Brian Dilkes WikiCV

Brian Dilkes

Dept. of Horticulture and Landscape Architecture Purdue University [1] WSLR room B036B Roy L. Whistler Hall of Agricultural Research 170 S. University Street West Lafayette, IN 47907-2072 (765) 494-2584 West Lafayette, IN eMail: bdilkes tohellwithspammers purdue.edu Brian Dilkes OWW project page Dilkes Lab Purdue Page

EDUCATION

2003 Ph. D., University of Arizona, Department of Plant Sciences

1993 B. L. A., Oberlin College, Biology

RESEARCH EXPERIENCE

2009- Assistant Professor, Department of Horticulture, Purdue University

2005-2008 Project manager for the NSF-funded “Functional Genomics of Plant Polyploids”, Department of Biology, University of Washington and Genome Center and Section of Plant Biology, University of California Davis, Prof. Luca Comai

2003-2005 USDA postdoctoral fellow, Biology Department, University of Washington, Prof. Luca Comai

1997-2002 Graduate research assistant, University of Arizona, Department of Plant Sciences, Prof. Brian Larkins

1992-1996 Undergraduate researcher, technician and graduate research assistant, University of Arizona, Department of Plant Sciences Prof. Ken Feldmann

AWARDS

USDA-CREES-NRI 2003-35300-13248 “Functional genomic analysis of plant responses to autopolyploidy” 2003-2005

Role: Project Director/PI

NSF Plant Genome Research Project grant DBI-0077774/DBI-0501712 “Functional genomics of plant polyploids” 2005-2010

Role: Project Manager, PI Comai

NIH R01 GM076103-01A1 “Dosage-dependent regulation in hybridization” 2006-2011

Role: Senior Personnel, PI Comai

Ag Alumni Seed, Inc. “Maize genetic research” 2010

Role: Recipient/PI

USDA Graduate Research Fellowship “Genetic and genomic investigation of water use efficiency in Zea mays” supporting two students (R. Robinson 2010-12, and E. Svedin 2012-14)

Role: Joint with M. Mickelbart / PI H. Ohm

Bill and Melinda Gates Foundation OPP1052924 “Developing a Functional Gene Discovery Platform for Sorghum Improvement” 2012-2015

Role: Co-PI/ PI M. Tuinstra

AFRI Competitive Grant No. 2012-67012-19817 “Maize endosperm development is affected by small RNA in interploidy crosses” 2012-2014

