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Ramos AM, Crooijmans RPMA, Affara NA, Amaral AJ, Archibald AL, Beever JE, Bendixen C, Churcher C, Clark R, Dehais P, Hansen MS, Hedegaard J, Hu ZL, Kerstens HH, Law AS, Megens HJ, Milan D, Nonneman DJ, Rohrer GA, Rothschild MF, Smith TPL, Schnabel RD, Van Tassell CP, Taylor JF, Wiedmann RT, Schook LB, Groenen MAM. Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology. PLoS One 2009; 4:e6524. [PMID: 19654876 PMCID: PMC2716536 DOI: 10.1371/journal.pone.0006524] [Citation(s) in RCA: 464] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2009] [Accepted: 06/21/2009] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND The dissection of complex traits of economic importance to the pig industry requires the availability of a significant number of genetic markers, such as single nucleotide polymorphisms (SNPs). This study was conducted to discover several hundreds of thousands of porcine SNPs using next generation sequencing technologies and use these SNPs, as well as others from different public sources, to design a high-density SNP genotyping assay. METHODOLOGY/PRINCIPAL FINDINGS A total of 19 reduced representation libraries derived from four swine breeds (Duroc, Landrace, Large White, Pietrain) and a Wild Boar population and three restriction enzymes (AluI, HaeIII and MspI) were sequenced using Illumina's Genome Analyzer (GA). The SNP discovery effort resulted in the de novo identification of over 372K SNPs. More than 549K SNPs were used to design the Illumina Porcine 60K+SNP iSelect Beadchip, now commercially available as the PorcineSNP60. A total of 64,232 SNPs were included on the Beadchip. Results from genotyping the 158 individuals used for sequencing showed a high overall SNP call rate (97.5%). Of the 62,621 loci that could be reliably scored, 58,994 were polymorphic yielding a SNP conversion success rate of 94%. The average minor allele frequency (MAF) for all scorable SNPs was 0.274. CONCLUSIONS/SIGNIFICANCE Overall, the results of this study indicate the utility of using next generation sequencing technologies to identify large numbers of reliable SNPs. In addition, the validation of the PorcineSNP60 Beadchip demonstrated that the assay is an excellent tool that will likely be used in a variety of future studies in pigs.
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Affiliation(s)
- Antonio M. Ramos
- Wageningen University, Animal Breeding and Genomics Centre, Wageningen, The Netherlands
| | | | - Nabeel A. Affara
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Andreia J. Amaral
- Wageningen University, Animal Breeding and Genomics Centre, Wageningen, The Netherlands
| | - Alan L. Archibald
- Division of Genetics and Genomics, The Roslin Institute and the Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin Midlothian, United Kingdom
| | - Jonathan E. Beever
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
| | | | - Carol Churcher
- The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Richard Clark
- The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Patrick Dehais
- INRA, Laboratoire de Génétique Cellulaire, Castanet Tolosan, France
| | - Mark S. Hansen
- Illumina, Inc., San Diego, California, United States of America
| | - Jakob Hedegaard
- Aarhus University, Faculty of Agricultural Sciences, Tjele, Denmark
| | - Zhi-Liang Hu
- Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Ames, Iowa, United States of America
| | - Hindrik H. Kerstens
- Wageningen University, Animal Breeding and Genomics Centre, Wageningen, The Netherlands
| | - Andy S. Law
- Division of Genetics and Genomics, The Roslin Institute and the Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin Midlothian, United Kingdom
| | - Hendrik-Jan Megens
- Wageningen University, Animal Breeding and Genomics Centre, Wageningen, The Netherlands
| | - Denis Milan
- INRA, Laboratoire de Génétique Cellulaire, Castanet Tolosan, France
| | - Danny J. Nonneman
- USDA, ARS, US Meat Animal Research Center, Clay Center, Nebraska, United States of America
| | - Gary A. Rohrer
- USDA, ARS, US Meat Animal Research Center, Clay Center, Nebraska, United States of America
| | - Max F. Rothschild
- Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Ames, Iowa, United States of America
| | - Tim P. L. Smith
- USDA, ARS, US Meat Animal Research Center, Clay Center, Nebraska, United States of America
| | - Robert D. Schnabel
- Division of Animal Sciences, University of Missouri-Columbia, Columbia, Missouri, United States of America
| | - Curt P. Van Tassell
