1. ¹Department of Biology, University of Florida, Gainesville, FL, USA
2. ²Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, USA
3. ³Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
4. ⁴Genetics Institute, University of Florida, Gainesville, FL, USA

Correspondence: Dr RJA Buggs, Department of Biology, University of Florida, Gainesville, FL 32611, USA. E-mail: buggs@ufl.edu

⁵These authors contributed equally to this work.

⁶Current address: Botany Department, Oklahoma State University, 104 Life Sciences East, Stillwater, OK 74078, USA.

⁷Current address: Massey University, Institute of Molecular Biosciences, Private Bag 11222, Palmerston North, New Zealand.

⁸Current address: Clemson University, Department of Genetics and Biochemistry, Biosystems Research Complex, 51 New Cherry Street, Clemson, SC 29634, USA.

Received 29 October 2008; Accepted 3 February 2009; Published online 11 March 2009.

Abstract

Whole-genome duplication (polyploidisation) is a widespread mechanism of speciation in plants. Over time, polyploid genomes tend towards a more diploid-like state, through downsizing and loss of duplicated genes (homoeologues), but relatively little is known about the timing of gene loss during polyploid formation and stabilisation. Several studies have also shown gene transcription to be affected by polyploidisation. Here, we examine patterns of gene loss in 10 sets of homoeologues in five natural populations of the allotetraploid Tragopogon miscellus that arose within the past 80 years following independent whole-genome duplication events. We also examine 44 first-generation synthetic allopolyploids of the same species. No cases of homoeologue loss arose in the first allopolyploid generation, but after 80 years, 1.6% of homoeologues were lost in natural populations. For seven homoeologue sets we also examined transcription, finding that 3.4% of retained homoeologues had been silenced in the natural populations, but none in the synthetic plants. The homoeologue losses and silencing events found were not fixed within natural populations and did not form a predictable pattern among populations. We therefore show haphazard loss and silencing of homoeologues, occurring within decades of polyploid formation in T. miscellus, but not in the initial generation.