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Pignon CP, Fernandes SB, Valluru R, Bandillo N, Lozano R, Buckler E, Gore MA, Long SP, Brown PJ, Leakey ADB. Phenotyping stomatal closure by thermal imaging for GWAS and TWAS of water use efficiency-related genes. Plant Physiol 2021; 187:2544-2562. [PMID: 34618072 PMCID: PMC8644692 DOI: 10.1093/plphys/kiab395] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 07/26/2021] [Indexed: 05/07/2023]
Abstract
Stomata allow CO2 uptake by leaves for photosynthetic assimilation at the cost of water vapor loss to the atmosphere. The opening and closing of stomata in response to fluctuations in light intensity regulate CO2 and water fluxes and are essential for maintaining water-use efficiency (WUE). However, a little is known about the genetic basis for natural variation in stomatal movement, especially in C4 crops. This is partly because the stomatal response to a change in light intensity is difficult to measure at the scale required for association studies. Here, we used high-throughput thermal imaging to bypass the phenotyping bottleneck and assess 10 traits describing stomatal conductance (gs) before, during and after a stepwise decrease in light intensity for a diversity panel of 659 sorghum (Sorghum bicolor) accessions. Results from thermal imaging significantly correlated with photosynthetic gas exchange measurements. gs traits varied substantially across the population and were moderately heritable (h2 up to 0.72). An integrated genome-wide and transcriptome-wide association study identified candidate genes putatively driving variation in stomatal conductance traits. Of the 239 unique candidate genes identified with the greatest confidence, 77 were putative orthologs of Arabidopsis (Arabidopsis thaliana) genes related to functions implicated in WUE, including stomatal opening/closing (24 genes), stomatal/epidermal cell development (35 genes), leaf/vasculature development (12 genes), or chlorophyll metabolism/photosynthesis (8 genes). These findings demonstrate an approach to finding genotype-to-phenotype relationships for a challenging trait as well as candidate genes for further investigation of the genetic basis of WUE in a model C4 grass for bioenergy, food, and forage production.
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Affiliation(s)
- Charles P Pignon
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Samuel B Fernandes
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Ravi Valluru
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
- Lincoln Institute for Agri-Food Technology, University of Lincoln, Lincoln LN1 3QE, UK
| | - Nonoy Bandillo
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota 58105, USA
| | - Roberto Lozano
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Edward Buckler
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
- United States Department of Agriculture, Agricultural Research Service (USDA-ARS) R.W. Holley Center for Agriculture and Health, Ithaca, New York 14853, USA
| | - Michael A Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Stephen P Long
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Lancaster Environment Centre, University of Lancaster, Lancaster LA1 1YX, UK
| | - Patrick J Brown
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Andrew D B Leakey
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
- Author for communication:
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Wang L, Pittman KJ, Barker JR, Salinas RE, Stanaway IB, Williams GD, Carroll RJ, Balmat T, Ingham A, Gopalakrishnan AM, Gibbs KD, Antonia AL, Heitman J, Lee SC, Jarvik GP, Denny JC, Horner SM, DeLong MR, Valdivia RH, Crosslin DR, Ko DC. An Atlas of Genetic Variation Linking Pathogen-Induced Cellular Traits to Human Disease. Cell Host Microbe 2018; 24:308-323.e6. [PMID: 30092202 PMCID: PMC6093297 DOI: 10.1016/j.chom.2018.07.007] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 05/28/2018] [Accepted: 07/05/2018] [Indexed: 12/18/2022]
Abstract
Pathogens have been a strong driving force for natural selection. Therefore, understanding how human genetic differences impact infection-related cellular traits can mechanistically link genetic variation to disease susceptibility. Here we report the Hi-HOST Phenome Project (H2P2): a catalog of cellular genome-wide association studies (GWAS) comprising 79 infection-related phenotypes in response to 8 pathogens in 528 lymphoblastoid cell lines. Seventeen loci surpass genome-wide significance for infection-associated phenotypes ranging from pathogen replication to cytokine production. We combined H2P2 with clinical association data from patients to identify a SNP near CXCL10 as a risk factor for inflammatory bowel disease. A SNP in the transcriptional repressor ZBTB20 demonstrated pleiotropy, likely through suppression of multiple target genes, and was associated with viral hepatitis. These data are available on a web portal to facilitate interpreting human genome variation through the lens of cell biology and should serve as a rich resource for the research community.