- Bovine Functional Genomics Laboratory, U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS), Beltsville, Maryland, United States of America
| | - Jeremy F. Taylor
- Division of Animal Sciences, University of Missouri-Columbia, Columbia, Missouri, United States of America
| | - Ralph T. Wiedmann
- USDA, ARS, US Meat Animal Research Center, Clay Center, Nebraska, United States of America
| | - Lawrence B. Schook
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
| | - Martien A. M. Groenen
- Wageningen University, Animal Breeding and Genomics Centre, Wageningen, The Netherlands
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Shayegan A, Petein M, Vanden Abbeele A. The use of beta-tricalcium phosphate, white MTA, white Portland cement and calcium hydroxide for direct pulp capping of primary pig teeth. Dent Traumatol 2009; 25:413-9. [DOI: 10.1111/j.1600-9657.2009.00799.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Jann OC, King A, Corrales NL, Anderson SI, Jensen K, Ait-ali T, Tang H, Wu C, Cockett NE, Archibald AL, Glass EJ. Comparative genomics of Toll-like receptor signalling in five species. BMC Genomics 2009; 10:216. [PMID: 19432955 PMCID: PMC2689273 DOI: 10.1186/1471-2164-10-216] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2008] [Accepted: 05/11/2009] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Over the last decade, several studies have identified quantitative trait loci (QTL) affecting variation of immune related traits in mammals. Recent studies in humans and mice suggest that part of this variation may be caused by polymorphisms in genes involved in Toll-like receptor (TLR) signalling. In this project, we used a comparative approach to investigate the importance of TLR-related genes in comparison with other immunologically relevant genes for resistance traits in five species by associating their genomic location with previously published immune-related QTL regions. RESULTS We report the genomic localisation of TLR1-10 and ten associated signalling molecules in sheep and pig using in-silico and/or radiation hybrid (RH) mapping techniques and compare their positions with their annotated homologues in the human, cattle and mouse whole genome sequences. We also report medium-density RH maps for porcine chromosomes 8 and 13. A comparative analysis of the positions of previously published relevant QTLs allowed the identification of homologous regions that are associated with similar health traits in several species and which contain TLR related and other immunologically relevant genes. Additional evidence was gathered by examining relevant gene expression and association studies. CONCLUSION This comparative genomic approach identified eight genes as potentially causative genes for variations of health related traits. These include susceptibility to clinical mastitis in dairy cattle, general disease resistance in sheep, cattle, humans and mice, and tolerance to protozoan infection in cattle and mice. Four TLR-related genes (TLR1, 6, MyD88, IRF3) appear to be the most likely candidate genes underlying QTL regions which control the resistance to the same or similar pathogens in several species. Further studies are required to investigate the potential role of polymorphisms within these genes.
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Affiliation(s)
- Oliver C Jann
- The Roslin Institute and R(D)SVS, University of Edinburgh, Roslin, Midlothian, Edinburgh, EH25 9PS, UK
| | - Annemarie King
- The Roslin Institute and R(D)SVS, University of Edinburgh, Roslin, Midlothian, Edinburgh, EH25 9PS, UK
| | | | - Susan I Anderson
- The Roslin Institute and R(D)SVS, University of Edinburgh, Roslin, Midlothian, Edinburgh, EH25 9PS, UK
| | - Kirsty Jensen
- The Roslin Institute and R(D)SVS, University of Edinburgh, Roslin, Midlothian, Edinburgh, EH25 9PS, UK
| | - Tahar Ait-ali
- The Roslin Institute and R(D)SVS, University of Edinburgh, Roslin, Midlothian, Edinburgh, EH25 9PS, UK
| | - Haizhou Tang
- The Roslin Institute and R(D)SVS, University of Edinburgh, Roslin, Midlothian, Edinburgh, EH25 9PS, UK
| | - Chunhua Wu
- Department of Animal, Dairy, and Veterinary Sciences, Utah State University, Logan, UT 844322-4700 USA
| | - Noelle E Cockett
- Department of Animal, Dairy, and Veterinary Sciences, Utah State University, Logan, UT 844322-4700 USA
| | - Alan L Archibald
- The Roslin Institute and R(D)SVS, University of Edinburgh, Roslin, Midlothian, Edinburgh, EH25 9PS, UK
| | - Elizabeth J Glass
- The Roslin Institute and R(D)SVS, University of Edinburgh, Roslin, Midlothian, Edinburgh, EH25 9PS, UK
