Faculty | Ecology & Evolution | University of Chicago

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Faculty : Students : Administrative Staff : Research Staff

Justin Borevitz, Ph.D.
Assistant Professor
Department of Ecology & Evolution
Committee on Evolutionary Biology

Office: Erman 305 | Phone: (773) 702-5948 | Fax: (773) 702-9740 | email:borevitz(at)uchicago(dot)edu
Subjects:Genetics of local adaptation in plants, genetic variation in environmental response, genomic approaches to natural variation, molecular systems to ecosystems: restoring biodiversity and biomass

Research Interests

For more detailed research information, see the Borevitz Lab Website.

Genetics of local adaptation in plants

Specific interests of the lab include the genetics of adaptation to seasonal light environments. Quantitative and population genetic approaches in Arabidopsis thaliana, Arabidopsis lyrata, Aquilegia (columbines), and switchgrass are used to dissect local and regional phenotypic variation. What genes and what alleles explain differential survival (germination/elongation) and reproduction (flowering time) in the field? Are these new variants or new combinations of existing polymorphisms? Are similar evolutionary steps occurring in related species living in a similar ecological context?
Environmental variation in growth chambersgrowth chambers

Genetic variation in environmental response

In Arabidopsis, we have revealed extensive genetic variation in world-wide collections for seedling elongation (Nature Genetics 2001) and flowering time (Genetics 2005) under unique light environments and determined quantitative trait loci (QTL) responsible for this variation (Genetics 2002,2004, PLoSONE, 2007). The next questions are what are the genes underlying these QTL and what are the functional allelic differences? How have the patterns of variation at these loci been shaped by natural selection? Can we find evidence for local adaptation and determine the ecological environmental differences driving selection?
Microarray analysis of genetic variationarray mapping

Genomic approaches to natural variation

A second focus is on the development of genomics methods to enable comprehensive studies of natural variation. Tools such as whole genome oligo-nucleotide SNP tiling arrays are being used for very high resolution studies of polymorphism, mapping (Genome Research 2003, Genetics 2004, PNAS 2005, Plant Phys 2005, COPB 2007) and haplotype analysis (PNAS 2007). These arrays which interrogate nearly every base of the A. thaliana genome, can reveal natural variation in gene or allelic expression and alternative splicing to identify candidate genes for QTL and their downstream responses (Annual Review 2004). SNPs, novel Single Feature Polymorphisms (SFPs) and CNPs can identify potential causative changes for QTL. We have also revealed natural variation in methylation by differential enzyme digestion followed by tiling array hybridization.
Little Bluestem (Northerly Island)

From molecular systems to ecosystems: restoring biodiversity and biomass

We use genomic profiling of RNA and methylation variation to understand cellular signaling pathways and their genetic control. These responses are the integration of environmental inputs through development resulting in altered organismal phenotypes of the adult plant. Whole plant structure and physiology affects the species community makeup and higher order inter-specific interactions. The resulting landscape effects, in turn have outputs measured as ecosystems services including biomass for biofuel, habitat for biodiversity, and carbon and nitrogen sequestration that input again on molecular cellular signaling.

Recent Publications

Emerson JJ, Cardoso-Moreira M, Borevitz JO, Long M. Natural selection shapes genome-wide patterns of copy-number polymorphism in Drosophila melanogaster. Science. 2008 Jun 20;320(5883):1629-31. Epub 2008 Jun 5.

Zhang X, Shiu S, Cal A, Borevitz JO. Global analysis of genetic, epigenetic and transcriptional polymorphisms in Arabidopsis thaliana using whole genome tiling arrays. PLoS Genet. 2008 Mar 21;4(3):e1000032.

Filiault DL, Wessinger CA, Dinneny JR, Lutes J, Borevitz JO, Weigel D, Chory J, Maloof JN. Amino acid polymorphisms in Arabidopsis phytochrome B cause differential responses to light. Proc Natl Acad Sci U S A. 2008 Feb 26;105(8):3157-62. Epub 2008 Feb 14. Erratum in: Proc Natl Acad Sci U S A. 2008 Jun 17;105(24):8482.

