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Sutera AM, Tolone M, Mastrangelo S, Di Gerlando R, Sardina MT, Portolano B, Pong-Wong R, Riggio V. Detection of genomic regions underlying milk production traits in Valle del Belice dairy sheep using regional heritability mapping. J Anim Breed Genet 2021; 138:552-561. [PMID: 34014003 PMCID: PMC8453569 DOI: 10.1111/jbg.12552] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 03/09/2021] [Accepted: 04/15/2021] [Indexed: 11/28/2022]
Abstract
The aim of this study was to identify genomic regions underlying milk production traits in the Valle del Belice dairy sheep using regional heritability mapping (RHM). Repeated measurements for milk yield (MY), fat percentage and yield (F% and FY) and protein percentage and yield (P% and PY), collected over a period of 6 years (2006–2012) on 481 Valle del Belice ewes, were used for the analysis. Animals were genotyped with the Illumina 50k SNP chip. Variance components, heritabilities and repeatabilities within and across lactations were estimated, fitting parity, litter size, season of lambing and fortnights in milk, as fixed; and additive genetic, permanent environment within and across lactations, flock by test‐day interaction and residual as random effects. For the RHM analysis, the model included the same fixed and random effects as before, plus an additional regional genomic additive effect (specific for the region being tested) as random. While the whole genomic additive effect was estimated using the genomic relationship matrix (GRM) constructed from all SNPs, the regional genomic additive effect was estimated from a GRM matrix constructed from the SNPs within each region. Heritability estimates ranged between 0.06 and 0.15, with repeatabilities being between 0.14 and 0.24 across lactations and between 0.23 and 0.39 within lactation for all milk production traits. A substantial effect of flock‐test‐day on milk production traits was also estimated. Significant genomic regions at either genome‐wide (p < .05) or suggestive (i.e., one false positive per genome scan) level were identified on chromosome (OAR) 2, 3 and 20 for F% and on OAR3 for P%, with the regions on OAR3 in common between the two traits. Our results confirmed the role of LALBA and AQP genes, on OAR3, as candidate genes for milk production traits in sheep.
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Affiliation(s)
- Anna Maria Sutera
- Dipartimento Scienze Veterinarie, Università di Messina, Messina, Italy
| | - Marco Tolone
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Palermo, Italy
| | - Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Palermo, Italy
| | - Rosalia Di Gerlando
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Palermo, Italy
| | - Maria Teresa Sardina
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Palermo, Italy
| | - Baldassare Portolano
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Palermo, Italy
| | - Ricardo Pong-Wong
- The Roslin Institute and R(D)SVS, Easter Bush Campus, Midlothian, UK
| | - Valentina Riggio
- The Roslin Institute and R(D)SVS, Easter Bush Campus, Midlothian, UK.,Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh, UK
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2
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Mosley YYC, Radder JE, HogenEsch H. Genetic Variation in the Magnitude and Longevity of the IgG Subclass Response to a Diphtheria-Tetanus-Acellular Pertussis (DTaP) Vaccine in Mice. Vaccines (Basel) 2019; 7:E124. [PMID: 31547158 PMCID: PMC6963843 DOI: 10.3390/vaccines7040124] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 09/04/2019] [Accepted: 09/05/2019] [Indexed: 11/17/2022] Open
Abstract
The type of IgG subclasses induced by vaccination is an important determinant of vaccine efficacy because the IgG subclasses vary in their biological function. The goal of this study was to determine the influence of the genetic background on the production and duration of vaccine-induced IgG subclasses. IgG1, IgG2b, and IgG3 titers against diphtheria toxoid (DT), pertussis toxin (PT), filamentous hemagglutinin (FHA), and pertactin (Prn) were measured in mice from 28 different inbred and wild-derived strains vaccinated with an aluminum hydroxide-adjuvanted DTaP vaccine. The titers and duration of vaccine-specific IgG subclass responses were different among mouse strains, indicating that genetic factors contribute to this variation. Statistical associations were used to identify potential mechanisms that contribute to antibody production and longevity. This analysis showed that the mechanisms guiding the magnitude of antibody production were antigen-dependent for IgG1 but antigen-independent for IgG2b and IgG3. However, the mechanisms driving the longevity of antibody titers were antigen-independent for IgG1, IgG2b, and IgG3. The ratio of IgG1 and IgG3 titers identified Th1 and Th2-prone mouse strains. TLR4-deficient C3H/HeJ mice had an enhanced IgG1 response compared with C3H/HeOuJ mice with intact TLR4. This work demonstrates that the genetic background contributes significantly to the magnitude and longevity of vaccine-induced IgG1, IgG2b, and IgG3 titers in mice.
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Affiliation(s)
- Yung-Yi C Mosley
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN 47907 USA.
| | - Josiah E Radder
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA.
| | - Harm HogenEsch
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN 47907 USA.
- Purdue Institute of Inflammation, Immunology, and Infectious Diseases, Purdue University, Indiana Purdue University, West Lafayette, IN 47907, USA.
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Brog YM, Osorio S, Yichie Y, Alseekh S, Bensal E, Kochevenko A, Zamir D, Fernie AR. A Solanum neorickii introgression population providing a powerful complement to the extensively characterized Solanum pennellii population. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:391-403. [PMID: 30230636 PMCID: PMC7379295 DOI: 10.1111/tpj.14095] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 09/01/2018] [Accepted: 09/04/2018] [Indexed: 05/31/2023]
Abstract
We present a complementary resource for trait fine-mapping in tomato to those based on the intra-specific cross between cultivated tomato and the wild tomato species Solanum pennellii, which have been extensively used for quantitative genetics in tomato over the last 20 years. The current population of backcross inbred lines (BILs) is composed of 107 lines derived after three backcrosses of progeny of the wild species Solanum neorickii (LA2133) and cultivated tomato (cultivar TA209) and is freely available to the scientific community. These S. neorickii BILs were genotyped using the 10K SolCAP single nucleotide polymorphism chip, and 3111 polymorphic markers were used to map recombination break points relative to the physical map of Solanum lycopersicum. The BILs harbor on average 4.3 introgressions per line, with a mean introgression length of 34.7 Mbp, allowing partitioning of the genome into 340 bins and thereby facilitating rapid trait mapping. We demonstrate the power of using this resource in comparison with archival data from the S. pennellii resources by carrying out metabolic quantitative trait locus analysis following gas chromatography-mass spectrometry on fruits harvested from the S. neorickii BILs. The metabolic candidate genes phenylalanine ammonia-lyase and cystathionine gamma-lyase were then tested and validated in F2 populations and via agroinfiltration-based overexpression in order to exemplify the fidelity of this method in identifying the genes that drive tomato metabolic phenotypes.
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Affiliation(s)
- Yaacov Micha Brog
- Faculty of AgricultureThe Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture at the Hebrew University of JerusalemRehovot76100Israel
| | - Sonia Osorio
- Department of Molecular Biology and BiochemistryInstituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’ – University of Malaga – Consejo Superior de Investigaciones Científicas (IHSM‐UMA‐CSIC)Campus de Teatinos29071MálagaSpain
- Max‐Planck‐Institute of Molecular Plant PhysiologyAm Mühlenberg 114476Potsdam‐GolmGermany
| | - Yoav Yichie
- Faculty of AgricultureThe Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture at the Hebrew University of JerusalemRehovot76100Israel
| | - Saleh Alseekh
- Max‐Planck‐Institute of Molecular Plant PhysiologyAm Mühlenberg 114476Potsdam‐GolmGermany
- Center of Plant Systems Biology and Biotechnology4000PlovdivBulgaria
| | - Elad Bensal
- Faculty of AgricultureThe Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture at the Hebrew University of JerusalemRehovot76100Israel
| | - Andriy Kochevenko
- Max‐Planck‐Institute of Molecular Plant PhysiologyAm Mühlenberg 114476Potsdam‐GolmGermany
| | - Dani Zamir
- Faculty of AgricultureThe Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture at the Hebrew University of JerusalemRehovot76100Israel
| | - Alisdair R. Fernie
- Max‐Planck‐Institute of Molecular Plant PhysiologyAm Mühlenberg 114476Potsdam‐GolmGermany
- Center of Plant Systems Biology and Biotechnology4000PlovdivBulgaria
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Radder JE, Gregory AD, Leme AS, Cho MH, Chu Y, Kelly NJ, Bakke P, Gulsvik A, Litonjua AA, Sparrow D, Beaty TH, Crapo JD, Silverman EK, Zhang Y, Berndt A, Shapiro SD. Variable Susceptibility to Cigarette Smoke-Induced Emphysema in 34 Inbred Strains of Mice Implicates Abi3bp in Emphysema Susceptibility. Am J Respir Cell Mol Biol 2017; 57:367-375. [PMID: 28441029 DOI: 10.1165/rcmb.2016-0220oc] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is caused by a complex interaction of environmental exposures, most commonly cigarette smoke, and genetic factors. Chronic cigarette smoke exposure in the mouse is a commonly used animal model of COPD. We aimed to expand our knowledge about the variable susceptibility of inbred strains to this model and test for genetic variants associated with this trait. To that end, we sought to measure differential susceptibility to cigarette smoke-induced emphysema in the mouse, identify genetic loci associated with this quantitative trait, and find homologous human genes associated with COPD. Alveolar chord length (CL) in 34 inbred strains of mice was measured after 6 months of exposure to cigarette smoke. After testing for association, we connected a murine candidate locus to a published meta-analysis of moderate-to-severe COPD. We identified deleterious mutations in a candidate gene in silico and measured gene expression in extreme strains. A/J was the most susceptible strain in our survey (Δ CL 7.0 ± 2.2 μm) and CBA/J was the least susceptible (Δ CL -0.3 ± 1.2 μm). By integrating mouse and human genome-wide scans, we identified the candidate gene Abi3bp. CBA/J mice harbor predicted deleterious variants in Abi3bp, and expression of the gene differs significantly between CBA/J and A/J mice. This is the first report of susceptibility to cigarette smoke-induced emphysema in 34 inbred strains of mice, and Abi3bp is identified as a potential contributor to this phenotype.