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Joller D, Jørgensen CB, Bertschinger HU, Python P, Edfors I, Cirera S, Archibald AL, Bürgi E, Karlskov-Mortensen P, Andersson L, Fredholm M, Vögeli P. Refined localization of the Escherichia coli F4ab/F4ac receptor locus on pig chromosome 13. Anim Genet 2009; 40:749-52. [PMID: 19392815 DOI: 10.1111/j.1365-2052.2009.01881.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Diarrhoea in newborn and weaned pigs caused by enterotoxigenic Escherichia coli (ETEC) expressing F4 fimbriae leads to considerable losses in pig production. In this study, we refined the mapping of the receptor locus for ETEC F4ab/F4ac adhesion (F4bcR) by joint analysis of Nordic and Swiss data. A total of 236 pigs from a Nordic experimental herd, 331 pigs from a Swiss experimental herd and 143 pigs from the Swiss performing station were used for linkage analysis. Genotyping data of six known microsatellite markers, two newly developed markers (MUC4gt and HSA125gt) and an intronic SNP in MUC4 (MUC4-8227) were used to create the linkage map. The region for F4bcR was refined to the interval SW207-S0075 on pig chromosome 13. The most probable position of F4bcR was in the SW207-MUC4 region. The order of six markers was supported by physical mapping on the BAC fingerprint contig from the Wellcome Trust Sanger Institute. Thus, the region for F4bcR could be reduced from 26 to 14 Mb.
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Affiliation(s)
- D Joller
- Institute of Animal Sciences, ETH Zurich, 8092 Zurich, Switzerland
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Uenishi H, Shinkai H. Porcine Toll-like receptors: the front line of pathogen monitoring and possible implications for disease resistance. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2009; 33:353-361. [PMID: 18590761 DOI: 10.1016/j.dci.2008.06.001] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2008] [Revised: 06/04/2008] [Accepted: 06/04/2008] [Indexed: 05/26/2023]
Abstract
Toll-like receptors (TLRs) are the most famous pattern-recognition receptors (PRRs); they monitor pathogen-associated molecular patterns and play a critical role in activation of the immune system against infection. TLR gene mutations may affect the gene products in terms of their ligand-binding ability or their signal transduction ability after ligand binding; such changes have a great influence on pathogen monitoring and disease resistance. Thirteen mammalian TLRs have been identified, and genes corresponding to all 10 TLR genes identified in humans have been fully cloned in pigs. Porcine TLR gene coding sequences possess a large number of nonsynonymous single nucleotide polymorphisms (SNPs). They are concentrated in ectodomains, and may increase the variability of pathogen recognition in pig populations. We summarize the current knowledge of TLR molecules in mammals and livestock (particularly pigs) and speculate on the relationship between SNPs in porcine TLRs and their application to vaccine design and disease-resistance breeding.
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Affiliation(s)
- Hirohide Uenishi
- Division of Animal Sciences, National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan.
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Genomic sequence encoding diversity segments of the pig TCR delta chain gene demonstrates productivity of highly diversified repertoire. Mol Immunol 2009; 46:1212-21. [PMID: 19128837 DOI: 10.1016/j.molimm.2008.11.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2008] [Revised: 11/18/2008] [Accepted: 11/19/2008] [Indexed: 11/21/2022]
Abstract
To better understand the function and diversity of gammadelta T cells, we determined the genomic sequence encoding diversity (D) segments of the porcine TCR delta chain and its upstream regions, because pigs and other artiodactyls have relatively high proportions of gammadelta T cells. The revealed sequence contained 28 variable (V) alpha/delta segments, including 4 TRDV1 and at least 6 Ddelta segments, a much higher number than in humans and mice. All 6 of the Ddelta segments that had canonical recombination signal sequences were functionally utilized in expressed TCR delta chain genes. The multiplicity of Ddelta segments enabled the use of more than 3 Ddelta segments in a single functional TCR delta chain. The increased number of TCR delta segments was acquired by the duplication of the germline sequence, which occurred after the divergence of artiodactyls from primates and rodents. These data demonstrate that the pig is able to generate a highly diversified repertoire of TCR delta chain molecules.
