Award Abstract #0501712
Functional Genomics of Plant Polyploids

NSF Org:	DBI Division of Biological Infrastructure
Initial Amendment Date:	September 5, 2005
Latest Amendment Date:	July 24, 2006
Award Number:	0501712
Award Instrument:	Cooperative Agreement
Program Manager:	Jane Silverthorne DBI Division of Biological Infrastructure BIO Directorate for Biological Sciences
Start Date:	September 1, 2005
Expires:	July 31, 2007 (Estimated)
Awarded Amount to Date:	$3132154
Investigator(s):	Luca Comai lcomai@ucdavis.edu (Principal Investigator) Robert Martienssen (Co-Principal Investigator) James Birchler (Co-Principal Investigator) Rebecca Doerge (Co-Principal Investigator) Z. Jeffrey Chen (Co-Principal Investigator)
Sponsor:	University of Washington 4333 Brooklyn Ave NE SEATTLE, WA 98195 206/543-4043
NSF Program(s):	PLANT GENOME RESEARCH PROJECT
Field Application(s):
Program Reference Code(s):	BIOT,9109
Program Element Code(s):	1329

ABSTRACT



PI: Luca Comai, University of Washington

Co-PI: James A. Birchler, University of Missouri

Co-PI: Z. Jeffrey Chen, Texas A&M University

Co-PI: R. W. Doerge, Purdue University

Co-PI: Robert A. Martienssen, Cold Spring Harbor Laboratory

Co-PI: J. Chris Pires, University of Missouri

Senior Personnel: Edward Himelblau, California Polytechnic State University San Luis Obispo

Senior Personnel: Andreas Madlung, University of Puget Sound

Polyploidy can be found throughout the evolutionary history and diversity of eukaryotes, including flowering plants. Several of the most important agricultural crops are polyploid, such as wheat and Brassica, and many have identifiable polyploidy in their ancestry, such as maize. Whole genome duplication creates an autopolyploid by multiplying a single genome or an allopolyploid by combining two or more divergent genomes. Auto- and allopolyploids exhibit functional divergence of duplicate genes, increased variation and result in novel genetic interactions leading to greater phenotypic variability and hybrid vigor (heterosis). In this project, several hypotheses will be tested concerning the mechanisms of dosage-dependent and non-additive gene regulation in three complementary plant systems: Arabidopsis, Brassica and corn. The genetic basis of inbreeding depression, allopolyploid sterility, and hybrid vigor will be determined. Models for the molecular basis of gene regulation in polyploids using transgenic reporters and endogenous genes will be determined. The roles of chromatin structure and RNA interference in non-additive gene regulation will be tested. Gene expression changes in new polyploidy populations will be compared to identify loci affecting de novo phenotypic variation and hybrid vigor in polyploids.

In the post-sequencing era, polyploidy is one of the most challenging fields in plant biology. Results from this research will not only illuminate our understanding of polyploidy and the genetic mechanisms of non-additive gene action, but may also enable the improvement of agricultural crops.

Microarray data analysis and management will be streamlined using genome informatics and statistical methodologies. Research and training activities will be updated monthly at the project website. The senior personnel from two primarily teaching colleges (University of Puget Sound and California Polytechnic State University San Luis Obispo) will implement contemporary polyploidy and genomics modules into traditional genetics and biology curricula. The PIs will actively participate in exposing underrepresented students to research and teaching career opportunities by organizing summer internships and workshops in research laboratories in collaboration with local high and middle schools.

Access to project outcomes

Project data will be available at http://www.polyploidy.org/. Seeds will be deposited in the Arabidopsis Biological Resource Center (ABRC: http://www.biosci.ohio-state.edu/~plantbio/Facilities/abrc/abrchome.htm) and the Maize Genetics Cooperation Stock Center (http://w3.ag.uiuc.edu/maize-coop/). DNA sequences will be deposited in GenBank (http://www.ncbi.nlm.nih.gov/Genbank/) and microarray data in the Gene Expression Omnibus (GEO: http://www.ncbi.nlm.nih.gov/Genbank/GenbankOverview.html).

PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH

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Akio Kato and James A. Birchler.  "Induction of tetraploid derivatives of maize inbred lines by nitrous oxide gas treatment.,"  Journal of Heredity,  v.97,  2006,  p. 39.