Jones-Rhoades MW, Borevitz JO, Preuss D.Genome-wide expression profiling of the Arabidopsis female gametophyte identifies families of small, secreted proteins. PLoS Genet. 2007 Oct;3(10):1848-61. Epub 2007 Aug 24.

Borevitz JO, Hazen SP, Michael TP, Morris GP, Baxter IR, Hu TT, Chen H, Werner JD, Nordborg M, Salt DE, Kay SA, Chory J, Weigel D, Jones JD, Ecker JR. Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana. Proc Natl Acad Sci U S A. 2007 Jul 17;104(29):12057-62. Epub 2007 Jul 12.

Hanada K, Zhang X, Borevitz JO, Li WH, Shiu SH.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. Genome Res. 2007 May;17(5):632-40. Epub 2007 Mar 29.

Smemo S, Borevitz JO. Redundancy in genotyping arrays. PLoS ONE. 2007 Mar 14;2(3):e287.

Zhang X, Richards EJ, Borevitz JO. Genetic and epigenetic dissection of cis regulatory variation. Curr Opin Plant Biol. 2007 Apr;10(2):142-8. Epub 2007 Feb 14. Review.

Li Y, Roycewicz P, Smith E, Borevitz JO. Genetics of local adaptation in the laboratory: flowering time quantitative trait loci under geographic and seasonal conditions in Arabidopsis. PLoS ONE. 2006 Dec 27;1:e105.

Shiu SH, Borevitz JO. The next generation of microarray research: applications in evolutionary and ecological genomics. Heredity. 2008 Feb;100(2):141-9. Epub 2006 Nov 8. Review.

Gilad Y, Borevitz J. Using DNA microarrays to study natural variation. Curr Opin Genet Dev. 2006 Dec;16(6):553-8. Epub 2006 Sep 27. Review.

Baxter IR, Borevitz JO. Mapping a plant's chemical vocabulary. Nat Genet. 2006 Jul;38(7):737-8.

Kidgell C, Volkman SK, Daily J, Borevitz JO, Plouffe D, Zhou Y, Johnson JR, Le Roch K, Sarr O, Ndir O, Mboup S, Batalov S, Wirth DF, Winzeler EA. A systematic map of genetic variation in Plasmodium falciparum. PLoS Pathog. 2006 Jun;2(6):e57. Epub 2006 Jun 23. Erratum in: PLoS Pathog. 2006 Aug;2(8):e96.

Borevitz J. Genotyping and mapping with high-density oligonucleotide arrays. Methods Mol Biol. 2006;323:137-45.

Jiang R, Marjoram P, Borevitz JO, Tavaré S. Inferring population parameters from single-feature polymorphism data. Genetics. 2006 Aug;173(4):2257-67. Epub 2006 May 15.

Kim SK, Borevitz J. Mining the HapMap to dissect complex traits. Genome Biol. 2006;7(3):310. Epub 2006 Mar 28.

Kim S, Zhao K, Jiang R, Molitor J, Borevitz JO, Nordborg M, Marjoram P. Association mapping with single-feature polymorphisms. Genetics. 2006 Jun;173(2):1125-33. Epub 2006 Mar 1.

Hazen SP, Schultz TF, Pruneda-Paz JL, Borevitz JO, Ecker JR, Kay SA. LUX ARRHYTHMO encodes a Myb domain protein essential for circadian rhythms. Proc Natl Acad Sci U S A. 2005 Jul 19;102(29):10387-92. Epub 2005 Jul 8.

Rostoks N, Borevitz JO, Hedley PE, Russell J, Mudie S, Morris J, Cardle L, Marshall DF, Waugh R. Single-feature polymorphism discovery in the barley transcriptome. Genome Biol. 2005;6(6):R54. Epub 2005 May 11.

Werner JD, Borevitz JO, Uhlenhaut NH, Ecker JR, Chory J, Weigel D. FRIGIDA-independent variation in flowering time of natural Arabidopsis thaliana accessions. Genetics. 2005 Jul;170(3):1197-207. Epub 2005 May 23.