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Genomic aspects of research involving polyploid plants

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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 evolutionary 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 polyploid 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 genomic 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.

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Acknowledgment

The writing of this review was supported by the U.S. DOE Office of Biological and Environmental Research, Genomic Science Program, and the U.S. DOE BioEnergy Science Center. The BioEnergy Science Center is a U.S. Department of Energy Bioenergy Research Center supported by the Office of Biological and Environmental Research in the DOE Office of Science. Oak Ridge National Laboratory is managed by UT-Battelle, LLC for the U.S. Department of Energy under Contract Number DE-AC05-00OR22725.

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Authors and Affiliations

  1. Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA

    Xiaohan Yang, Chu-Yu Ye, Timothy J. Tschaplinski & Gerald A. Tuskan

  2. BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA

    Xiaohan Yang, Chu-Yu Ye, Zong-Ming Cheng, Timothy J. Tschaplinski & Gerald A. Tuskan

  3. Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA

    Stan D. Wullschleger

  4. Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA

    Zong-Ming Cheng

  5. National Engineering Laboratory for Tree Breeding, Beijing Forestry University, 100083, Beijing, China

    Weilun Yin & Xinli Xia

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  1. Xiaohan Yang
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Yang, X., Ye, CY., Cheng, ZM. et al. Genomic aspects of research involving polyploid plants. Plant Cell Tiss Organ Cult 104, 387–397 (2011). https://doi.org/10.1007/s11240-010-9826-1

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