Justin O Borevitz

Summary

Affiliation: University of Chicago
Country: USA

Publications

  1. pmc Global analysis of genetic, epigenetic and transcriptional polymorphisms in Arabidopsis thaliana using whole genome tiling arrays
    Xu Zhang
    Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
    PLoS Genet 4:e1000032. 2008
  2. pmc Redundancy in genotyping arrays
    Scott Smemo
    Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
    PLoS ONE 2:e287. 2007
  3. pmc The scale of population structure in Arabidopsis thaliana
    Alexander Platt
    Molecular and Computational Biology, University of Southern California, Los Angeles, California, USA
    PLoS Genet 6:e1000843. 2010
  4. pmc Single-feature polymorphism discovery in the barley transcriptome
    Nils Rostoks
    Scottish Crop Research Institute, Genome Dynamics, Invergowrie, Dundee, DD2 5DA, Scotland, UK
    Genome Biol 6:R54. 2005
  5. pmc Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana
    Justin O Borevitz
    Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
    Proc Natl Acad Sci U S A 104:12057-62. 2007
  6. pmc Cis-regulatory changes at FLOWERING LOCUS T mediate natural variation in flowering responses of Arabidopsis thaliana
    Christopher Schwartz
    Plant Biology Laboratory, Howard Hughes Medical Institute, The Salk Institute for Biological Sciences, La Jolla, California 92037, USA
    Genetics 183:723-32, 1SI-7SI. 2009
  7. pmc Quantitative trait locus mapping and DNA array hybridization identify an FLM deletion as a cause for natural flowering-time variation
    Jonathan D Werner
    Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
    Proc Natl Acad Sci U S A 102:2460-5. 2005
  8. pmc Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines
    Susanna Atwell
    Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089, USA
    Nature 465:627-31. 2010
  9. pmc LUX ARRHYTHMO encodes a Myb domain protein essential for circadian rhythms
    Samuel P Hazen
    Department of Cell Biology and Institute for Childhood and Neglected Diseases, The Scripps Research Institute, La Jolla, CA 92037, USA
    Proc Natl Acad Sci U S A 102:10387-92. 2005
  10. pmc Exploring the transcriptional landscape of plant circadian rhythms using genome tiling arrays
    Samuel P Hazen
    Section of Cell and Developmental Biology, University of California San Diego, Gilman Drive, La Jolla, CA 92093 0130, USA
    Genome Biol 10:R17. 2009