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Affiliation(s)
- Josiah E Radder
- 1 Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Alyssa D Gregory
- 1 Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Adriana S Leme
- 1 Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Michael H Cho
- 2 Channing Division of Network Medicine, and.,3 Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts
| | - Yanxia Chu
- 1 Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Neil J Kelly
- 1 Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Per Bakke
- 4 Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Amund Gulsvik
- 4 Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Augusto A Litonjua
- 2 Channing Division of Network Medicine, and.,3 Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts
| | - David Sparrow
- 5 School of Public Health and.,6 School of Medicine, Boston University, Boston, Massachusetts.,7 Veterans Affairs Boston Healthcare System, Boston, Massachusetts
| | - Terri H Beaty
- 8 Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland; and
| | - James D Crapo
- 9 Department of Radiology, National Jewish Health, Denver, Colorado
| | - Edwin K Silverman
- 2 Channing Division of Network Medicine, and.,3 Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts
| | - Yingze Zhang
- 1 Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Annerose Berndt
- 1 Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Steven D Shapiro
- 1 Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
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Dassano A, Pintarelli G, Cotroneo CE, Pettinicchio A, Forcati E, De Cecco L, Borrego A, Colombo F, Dragani TA, Manenti G. Complex genetic control of lung tumorigenesis in resistant mice strains. Cancer Sci 2017; 108:2281-2286. [PMID: 28796413 PMCID: PMC5666032 DOI: 10.1111/cas.13349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 07/27/2017] [Accepted: 08/05/2017] [Indexed: 12/18/2022] Open
Abstract
The SM/J mouse strain is resistant to chemically‐induced lung tumorigenesis despite having a haplotype, in the pulmonary adenoma susceptibility locus (Pas1) locus, that confers tumor susceptibility in other strains. To clarify this inconsistent genotype‐phenotype correlation, we crossed SM/J mice with another resistant strain and conducted genome‐wide linkage analysis in the (C57BL/6J × SM/J)F2 progeny exposed to urethane to induce lung tumors. Overall, >80% of F2 mice of both sexes developed from 1 to 20 lung tumors. Genotyping of 372 F2 mice for 744 informative non‐redundant SNPs dispersed over all autosomal chromosomes revealed four quantitative trait loci (QTLs) affecting lung tumor multiplicity, on chromosomes 3 (near rs13477379), 15 (rs6285067), 17 (rs33373629) and 18 (rs3706601), all with logarithm of the odds (LOD) scores >5. Four QTLs modulated total lung tumor volume, on chromosome 3 (rs13477379), 10 (rs13480702), 15 (rs6285067) and 17 (rs3682923), all with LOD scores >4. No QTL modulating lung tumor multiplicity or total volume was detected in Pas1 on chromosome 6. The present study demonstrates that the SM/J strain carries, at the Pas1 locus, the resistance allele: a finding that will facilitate identification of the Pas1 causal element. More generally, it demonstrates that lung tumorigenesis is under complex polygenic control even in a pedigree with low susceptibility to this neoplasia, suggesting that the genetics of lung tumorigenesis is much more complex than evidenced by the pulmonary adenoma susceptibility and resistance loci that have, so far, been mapped in a small number of crosses between a few inbred strains.
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Affiliation(s)
- Alice Dassano
- Department of Predictive and Preventive Medicine, Fondazione IRCCS, Istituto Nazionale dei Tumori, Milan, Italy
| | - Giulia Pintarelli
- Department of Predictive and Preventive Medicine, Fondazione IRCCS, Istituto Nazionale dei Tumori, Milan, Italy
| | - Chiara E Cotroneo
- Department of Predictive and Preventive Medicine, Fondazione IRCCS, Istituto Nazionale dei Tumori, Milan, Italy
| | - Angela Pettinicchio
- Department of Predictive and Preventive Medicine, Fondazione IRCCS, Istituto Nazionale dei Tumori, Milan, Italy
| | - Elena Forcati
- Department of Predictive and Preventive Medicine, Fondazione IRCCS, Istituto Nazionale dei Tumori, Milan, Italy
| | - Loris De Cecco
- Department of Predictive and Preventive Medicine, Fondazione IRCCS, Istituto Nazionale dei Tumori, Milan, Italy.,Department of Experimental Oncology and Molecular medicine, Fondazione IRCCS, Istituto Nazionale dei Tumori, Milan, Italy
| | - Andrea Borrego
- Laboratory of Immunogenetics, Instituto Butantan, São Paulo, Brazil
| | - Francesca Colombo
- Department of Predictive and Preventive Medicine, Fondazione IRCCS, Istituto Nazionale dei Tumori, Milan, Italy
| | - Tommaso A Dragani
- Department of Predictive and Preventive Medicine, Fondazione IRCCS, Istituto Nazionale dei Tumori, Milan, Italy
| | - Giacomo Manenti
- Department of Predictive and Preventive Medicine, Fondazione IRCCS, Istituto Nazionale dei Tumori, Milan, Italy
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6
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Khajavi M, Zhou Y, Birsner AE, Bazinet L, Rosa Di Sant A, Schiffer AJ, Rogers MS, Krishnaji ST, Hu B, Nguyen V, Zon L, D’Amato RJ. Identification of Padi2 as a novel angiogenesis-regulating gene by genome association studies in mice. PLoS Genet 2017; 13:e1006848. [PMID: 28617813 PMCID: PMC5491319 DOI: 10.1371/journal.pgen.1006848] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 06/29/2017] [Accepted: 06/01/2017] [Indexed: 11/18/2022] Open
Abstract
Recent findings indicate that growth factor-driven angiogenesis is markedly influenced by genetic variation. This variation in angiogenic responsiveness may alter the susceptibility to a number of angiogenesis-dependent diseases. Here, we utilized the genetic diversity available in common inbred mouse strains to identify the loci and candidate genes responsible for differences in angiogenic response. The corneal micropocket neovascularization assay was performed on 42 different inbred mouse strains using basic fibroblast growth factor (bFGF) pellets. We performed a genome-wide association study utilizing efficient mixed-model association (EMMA) mapping using the induced vessel area from all strains. Our analysis yielded five loci with genome-wide significance on chromosomes 4, 8, 11, 15 and 16. We further refined the mapping on chromosome 4 within a haplotype block containing multiple candidate genes. These genes were evaluated by expression analysis in corneas of various inbred strains and in vitro functional assays in human microvascular endothelial cells (HMVECs). Of these, we found the expression of peptidyl arginine deiminase type II (Padi2), known to be involved in metabolic pathways, to have a strong correlation with a haplotype shared by multiple high angiogenic strains. In addition, inhibition of Padi2 demonstrated a dosage-dependent effect in HMVECs. To investigate its role in vivo, we knocked down Padi2 in transgenic kdrl:zsGreen zebrafish embryos using morpholinos. These embryos had disrupted vessel formation compared to control siblings. The impaired vascular pattern was partially rescued by human PADI2 mRNA, providing evidence for the specificity of the morphant phenotype. Taken together, our study is the first to indicate the potential role of Padi2 as an angiogenesis-regulating gene. The characterization of Padi2 and other genes in associated pathways may provide new understanding of angiogenesis regulation and novel targets for diagnosis and treatment of a wide variety of angiogenesis-dependent diseases.
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Affiliation(s)
- Mehrdad Khajavi
- The Vascular Biology Program and Department of Surgery, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Yi Zhou
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Amy E. Birsner
- The Vascular Biology Program and Department of Surgery, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Lauren Bazinet
- The Vascular Biology Program and Department of Surgery, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Amanda Rosa Di Sant
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Alex J. Schiffer
- The Vascular Biology Program and Department of Surgery, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Michael S. Rogers
- The Vascular Biology Program and Department of Surgery, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Subrahmanian Tarakkad Krishnaji
- The Vascular Biology Program and Department of Surgery, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Bella Hu
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Vy Nguyen
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Leonard Zon
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Boston, Massachusetts, United States of America
| | - Robert J. D’Amato
- The Vascular Biology Program and Department of Surgery, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail:
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7
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Zhong Z, Marcel TC, Hartmann FE, Ma X, Plissonneau C, Zala M, Ducasse A, Confais J, Compain J, Lapalu N, Amselem J, McDonald BA, Croll D, Palma-Guerrero J. A small secreted protein in Zymoseptoria tritici is responsible for avirulence on wheat cultivars carrying the Stb6 resistance gene. THE NEW PHYTOLOGIST 2017; 214:619-631. [PMID: 28164301 DOI: 10.1111/nph.14434] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 12/09/2016] [Indexed: 05/06/2023]
Abstract
Zymoseptoria tritici is the causal agent of Septoria tritici blotch, a major pathogen of wheat globally and the most damaging pathogen of wheat in Europe. A gene-for-gene (GFG) interaction between Z. tritici and wheat cultivars carrying the Stb6 resistance gene has been postulated for many years, but the genes have not been identified. We identified AvrStb6 by combining quantitative trait locus mapping in a cross between two Swiss strains with a genome-wide association study using a natural population of c. 100 strains from France. We functionally validated AvrStb6 using ectopic transformations. AvrStb6 encodes a small, cysteine-rich, secreted protein that produces an avirulence phenotype on wheat cultivars carrying the Stb6 resistance gene. We found 16 nonsynonymous single nucleotide polymorphisms among the tested strains, indicating that AvrStb6 is evolving very rapidly. AvrStb6 is located in a highly polymorphic subtelomeric region and is surrounded by transposable elements, which may facilitate its rapid evolution to overcome Stb6 resistance. AvrStb6 is the first avirulence gene to be functionally validated in Z. tritici, contributing to our understanding of avirulence in apoplastic pathogens and the mechanisms underlying GFG interactions between Z. tritici and wheat.