Role: Mentor / PD: E. Buescher

REFEREED PUBLICATIONS

1. Hollister JD, Arnold BJ, Svedin E, Xue KS, Dilkes BP, Bomblies K 2012 Genetic Adaptation Associated with Genome-Doubling in Autotetraploid Arabidopsis arenosa. PLoS Genet 8(12): e1003093. doi:10.1371/journal.pgen.1003093
2. Albertin CB et al., 2012 Cephalopod Genomics: A plan of strategies and organization. Standards in Genomic Sciences 7(1)
3. Dilkes BP* and I Baxter* 2012 Elemental profiles reflect plant adaptations to the environment. Science 336 (6089): 1661-1663
4. Burkart-Waco D, Josefsson C, Dilkes BP, Kozloff N, Torjek O, Meyer R, Altmann T and Comai L 2011 Hybrid incompatibility in Arabidopsis is determined by a multi-locus genetic network.Plant Physiology 158(2):801-12.
5. Correa R, Stanga J, Larget B, Roznowski A, Shu G, Dilkes B, Baum DA. 2011 An assessment of transgenomics as a tool for identifying genes involved in the evolutionary differentiation of closely related plant species. New Phytologist 193(2):494-503. doi: 10.1111/j.1469-8137.2011.03949.x.
6. Chang PL, Dilkes BP, McMahon M, Comai L and Nuzhdin SV. Homoeolog-specific retention and use in allotetraploid Arabidopsis suecica depends on parent of origin and network partners. Genome Biology 2010, 11:R125
7. Henry IM, Dilkes BP, Miller ES, Burkart-Waco D, Comai L. 2010 Phenotypic Consequences of Aneuploidy in Arabidopsis thaliana. Genetics. 186(4):1231-1245
8. Pignatta D, Dilkes BP, Yoo, SY, Henry IM Madlung, A, Doerge, RW, Chen, JZ, Comai L. 2010 Differential sensitivity of the Arabidopsis thaliana transcriptome and enhancers to the effects of genome doubling. New Phytologist 186(1):194-206
9. Henry IM, Dilkes BP, Tyagi A, Lin H-S, and Comai L 2009 Dosage and parent-of-origin effects shaping aneuploid swarms in A. thaliana. Heredity doi: 10.1038/hdy.2009.81
10. Walia H, Josefsson C. Dilkes BP, Kirkbride R, Harada J and Comai L. 2009 Dosage-dependent deregulation of an AGAMOUS LIKE GENES cluster contributes to interspecific incompatibility. Current Biology 19(13):1128-32
11. Dilkes BP, Spielman M, Wiezbauer R, Burkart-Waco D, Watson B, Scott R, and Comai L 2008 The maternally-expressed WRKY transcription factor TTG2 controls lethality in interploidy crosses of Arabidopsis. PLoS Biol 6(12): e308 doi:10.1371/journal.pbio.0060308
12. Pignatta D, Dilkes BP, Wroblewski T, Michelmore RW, Comai L 2008 Transgene-induced gene silencing is not affected by a change in ploidy level. PLoS ONE 3(8): e3061. doi:10.1371/journal.pone.0003061
13. Henry IM, Dilkes BP, Comai L 2007 Genetic basis for dosage sensitivity in Arabidopsis thaliana. PLoS Genet 3(4): e70 doi:10.1371/journal.pgen.0030070
14. Henry IM, Dilkes BP, Comai L 2006 Molecular karyotyping and aneuploidy detection in A. thaliana using quantitative fluorescent PCR. Plant Journal, 48:307-319
15. Josefsson C, Dilkes B, Comai L 2006 Parent-dependent loss of gene silencing during interspecies hybridization. Current Biology 16:1322-1328
16. Coelho CM, Dante RA, Sabelli PA, Sun Y, Dilkes BP, Gordon-Kamm WJ Larkins BA 2005 Cyclin-dependent kinase inhibitors in maize endosperm and their potential role in endoreduplication. Plant Physiology 138: 2323-36
17. Henry IM, Dilkes BP, Young K, Watson B, Wu H, Comai L 2005 Aneuploidy and genetic variation in the Arabidopsis thaliana triploid bridge. Genetics 170: 1979-88
18. Dilkes BP, Comai L 2004 A differential dosage hypothesis for parental effects in seed development. Plant Cell 16:3174-80
19. Hunter BG, Beatty MK, Singletary GW, Hamaker BR, Dilkes BP, Larkins BA, and Jung R 2002 Maize opaque endosperm mutations create extensive changes in patterns of gene expression. Plant Cell 14: 14:2591-2612
20. Gordon-Kamm WJ, Dilkes BP, Lowe KS, Hoerster G, Sun X, Ross M, Church L, Bunde C, Farrell J, Hill P, Maddock S, Snyder J, Li X, Woo Y, Bidney D and Larkins BA 2002 Stimulation of the cell cycle and maize transformation by disruption of the plant retinoblastoma pathway. Proc. Natl. Acad. Sci. U S A 99: 11975-11980
21. Dilkes BP, Dante RD, Coelho C, Larkins BA. 2002 Genetic analyses of endoreduplication in Zea mays endosperm: evidence of sporophytic and zygotic maternal control. Genetics 160: 1163-117
22. Larkins BA, Dilkes BP, Dante RA, Coelho CM, Woo Y, Liu Y 2001 Investigating the hows and whys of DNA endoreduplication. J. Exp. Bot. 52: 183-92
23. Sun Y, Dilkes BP, Zhang C, Dante RA, Carneiro NP, Lowe KS, Jung R, Gordon-Kamm WJ, Larkins BA 1999 Characterization of maize (Zea mays L.) Wee1 and its activity in developing endosperm. Proc. Natl. Acad. Sci. U S A 96: 4180-5
24. Choe S, Dilkes BP, Gregory BD, Ross AS, Yuan H, Noguchi T, Fujioka S, Takatsuto S, Tanaka A, Yoshida S, Tax FE, Feldmann KA 1999 The Arabidopsis dwarf1 mutant is defective in the conversion of 24-methylenecholesterol to campesterol in brassinosteroid biosynthesis. Plant Physiol. 119: 897-907
25. Choe S, Dilkes BP, Fujioka S, Takatsuto S, Sakurai A, Feldmann KA 1998 The DWF4 gene of Arabidopsis encodes a cytochrome P450 that mediates multiple 22alpha-hydroxylation steps in brassinosteroid biosynthesis. Plant Cell 10: 231-43

RELEVANT TECHNICAL PUBLICATIONS

1. Gordon-Kamm WJ, Lowe KS, Gregory CA, Hoerster GJ, Larkins BA, Dilkes B, Burnett R 2004 Methods of using viral replicase polynucleotides and polypeptides. U.S. Patent 6,770,800
2. Sun Y, Dilkes B, Larkins BA, Lowe KS, Gordon-Kamm WJ, Dante RA 2004 Cell cycle nucleic acids, polypeptides and uses thereof. U.S. Patent 6,777,590
3. Gordon-Kamm WJ, Lowe KS Bailey MA, Gregory CA, Hoerster GJ, Larkins BA, Dilkes B, Burnett R, Woo, Y 2002 Methods of using viral replicase polynucleotides and polypeptides. U.S. Patent 6,452,070
4. Gordon-Kamm WJ, Lowe KS Bailey MA, Gregory CA, Hoerster GJ, Larkins BA, Dilkes B, Burnett R, Woo, Y 2001 Methods of using viral replicase polynucleotides and polypeptides. U.S. Patent 6,284,947
5. Dilkes, BP and Larkins BA 1999 "Transgenic plants: where is this technology leading us" in Biowork II (A. Borem, M.P. Giudice and N.S. Sakiyama, eds.), Federal University of Vicosa, Vicosa, Brasil, 213-240
6. Dilkes BP, , Feldmann KA 1998 Cloning genes from T-DNA tagged mutants. Methods Mol. Biol. 82: 339-51
7. Schulz B, Bennett MJ, Dilkes BP, and Feldmann KA 1995 “T-DNA tagging in Arabidopsis thaliana: cloning by gene disruption” in Plant Molecular Biology Manual (Gelvin, S, ed.) Kluwer Academic Publishers, The Netherlands pp. K3:1-17

CURRENT TEACHING ASSIGNMENTS

Undergraduate level

Agronomy 320 - This is an introductory genetics course required for a number majors in the College of Agriculture at Purdue University. The course is offered every semester. I teach it every Fall in collaboration with Clifford Weil of the Agronomy Department at Purdue.

Graduate level

Agronomy 530 - This is an advanced genetics course available to students interested in deepening their understanding of modern genetics and forging links between genomics, population genetics, classical genetics, and development. This is a primary literature-driven course.