REVIEW Genomic aspects of research involving polyploid plants Xiaohan Yang • Chu-Yu Ye • Zong-Ming Cheng • Timothy J. Tschaplinski • Stan D. Wullschleger • Weilun Yin • Xinli Xia • Gerald A. Tuskan Received: 19 June 2010 / Accepted: 13 August 2010 / Published online: 31 August 2010 Ó Springer Science+Business Media B.V. 2010 Abstract Almost all extant plant species have doubled their genomes at least once in their evolutionary histories, resulting in polyploidy which provided a rich genomic resource for evolutionary processes. Moreover, superior polyploid clones have been developed during the process of crop domestication. Polyploid plants generated by evolu- tionary processes and/or crop domestication have been the intentional or serendipitous focus of research dealing with the dynamics and consequences of genome evolution. One of the new trends in genomics research is to create synthetic polyploid plants which provide materials for studying the initial genomic changes/responses immediately after poly- ploid formation. Polyploid plants are also used in functional genomics research to study gene expression in a complex genomic background. In this review, we summarize recent progress in genomics research involving ancient, young, and synthetic polyploid plants, with a focus on genome size evolution, genomic diversity, genomic rearrangement, genetic and epigenetic changes in duplicated genes, gene discovery, and comparative genomics. Implications on plant sciences including evolution, functional genomics, and plant breeding are presented. Polyploids will be a focus of geno- mic research in the future as rapid advances in DNA sequencing technology create unprecedented opportunities for discovering and monitoring genomic and transcriptomic changes. The accumulation of knowledge on polyploid formation, maintenance, and divergence at whole-genome and subgenome levels will not only help plant biologists understand how plants have evolved and diversified, but also assist plant breeders in designing new strategies for crop improvement. Keywords Evolution Á Genetics Á Epigenetics Introduction Polyploidy (genome doubling), discovered in 1907, is an important driver of eukaryotic evolution, evident in many animals, fungi, and plants (Grant 1981; Hovav et al. 2008; Wood et al. 2009). Almost all eukaryotes have had a history of ancient polyploidization events followed by diploidiza- tion and then repeated polyploidization (Birchler and Veitia 2010; Salmon and Ainouche 2010). Polyploid plants have been generated from evolutionary processes, crop domesti- cation, and/or artificial synthesis via chemical or physical mutations. Traditionally, polyploid plants have been studied from the perspectives of crop domestication, e.g., creating crops with specific traits such as larger flowers and fruits. This type of research has been reviewed extensively in the X. Yang (&) Á C.-Y. Ye Á T. J. Tschaplinski Á G. A. Tuskan Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA e-mail: yangx@ornl.gov X. Yang Á C.-Y. Ye Á Z.-M. Cheng Á T. J. Tschaplinski Á G. A. Tuskan BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA S. D. Wullschleger Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA Z.-M. Cheng Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA W. Yin Á X. Xia National Engineering Laboratory for Tree Breeding, Beijing Forestry University, 100083 Beijing, China 123 Plant Cell Tiss Organ Cult (2011) 104:387–397 DOI 10.1007/s11240-010-9826-1