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Kerstens HH, Kollers S, Kommadath A, Del Rosario M, Dibbits B, Kinders SM, Crooijmans RP, Groenen MA. Mining for single nucleotide polymorphisms in pig genome sequence data. BMC Genomics 2009; 10:4. [PMID: 19126189 PMCID: PMC2637895 DOI: 10.1186/1471-2164-10-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2008] [Accepted: 01/06/2009] [Indexed: 11/30/2022] Open
Abstract
Background Single nucleotide polymorphisms (SNPs) are ideal genetic markers due to their high abundance and the highly automated way in which SNPs are detected and SNP assays are performed. The number of SNPs identified in the pig thus far is still limited. Results A total of 4.8 million whole genome shotgun sequences obtained from the NCBI trace-repository with center name "SDJVP", and project name "Sino-Danish Pig Genome Project" were analysed for the presence of SNPs. Available BAC and BAC-end sequences and their naming and mapping information, all obtained from SangerInstitute FTP site, served as a rough assembly of a reference genome. In 1.2 Gb of pig genome sequence, we identified 98,151 SNPs in which one of the sequences in the alignment represented the polymorphism and 6,374 SNPs in which two sequences represent an identical polymorphism. To benchmark the SNP identification method, 163 SNPs, in which the polymorphism was represented twice in the sequence alignment, were selected and tested on a panel of three purebred boar lines and wild boar. Of these 163 in silico identified SNPs, 134 were shown to be polymorphic in our animal panel. Conclusion This SNP identification method, which mines for SNPs in publicly available porcine shotgun sequences repositories, provides thousands of high quality SNPs. Benchmarking in an animal panel showed that more than 80% of the predicted SNPs represented true genetic variation.
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Affiliation(s)
- Hindrik Hd Kerstens
- Animal Breeding and Genetics Group, Wageningen University, Wageningen, the Netherlands.
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Nelson L, Anderson S, Archibald AL, Rhind S, Lu ZH, Condie A, McIntyre N, Thompson J, Nenutil R, Vojtesek B, Whitelaw CBA, Little TJ, Hupp T. An animal model to evaluate the function and regulation of the adaptively evolving stress protein SEP53 in oesophageal bile damage responses. Cell Stress Chaperones 2008; 13:375-85. [PMID: 18465210 PMCID: PMC2673944 DOI: 10.1007/s12192-008-0037-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2007] [Revised: 03/04/2008] [Accepted: 03/12/2008] [Indexed: 01/19/2023] Open
Abstract
Squamous epithelium in mammals has evolved an atypical stress response involving down-regulation of the classic HSP70 protein and induction of sets of proteins including one named SEP53. This atypical stress response might be due to the unusual environmental pressures placed on squamous tissue. In fact, SEP53 plays a role as an anti-apoptotic factor in response to DNA damage induced by deoxycholic acid stresses implicated in oesophageal reflux disease. SEP53 also has a genetic signature characteristic of an adaptively and rapidly evolving gene, and this observation has been used to imply a role for SEP53 in immunity. Physiological models of squamous tissue are required to further define the regulation and function of SEP53. We examined whether porcine squamous epithelium would be a good model to study SEP53, since this animal suffers from a bile-reflux disease in squamous oesophageal tissue. We have (1) cloned and sequenced the porcine SEP53 locus from porcine bacterial artificial chromosome genomic DNA, (2) confirmed the strikingly divergent nature of the C-terminal portion of the SEP53 gene amongst mammals, (3) discovered that a function of the conserved N-terminal domain of the gene is to maintain cytoplasmic localisation, and (4) examined SEP53 expression in normal and diseased porcine pars oesophagea. SEP53 expression in porcine tissue was relatively confined to gastric squamous epithelium, consistent with its expression in normal human squamous epithelium. Immunohistochemical staining for SEP53 protein in normal and damaged pars oesophagea demonstrated significant stabilisation of SEP53 protein in the injured tissue. These results suggest that porcine squamous epithelium would be a robust physiological model to examine the evolution and function of the SEP53 stress pathway in modulating stress-induced responses in squamous tissue.