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Affiliation(s)
- Ziming Zhong
- Plant Pathology Group, ETH Zürich, Universitätstrasse 2, 8092, Zürich, Switzerland
| | - Thierry C Marcel
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, 78850, Thiverval-Grignon, France
| | - Fanny E Hartmann
- Plant Pathology Group, ETH Zürich, Universitätstrasse 2, 8092, Zürich, Switzerland
| | - Xin Ma
- Plant Pathology Group, ETH Zürich, Universitätstrasse 2, 8092, Zürich, Switzerland
| | - Clémence Plissonneau
- Plant Pathology Group, ETH Zürich, Universitätstrasse 2, 8092, Zürich, Switzerland
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, 78850, Thiverval-Grignon, France
| | - Marcello Zala
- Plant Pathology Group, ETH Zürich, Universitätstrasse 2, 8092, Zürich, Switzerland
| | - Aurélie Ducasse
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, 78850, Thiverval-Grignon, France
| | - Johann Confais
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, 78850, Thiverval-Grignon, France
| | - Jérôme Compain
- UR URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Nicolas Lapalu
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, 78850, Thiverval-Grignon, France
- UR URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Joëlle Amselem
- UR URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Bruce A McDonald
- Plant Pathology Group, ETH Zürich, Universitätstrasse 2, 8092, Zürich, Switzerland
| | - Daniel Croll
- Plant Pathology Group, ETH Zürich, Universitätstrasse 2, 8092, Zürich, Switzerland
- Laboratory of Evolutionary Genetics, University of Neuchâtel Institute of Biology Rue Emile-Argand 11, CH-2000, Neuchâtel, Switzerland
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8
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Emebiri LC, Tan MK, El-Bouhssini M, Wildman O, Jighly A, Tadesse W, Ogbonnaya FC. QTL mapping identifies a major locus for resistance in wheat to Sunn pest (Eurygaster integriceps) feeding at the vegetative growth stage. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:309-318. [PMID: 27744491 DOI: 10.1007/s00122-016-2812-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 10/08/2016] [Indexed: 06/06/2023]
Abstract
This research provides the first report of a major locus controlling wheat resistance to Sunn pest. It developed and validated SNP markers that will be useful for marker-assisted selection. Sunn pest (Eurygaster integriceps Puton) is the most destructive insect pest of bread wheat and durum wheat in West and Central Asia and East Europe. Breeding for resistance at the vegetative stage of growth is vital in reducing the damage caused by overwintered adult populations that feed on shoot and leaves of seedlings, and in reducing the next generation of pest populations (nymphs and adults), which can cause damage to grain quality by feeding on spikes. In the present study, two doubled haploid (DH) populations involving resistant landraces from Afghanistan were genotyped with the 90k SNP iSelect assay and candidate gene-based KASP markers. The DH lines and parents were phenotyped for resistance to Sunn pest feeding, using artificial infestation cages at Terbol station, in Lebanon, over three years. Quantitative trait locus (QTL) analysis identified a single major locus on chromosome 4BS in the two populations, with the resistance allele derived from the landrace accessions, IG139431 and IG139883. The QTL explained a maximum of 42 % of the phenotypic variation in the Cham6 × IG139431 and 56 % in the Cham6 × IG139883 populations. SNP markers closest to the QTL showed high similarity to rice genes that putatively encode proteins for defense response to herbivory and wounding. The markers were validated in a large, unrelated population of parental wheat genotypes. All wheat lines carrying the 'C-G' haplotype at the identified SNPs were resistant, suggesting that selection based on a haplotype of favourable alleles would be effective in predicting resistance status of unknown genotypes.
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Affiliation(s)
- L C Emebiri
- Graham Centre for Agricultural Innovation (NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga, NSW, 2650, Australia.
| | - M-K Tan
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Rd, Menangle NSW, Menangle, NSW, 2568, Australia
| | - M El-Bouhssini
- The International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat Instituts, P. O. Box 6299, Rabat, Morocco
| | - O Wildman
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Rd, Menangle NSW, Menangle, NSW, 2568, Australia
| | - A Jighly
- The International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat Instituts, P. O. Box 6299, Rabat, Morocco
| | - W Tadesse
- The International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat Instituts, P. O. Box 6299, Rabat, Morocco
| | - F C Ogbonnaya
- The International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat Instituts, P. O. Box 6299, Rabat, Morocco
- Grains Research and Development Corporation, P. O. Box 5367, Kingston, ACT, 2604, Australia
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Klein AD. Modeling diseases in multiple mouse strains for precision medicine studies. Physiol Genomics 2017; 49:177-179. [PMID: 28130429 DOI: 10.1152/physiolgenomics.00123.2016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 01/13/2017] [Accepted: 01/13/2017] [Indexed: 12/12/2022] Open
Abstract
The genetic basis of the phenotypic variability observed in patients can be studied in mice by generating disease models through genetic or chemical interventions in many genetic backgrounds where the clinical phenotypes can be assessed and used for genome-wide association studies (GWAS). This is particularly relevant for rare disorders, where patients sharing identical mutations can present with a wide variety of symptoms, but there are not enough number of patients to ensure statistical power of GWAS. Inbred strains are homozygous for each loci, and their single nucleotide polymorphisms catalogs are known and freely available, facilitating the bioinformatics and reducing the costs of the study, since it is not required to genotype every mouse. This kind of approach can be applied to pharmacogenomics studies as well.
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Affiliation(s)
- Andrés D Klein
- Telethon Institute of Genetics and Medicine, Pozzuoli (NA), Italy
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10
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Shirali M, Pong-Wong R, Navarro P, Knott S, Hayward C, Vitart V, Rudan I, Campbell H, Hastie ND, Wright AF, Haley CS. Regional heritability mapping method helps explain missing heritability of blood lipid traits in isolated populations. Heredity (Edinb) 2015; 116:333-8. [PMID: 26696135 PMCID: PMC4751621 DOI: 10.1038/hdy.2015.107] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 10/23/2015] [Accepted: 10/26/2015] [Indexed: 11/21/2022] Open
Abstract
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 were compared with large meta-analyses of these traits for validation. Using RHM, two significant regions affecting HDL on chromosomes 15 and 16 and one affecting LDL on chromosome 19 were identified. These regions covered the most significant SNPs associated with HDL and LDL from the meta-analysis. The chromosome 19 region was identified in our data despite the fact that the most significant SNP in the meta-analysis (or any SNP tagging it) was not genotyped in our SNP array. The SSGWAS identified one SNP associated with HDL on chromosome 16 (the top meta-analysis SNP) and one on chromosome 10 (not reported by RHM or in the meta-analysis and hence possibly a false positive association). The results further confirm that RHM can have better power than SSGWAS in detecting causal regions including regions containing crucial ungenotyped variants. This study suggests that RHM can be a useful tool to explain some of the ‘missing heritability' of complex trait variation.
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Affiliation(s)
- M Shirali
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - R Pong-Wong
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, UK
| | - P Navarro
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - S Knott
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - C Hayward
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - V Vitart
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - I Rudan
- Croatian Centre for Global Health, Faculty of Medicine, University of Split, Split, Croatia.,Centre for Population Health sciences, University of Edinburgh, Edinburgh, UK
| | - H Campbell
- Centre for Population Health sciences, University of Edinburgh, Edinburgh, UK
| | - N D Hastie
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - A F Wright
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - C S Haley
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.,Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, UK
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11
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Wang Y, Hao C, Zheng J, Ge H, Zhou Y, Ma Z, Zhang X. A haplotype block associated with thousand-kernel weight on chromosome 5DS in common wheat (Triticum aestivum L.). JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2015; 57:662-672. [PMID: 25318826 DOI: 10.1111/jipb.12294] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2014] [Accepted: 10/09/2014] [Indexed: 06/04/2023]
Abstract
Spike number per unit area, number of grains per spike, and thousand-kernel weight (TKW) are important yield components for wheat (Triticum aestivum L.). TKW has the highest heritability among the three components. We validated 27 simple sequence repeat (SSR) loci associated with TKW in an F(2:5) breeding population grown in four environments. A cfd7(8265bp) marker on chromosome 5DS showed the strongest association with TKW and had a significantly positive effect on TKW compared to allele cfd7(8259bp), with mean increases of 5.17, 3.63, 4.11, and 5.16 g in the four environments. Markers cfd67 and cfd40 flanking cfd78 also showed significantly positive associations with TKW with increases of 5.11, 3.29, 4.31, and 4.50 g for cfd67(205), and 4.98, 3.49, 4.06, and 4.84 g for cfd40(187) compared with cfd67(203) and cfd40(190) in the four environments, respectively. A major quantitative trait locus for TKW spanning 2.94 cM on chromosome 5DS was detected by association mapping. Strong linkage disequilibrium (LD) (r(2) > 0.2) was detected among the three linked markers, which formed three haplotype blocks in the F(2:5) breeding population. Mean TKW differences between HapB-I and HapB-II were 5.80, 4.41, 4.02, and 5.06 g in the four environments, respectively. Moreover, significant LD was detected only between cfd78 and cfd67 and between cfd67 and cfd40 in a germplasm collection. This study provides a base for cloning genes related to TKW on chromosome 5DS.