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Affiliation(s)
- Liuyang Wang
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Kelly J Pittman
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Jeffrey R Barker
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Raul E Salinas
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Ian B Stanaway
- Department of Biomedical Informatics and Medical Education, School of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Graham D Williams
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Robert J Carroll
- Department of Biomedical Informatics, School of Medicine, Vanderbilt University, Nashville, TN 37212, USA
| | - Tom Balmat
- Social Science Research Institute, Duke University, Durham, NC 27710, USA
| | - Andy Ingham
- Duke Research Computing, Duke University, Durham, NC 27710, USA
| | - Anusha M Gopalakrishnan
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Kyle D Gibbs
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Alejandro L Antonia
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA; Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Soo Chan Lee
- South Texas Center for Emerging Infectious Diseases (STCEID), Department of Biology, College of Sciences, the University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Gail P Jarvik
- Department of Medicine, Division of Medical Genetics, School of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Joshua C Denny
- Department of Biomedical Informatics, School of Medicine, Vanderbilt University, Nashville, TN 37212, USA
| | - Stacy M Horner
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA; Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Mark R DeLong
- Duke Research Computing, Duke University, Durham, NC 27710, USA
| | - Raphael H Valdivia
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - David R Crosslin
- Department of Biomedical Informatics and Medical Education, School of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Dennis C Ko
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA; Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, NC 27710, USA.
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Keating BJ, Tischfield S, Murray SS, Bhangale T, Price TS, Glessner JT, Galver L, Barrett JC, Grant SFA, Farlow DN, Chandrupatla HR, Hansen M, Ajmal S, Papanicolaou GJ, Guo Y, Li M, DerOhannessian S, de Bakker PIW, Bailey SD, Montpetit A, Edmondson AC, Taylor K, Gai X, Wang SS, Fornage M, Shaikh T, Groop L, Boehnke M, Hall AS, Hattersley AT, Frackelton E, Patterson N, Chiang CWK, Kim CE, Fabsitz RR, Ouwehand W, Price AL, Munroe P, Caulfield M, Drake T, Boerwinkle E, Reich D, Whitehead AS, Cappola TP, Samani NJ, Lusis AJ, Schadt E, Wilson JG, Koenig W, McCarthy MI, Kathiresan S, Gabriel SB, Hakonarson H, Anand SS, Reilly M, Engert JC, Nickerson DA, Rader DJ, Hirschhorn JN, FitzGerald GA. Concept, design and implementation of a cardiovascular gene-centric 50 k SNP array for large-scale genomic association studies. PLoS One 2008; 3:e3583. [PMID: 18974833 PMCID: PMC2571995 DOI: 10.1371/journal.pone.0003583] [Citation(s) in RCA: 327] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2008] [Accepted: 09/16/2008] [Indexed: 11/19/2022] Open
Abstract
A wealth of genetic associations for cardiovascular and metabolic phenotypes in humans has been accumulating over the last decade, in particular a large number of loci derived from recent genome wide association studies (GWAS). True complex disease-associated loci often exert modest effects, so their delineation currently requires integration of diverse phenotypic data from large studies to ensure robust meta-analyses. We have designed a gene-centric 50 K single nucleotide polymorphism (SNP) array to assess potentially relevant loci across a range of cardiovascular, metabolic and inflammatory syndromes. The array utilizes a "cosmopolitan" tagging approach to capture the genetic diversity across approximately 2,000 loci in populations represented in the HapMap and SeattleSNPs projects. The array content is informed by GWAS of vascular and inflammatory disease, expression quantitative trait loci implicated in atherosclerosis, pathway based approaches and comprehensive literature searching. The custom flexibility of the array platform facilitated interrogation of loci at differing stringencies, according to a gene prioritization strategy that allows saturation of high priority loci with a greater density of markers than the existing GWAS tools, particularly in African HapMap samples. We also demonstrate that the IBC array can be used to complement GWAS, increasing coverage in high priority CVD-related loci across all major HapMap populations. DNA from over 200,000 extensively phenotyped individuals will be genotyped with this array with a significant portion of the generated data being released into the academic domain facilitating in silico replication attempts, analyses of rare variants and cross-cohort meta-analyses in diverse populations. These datasets will also facilitate more robust secondary analyses, such as explorations with alternative genetic models, epistasis and gene-environment interactions.