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Affiliation(s)
- Lenny Nelson
- CRUK p53 Signal Transduction Group, University of Edinburgh, South Crewe Road, Edinburgh, EH4 2XR UK
| | - Susan Anderson
- Division of Genomics and Genetics, Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin, Midlothian, EH25 9PS UK
| | - Alan L. Archibald
- Division of Genomics and Genetics, Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin, Midlothian, EH25 9PS UK
| | - Susan Rhind
- Division of Animal Health and Welfare, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Roslin, Midlothian, EH25 9RG UK
| | - Zen H. Lu
- Division of Genomics and Genetics, Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin, Midlothian, EH25 9PS UK
| | - Alison Condie
- Wellcome Trust Clinical Research Facility, South Crewe Road, Edinburgh, EH4 2XU UK
| | - Neal McIntyre
- Division of Animal Health and Welfare, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Roslin, Midlothian, EH25 9RG UK
| | - Jill Thompson
- SAC Veterinary Services (Edinburgh), Bush Estate, Penicuik, Midlothian, EH26 0QE UK
| | | | | | - C. Bruce A. Whitelaw
- Division of Genomics and Genetics, Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin, Midlothian, EH25 9PS UK
| | - Tom J. Little
- Institute of Evolutionary Biology, University of Edinburgh, School of Biology, Kings Buildings, EH9 3JT Edinburgh, UK
| | - Ted Hupp
- CRUK p53 Signal Transduction Group, University of Edinburgh, South Crewe Road, Edinburgh, EH4 2XR UK
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Shayegan A, Petein M, Abbeele AV. Beta-tricalcium phosphate, white mineral trioxide aggregate, white Portland cement, ferric sulfate, and formocresol used as pulpotomy agents in primary pig teeth. ACTA ACUST UNITED AC 2008; 105:536-42. [DOI: 10.1016/j.tripleo.2007.10.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2007] [Revised: 10/09/2007] [Accepted: 10/11/2007] [Indexed: 10/22/2022]
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Humphray SJ, Scott CE, Clark R, Marron B, Bender C, Camm N, Davis J, Jenks A, Noon A, Patel M, Sehra H, Yang F, Rogatcheva MB, Milan D, Chardon P, Rohrer G, Nonneman D, de Jong P, Meyers SN, Archibald A, Beever JE, Schook LB, Rogers J. A high utility integrated map of the pig genome. Genome Biol 2008; 8:R139. [PMID: 17625002 PMCID: PMC2323232 DOI: 10.1186/gb-2007-8-7-r139] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2007] [Revised: 06/21/2007] [Accepted: 07/11/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The domestic pig is being increasingly exploited as a system for modeling human disease. It also has substantial economic importance for meat-based protein production. Physical clone maps have underpinned large-scale genomic sequencing and enabled focused cloning efforts for many genomes. Comparative genetic maps indicate that there is more structural similarity between pig and human than, for example, mouse and human, and we have used this close relationship between human and pig as a way of facilitating map construction. RESULTS Here we report the construction of the most highly continuous bacterial artificial chromosome (BAC) map of any mammalian genome, for the pig (Sus scrofa domestica) genome. The map provides a template for the generation and assembly of high-quality anchored sequence across the genome. The physical map integrates previous landmark maps with restriction fingerprints and BAC end sequences from over 260,000 BACs derived from 4 BAC libraries and takes advantage of alignments to the human genome to improve the continuity and local ordering of the clone contigs. We estimate that over 98% of the euchromatin of the 18 pig autosomes and the X chromosome along with localized coverage on Y is represented in 172 contigs, with chromosome 13 (218 Mb) represented by a single contig. The map is accessible through pre-Ensembl, where links to marker and sequence data can be found. CONCLUSION The map will enable immediate electronic positional cloning of genes, benefiting the pig research community and further facilitating use of the pig as an alternative animal model for human disease. The clone map and BAC end sequence data can also help to support the assembly of maps and genome sequences of other artiodactyls.