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Affiliation(s)
- Yuquan Wang
- Crop Genomics and Bioinformatics Center and National Key Lab of Crop Genetics and Germplasm Enhancement, College of Agricultural Sciences, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture/Institute of Crop Science, the Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chenyang Hao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture/Institute of Crop Science, the Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jun Zheng
- Crop Genomics and Bioinformatics Center and National Key Lab of Crop Genetics and Germplasm Enhancement, College of Agricultural Sciences, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture/Institute of Crop Science, the Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hongmei Ge
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture/Institute of Crop Science, the Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yang Zhou
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture/Institute of Crop Science, the Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhengqiang Ma
- Crop Genomics and Bioinformatics Center and National Key Lab of Crop Genetics and Germplasm Enhancement, College of Agricultural Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xueyong Zhang
- Crop Genomics and Bioinformatics Center and National Key Lab of Crop Genetics and Germplasm Enhancement, College of Agricultural Sciences, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture/Institute of Crop Science, the Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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12
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Li C, Zuo W, Tong X, Hu H, Qiao L, Song J, Xiong G, Gao R, Dai F, Lu C. A composite method for mapping quantitative trait loci without interference of female achiasmatic and gender effects in silkworm,Bombyx mori. Anim Genet 2015; 46:426-32. [DOI: 10.1111/age.12311] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/15/2015] [Indexed: 11/27/2022]
Affiliation(s)
- C. Li
- State Key Laboratory of Silkworm Genome Biology; Southwest University; Chongqi-ng 400716 China
- Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry; Southwest University; Chongqing 400716 China
| | - W. Zuo
- State Key Laboratory of Silkworm Genome Biology; Southwest University; Chongqi-ng 400716 China
- Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry; Southwest University; Chongqing 400716 China
| | - X. Tong
- State Key Laboratory of Silkworm Genome Biology; Southwest University; Chongqi-ng 400716 China
- Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry; Southwest University; Chongqing 400716 China
| | - H. Hu
- State Key Laboratory of Silkworm Genome Biology; Southwest University; Chongqi-ng 400716 China
- Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry; Southwest University; Chongqing 400716 China
| | - L. Qiao
- Institute of Entomology and Molecular Biology; College of Life Sciences; Chongqing Normal University; Chongqing 401331 China
| | - J. Song
- State Key Laboratory of Silkworm Genome Biology; Southwest University; Chongqi-ng 400716 China
- Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry; Southwest University; Chongqing 400716 China
| | - G. Xiong
- State Key Laboratory of Silkworm Genome Biology; Southwest University; Chongqi-ng 400716 China
- Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry; Southwest University; Chongqing 400716 China
| | - R. Gao
- State Key Laboratory of Silkworm Genome Biology; Southwest University; Chongqi-ng 400716 China
- Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry; Southwest University; Chongqing 400716 China
| | - F. Dai
- State Key Laboratory of Silkworm Genome Biology; Southwest University; Chongqi-ng 400716 China
- Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry; Southwest University; Chongqing 400716 China
| | - C. Lu
- State Key Laboratory of Silkworm Genome Biology; Southwest University; Chongqi-ng 400716 China
- Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry; Southwest University; Chongqing 400716 China
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13
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Wang L, Jiao Y, Cao Y, Liu G, Wang Y, Gu W. Limitation of number of strains and persistence of false positive loci in QTL mapping using recombinant inbred strains. PLoS One 2014; 9:e102307. [PMID: 25032693 PMCID: PMC4102522 DOI: 10.1371/journal.pone.0102307] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 06/17/2014] [Indexed: 01/21/2023] Open
Abstract
While the identification of causal genes of quantitative trait loci (QTL) remains a difficult problem in the post-genome era, the number of QTL continues to accumulate, mainly identified using the recombinant inbred (RI) strains. Over the last decade, hundreds of publications have reported nearly a thousand QTL identified from RI strains. We hypothesized that the inaccuracy of most of these QTL makes it difficult to identify causal genes. Using data from RI strains derived from C57BL/6J (B6) X DBA/2J (D2), we tested the possibility of detection of reliable QTL with different numbers of strains in the same trait in five different traits. Our results indicated that studies using RI strains of less than 30 in general have a higher probability of failing to detect reliable QTL. Errors in many studies could include false positive loci, switches between QTL with small and major effects, and missing the real major loci. The similar data was obtained from a RI strain population derived from a different pair of parents and a RI strain population of rat. Thus, thousands of reported QTL from studies of RI strains may need to be double-checked for accuracy before proceeding to causal gene identification.
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Affiliation(s)
- Lishi Wang
- Department of Orthopedic Surgery and BME, Campbell-Clinic, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
- Department of Basic Medical Research, Inner Mongolia Medical University, Inner Mongolia, China
| | - Yan Jiao
- Department of Orthopedic Surgery and BME, Campbell-Clinic, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
- Mudanjiang Medical College, Mudanjiang, PR China
| | - Yanhong Cao
- Department of Orthopedic Surgery and BME, Campbell-Clinic, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
- Institute of Kaschin-Beck Disease, Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University; Key Laboratory of Etiologic Epidemiology, Education Bureau of Heilongjiang Province and Ministry of Health (23618104), Harbin, China
| | - Gaifen Liu
- Department. of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yongjun Wang
- Department. of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Weikuan Gu
- Department of Orthopedic Surgery and BME, Campbell-Clinic, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
- * E-mail:
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14
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Jing S, Zhang L, Ma Y, Liu B, Zhao Y, Yu H, Zhou X, Qin R, Zhu L, He G. Genome-wide mapping of virulence in brown planthopper identifies loci that break down host plant resistance. PLoS One 2014; 9:e98911. [PMID: 24911169 PMCID: PMC4049697 DOI: 10.1371/journal.pone.0098911] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 04/14/2014] [Indexed: 12/26/2022] Open
Abstract
Insects and plants have coexisted for over 350 million years and their interactions have affected ecosystems and agricultural practices worldwide. Variation in herbivorous insects' virulence to circumvent host resistance has been extensively documented. However, despite decades of investigation, the genetic foundations of virulence are currently unknown. The brown planthopper (Nilaparvata lugens) is the most destructive rice (Oryza sativa) pest in the world. The identification of the resistance gene Bph1 and its introduction in commercial rice varieties prompted the emergence of a new virulent brown planthopper biotype that was able to break the resistance conferred by Bph1. In this study, we aimed to construct a high density linkage map for the brown planthopper and identify the loci responsible for its virulence in order to determine their genetic architecture. Based on genotyping data for hundreds of molecular markers in three mapping populations, we constructed the most comprehensive linkage map available for this species, covering 96.6% of its genome. Fifteen chromosomes were anchored with 124 gene-specific markers. Using genome-wide scanning and interval mapping, the Qhp7 locus that governs preference for Bph1 plants was mapped to a 0.1 cM region of chromosome 7. In addition, two major QTLs that govern the rate of insect growth on resistant rice plants were identified on chromosomes 5 (Qgr5) and 14 (Qgr14). This is the first study to successfully locate virulence in the genome of this important agricultural insect by marker-based genetic mapping. Our results show that the virulence which overcomes the resistance conferred by Bph1 is controlled by a few major genes and that the components of virulence originate from independent genetic characters. The isolation of these loci will enable the elucidation of the molecular mechanisms underpinning the rice-brown planthopper interaction and facilitate the development of durable approaches for controlling this most destructive agricultural insect.
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Affiliation(s)
- Shengli Jing
- State Key Laboratory of Hybrid Rice, College of Life Science, Wuhan University, Wuhan, China
| | - Lei Zhang
- Engineering Research Center of Protection and Utilization for Biological Resources in Minority Regions, College of Life Science, South-Central University for Nationalities, Wuhan, China
| | - Yinhua Ma
- State Key Laboratory of Hybrid Rice, College of Life Science, Wuhan University, Wuhan, China
| | - Bingfang Liu
- State Key Laboratory of Hybrid Rice, College of Life Science, Wuhan University, Wuhan, China
| | - Yan Zhao
- State Key Laboratory of Hybrid Rice, College of Life Science, Wuhan University, Wuhan, China
| | - Hangjin Yu
- State Key Laboratory of Hybrid Rice, College of Life Science, Wuhan University, Wuhan, China
| | - Xi Zhou
- State Key Laboratory of Hybrid Rice, College of Life Science, Wuhan University, Wuhan, China
| | - Rui Qin
- Engineering Research Center of Protection and Utilization for Biological Resources in Minority Regions, College of Life Science, South-Central University for Nationalities, Wuhan, China
| | - Lili Zhu
- State Key Laboratory of Hybrid Rice, College of Life Science, Wuhan University, Wuhan, China
| | - Guangcun He
- State Key Laboratory of Hybrid Rice, College of Life Science, Wuhan University, Wuhan, China
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15
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Du Q, Xu B, Pan W, Gong C, Wang Q, Tian J, Li B, Zhang D. Allelic variation in a cellulose synthase gene (PtoCesA4) associated with growth and wood properties in Populus tomentosa. G3 (BETHESDA, MD.) 2013; 3:2069-84. [PMID: 24048648 PMCID: PMC3815066 DOI: 10.1534/g3.113.007724] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 09/11/2013] [Indexed: 12/12/2022]
Abstract
Lignocellulosic biomass from trees provides a renewable feedstock for biofuels, lumber, pulp, paper, and other uses. Dissecting the mechanism underlying natural variation of the complex traits controlling growth and lignocellulose biosynthesis in trees can enable marker-assisted breeding to improve wood quality and yield. Here, we combined linkage disequilibrium (LD)-based association analysis with traditional linkage analysis to detect the genetic effect of a Populus tomentosa cellulose synthase gene, PtoCesA4. PtoCesA4 is strongly expressed in developing xylem and leaves. Nucleotide diversity and LD in PtoCesA4, sampled from the P. tomentosa natural distribution, revealed that PtoCesA4 harbors high single nucleotide polymorphism (SNP) diversity (πT = 0.0080 and θw = 0.0098) and low LD (r(2) ≥ 0.1, within 1400 bp), demonstrating that the potential of a candidate-gene-based LD approach in understanding the molecular basis underlying quantitative variation in this species. By combining single SNP, multi-SNP, and haplotype-based associations in an association population of 460 individuals with single SNP linkage analysis in a family-based linkage populations (1200 individuals), we identified three strong associations (false discovery rate Q < 0.05) in both populations. These include two nonsynonymous markers (SNP49 associated with α-cellulose content and SNP59 associated with fiber width) and a noncoding marker (SNP18 associated with α-cellulose content). Variation in RNA transcript abundance among genotypic classes of SNP49 was confirmed in these two populations. Therefore, combining different methods allowed us to examine functional PtoCesA4 allelic variation underlying natural variation in complex quantitative traits related to growth and lignocellulosic biosynthesis.
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Affiliation(s)
- Qingzhang Du
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, People’s Republic of China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, People’s Republic of China
| | - Baohua Xu
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, People’s Republic of China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, People’s Republic of China
| | - Wei Pan
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, People’s Republic of China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, People’s Republic of China
| | - Chenrui Gong
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, People’s Republic of China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, People’s Republic of China
| | - Qingshi Wang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, People’s Republic of China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, People’s Republic of China
| | - Jiaxing Tian
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, People’s Republic of China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, People’s Republic of China
| | - Bailian Li
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, People’s Republic of China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, People’s Republic of China
- Department of Forestry, North Carolina State University, Raleigh, North Carolina 27695-8203
| | - Deqiang Zhang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, People’s Republic of China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, People’s Republic of China
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Iguchi M, Osanai M, Hayashi Y, Koentgen F, Lee GH. The error-prone DNA polymerase ι provides quantitative resistance to lung tumorigenesis and mutagenesis in mice. Oncogene 2013; 33:3612-7. [DOI: 10.1038/onc.2013.331] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 05/19/2013] [Accepted: 06/25/2013] [Indexed: 12/24/2022]
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17
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Paun A, Lemay AM, Tomko TG, Haston CK. Association Analysis Reveals Genetic Variation Altering Bleomycin-Induced Pulmonary Fibrosis in Mice. Am J Respir Cell Mol Biol 2013; 48:330-6. [DOI: 10.1165/rcmb.2012-0078oc] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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18
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Genomic and genome-wide association of susceptibility to radiation-induced fibrotic lung disease in mice. Radiother Oncol 2012; 105:350-7. [DOI: 10.1016/j.radonc.2012.08.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Revised: 07/10/2012] [Accepted: 08/11/2012] [Indexed: 12/13/2022]
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Abstract
Genome-wide association studies (GWASs) have transformed the field of human genetics and have led to the discovery of hundreds of genes that are implicated in human disease. The technological advances that drove this revolution are now poised to transform genetic studies in model organisms, including mice. However, the design of GWASs in mouse strains is fundamentally different from the design of human GWASs, creating new challenges and opportunities. This Review gives an overview of the novel study designs for mouse GWASs, which dramatically improve both the statistical power and resolution compared to classical gene-mapping approaches.
