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Open Access Research

Homoeolog-specific retention and use in allotetraploid Arabidopsis suecica depends on parent of origin and network partners

Peter L Chang1, Brian P Dilkes23, Michelle McMahon4, Luca Comai2 and Sergey V Nuzhdin1*

Author Affiliations

1 Molecular and Computational Biology, University of Southern California, 1050 Childs Way, RRI 201, Los Angeles, CA 90089-2910, USA

2 Genome Center and Department of Plant Biology, University of California at Davis, 451 Health Services Drive, Davis, CA 95616, USA

3 Current address: Department of Horticulture and Landscape Architecture, Purdue University, 625 Agriculture Mall Drive, West Lafayette, IN 47907-2010, USA

4 School of Plant Sciences, University of Arizona, 1140 E. South Campus Drive, Forbes Building, Room 303, Tucson, AZ 85721-0036, USA

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Genome Biology 2010, 11:R125  doi:10.1186/gb-2010-11-12-r125

Published: 23 December 2010

Abstract

Background

Allotetraploids carry pairs of diverged homoeologs for most genes. With the genome doubled in size, the number of putative interactions is enormous. This poses challenges on how to coordinate the two disparate genomes, and creates opportunities by enhancing the phenotypic variation. New combinations of alleles co-adapt and respond to new environmental pressures. Three stages of the allopolyploidization process - parental species divergence, hybridization, and genome duplication - have been well analyzed. The last stage of evolutionary adjustments remains mysterious.

Results

Homoeolog-specific retention and use were analyzed in Arabidopsis suecica (As), a species derived from A. thaliana (At) and A. arenosa (Aa) in a single event 12,000 to 300,000 years ago. We used 405,466 diagnostic features on tiling microarrays to recognize At and Aa contributions to the As genome and transcriptome: 324 genes lacked Aa contributions and 614 genes lacked At contributions within As. In leaf tissues, 3,458 genes preferentially expressed At homoeologs while 4,150 favored Aa homoeologs. These patterns were validated with resequencing. Genes with preferential use of Aa homoeologs were enriched for expression functions, consistent with the dominance of Aa transcription. Heterologous networks - mixed from At and Aa transcripts - were underrepresented.

Conclusions

Thousands of deleted and silenced homoeologs in the genome of As were identified. Since heterologous networks may be compromised by interspecies incompatibilities, these networks evolve co-biases, expressing either only Aa or only At homoeologs. This progressive change towards predominantly pure parental networks might contribute to phenotypic variability and plasticity, and enable the species to exploit a larger range of environments.