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Affiliation(s)
- Sean J Humphray
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA UK
| | - Carol E Scott
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA UK
| | - Richard Clark
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA UK
| | - Brandy Marron
- College of Agriculture, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 USA
| | - Clare Bender
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA UK
| | - Nick Camm
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA UK
| | - Jayne Davis
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA UK
| | - Andrew Jenks
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA UK
| | - Angela Noon
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA UK
| | - Manish Patel
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA UK
| | - Harminder Sehra
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA UK
| | - Fengtang Yang
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA UK
| | - Margarita B Rogatcheva
- College of Agriculture, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 USA
| | - Denis Milan
- Laboratoire de Génétique Cellulaire, INRA, 31326 Castanet-Tolosan, France
| | - Patrick Chardon
- INRA-CEA, Domaine de Vilvert, 78352, Jouy en Josas cedex, France
| | - Gary Rohrer
- US Department of Agriculture, Agricultural Research Service, US Meat Animal Research Center, Clay Center, NE 68933-0166, USA
| | - Dan Nonneman
- US Department of Agriculture, Agricultural Research Service, US Meat Animal Research Center, Clay Center, NE 68933-0166, USA
| | - Pieter de Jong
- Children's Hospital Oakland-BACPAC Resources, Oakland, California 94609, USA
| | - Stacey N Meyers
- College of Agriculture, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 USA
| | | | - Jonathan E Beever
- College of Agriculture, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 USA
| | - Lawrence B Schook
- College of Agriculture, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 USA
| | - Jane Rogers
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA UK
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Rothschild MF, Plastow GS. Impact of genomics on animal agriculture and opportunities for animal health. Trends Biotechnol 2008; 26:21-5. [PMID: 18022262 PMCID: PMC7114270 DOI: 10.1016/j.tibtech.2007.10.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2007] [Revised: 10/09/2007] [Accepted: 10/10/2007] [Indexed: 11/24/2022]
Abstract
Livestock production is an important source of animal protein worldwide. In the developed world meat consumption will remain steady but demand is forecast to grow enormously in developing countries. The use of genomics will speed genetic improvement and increase levels of production quickly in the developed world but might face problems in the developing world, including scientific, economic and political challenges. Considerable increases in public and private research funding will be required to develop and utilize novel tools and collections of detailed trait information on appropriate animals. The development of policies protecting the environment and managing all genetic resources will also be needed. Advances in livestock genomics have major implications for increasing food output as well as improving human health.
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Affiliation(s)
- Max F Rothschild
- Department of Animal Science, Center for Integrated Animal Genomics, Iowa State University, Ames, IA 50011, USA.
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Lewis CR, Ait-Ali T, Clapperton M, Archibald AL, Bishop S. Genetic Perspectives on Host Responses to Porcine Reproductive and Respiratory Syndrome (PRRS). Viral Immunol 2007; 20:343-58. [DOI: 10.1089/vim.2007.0024] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Craig R.G. Lewis
- Division of Genetics and Genomics, Roslin Institute (Edinburgh), Roslin, Midlothian, United Kingdom
| | - Tahar Ait-Ali
- Division of Genetics and Genomics, Roslin Institute (Edinburgh), Roslin, Midlothian, United Kingdom
| | - Mary Clapperton
- Division of Genetics and Genomics, Roslin Institute (Edinburgh), Roslin, Midlothian, United Kingdom
| | - Alan L. Archibald
- Division of Genetics and Genomics, Roslin Institute (Edinburgh), Roslin, Midlothian, United Kingdom
| | - Stephen Bishop
- Division of Genetics and Genomics, Roslin Institute (Edinburgh), Roslin, Midlothian, United Kingdom
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Chen K, Baxter T, Muir WM, Groenen MA, Schook LB. Genetic resources, genome mapping and evolutionary genomics of the pig (Sus scrofa). Int J Biol Sci 2007; 3:153-65. [PMID: 17384734 PMCID: PMC1802013 DOI: 10.7150/ijbs.3.153] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2006] [Accepted: 01/09/2007] [Indexed: 02/01/2023] Open
Abstract
The pig, a representative of the artiodactyla clade, is one of the first animals domesticated, and has become an important agriculture animal as one of the major human nutritional sources of animal based protein. The pig is also a valuable biomedical model organism for human health. The pig's importance to human health and nutrition is reflected in the decision to sequence its genome (3X). As an animal species with its wild ancestors present in the world, the pig provides a unique opportunity for tracing mammalian evolutionary history and defining signatures of selection resulting from both domestication and natural selection. Completion of the pig genome sequencing project will have significant impacts on both agriculture and human health. Following the pig whole genome sequence drafts, along with large-scale polymorphism data, it will be possible to conduct genome sweeps using association mapping, and identify signatures of selection. Here, we provide a description of the pig genome sequencing project and perspectives on utilizing genomic technologies to exploit pig genome evolution and the molecular basis for phenotypic traits for improving pig production and health.