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Affiliation(s)
- Jonathan Flint
- The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
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20
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Stearns TM, Cario CL, Savage HS, Sundberg JP, Paigen B, Berndt A. Early gene expression differences in inbred mouse strains with susceptibility to pulmonary adenomas. Exp Mol Pathol 2012; 93:455-61. [PMID: 23026400 DOI: 10.1016/j.yexmp.2012.09.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Accepted: 09/20/2012] [Indexed: 10/27/2022]
Abstract
Lung cancer is the most common cause of cancer-related deaths in both men and women, and effective preventatives are rare due to the difficulty of early detection. Specific gene expression signatures have been identified in individuals that already developed lung cancer. To identify if gene expression differences could be detected in individuals before the onset of the disease, we obtained lung tissues for microarray analysis from young, healthy mice of 9 inbred strains with known differences in their susceptibility to spontaneous pulmonary adenomas when aged. We found that the most common differentially expressed genes among all possible 36 strain comparisons showed significant associations with cancer- and inflammation-related processes. Significant expression differences between susceptible and resistant strains were detected for Aldh3a1, Cxcr1 and 7, Dpt, and Nptx1-genes with known cancer-related functions, and Cd209, Cxcr1 and 7, and Plag2g1b-genes with known inflammatory-related functions. Whereas Aldh3a1, Cd209, Dpt, and Pla2g1b had increased expression, Cxcr1 and 7, and Nptx1 had decreased expression in strains susceptible to pulmonary adenomas. Thus, our study shows that expression differences between susceptible and resistant strains can be detected in young and healthy mice without manifestation of pulmonary adenomas and, thus, may provide an opportunity of early detection. Finally, the identified genes have previously been reported for human non-small cell lung cancer suggesting that molecular pathways may be shared between these two cancer types.
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Courtney SM, Massett MP. Identification of exercise capacity QTL using association mapping in inbred mice. Physiol Genomics 2012; 44:948-55. [PMID: 22911454 DOI: 10.1152/physiolgenomics.00051.2012] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
There are large interindividual differences in exercise capacity. It is well established that there is a genetic basis for these differences. However, the genetic factors underlying this variation are undefined. Therefore, the purpose of this study was to identify novel putative quantitative trait loci (QTL) for exercise capacity by measuring exercise capacity in inbred mice and performing genome-wide association mapping. Exercise capacity, defined as run time and work, was assessed in male mice (n = 6) from 34 strains of classical and wild-derived inbred mice performing a graded treadmill test. Genome-wide association mapping was performed with an efficient mixed-model association (EMMA) algorithm to identify QTL. Exercise capacity was significantly different across strains. Run time varied by 2.7-fold between the highest running strain (C58/J) and the lowest running strain (A/J). These same strains showed a 16.5-fold difference in work. Significant associations were identified for exercise time on chromosomes 1, 2, 7, 11, and 13. The QTL interval on chromosome 2 (~168 Mb) contains one gene, Nfatc2, and overlaps with a suggestive QTL for training responsiveness in humans. These results provide phenotype data on the widest range of inbred strains tested thus far and indicate that genetic background significantly influences exercise capacity. Furthermore, the novel QTLs identified in the current study provide new targets for investigating the underlying mechanisms for variation in exercise capacity.
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Affiliation(s)
- Sean M Courtney
- Department of Health and Kinesiology, Texas A&M University, College Station, Texas 77843-4243, USA
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Abstract
The Collaborative Cross Consortium reports here on the development of a unique genetic resource population. The Collaborative Cross (CC) is a multiparental recombinant inbred panel derived from eight laboratory mouse inbred strains. Breeding of the CC lines was initiated at multiple international sites using mice from The Jackson Laboratory. Currently, this innovative project is breeding independent CC lines at the University of North Carolina (UNC), at Tel Aviv University (TAU), and at Geniad in Western Australia (GND). These institutions aim to make publicly available the completed CC lines and their genotypes and sequence information. We genotyped, and report here, results from 458 extant lines from UNC, TAU, and GND using a custom genotyping array with 7500 SNPs designed to be maximally informative in the CC and used a novel algorithm to infer inherited haplotypes directly from hybridization intensity patterns. We identified lines with breeding errors and cousin lines generated by splitting incipient lines into two or more cousin lines at early generations of inbreeding. We then characterized the genome architecture of 350 genetically independent CC lines. Results showed that founder haplotypes are inherited at the expected frequency, although we also consistently observed highly significant transmission ratio distortion at specific loci across all three populations. On chromosome 2, there is significant overrepresentation of WSB/EiJ alleles, and on chromosome X, there is a large deficit of CC lines with CAST/EiJ alleles. Linkage disequilibrium decays as expected and we saw no evidence of gametic disequilibrium in the CC population as a whole or in random subsets of the population. Gametic equilibrium in the CC population is in marked contrast to the gametic disequilibrium present in a large panel of classical inbred strains. Finally, we discuss access to the CC population and to the associated raw data describing the genetic structure of individual lines. Integration of rich phenotypic and genomic data over time and across a wide variety of fields will be vital to delivering on one of the key attributes of the CC, a common genetic reference platform for identifying causative variants and genetic networks determining traits in mammals.
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Turner TL, Miller PM. Investigating natural variation in Drosophila courtship song by the evolve and resequence approach. Genetics 2012; 191:633-42. [PMID: 22466043 PMCID: PMC3374323 DOI: 10.1534/genetics.112.139337] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Accepted: 03/18/2012] [Indexed: 12/13/2022] Open
Abstract
A primary goal of population genetics is to determine the genetic basis of natural trait variation. We could significantly advance this goal by developing comprehensive genome-wide approaches to link genotype and phenotype in model organisms. Here we combine artificial selection with population-based resequencing to investigate the genetic basis of variation in the interpulse interval (IPI) of Drosophila melanogaster courtship song. We performed divergent selection on replicate populations for only 14 generations, but had considerable power to differentiate alleles that evolved due to selection from those that evolved stochastically. We identified a large number of variants that changed frequency in response to selection for this simple behavior, and they are highly underrepresented on the X chromosome. Though our power was adequate using this experimental technique, the ability to differentiate causal variants from those affected by linked selection requires further development.
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Affiliation(s)
- Thomas L Turner
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, California 93106, USA.
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Increasing association mapping power and resolution in mouse genetic studies through the use of meta-analysis for structured populations. Genetics 2012; 191:959-67. [PMID: 22505625 DOI: 10.1534/genetics.112.140277] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Genetic studies in mouse models have played an integral role in the discovery of the mechanisms underlying many human diseases. The primary mode of discovery has been the application of linkage analysis to mouse crosses. This approach results in high power to identify regions that affect traits, but in low resolution, making it difficult to identify the precise genomic location harboring the causal variant. Recently, a panel of mice referred to as the hybrid mouse diversity panel (HMDP) has been developed to overcome this problem. However, power in this panel is limited by the availability of inbred strains. Previous studies have suggested combining results across multiple panels as a means to increase power, but the methods employed may not be well suited to structured populations, such as the HMDP. In this article, we introduce a meta-analysis-based method that may be used to combine HMDP studies with F2 cross studies to gain power, while increasing resolution. Due to the drastically different genetic structure of F2s and the HMDP, the best way to combine two studies for a given SNP depends on the strain distribution pattern in each study. We show that combining results, while accounting for these patterns, leads to increased power and resolution. Using our method to map bone mineral density, we find that two previously implicated loci are replicated with increased significance and that the size of the associated is decreased. We also map HDL cholesterol and show a dramatic increase in the significance of a previously identified result.
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Abstract
In a previous study, we identified a candidate fragment length polymorphism associated with flowering time variation after seven generations of selection for flowering time, starting from the maize inbred line F252. Here, we characterized the candidate region and identified underlying polymorphisms. Then, we combined QTL mapping, association mapping, and developmental characterization to dissect the genetic mechanisms responsible for the phenotypic variation. The candidate region contained the Eukaryotic Initiation Factor (eIF-4A) and revealed a high level of sequence and structural variation beyond the 3'-UTR of eIF-4A, including several insertions of truncated transposable elements. Using a biallelic single-nucleotide polymorphism (SNP) (C/T) in the candidate region, we confirmed its association with flowering time variation in a panel of 317 maize inbred lines. However, while the T allele was correlated with late flowering time within the F252 genetic background, it was correlated with early flowering time in the association panel with pervasive interactions between allelic variation and the genetic background, pointing to underlying epistasis. We also detected pleiotropic effects of the candidate polymorphism on various traits including flowering time, plant height, and leaf number. Finally, we were able to break down the correlation between flowering time and leaf number in the progeny of a heterozygote (C/T) within the F252 background consistent with causal loci in linkage disequilibrium. We therefore propose that both a cluster of tightly linked genes and epistasis contribute to the phenotypic variation for flowering time.
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Hollander M, Zhou X, Maier CR, Patterson AD, Ding X, Dennis PA. A Cyp2a polymorphism predicts susceptibility to NNK-induced lung tumorigenesis in mice. Carcinogenesis 2011; 32:1279-84. [PMID: 21625009 PMCID: PMC3149208 DOI: 10.1093/carcin/bgr097] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Revised: 04/21/2011] [Accepted: 05/17/2011] [Indexed: 02/06/2023] Open
Abstract
Lung tumors from smokers as well as lung tumors from mice exposed to tobacco carcinogens such as 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK), often carry mutations in K-ras, which activates downstream-signaling pathways such as PI3K/AKT/mTOR pathway. Mice with genetic deletion of one of three isoforms of AKT were used to investigate the role of AKT in mutant K-ras-induced lung tumorigenesis in mice. Although deletion of Akt1 or Akt2 decreased NNK-induced lung tumor formation by 90%, deletion of Akt2 failed to decrease lung tumorigenesis in two other mouse models driven by mutant K-ras. Genetic mapping showed that Akt2 was tightly linked to the cytochrome P450 Cyp2a locus on chromosome 7. Consequently, targeted deletion of Akt2 created linkage to a strain-specific Cyp2a5 polymorphism that decreased activation of NNK in vitro. Mice with this Cyp2a5 polymorphism had decreased NNK-induced DNA adduct formation in vivo and decreased NNK-induced lung tumorigenesis. These studies support human epidemiological studies linking CYP2A polymorphisms with lung cancer risk in humans and highlight the need to confirm phenotypes of genetically engineered mice in multiple mouse strains.
