Originally published as Genetics Published Articles Ahead of Print on April 28, 2006.

Genetics, Vol. 173, 1599-1611, July 2006, Copyright © 2006
doi:10.1534/genetics.106.057646

Evolution and Expression of Homeologous Loci in Tragopogon miscellus (Asteraceae), a Recent and Reciprocally Formed Allopolyploid

Jennifer A. Tate*,1, Zhongfu Ni{dagger}, Anne-Cathrine Scheen{ddagger}, Jin Koh*, Candace A. Gilbert*, David Lefkowitz*, Z. Jeffrey Chen{dagger}, Pamela S. Soltis§ and Douglas E. Soltis*

* Department of Botany, University of Florida, Gainesville, Florida 32611, {dagger} Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas 78712, {ddagger} Natural History Museum, University of Oslo, N-0318 Oslo, Norway and § Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611

1 Corresponding author: Institute of Molecular Biosciences, Massey University, Private Bag 11-222, Palmerston North, New Zealand.
E-mail: jtate{at}ufl.edu

On both recent and ancient time scales, polyploidy (genome doubling) has been a significant evolutionary force in plants. Here, we examined multiple individuals from reciprocally formed populations of Tragopogon miscellus, an allotetraploid that formed repeatedly within the last 80 years from the diploids T. dubius and T. pratensis. Using cDNA–AFLPs followed by genomic and cDNA cleaved amplified polymorphic sequence (CAPS) analyses, we found differences in the evolution and expression of homeologous loci in T. miscellus. Fragment variation within T. miscellus, possibly attributable to reciprocal formation, comprised 0.6% of the cDNA–AFLP bands. Genomic and cDNA CAPS analyses of 10 candidate genes revealed that only one "transcript-derived fragment" (TDF44) showed differential expression of parental homeologs in T. miscellus; the T. pratensis homeolog was preferentially expressed by most polyploids in both populations. Most of the cDNA–AFLP polymorphisms apparently resulted from loss of parental fragments in the polyploids. Importantly, changes at the genomic level have occurred stochastically among individuals within the independently formed populations. Synthetic F1 hybrids between putative diploid progenitors are additive of their parental genomes, suggesting that polyploidization rather than hybridization induces genomic changes in Tragopogon.




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