The development of an Arabidopsis model system for genome-wide analysis of polyploidy effects

Jeffrey Chen, Z., Wang, J., Tian, L., Lee, H. S., Wang, J. J., Chen, M., Lee, J. J., Josefsson, C., Madlung, A., Watson, B., Lippman, Z., Vaughn, M., Chris Pires, J., Colot, V., Doerge, R. W., Martienssen, R. A., Comai, L., Osborn, T. C. (2004) The development of an Arabidopsis model system for genome-wide analysis of polyploidy effects. Biological journal of the Linnean Society. Linnean Society of London, 82 (4). pp. 689-700. ISSN 0024-4066 (Print)0024-4066 (Linking)

URL: http://www.ncbi.nlm.nih.gov/pubmed/18079994
DOI: 10.1111/j.1095-8312.2004.00351.x

Abstract

Arabidopsis is a model system not only for studying numerous aspects of plant biology, but also for understanding mechanisms of the rapid evolutionary process associated with genome duplication and polyploidization. Although in animals interspecific hybrids are often sterile and aneuploids are related to disease syndromes, both Arabidopsis autopolyploids and allopolyploids occur in nature and can be readily formed in the laboratory, providing an attractive system for comparing changes in gene expression and genome structure among relatively 'young' and 'established' or 'ancient' polyploids. Powerful reverse and forward genetics in Arabidopsis offer an exceptional means by which regulatory mechanisms of gene and genome duplication may be revealed. Moreover, the Arabidopsis genome is completely sequenced; both coding and non-coding sequences are available. We have developed spotted oligo-gene and chromosome microarrays using the complete Arabidopsis genome sequence. The oligo-gene microarray consists of ~26 000 70-mer oligonucleotides that are designed from all annotated genes in Arabidopsis, and the chromosome microarray contains 1 kb genomic tiling fragments amplified from a chromosomal region or the complete sequence of chromosome 4. We have demonstrated the utility of microarrays for genome-wide analysis of changes in gene expression, genome organization and chromatin structure in Arabidopsis polyploids and related species.

Item Type: Paper
Subjects: organism description > plant > Arabidopsis
bioinformatics > genomics and proteomics > genetics & nucleic acid processing
bioinformatics > genomics and proteomics
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes
organism description > plant
CSHL Authors:
Communities: CSHL labs > Lippman lab
CSHL labs > Martienssen lab
Watson School > Publications
Depositing User: Matt Covey
Date Deposited: 04 Mar 2013 20:25
Last Modified: 19 Sep 2014 14:52
PMCID: PMC2136415
URI: http://repository.cshl.edu/id/eprint/27724

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