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Affiliation(s)
- Kefei Chen
- 1. Department of Animal Sciences, University of Illinois at Urbana-Champaign, 1201 W. Gregory Dr., Urbana, IL 61801, USA
| | - Tara Baxter
- 1. Department of Animal Sciences, University of Illinois at Urbana-Champaign, 1201 W. Gregory Dr., Urbana, IL 61801, USA
| | - William M. Muir
- 2. Department of Animal Science, Purdue University, West Lafayette, Indiana 47907-1151, USA
| | - Martien A. Groenen
- 3. Animal Breeding and Genetics Group, Wageningen University, PO Box 9101, Wageningen, 6701 BH, The Netherlands
| | - Lawrence B. Schook
- 1. Department of Animal Sciences, University of Illinois at Urbana-Champaign, 1201 W. Gregory Dr., Urbana, IL 61801, USA
- 4. Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W. Gregory Dr., Urbana, IL 61801, USA
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Du ZQ, Vincent-Naulleau S, Gilbert H, Vignoles F, Créchet F, Shimogiri T, Yasue H, Leplat JJ, Bouet S, Gruand J, Horak V, Milan D, Le Roy P, Geffrotin C. Detection of novel quantitative trait loci for cutaneous melanoma by genome-wide scan in the MeLiM swine model. Int J Cancer 2007; 120:303-20. [PMID: 17066441 DOI: 10.1002/ijc.22289] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Human cutaneous melanoma is a complex trait inherited in about 10% of cases. Although 2 high-risk genes, CDKN2A and CDK4, and 1 low risk gene, MC1R, have been identified, susceptibility genes remain to be discovered. Here, we attempted to determine new genomic regions linked to melanoma using the pig MeLiM strain, which develops hereditary cutaneous melanomas. We applied quantitative trait loci (QTL) mapping method to a significant genome-wide scan performed on 331 backcross pigs derived from this strain. QTLs were detected at chromosome-wide level for a melanoma synthetic trait corresponding to the development of melanoma. The peak positions on Sus scrofa chromosomes (SSC) were at 49.4 and 88.0 cM (SSC1), 56.0 cM (SSC13), 86.5 cM (SSC15) and 39.8 cM (SSC17), and, on SSC2, at 16.9 cM, in families derived from F1 males only (p < 0.05, except for SSC13, p < 0.01). Analysis of 7 precise specific traits revealed highly significant QTLs on SSC10 (ulceration), on SSC12 (presence of melanoma at birth), on SSC13 (lesion type), and on SSC16 and SSC17 (number of aggressive melanomas) at the respective positions 42.0, 95.6, 81.0, 45.3 and 44.8 cM (p < 0.001 and p < 0.05 respectively at the chromosome- and genome-wide levels). We also showed that MeLiM MC1R*2 allele, which determines black coat colour in pigs, predisposes significantly to melanoma. Interactions were observed between MC1R and markers located on SSC1 (p < 0.05). Taken together, these results indicate that MeLiM swine is a model for human multigenic diseases. Comparative mapping revealed human regions of interest to search for new melanoma susceptibility candidates.