Chen, Z. J. and Z. Ni.  "Mechanisms of genomic rearrangements and gene expression changes in plant polyploids,"  BioEssays,  v.28,  2006,  p. 240.

Chen, Z. J., Ha, M., and Soltis, D. E..  "Polyploidy: Genome obesity and its consequences,"  New Pytologist,  v.174,  2007,  p. 177.

Comai, L.  "The advantages and disadvantages of being polyploid,"  Nat Rev Genet 6: 836-846.,  v.6,  2005,  p. 836.

COMAI, L., and R. A. CARTWRIGHT.  "A toxic mutator and selection alternative to the non-Mendelian RNA cache hypothesis for hothead reversion,"  Plant Cell,  v.17,  2005,  p. 2856.

Fong, P. M., L. Tian, and Z. J. Chen.  "Arabidopsis thaliana histone deacetylase 1 (AtHD1) is localized in euchromatic regions and demonstrates histone deacetylase activity in vitro,"  Cell Research,  v.16,  2006,  p. 479.

Gendrel, A.V., Lippman, Z., Martienssen, R., and Colot, V..  "Profiling histone modification patterns in plants using genomic tiling microarrays.,"  Nature Methods,  v.2,  2005,  p. 213.

H. Jiang and R.W. Doerge.  "A two step multiple comparison procedure for a large number of tests and multiple treatments,"  Statistical Applications in Genetics and Molecular Biology,  v.5,  2006,  p. 28.

Ha, M., Li, W.-H., and Z. J. Chen.  "External factors accelerate expression divergence between duplicate genes,"  Trends in Genetics,  v.23,  2007,  p. 162.

Henry IM, Dilkes BP, Comai L.  "Genetic basis for dosage sensitivity in Arabidopsis thaliana,"  PLoS Genetics,  v.3,  2007,  p. e70.

HENRY, I. M., B. P. DILKES, and L. COMAI.  "Molecular karyotyping and aneuploidy detection in A. thaliana using quantitative fluorescent PCR. Plant Journal (Accepted with revision),"  The Plant Journal,  v.48,  2006,  p. 307.

HENRY, I. M., B. P. DILKES, K. YOUNG, B. WATSON, H. WU, and L. COMAI,.  "Aneuploidy and genetic variation in the Arabidopsis thaliana triploid response. Genetics 170: 1979-1988.,"  Genetics,  v.170,  2005,  p. 1979.

J. Stevens and R.W. Doerge.  "Combining Affymetrix microarray results,"  BioMed Central Bioinformatics,  v.6,  2005,  p. 57.

J. Wang, L. Tian, H-S Lee, N.E. Wei, H. Jiang, B. Watson, A. Madlung, T.C. Osborn, R.W. Doerge, L. Comai, and Z.J. Chen.  "Genome-wide non-additive gene regulation in Arabidopsis allotetraploids,"  Genetics,  v.172,  2006,  p. 507.

James A. Birchler, Hong Yao and Sivanandan Chudalayandi.  "Unraveling the genetic basis of hybrid vigor,"  Proc. Natl. Acad. Sci. USA,  v.103,  2006,  p. 12957.

JOSSEFSSON, C., B. P. DILKES, and L. COMAI,.  "Parent-dependent loss of gene silencing during interspecies hybridization.,"  Current Biology,  v.16,  2006,  p. 1322.

Katari, M.S., Balija, V., Wilson, R.K., Martienssen, R.A., and McCombie, W.R..  "Comparing low coverage random shotgun sequence data from Brassica oleracea and Oryza sativa genome sequence for their ability to add to the annotation of Arabidopsis thaliana.,"  Genome Research,  v.15,  2005,  p. 496.

L. An, N. Riddle, J. Bircherl, and R.W. Doerge.  "Clustering a series of replicated polyploid gene expression experiments,"  The Proceedings of the Kansas State University Conference on Applied Statistics in Agriculture,  2006,  p. 52.

Lippman, Z., Gendrel, A.V., Colot, V., and Martienssen, R..  "Profiling DNA methylation patterns using genomic tiling microarrays.,"  Nature Methods,  v.2,  2005,  p. 219.

Lukens LN, JC Pires, E Leon, RD Vogelzang, L Oslach, and TC Osborn.  "Patterns of sequence loss and cytosine methylation within a population of newly resynthesized Brassica napus.,"  Plant Physiology,  v.140,  2006,  p. 336.


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