Collaborators

Detail Information

Publications40

  1. pmc Global analysis of genetic, epigenetic and transcriptional polymorphisms in Arabidopsis thaliana using whole genome tiling arrays
    Xu Zhang
    Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
    PLoS Genet 4:e1000032. 2008
    ..Our results demonstrated extensive genetic and epigenetic polymorphisms between Arabidopsis accessions and suggested a possible relationship between natural CG methylation variation and gene expression variation...
  2. pmc Redundancy in genotyping arrays
    Scott Smemo
    Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
    PLoS ONE 2:e287. 2007
    ..3% with the full data set. Removal of this redundancy will allow for more comprehensive whole-genome association studies with increased SNP density and larger sample sizes...
  3. pmc The scale of population structure in Arabidopsis thaliana
    Alexander Platt
    Molecular and Computational Biology, University of Southern California, Los Angeles, California, USA
    PLoS Genet 6:e1000843. 2010
    ..Any model based on discrete clusters of interchangeable individuals will be an uneasy fit to organisms like A. thaliana which exhibit continuous isolation by distance on many scales...
  4. pmc Single-feature polymorphism discovery in the barley transcriptome
    Nils Rostoks
    Scottish Crop Research Institute, Genome Dynamics, Invergowrie, Dundee, DD2 5DA, Scotland, UK
    Genome Biol 6:R54. 2005
    ..This method is applicable to all oligonucleotide microarray data, accounts for SNP effects in gene-expression data and represents an efficient and versatile approach for highly parallel marker identification in large genomes...
  5. pmc Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana
    Justin O Borevitz
    Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
    Proc Natl Acad Sci U S A 104:12057-62. 2007
    ..SFPs identified with the gene expression array also provide an empirical hybridization polymorphism background for studies of gene expression polymorphism and are available through the genome browser http://signal.salk.edu/cgi-bin/AtSFP...
  6. pmc Cis-regulatory changes at FLOWERING LOCUS T mediate natural variation in flowering responses of Arabidopsis thaliana
    Christopher Schwartz
    Plant Biology Laboratory, Howard Hughes Medical Institute, The Salk Institute for Biological Sciences, La Jolla, California 92037, USA
    Genetics 183:723-32, 1SI-7SI. 2009
    ..Taken together, these results indicate that allelic variation at pathway integrator genes such as FT can underlie phenotypic variability and that this may be achieved through cis-regulatory changes...
  7. pmc Quantitative trait locus mapping and DNA array hybridization identify an FLM deletion as a cause for natural flowering-time variation
    Jonathan D Werner
    Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
    Proc Natl Acad Sci U S A 102:2460-5. 2005
    ..Analysis of near isogenic lines and quantitative transgenic complementation experiments confirmed that the FLM deletion is, in large part, responsible for the early flowering of the Nd accession...
  8. pmc Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines
    Susanna Atwell
    Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089, USA
    Nature 465:627-31. 2010
    ..Our study demonstrates the feasibility of GWA studies in A. thaliana and suggests that the approach will be appropriate for many other organisms...
  9. pmc LUX ARRHYTHMO encodes a Myb domain protein essential for circadian rhythms
    Samuel P Hazen
    Department of Cell Biology and Institute for Childhood and Neglected Diseases, The Scripps Research Institute, La Jolla, CA 92037, USA
    Proc Natl Acad Sci U S A 102:10387-92. 2005
    ..The data are also consistent with LUX being necessary for activation of CCA1 and LHY expression...
  10. pmc Exploring the transcriptional landscape of plant circadian rhythms using genome tiling arrays
    Samuel P Hazen
    Section of Cell and Developmental Biology, University of California San Diego, Gilman Drive, La Jolla, CA 92093 0130, USA
    Genome Biol 10:R17. 2009
    ..Here we explore, using whole genome tiling arrays, the extent of rhythmic expression patterns genome-wide, with an unbiased analysis of coding and noncoding regions of the Arabidopsis genome...
  11. pmc Large-scale identification of single-feature polymorphisms in complex genomes
    Justin O Borevitz
    Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
    Genome Res 13:513-23. 2003
    ..The extension of these tools to organisms with complex genomes, such as Arabidopsis, will greatly increase our ability to map and clone quantitative trait loci (QTL)...
  12. doi request reprint Source verification of mis-identified Arabidopsis thaliana accessions
    Alison E Anastasio
    Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
    Plant J 67:554-66. 2011
    ..Finally, we discuss possibilities for maintaining the integrity of stock lines...
  13. pmc FRIGIDA-independent variation in flowering time of natural Arabidopsis thaliana accessions
    Jonathan D Werner
    Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
    Genetics 170:1197-207. 2005
    ..Finally, eXtreme array mapping identified genomic regions linked to the vernalization-independent, late-flowering habit of Bur-0, which has an alternatively spliced FLC allele that behaves as a null allele...
  14. pmc Inferring population parameters from single-feature polymorphism data
    Rong Jiang
    Molecular and Computational Biology Program, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles 90089, USA
    Genetics 173:2257-67. 2006
    ..A coalescent simulation study is used to investigate the accuracy and robustness of our method. Our approach allows the utilization of single-feature polymorphism data for inference in population genetics...
  15. pmc Genetic architecture of regulatory variation in Arabidopsis thaliana
    Xu Zhang
    Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA
    Genome Res 21:725-33. 2011
    ..Finally, we identify candidate genes for 59 diverse phenotypic traits that were mapped to eQTL...
  16. pmc Global analysis of allele-specific expression in Arabidopsis thaliana
    Xu Zhang
    Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA
    Genetics 182:943-54. 2009
    ..Our findings demonstrate a method of global functional characterization of allele-specific expression and highlight that chromatin structure is intertwined with evolution of cis- and trans-regulatory variation...
  17. pmc Association mapping with single-feature polymorphisms
    Sung Kim
    Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089 2910, USA
    Genetics 173:1125-33. 2006
    ..Finally, we show how power depends on the accuracy with which single-feature polymorphisms are called...
  18. pmc Rapid array mapping of circadian clock and developmental mutations in Arabidopsis
    Samuel P Hazen
    Department of Cell Biology and Institute for Childhood and Neglected Diseases, Scripps Research Institute, La Jolla, California 92037, USA
    Plant Physiol 138:990-7. 2005
    ..We demonstrate this by resolving two deletions, the 77-kb flavin-binding, kelch repeat, f-box 1 and the 7-kb cryptochrome2-1 deletions, via direct hybridization of mutant DNA to ATH1 expression arrays...
  19. pmc Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel
    Matthew W Horton
    Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, USA
    Nat Genet 44:212-6. 2012
    ..We have made the seeds we used to produce this Regional Mapping (RegMap) panel publicly available. This panel comprises one of the largest genomic mapping resources currently available for global natural isolates of a non-human species...