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Affiliation(s)
- Zhi-Qiang Du
- CEA, DSV, DRR, Laboratoire de Radiobiologie et d'Etude du Génome, INRA Jouy-en-Josas, F-78352 France
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66
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Uenishi H, Eguchi-Ogawa T, Shinkai H, Okumura N, Suzuki K, Toki D, Hamasima N, Awata T. PEDE (Pig EST Data Explorer) has been expanded into Pig Expression Data Explorer, including 10 147 porcine full-length cDNA sequences. Nucleic Acids Res 2006; 35:D650-3. [PMID: 17145712 PMCID: PMC1751553 DOI: 10.1093/nar/gkl954] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We formerly released the porcine expressed sequence tag (EST) database Pig EST Data Explorer (PEDE; ), which comprised 68 076 high-quality ESTs obtained by using full-length-enriched cDNA libraries derived from seven tissues. We have added eight tissues and cell types to the EST analysis and have integrated 94 555 additional high-quality ESTs into the database. We also fully sequenced the inserts of 10 147 of the cDNA clones that had undergone EST analysis; the sequences and annotation of the cDNA clones were stored in the database. Further, we constructed an interface that can be used to perform various searches in the database. The PEDE database is the primary resource of expressed pig genes that are supported by full-length cDNA sequences. This resource not only enables us to pick cDNA clones of interest for a particular analysis, but it also confirms and thus contributes to the sequencing integrity of the pig genome, which is now being compiled by an international consortium (). PEDE has therefore evolved into what we now call ‘Pig Expression Data Explorer’.
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Affiliation(s)
- Hirohide Uenishi
- Animal Genome Research Unit, Division of Animal Sciences, National Institute of Agrobiological Sciences, 2 Ikenodai, Tsukuba, Ibaraki 305-8602, Japan.
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67
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Lahbib-Mansais Y, Mompart F, Milan D, Leroux S, Faraut T, Delcros C, Yerle M. Evolutionary breakpoints through a high-resolution comparative map between porcine chromosomes 2 and 16 and human chromosomes. Genomics 2006; 88:504-12. [PMID: 16765019 DOI: 10.1016/j.ygeno.2006.04.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2006] [Revised: 04/11/2006] [Accepted: 04/20/2006] [Indexed: 11/20/2022]
Abstract
This study reports a high-resolution comparative map between human chromosomes and porcine chromosomes 2 (SSC2) and 16 (SSC16), pointing out new homologies and evolutionary breakpoints. SSC2 is of particular interest because of the presence of several important QTLs. Among 226 porcine ESTs selected according to their expected localization, 151 were RH mapped and ordered on SSC2. This study confirmed the extensive conservation between SSC2 and HSA11 and HSA19 and refined the homology with HSA5 (three blocks defined). Furthermore the SSC2q pericentromeric region was shown to be homologous to another human chromosome (HSA1). A complex organization of these syntenies was demonstrated on SSC2q. Our strategy led us to improve also the SSC16 RH map by adding 45 markers. Two-color fluorescence in situ hybridization of markers representative of each synteny confirmed block order. Finally, 29 breakpoints were identified in both species, and porcine BACs containing two breakpoints were isolated.
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Affiliation(s)
- Yvette Lahbib-Mansais
- Institut National de la Recherche Agronomique, Laboratoire de Génétique Cellulaire, BP52627, 31326 Castanet-Tolosan, France.
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68
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Foster HA, Bridger JM. The genome and the nucleus: a marriage made by evolution. Genome organisation and nuclear architecture. Chromosoma 2005; 114:212-29. [PMID: 16133352 DOI: 10.1007/s00412-005-0016-6] [Citation(s) in RCA: 109] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2005] [Revised: 06/29/2005] [Accepted: 07/04/2005] [Indexed: 01/15/2023]
Abstract
Genomes are housed within cell nuclei as individual chromosome territories. Nuclei contain several architectural structures that interact and influence the genome. In this review, we discuss how the genome may be organised within its nuclear environment with the position of chromosomes inside nuclei being either influenced by gene density or by chromosomes size. We compare interphase genome organisation in diverse species and reveal similarities and differences between evolutionary divergent organisms. Genome organisation is also discussed with relevance to regulation of gene expression, development and differentiation and asks whether large movements of whole chromosomes are really observed during differentiation. Literature and data describing alterations to genome organisation in disease are also discussed. Further, the nuclear structures that are involved in genome function are described, with reference to what happens to the genome when these structures contain protein from mutant genes as in the laminopathies.
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Affiliation(s)
- Helen A Foster
- Laboratory of Nuclear and Genomic Health, Cell and Chromosome Biology Group, Division of Biosciences, School of Health Sciences and Social Care, Brunel University, Uxbridge UB8 3PH, UK
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69
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2005. [PMCID: PMC2447491 DOI: 10.1002/cfg.425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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