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Affiliation(s)
| | - Xin Zhou
- Wadsworth Center, New York State Department of Health and School of Public Health, State University of New York at Albany, Albany, NY 12201, USA
| | | | - Andrew D. Patterson
- Laboratory of Metabolism, National Cancer Institute, Bethesda, MD 20892, USA
| | - Xinxin Ding
- Wadsworth Center, New York State Department of Health and School of Public Health, State University of New York at Albany, Albany, NY 12201, USA
| | - Phillip A. Dennis
- To whom correspondence should be addressed. Tel: 301-496-0929 Fax: 301-435-4345
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Berndt A, Cario CL, Silva KA, Kennedy VE, Harrison DE, Paigen B, Sundberg JP. Identification of fat4 and tsc22d1 as novel candidate genes for spontaneous pulmonary adenomas. Cancer Res 2011; 71:5779-91. [PMID: 21764761 DOI: 10.1158/0008-5472.can-11-1418] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Genetic influences that underlie spontaneous lung oncogenesis are poorly understood. The objective of this study was to determine the genetic influences on spontaneous pulmonary adenoma frequency and severity in 28 strains of mice as part of a large-scale aging study conducted at the Jackson Aging Center (http://agingmice.jax.org/). Genome-wide association studies were conducted in these strains with both low-density (132,000) and high-density (4,000,000) panel of single-nucleotide polymorphisms (SNP). Our analysis revealed that adenomas were relatively less frequent and less severe in females than males, and that loci implicated in frequency and severity were often different between male and female mice. While some of the significant loci identified mapped to genomic locations known to be responsible for carcinogen-induced cancers (e.g., Pas1), others were unique to our study. In particular, Fat4 was influential in males and Tsc22d1 was influential in females. SNPs implicated were predicted to alter amino acid sequence and change protein function. In summary, our results suggested that genetic influences that underlie pulmonary adenoma frequency are dependent on gender, and that Fat4 and Tsc22d1 are likely candidate genes to influence formation of spontaneous pulmonary adenoma in aging male and female mice, respectively.
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Affiliation(s)
- Annerose Berndt
- Berndt Laboratory, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.
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28
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Dougan M, Li D, Neuberg D, Mihm M, Googe P, Wong KK, Dranoff G. A dual role for the immune response in a mouse model of inflammation-associated lung cancer. J Clin Invest 2011; 121:2436-46. [PMID: 21537082 DOI: 10.1172/jci44796] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Accepted: 03/02/2011] [Indexed: 12/28/2022] Open
Abstract
Lung cancer is the leading cause of cancer death worldwide. Both principal factors known to cause lung cancer, cigarette smoke and asbestos, induce pulmonary inflammation, and pulmonary inflammation has recently been implicated in several murine models of lung cancer. To further investigate the role of inflammation in the development of lung cancer, we generated mice with combined loss of IFN-γ and the β-common cytokines GM-CSF and IL-3. These immunodeficient mice develop chronic pulmonary inflammation and lung tumors at a high frequency. Examination of the relationship between these tumors and their inflammatory microenvironment revealed a dual role for the immune system in tumor development. The inflammatory cytokine IL-6 promoted optimal tumor growth, yet wild-type mice rejected transplanted tumors through the induction of adaptive immunity. These findings suggest a model whereby cytokine deficiency leads to oncogenic inflammation that combines with defective antitumor immunity to promote lung tumor formation, representing a unique system for studying the role of the immune system in lung tumor development.
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Affiliation(s)
- Michael Dougan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
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29
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Radovanovic I, Mullick A, Gros P. Genetic control of susceptibility to infection with Candida albicans in mice. PLoS One 2011; 6:e18957. [PMID: 21533108 PMCID: PMC3080400 DOI: 10.1371/journal.pone.0018957] [Citation(s) in RCA: 29] [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: 12/14/2010] [Accepted: 03/15/2011] [Indexed: 12/17/2022] Open
Abstract
Candida albicans is an opportunistic pathogen that causes acute disseminated infections in immunocompromised hosts, representing an important cause of morbidity and mortality in these patients. To study the genetic control of susceptibility to disseminated C. albicans in mice, we phenotyped a group of 23 phylogenetically distant inbred strains for susceptibility to infection as measured by extent of fungal replication in the kidney 48 hours following infection. Susceptibility was strongly associated with the loss-of-function mutant complement component 5 (C5/Hc) allele, which is known to be inherited by approximately 40% of inbred strains. Our survey identified 2 discordant strains, AKR/J (C5-deficient, resistant) and SM/J (C5-sufficient, susceptible), suggesting that additional genetic effects may control response to systemic candidiasis in these strains. Haplotype association mapping in the 23 strains using high density SNP maps revealed several putative loci regulating the extent of C. albicans replication, amongst which the most significant were C5 (P value = 2.43×10(-11)) and a novel effect on distal chromosome 11 (P value = 7.63×10(-9)). Compared to other C5-deficient strains, infected AKR/J strain displays a reduced fungal burden in the brain, heart and kidney, and increased survival, concomitant with uniquely high levels of serum IFNγ. C5-independent genetic effects were further investigated by linkage analysis in an [A/JxAKR/J]F2 cross (n = 158) where the mutant Hc allele is fixed. These studies identified a chromosome 11 locus (Carg4, Candida albicans resistance gene 4; LOD = 4.59), and a chromosome 8 locus (Carg3; LOD = 3.95), both initially detected by haplotype association mapping. Alleles at both loci were inherited in a co-dominant manner. Our results verify the important effect of C5-deficiency in inbred mouse strains, and further identify two novel loci, Carg3 and Carg4, which regulate resistance to C. albicans infection in a C5-independent manner.
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Affiliation(s)
- Irena Radovanovic
- Biochemistry Department, McGill University, Montréal, Québec, Canada
| | - Alaka Mullick
- Biotechnology Research Institute, Montréal, Québec, Canada
| | - Philippe Gros
- Biochemistry Department, McGill University, Montréal, Québec, Canada
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Yan J, Warburton M, Crouch J. Association Mapping for Enhancing Maize ( Zea maysL.) Genetic Improvement. CROP SCIENCE 2011; 51:433-449. [PMID: 0 DOI: 10.2135/cropsci2010.04.0233] [Citation(s) in RCA: 181] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Affiliation(s)
- Jianbing Yan
- National Maize Improvement Center of China; China Agricultural Univ.; Beijing 100193 China
- International Maize and Wheat Improvement Center (CIMMYT); Apartado Postal 6-640 06600 Mexico DF Mexico
| | - Marilyn Warburton
- USDA-ARS; Corn Host Plant Resistance Research Unit; Box 9555 Mississippi State MS 39762
| | - Jonathan Crouch
- International Maize and Wheat Improvement Center (CIMMYT); Apartado Postal 6-640 06600 Mexico DF Mexico
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31
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Bergelson J, Roux F. Towards identifying genes underlying ecologically relevant traits in Arabidopsis thaliana. Nat Rev Genet 2010; 11:867-79. [PMID: 21085205 DOI: 10.1038/nrg2896] [Citation(s) in RCA: 210] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A major challenge in evolutionary biology and plant breeding is to identify the genetic basis of complex quantitative traits, including those that contribute to adaptive variation. Here we review the development of new methods and resources to fine-map intraspecific genetic variation that underlies natural phenotypic variation in plants. In particular, the analysis of 107 quantitative traits reported in the first genome-wide association mapping study in Arabidopsis thaliana sets the stage for an exciting time in our understanding of plant adaptation. We also argue for the need to place phenotype-genotype association studies in an ecological context if one is to predict the evolutionary trajectories of plant species.
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Affiliation(s)
- Joy Bergelson
- Department of Ecology and Evolution, University of Chicago, Illinois 60637, USA.
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32
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McLachlan S, Lee SM, Steele TM, Hawthorne PL, Zapala MA, Eskin E, Schork NJ, Anderson GJ, Vulpe CD. In silico QTL mapping of basal liver iron levels in inbred mouse strains. Physiol Genomics 2010; 43:136-47. [PMID: 21062905 DOI: 10.1152/physiolgenomics.00025.2010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Both iron deficiency and iron excess are detrimental in many organisms, and previous studies in both mice and humans suggest that genetic variation may influence iron status in mammals. However, these genetic factors are not well defined. To address this issue, we measured basal liver iron levels in 18 inbred strains of mice of both sexes on a defined iron diet and found ∼4-fold variation in liver iron in males (lowest 153 μg/g, highest 661 μg/g) and ∼3-fold variation in females (lowest 222 μg/g, highest 658 μg/g). We carried out a genome-wide association mapping to identify haplotypes underlying differences in liver iron and three other related traits (copper and zinc liver levels, and plasma diferric transferrin levels) in a subset of 14 inbred strains for which genotype information was available. We identified two putative quantitative trait loci (QTL) that contain genes with a known role in iron metabolism: Eif2ak1 and Igf2r. We also identified four putative QTL that reside in previously identified iron-related QTL and 22 novel putative QTL. The most promising putative QTL include a 0.22 Mb region on Chromosome 7 and a 0.32 Mb region on Chromosome 11 that both contain only one candidate gene, Adam12 and Gria1, respectively. Identified putative QTL are good candidates for further refinement and subsequent functional studies.