  20. pmc Association mapping of local climate-sensitive quantitative trait loci in Arabidopsis thaliana
    Yan Li
    Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
    Proc Natl Acad Sci U S A 107:21199-204. 2010
    ..Our results suggest that these major, environmentally sensitive FT QTL play an important role in spatial and temporal adaptation...
  21. ncbi request reprint The extent of linkage disequilibrium in Arabidopsis thaliana
    Magnus Nordborg
    Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
    Nat Genet 30:190-3. 2002
    ..The combination of a relatively high level of polymorphism and extensive haplotype structure bodes well for developing a genome-wide LD map in A. thaliana...
  22. pmc Whole genome transcriptome polymorphisms in Arabidopsis thaliana
    Xu Zhang
    Department of Ecology and Evolution, University of Chicago, 1101 E, 57th Street, Chicago, IL 60637, USA
    Genome Biol 9:R165. 2008
    ..Our study demonstrates that whole genome tiling arrays are a powerful platform for dissecting natural transcriptome variation at multi-dimension and high resolution...
  23. pmc A systematic map of genetic variation in Plasmodium falciparum
    Claire Kidgell
    Department of Cell Biology, The Scripps Research Institute, La Jolla, California, USA
    PLoS Pathog 2:e57. 2006
    ..We speculate that an amplification of the GTP cyclohydrolase enzyme in the folate biosynthesis pathway may increase flux through this pathway and facilitate parasite resistance to antifolate drugs...
  24. pmc Genome-wide association studies in plants: the missing heritability is in the field
    Benjamin Brachi
    Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
    Genome Biol 12:232. 2011
    ..Genome-wide association studies (GWAS) have been even more successful in plants than in humans. Mapping approaches can be extended to dissect adaptive genetic variation from structured background variation in an ecological context...
  25. pmc The impact of genomics on the study of natural variation in Arabidopsis
    Justin O Borevitz
    Plant Biology, Salk Institute, 10010 North Torrey Pines Rd, La Jolla, California 92037, USA
    Plant Physiol 132:718-25. 2003
  26. ncbi request reprint Genetic and epigenetic dissection of cis regulatory variation
    Xu Zhang
    Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois 60637, USA
    Curr Opin Plant Biol 10:142-8. 2007
    ....
  27. pmc Genome-wide expression profiling of the Arabidopsis female gametophyte identifies families of small, secreted proteins
    Matthew W Jones-Rhoades
    Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, Illinois, USA
    PLoS Genet 3:1848-61. 2007
    ..The coexpression of highly similar proteins suggests a high degree of functional redundancy among embryo sac genes...
  28. pmc Quantitative trait loci controlling light and hormone response in two accessions of Arabidopsis thaliana
    Justin O Borevitz
    Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
    Genetics 160:683-96. 2002
    ..The phenotype and map position of LIGHT2 suggest the photoreceptor PHYB as a candidate gene. Natural variation in light and hormone response thus defines both new genes and known genes that control light response in wild accessions...
  29. ncbi request reprint Genomics tools for QTL analysis and gene discovery
    Justin O Borevitz
    Plant Biology Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Road, La Jolla, California 92037, USA
    Curr Opin Plant Biol 7:132-6. 2004
    ..Genome sequences, tens of thousands of molecular markers, microarrays, and knock-out collections are being applied to QTL mapping, facilitating the use of natural accessions for gene discovery...
  30. pmc A common and unstable copy number variant is associated with differences in Glo1 expression and anxiety-like behavior
    Richard Williams
    Committee on Computational Neuroscience, University of Chicago, Chicago, Illinois, United States of America
    PLoS ONE 4:e4649. 2009
    ..Finally, these data provide an example of biologically significant phenotypic variability in model organisms that can be attributed to CNVs...
  31. pmc Population genomic variation reveals roles of history, adaptation and ploidy in switchgrass
    Paul P Grabowski
    U S Dairy Forage Research Center, USDA ARS, 1925 Linden Drive, Madison, WI 53706, USA Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA
    Mol Ecol 23:4059-73. 2014
    ..These results provide new insights into the mechanisms shaping variation in widespread species and provide a foundation for dissecting the genetic basis of adaptation in switchgrass. ..
  32. pmc Genomic diversity in switchgrass (Panicum virgatum): from the continental scale to a dune landscape
    Geoffrey P Morris
    Department of Ecology and Evolution, University of Chicago, 1101 East 57th St, Chicago, IL 60637, USA
    Mol Ecol 20:4938-52. 2011
    ..Nuclear markers also support a deep lowland-upland split, followed by limited gene flow, and show extensive gene flow in the local population of the Indiana Dunes...
  33. ncbi request reprint Natural selection shapes genome-wide patterns of copy-number polymorphism in Drosophila melanogaster
    J J Emerson
    Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
    Science 320:1629-31. 2008
    ..Among duplications, those overlapping exons or introns, as well as those falling on the X chromosome, seem to be subject to stronger purifying selection...
  34. ncbi request reprint Plant genomics: the third wave
    Justin O Borevitz
    Genomic Analysis Laboratory, Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
    Annu Rev Genomics Hum Genet 5:443-77. 2004
    ..Genomics provides the essential tools to speed the work of the traditional molecular geneticist and is now a scientific discipline in its own right...
  35. pmc Genetic Variation for Life History Sensitivity to Seasonal Warming in Arabidopsis thaliana
    Yan Li
    Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637
    Genetics 196:569-77. 2014
    ..95) that has application for genomic selection of adaptive genotypes for future environments. This work may serve as a reference for breeding and conservation genetic studies under changing environments. ..
  36. pmc Light-response quantitative trait loci identified with composite interval and eXtreme array mapping in Arabidopsis thaliana
    David J Wolyn
    Department of Plant Agriculture, University of Guelph, Ontario N1G 2W1, Canada
    Genetics 167:907-17. 2004
    ..The RED2 QTL was identified clearly; differences exceeded a threshold of significance determined by simulations. The sensitivities of XAM to population type and size and genetic models were also determined by simulation analysis...
  37. pmc A large number of novel coding small open reading frames in the intergenic regions of the Arabidopsis thaliana genome are transcribed and/or under purifying selection
    Kousuke Hanada
    Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824, USA
    Genome Res 17:632-40. 2007
    ..thaliana genome...
  38. pmc Amino acid polymorphisms in Arabidopsis phytochrome B cause differential responses to light
    Daniele L Filiault
    Section of Plant Biology, College of Biological Sciences, University of California, One Shields Avenue, Davis, CA 95616, USA
    Proc Natl Acad Sci U S A 105:3157-62. 2008
    ..Together with earlier studies linking variation in light sensitivity to photoreceptor genes, our work suggests that photoreceptors may be a common target of natural selection...
  39. ncbi request reprint Mapping a plant's chemical vocabulary
    Ivan R Baxter
    Nat Genet 38:737-8. 2006