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Affiliation(s)
- Brendan J. Keating
- The Institute for Translational Medicine and Therapeutics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvannia, United States of America
| | - Sam Tischfield
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Divisions of Genetics, Endocrinology & Program in Genomics, Children's Hospital, Boston, Massachusetts, United States of America
| | - Sarah S. Murray
- Scripps Genomic Medicine, La Jolla, California, United States of America
| | - Tushar Bhangale
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Thomas S. Price
- MRC SGDP Centre, Institute of Psychiatry, London, United Kingdom
| | - Joseph T. Glessner
- The Center for Applied Genomics, Division of Human Genetics, Department of Pediatrics, The Childrens' Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Luana Galver
- Illumina Incorporated, San Diego, California, United States of America
| | - Jeffrey C. Barrett
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Struan F. A. Grant
- The Center for Applied Genomics, Division of Human Genetics, Department of Pediatrics, The Childrens' Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Deborah N. Farlow
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Hareesh R. Chandrupatla
- The Cardiovascular Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Mark Hansen
- Illumina Incorporated, San Diego, California, United States of America
| | - Saad Ajmal
- The Cardiovascular Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - George J. Papanicolaou
- Division of Prevention and Population Sciences, National Heart, Lung, and Blood Institute, Bethesda, Maryland, United States of America
| | - Yiran Guo
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Mingyao Li
- The Cardiovascular Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Stephanie DerOhannessian
- The Cardiovascular Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Paul I. W. de Bakker
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Swneke D. Bailey
- Departments of Medicine and Human Genetics, McGill University, Montréal, Québec, Canada
| | | | - Andrew C. Edmondson
- The Cardiovascular Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Kent Taylor
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Xiaowu Gai
- The Center for Applied Genomics, Division of Human Genetics, Department of Pediatrics, The Childrens' Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Susanna S. Wang
- Department of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Myriam Fornage
- Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Tamim Shaikh
- The Center for Applied Genomics, Division of Human Genetics, Department of Pediatrics, The Childrens' Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Leif Groop
- Department of Clinical Science Malmoe, Diabetes and Endocrinology, Lund University, Sweden and Department of Medicine, Helsinki University Hospital, Helsinki, Finland
| | - Michael Boehnke
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Alistair S. Hall
- Leeds Institute of Genetics, Health & Therapeutics, University of Leeds, Leeds, United Kingdom
| | - Andrew T. Hattersley
- Diabetes Genetics Group, Institute of Biomedical and Clinical Science, Peninsula Medical School, Exeter, United Kingdom
| | - Edward Frackelton
- The Center for Applied Genomics, Division of Human Genetics, Department of Pediatrics, The Childrens' Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Nick Patterson
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Charleston W. K. Chiang
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Cecelia E. Kim
- The Center for Applied Genomics, Division of Human Genetics, Department of Pediatrics, The Childrens' Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Richard R. Fabsitz
- Division of Prevention and Population Sciences, National Heart, Lung, and Blood Institute, Bethesda, Maryland, United States of America
| | - Willem Ouwehand
- Department of Haematology and NHS Blood and Transplant, University of Cambridge, Cambridge, United Kingdom
| | - Alkes L. Price
- Departments of Epidemiology and Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Patricia Munroe
- Department of Clinical Pharmacology, Barts and The London, Charterhouse Square, London, United Kingdom
- William Harvey Research Institute, Barts and The London, Charterhouse Square, London, United Kingdom
| | - Mark Caulfield
- William Harvey Research Institute, Barts and The London, Charterhouse Square, London, United Kingdom
| | - Thomas Drake
- Department of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Eric Boerwinkle
- Human Genetics Center, University of Texas Health Science Center, Houston, Texas, United States of America
| | - David Reich
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - A. Stephen Whitehead
- The Institute for Translational Medicine and Therapeutics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvannia, United States of America
| | - Thomas P. Cappola
- The Cardiovascular Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Nilesh J. Samani
- Department of Cardiovascular Sciences, University of Leicester, Leicester, United Kingdom
| | - A. Jake Lusis
- Department of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles School of Medicine, Los Angeles, California, United States of America
| | - Eric Schadt
- Rosetta Inpharmatics, LLC, Merck & Co. Inc., Seattle, Washington, United States of America
| | - James G. Wilson
- V.A. Medical Center and the University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Wolfgang Koenig
- Department of Internal Medicine II - Cardiology, University of Ulm Medical Center, Ulm, Germany
| | - Mark I. McCarthy
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Oxford Center for Diabetes, Endocrinology and Metabolism and Oxford NIHR Biomedical Research Center, Churchill Hospital, University of Oxford, Oxford, United Kingdom
| | - Sekar Kathiresan
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Cardiology Division, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Stacey B. Gabriel
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Hakon Hakonarson
- The Center for Applied Genomics, Division of Human Genetics, Department of Pediatrics, The Childrens' Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Sonia S. Anand
- Department of Medicine and Clinical Epidemiology and Biostatistics, Population Genomics Program, McMaster University, Hamilton Health Sciences, Hamilton General Hospital, Hamilton, Ontario, Canada
| | - Muredach Reilly
- The Institute for Translational Medicine and Therapeutics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvannia, United States of America
- The Cardiovascular Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - James C. Engert
- Departments of Medicine and Human Genetics, McGill University, Montréal, Québec, Canada
| | - Deborah A. Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Daniel J. Rader
- The Institute for Translational Medicine and Therapeutics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvannia, United States of America
- The Cardiovascular Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Joel N. Hirschhorn
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Divisions of Genetics, Endocrinology & Program in Genomics, Children's Hospital, Boston, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Garret A. FitzGerald
- The Institute for Translational Medicine and Therapeutics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvannia, United States of America
- * E-mail:
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