enrique Sánchez-Molano, Ricardo Pong-Wong, John M. Hickey, Marie J. Haskell & Pamela Wiener
A favourable genetic structure and diversity of behavioural features highlights the potential of dogs for studying the genetic architecture of behaviour traits. However, behaviours are complex traits, which have been shown to be influenced by numerous genetic and non-genetic factors, complicating their analysis. In this study, the genetic contribution to behaviour variation in German Shepherd dogs (GSDs) was analysed using genomic approaches. GSDs were phenotyped for behaviour traits using the established Canine Behavioral Assessment and...

Data from: Genetic susceptibility to infectious disease in East African Shorthorn Zebu: a genome-wide analysis of the effect of heterozygosity and exotic introgression

Gemma G. R. Murray, Mark E. J. Woolhouse, Miika Tapio, Mary N. Mbole-Kariuki, Tad S. Sonstegard, Samuel M. Thumbi, Amy E. Jennings, Ilana Conradie Van Wyk, Margo Chase-Topping, Henry Kiara, Phil Toye, Koos Coetzer, Barend M. De C. Bronsvoort & Olivier Hanotte
Genotyping 50kSNPs East African Shorthorn ZebuPlink files with no QC50kSNPs.ped

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