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Affiliation(s)
- Stela McLachlan
- Department of Nutritional Science and Toxicology, University of California Berkeley, Berkeley, CA 94720, USA
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Spach KM, Case LK, Noubade R, Petersen CB, McElvany B, Zalik N, Hickey WF, Blankenhorn EP, Teuscher C. Multiple linked quantitative trait loci within the Tmevd2/Eae3 interval control the severity of experimental allergic encephalomyelitis in DBA/2J mice. Genes Immun 2010; 11:649-59. [PMID: 20861860 PMCID: PMC2995842 DOI: 10.1038/gene.2010.40] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Theiler’s murine encephalomyelitis virus-induced demyelination (TMEVD) and experimental allergic encephalomyelitis (EAE) are the principal animal models of multiple sclerosis (MS). Previously we provided evidence that Tmevd2 and Eae3 may represent either a shared susceptibility locus or members of a gene complex controlling susceptibility to CNS inflammatory demyelinating disease. To explore the genetic relationship between Tmevd2 and Eae3, we generated a D2.C-Tmevd2 interval-specific congenic (ISC) line and three overlapping interval-specific recombinant congenic (ISRC) lines in which the Tmevd2 resistant allele from BALB/cByJ was introgressed onto the TMEVD-susceptible DBA/2J background. These mice, all H2d, were studied for susceptibility to EAE elicited by immunization with PLP180–199. Compared to DBA/2J mice, D2.C-Tmevd2 mice developed a significantly less severe clinical disease course and EAE pathology in the spinal cord, confirming the existence of Eae3 and its linkage to Tmevd2 in this strain combination. Compare to DBA/2J and D2.C-Tmevd2, all three ISRC lines exhibited clinical disease courses of intermediate severity. Neither differences in ex vivo antigen-specific cytokine nor proliferative responses uniquely cosegregated with differences in disease severity. These results indicate that multiple QTL within the Tmevd2/Eae3 interval influence EAE severity, one of which includes a homology region for a QTL found in MS by admixture mapping.
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Affiliation(s)
- K M Spach
- Department of Medicine, University of Vermont, Burlington, VT 05405, USA
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Abstract
A substantial genetic contribution underlies variation in baseline peripheral blood counts. We performed quantitative trait locus/loci analyses to identify chromosome regions harboring genes influencing red cell hemoglobin concentration using the cell hemoglobin concentration mean (CHCM), a directly measured parameter analogous to the mean cell hemoglobin concentration. Fourteen significant loci (gene symbols Chcmq1-Chcmq14) were detected. Seven of these influenced CHCM in a sex-specific fashion, and 2 showed significant interactive effects (epistasis). For quantitative trait locus/loci detected in multiple crosses, confidence intervals were narrowed using statistical and bioinformatic approaches. Two strong candidate genes emerged and were further analyzed: adult β-globin (Hbb) for Chcmq3 on Chr 7, and transferrin (Trf) for Chcmq2 on Chr 9. High and low allele parental strains in crosses detecting Chcmq3 segregate 100% with the known ancestral haplotype blocks, hemoglobin (Hb) diffuse (Hbb(d)) and Hb single (Hbb(s)), respectively. Hbb(d) consists of nonidentical major and minor polypeptides and exhibits an increased positive charge relative to Hbb(s) due to the net loss of 2 negative residues in the Hbb(dminor) polypeptide, resulting in a pI of 7.85 versus 7.13. Thus, as shown in human erythrocytes, positively charged Hbs are associated with cell dehydration and increased CHCM in mouse erythrocytes.
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35
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Berndt A, Leme AS, Williams LK, Von Smith R, Savage HS, Stearns TM, Tsaih SW, Shapiro SD, Peters LL, Paigen B, Svenson KL. Comparison of unrestrained plethysmography and forced oscillation for identifying genetic variability of airway responsiveness in inbred mice. Physiol Genomics 2010; 43:1-11. [PMID: 20823217 DOI: 10.1152/physiolgenomics.00108.2010] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Lung function detection in mice is currently most accurately measured by invasive techniques, which are costly, labor intensive, and terminal. This limits their use for large-scale or longitudinal studies. Noninvasive assays are often used instead, but their accuracy for measuring lung function parameters such as resistance and elastance has been questioned in studies involving small numbers of mouse strains. Here we compared parameters detected by two different methods using 29 inbred mouse strains: enhanced pause (Penh), detected by unrestrained plethysmography, and central airway resistance and lung elastance, detected by a forced oscillation technique. We further tested whether the phenotypic variations were determined by the same genomic location in genome-wide association studies using a linear mixed model algorithm. Penh, resistance, and elastance were measured in nonexposed mice or mice exposed to saline and increasing doses of aerosolized methacholine. Because Penh differed from airway resistance in several strains and because the peak genetic associations found for Penh, resistance, or elastance were located at different genomic regions, we conclude that using Penh as an indicator for lung function changes in high-throughput genetic studies (i.e., genome-wide association studies or quantitative trait locus studies) measures something fundamentally different than airway resistance and lung elastance.
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36
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Galvan A, Vorraro F, Cabrera WHK, Ribeiro OG, Pazzaglia S, Mancuso M, Zolin A, Milani S, Saran A, Ibañez OM, Dragani TA. Genetic heterogeneity of inflammatory response and skin tumorigenesis in phenotypically selected mouse lines. Cancer Lett 2010; 295:54-8. [DOI: 10.1016/j.canlet.2010.02.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2009] [Revised: 02/11/2010] [Accepted: 02/12/2010] [Indexed: 10/19/2022]
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Flint J. Mapping quantitative traits and strategies to find quantitative trait genes. Methods 2010; 53:163-74. [PMID: 20643209 PMCID: PMC3036800 DOI: 10.1016/j.ymeth.2010.07.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Accepted: 07/12/2010] [Indexed: 12/17/2022] Open
Abstract
In 1999 a meeting took place at the Jackson Laboratory, a large mouse research centre in Bar Harbor, Maine, to consider the value of systematically collecting phenotypes on inbred strains of mice (Paigen and Eppig (2000) [1]). The group concluded that cataloguing the extensive phenotypic diversity present among laboratory mice, and in particular providing the research community with data from cohorts of animals, phenotyped according to standardized protocols, was essential if we were to take advantage of the possibilities of mouse genetics. Beginning with the collection of basic physiological, biochemical and behavioral data on nine commonly used inbred strains, the project has expanded so that by the beginning of 2010 data for 178 strains had been collected, with 105 phenotype projects yielding over 2000 different measurements (Bogue et al. (2007) [2].
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Affiliation(s)
- Jonathan Flint
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK.
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Sillanpää MJ. Overview of techniques to account for confounding due to population stratification and cryptic relatedness in genomic data association analyses. Heredity (Edinb) 2010; 106:511-9. [PMID: 20628415 DOI: 10.1038/hdy.2010.91] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Population-based genomic association analyses are more powerful than within-family analyses. However, population stratification (unknown or ignored origin of individuals from multiple source populations) and cryptic relatedness (unknown or ignored covariance between individuals because of their relatedness) are confounding factors in population-based genomic association analyses, which inflate the false-positive rate. As a consequence, false association signals may arise in genomic data association analyses for reasons other than true association between the tested genomic factor (marker genotype, gene or protein expression) and the study phenotype. It is therefore important to correct or account for these confounders in population-based genomic data association analyses. The common correction techniques for population stratification and cryptic relatedness problems are presented here in the phenotype-marker association analysis context, and comments on their suitability for other types of genomic association analyses (for example, phenotype-expression association) are also provided. Even though many of these techniques have originally been developed in the context of human genetics, most of them are also applicable to model organisms and breeding populations.
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Affiliation(s)
- M J Sillanpää
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland.
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Brachi B, Faure N, Horton M, Flahauw E, Vazquez A, Nordborg M, Bergelson J, Cuguen J, Roux F. Linkage and association mapping of Arabidopsis thaliana flowering time in nature. PLoS Genet 2010; 6:e1000940. [PMID: 20463887 PMCID: PMC2865524 DOI: 10.1371/journal.pgen.1000940] [Citation(s) in RCA: 305] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Accepted: 04/06/2010] [Indexed: 12/28/2022] Open
Abstract
Flowering time is a key life-history trait in the plant life cycle. Most studies to unravel the genetics of flowering time in Arabidopsis thaliana have been performed under greenhouse conditions. Here, we describe a study about the genetics of flowering time that differs from previous studies in two important ways: first, we measure flowering time in a more complex and ecologically realistic environment; and, second, we combine the advantages of genome-wide association (GWA) and traditional linkage (QTL) mapping. Our experiments involved phenotyping nearly 20,000 plants over 2 winters under field conditions, including 184 worldwide natural accessions genotyped for 216,509 SNPs and 4,366 RILs derived from 13 independent crosses chosen to maximize genetic and phenotypic diversity. Based on a photothermal time model, the flowering time variation scored in our field experiment was poorly correlated with the flowering time variation previously obtained under greenhouse conditions, reinforcing previous demonstrations of the importance of genotype by environment interactions in A. thaliana and the need to study adaptive variation under natural conditions. The use of 4,366 RILs provides great power for dissecting the genetic architecture of flowering time in A. thaliana under our specific field conditions. We describe more than 60 additive QTLs, all with relatively small to medium effects and organized in 5 major clusters. We show that QTL mapping increases our power to distinguish true from false associations in GWA mapping. QTL mapping also permits the identification of false negatives, that is, causative SNPs that are lost when applying GWA methods that control for population structure. Major genes underpinning flowering time in the greenhouse were not associated with flowering time in this study. Instead, we found a prevalence of genes involved in the regulation of the plant circadian clock. Furthermore, we identified new genomic regions lacking obvious candidate genes.
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Affiliation(s)
- Benjamin Brachi
- Laboratoire Génétique et Evolution des Populations Végétales, Unité Mixte de Recherche CNRS 8016, Université des Sciences et Technologies de Lille 1, Villeneuve d'Ascq, France
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40
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Abstract
The genetics of phenotypic variation in inbred mice has for nearly a century provided a primary weapon in the medical research arsenal. A catalog of the genetic variation among inbred mouse strains, however, is required to enable powerful positional cloning and association techniques. A recent whole-genome resequencing study of 15 inbred mouse strains captured a significant fraction of the genetic variation among a limited number of strains, yet the common use of hundreds of inbred strains in medical research motivates the need for a high-density variation map of a larger set of strains. Here we report a dense set of genotypes from 94 inbred mouse strains containing 10.77 million genotypes over 121,433 single nucleotide polymorphisms (SNPs), dispersed at 20-kb intervals on average across the genome, with an average concordance of 99.94% with previous SNP sets. Through pairwise comparisons of the strains, we identified an average of 4.70 distinct segments over 73 classical inbred strains in each region of the genome, suggesting limited genetic diversity between the strains. Combining these data with genotypes of 7570 gap-filling SNPs, we further imputed the untyped or missing genotypes of 94 strains over 8.27 million Perlegen SNPs. The imputation accuracy among classical inbred strains is estimated at 99.7% for the genotypes imputed with high confidence. We demonstrated the utility of these data in high-resolution linkage mapping through power simulations and statistical power analysis and provide guidelines for developing such studies. We also provide a resource of in silico association mapping between the complex traits deposited in the Mouse Phenome Database with our genotypes. We expect that these resources will facilitate effective designs of both human and mouse studies for dissecting the genetic basis of complex traits.