Research Grants7

  1. GENOME WIDE ASSOCIATION MAPPING IN ARABIDOPSIS THALIANA
    Justin Borevitz; Fiscal Year: 2006
    ..The studies proposed here in Arabidopsis will suggest successful paths for this daunting undertaking, as associations can be quickly confirmed to identify novel QTL. [unreadable] [unreadable]..
  2. GENOME WIDE ASSOCIATION MAPPING IN ARABIDOPSIS THALIANA
    Justin Borevitz; Fiscal Year: 2007
    ..The studies proposed here in Arabidopsis will suggest successful paths for this daunting undertaking, as associations can be quickly confirmed to identify novel QTL. [unreadable] [unreadable]..
  3. GENOME WIDE ASSOCIATION MAPPING IN ARABIDOPSIS THALIANA
    Justin Borevitz; Fiscal Year: 2006
    ..The studies proposed here in Arabidopsis will suggest successful paths for this daunting undertaking, as associations can be quickly confirmed to identify novel QTL. [unreadable] [unreadable]..
  4. GENOME WIDE ASSOCIATION MAPPING IN ARABIDOPSIS THALIANA
    Justin Borevitz; Fiscal Year: 2008
    ..The studies proposed here in Arabidopsis will suggest successful paths for this daunting undertaking, as associations can be quickly confirmed to identify novel QTL. ..
  5. GENOME WIDE ASSOCIATION MAPPING IN ARABIDOPSIS THALIANA
    Justin Borevitz; Fiscal Year: 2009
    ..The studies proposed here in Arabidopsis will suggest successful paths for this daunting undertaking, as associations can be quickly confirmed to identify novel QTL. ..
  6. GENOME WIDE ASSOCIATION MAPPING IN ARABIDOPSIS THALIANA
    Justin O Borevitz; Fiscal Year: 2010
    ..The studies proposed here in Arabidopsis will suggest successful paths for this daunting undertaking, as associations can be quickly confirmed to identify novel QTL. ..
  7. GENOME WIDE ASSOCIATION MAPPING IN ARABIDOPSIS THALIANA
    Justin Borevitz; Fiscal Year: 2009
    ..The studies proposed here in Arabidopsis will suggest successful paths for this daunting undertaking, as associations can be quickly confirmed to identify novel QTL. ..