%0 Journal Article
%T Homoeolog-specific retention and use in allotetraploid Arabidopsis suecica depends on parent of origin and network partners
%A Peter L Chang
%A Brian P Dilkes
%A Michelle McMahon
%A Luca Comai
%A Sergey V Nuzhdin
%J Genome Biology
%D 2010
%I BioMed Central
%R 10.1186/gb-2010-11-12-r125
%X 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.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.An allotetraploid is formed when diploids from two different species, which may have diverged for millions of years, hybridize. The resulting plant, if viable, might have a competitive edge, such as broader ecological tolerance compared to its parents [1-3]. The evolutionary importance of polyploidy, of which allotetraploidy is a common form, is reflected in its prevalence in flowering plants [4]: ancient polyploidy is apparent in all plant genomes sequenced to date and is estimated to have been involved in 15% of all plant speciation events [5]. Furthermore, most cultivated crops have undergone polyploidization during their ancestry [5,6]. Why are polyploids so evolutionarily, ecologically, and agriculturally successful? To answer this question, one has to consider the evolutiona
%U http://genomebiology.com/2010/11/12/R125