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Su WL, Sieberts SK, Kleinhanz RR, Lux K, Millstein J, Molony C, Schadt EE. Assessing the prospects of genome-wide association studies performed in inbred mice. Mamm Genome 2010; 21:143-52. [PMID: 20135320 DOI: 10.1007/s00335-010-9249-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Accepted: 01/05/2010] [Indexed: 01/18/2023]
Abstract
The remarkable success in mapping genes linked to a number of disease traits using genome-wide association studies (GWAS) in human cohorts has renewed interest in applying this same technique in model organisms such as inbred laboratory mice. Unlike humans, however, the limited genetic diversity in the ancestry of laboratory mice combined with selection pressure over the past decades have yielded an intricate population genetic structure that can complicate the results obtained from association studies. This problem is further exacerbated by the small number of strains typically used in such studies where multiple spurious associations arise as a result of random chance. We sought to empirically assess the viability of GWAS in inbred mice using hundreds of expression traits for which the true location of the expression quantitative trait locus was known a priori. We then measured transcript abundance levels for these expression traits in 16 classical and 3 wild-derived inbred strains and carried out a genome-wide association scan, demonstrating the low statistical power of such studies and empirically estimating the large extent to which allelic association of transcripts gives rise to spurious associations. We provide evidence illustrating that in a large fraction of cases, the marker with the most significant p values fails to map to the location of the true eQTL. Finally, we provide experimental support for hundreds of traits, and that combining linkage analysis with association mapping provides significant increases in statistical power over a stand-alone GWAS as well as significantly higher mapping resolution than either study alone.
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Affiliation(s)
- Wan-Lin Su
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
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Bennett BJ, Farber CR, Orozco L, Kang HM, Ghazalpour A, Siemers N, Neubauer M, Neuhaus I, Yordanova R, Guan B, Truong A, Yang WP, He A, Kayne P, Gargalovic P, Kirchgessner T, Pan C, Castellani LW, Kostem E, Furlotte N, Drake TA, Eskin E, Lusis AJ. A high-resolution association mapping panel for the dissection of complex traits in mice. Genome Res 2010; 20:281-90. [PMID: 20054062 DOI: 10.1101/gr.099234.109] [Citation(s) in RCA: 252] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Systems genetics relies on common genetic variants to elucidate biologic networks contributing to complex disease-related phenotypes. Mice are ideal model organisms for such approaches, but linkage analysis has been only modestly successful due to low mapping resolution. Association analysis in mice has the potential of much better resolution, but it is confounded by population structure and inadequate power to map traits that explain less than 10% of the variance, typical of mouse quantitative trait loci (QTL). We report a novel strategy for association mapping that combines classic inbred strains for mapping resolution and recombinant inbred strains for mapping power. Using a mixed model algorithm to correct for population structure, we validate the approach by mapping over 2500 cis-expression QTL with a resolution an order of magnitude narrower than traditional QTL analysis. We also report the fine mapping of metabolic traits such as plasma lipids. This resource, termed the Hybrid Mouse Diversity Panel, makes possible the integration of multiple data sets and should prove useful for systems-based approaches to complex traits and studies of gene-by-environment interactions.
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Affiliation(s)
- Brian J Bennett
- Department of Medicine/Division of Cardiology, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA
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Burgess-Herbert SL, Tsaih SW, Stylianou IM, Walsh K, Cox AJ, Paigen B. An experimental assessment of in silico haplotype association mapping in laboratory mice. BMC Genet 2009; 10:81. [PMID: 20003225 PMCID: PMC2797012 DOI: 10.1186/1471-2156-10-81] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2009] [Accepted: 12/09/2009] [Indexed: 11/10/2022] Open
Abstract
Background To assess the utility of haplotype association mapping (HAM) as a quantitative trait locus (QTL) discovery tool, we conducted HAM analyses for red blood cell count (RBC) and high density lipoprotein cholesterol (HDL) in mice. We then experimentally tested each HAM QTL using published crosses or new F2 intercrosses guided by the haplotype at the HAM peaks. Results The HAM for RBC, using 33 classic inbred lines, revealed 8 QTLs; 2 of these were true positives as shown by published crosses. A HAM-guided (C57BL/6J × CBA/J)F2 intercross we carried out verified 2 more as true positives and 4 as false positives. The HAM for HDL, using 81 strains including recombinant inbred lines and chromosome substitution strains, detected 46 QTLs. Of these, 36 were true positives as shown by published crosses. A HAM-guided (C57BL/6J × A/J)F2 intercross that we carried out verified 2 more as true positives and 8 as false positives. By testing each HAM QTL for RBC and HDL, we demonstrated that 78% of the 54 HAM peaks were true positives and 22% were false positives. Interestingly, all false positives were in significant allelic association with one or more real QTL. Conclusion Because type I errors (false positives) can be detected experimentally, we conclude that HAM is useful for QTL detection and narrowing. We advocate the powerful and economical combined approach demonstrated here: the use of HAM for QTL discovery, followed by mitigation of the false positive problem by testing the HAM-predicted QTLs with small HAM-guided experimental crosses.
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Genetic loci that regulate healing and regeneration in LG/J and SM/J mice. Mamm Genome 2009; 20:720-33. [PMID: 19760323 DOI: 10.1007/s00335-009-9216-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2009] [Accepted: 08/06/2009] [Indexed: 10/20/2022]
Abstract
MRL mice display unusual healing properties. When MRL ear pinnae are hole punched, the holes close completely without scarring, with regrowth of cartilage and reappearance of both hair follicles and sebaceous glands. Studies using (MRL/lpr x C57BL/6)F(2) and backcross mice first showed that this phenomenon was genetically determined and that multiple loci contributed to this quantitative trait. The lpr mutation itself, however, was not one of them. In the present study we examined the genetic basis of healing in the Large (LG/J) mouse strain, a parent of the MRL mouse and a strain that shows the same healing phenotype. LG/J mice were crossed with Small (SM/J) mice and the F(2) population was scored for healing and their genotypes determined at more than 200 polymorphic markers. As we previously observed for MRL and (MRL x B6)F(2) mice, the wound-healing phenotype was sexually dimorphic, with female mice healing more quickly and more completely than male mice. We found quantitative trait loci (QTLs) on chromosomes (Chrs) 9, 10, 11, and 15. The heal QTLs on Chrs 11 and 15 were linked to differential healing primarily in male animals, whereas QTLs on Chrs 9 and 10 were not sexually dimorphic. A comparison of loci identified in previous crosses with those in the present report using LG/J x SM/J showed that loci on Chrs 9, 11, and 15 colocalized with those seen in previous MRL crosses, whereas the locus on Chr 10 was not seen before and is contributed by SM/J.
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Myles S, Peiffer J, Brown PJ, Ersoz ES, Zhang Z, Costich DE, Buckler ES. Association mapping: critical considerations shift from genotyping to experimental design. THE PLANT CELL 2009; 21:2194-202. [PMID: 19654263 PMCID: PMC2751942 DOI: 10.1105/tpc.109.068437] [Citation(s) in RCA: 445] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2009] [Revised: 07/06/2009] [Accepted: 07/13/2009] [Indexed: 05/18/2023]
Abstract
The goal of many plant scientists' research is to explain natural phenotypic variation in terms of simple changes in DNA sequence. Traditionally, linkage mapping has been the most commonly employed method to reach this goal: experimental crosses are made to generate a family with known relatedness, and attempts are made to identify cosegregation of genetic markers and phenotypes within this family. In vertebrate systems, association mapping (also known as linkage disequilibrium mapping) is increasingly being adopted as the mapping method of choice. Association mapping involves searching for genotype-phenotype correlations in unrelated individuals and often is more rapid and cost-effective than traditional linkage mapping. We emphasize here that linkage and association mapping are complementary approaches and are more similar than is often assumed. Unlike in vertebrates, where controlled crosses can be expensive or impossible (e.g., in humans), the plant scientific community can exploit the advantages of both controlled crosses and association mapping to increase statistical power and mapping resolution. While the time and money required for the collection of genotype data were critical considerations in the past, the increasing availability of inexpensive DNA sequencing and genotyping methods should prompt researchers to shift their attention to experimental design. This review provides thoughts on finding the optimal experimental mix of association mapping using unrelated individuals and controlled crosses to identify the genes underlying phenotypic variation.
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Affiliation(s)
- Sean Myles
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853-2703, USA.
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Gatti DM, Harrill AH, Wright FA, Threadgill DW, Rusyn I. Replication and narrowing of gene expression quantitative trait loci using inbred mice. Mamm Genome 2009; 20:437-46. [PMID: 19609828 DOI: 10.1007/s00335-009-9199-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2009] [Accepted: 06/02/2009] [Indexed: 10/20/2022]
Abstract
Gene expression quantitative trait locus (eQTL) mapping has become a powerful tool in systems biology. While many authors have made important discoveries using this approach, one persistent challenge in eQTL studies is the selection of loci and genes that should receive further biological investigation. In this study we compared eQTL generated from gene expression profiling in the livers of two panels of mouse strains: 41 BXD recombinant inbred and 36 Mouse Diversity Panel (MDP) strains. Cis-eQTL, loci in which the transcript and its maximum QTL are colocated, have been shown to be more reproducible than trans-eQTL, which are not colocated with the transcript. We observed that between 9.9 and 12.1% of cis-eQTL and between 2.0 and 12.6% of trans-eQTL replicated between the two panels depending on the degree of statistical stringency. Notably, a significant eQTL hotspot on distal chromosome 12 observed in the BXD panel was reproduced in the MDP. Furthermore, the shorter linkage disequilibrium in the MDP strains allowed us to considerably narrow the locus and limit the number of candidate genes to a cluster of Serpin genes, which code for extracellular proteases. We conclude that this strategy has some utility in increasing confidence and resolution in eQTL mapping studies; however, due to the high false-positive rate in the MDP, eQTL mapping in inbred strains is best carried out in combination with an eQTL linkage study.
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Affiliation(s)
- Daniel M Gatti
- Department of Environmental Sciences & Engineering, University of North Carolina, CB 7431, Chapel Hill, NC 27599, USA
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