Originally published as Genetics Published Articles Ahead of Print on April 10, 2009.

Genetics, Vol. 182, 503-517, June 2009, Copyright © 2009
doi:10.1534/genetics.109.102608

Reciprocal Silencing, Transcriptional Bias and Functional Divergence of Homeologs in Polyploid Cotton (Gossypium)

Bhupendra Chaudhary*,1, Lex Flagel*,1, Robert M. Stupar{dagger}, Joshua A. Udall{ddagger}, Neetu Verma*, Nathan M. Springer§ and Jonathan F. Wendel*,2

* Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011, {dagger} Departments of Agronomy and Plant Genetics and § Plant Biology, University of Minnesota, St. Paul, Minnesota 55108 and {ddagger} Department of Plant and Wildlife Sciences, Brigham Young University, Provo, Utah 84602

2 Corresponding author: Department of Ecology, Evolution, and Organismal Biology, 251 Bessey Hall, Iowa State University, Ames, IA 50011.
E-mail: jfw{at}iastate.edu

Polyploidy is an important force in the evolution of flowering plants. Genomic merger and doubling induce an extensive array of genomic effects, including immediate and long-term alterations in the expression of duplicate genes ("homeologs"). Here we employed a novel high-resolution, genome-specific, mass-spectrometry technology and a well-established phylogenetic framework to investigate relative expression levels of each homeolog for 63 gene pairs in 24 tissues in naturally occurring allopolyploid cotton (Gossypium L.), a synthetic allopolyploid of the same genomic composition, and models of the diploid progenitor species. Results from a total of 2177 successful expression assays permitted us to determine the extent of expression evolution accompanying genomic merger of divergent diploid parents, genome doubling, and genomic coevolution in a common nucleus subsequent to polyploid formation. We demonstrate that 40% of homeologs are transcriptionally biased in at least one stage of cotton development, that genome merger per se has a large effect on relative expression of homeologs, and that the majority of these alterations are caused by cis-regulatory divergence between the diploid progenitors. We describe the scope of transcriptional subfunctionalization and 15 cases of probable neofunctionalization among 8 tissues. To our knowledge, this study represents the first characterization of transcriptional neofunctionalization in an allopolyploid. These results provide a novel temporal perspective on expression evolution of duplicate genomes and add to our understanding of the importance of polyploidy in plants.


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Genetics 2009 182: NP. [Full Text]