Send to:

Choose Destination
See comment in PubMed Commons below
Plant J. 2013 Jan;73(1):143-53. doi: 10.1111/tpj.12026. Epub 2012 Oct 22.

The fate of duplicated genes in a polyploid plant genome.

Author information

  • 1Institute for Plant Breeding, Genetics and Genomics, University of Georgia, 111 Riverbend Road, Athens, GA, 30602, USA.
  • 2Zoologisches Institut, Universität Basel, Vesalgasse 1, CH-4051, Basel, Switzerland.
  • 3Department of Statistics, Purdue University, West Lafayette, IN, 47907, USA.
  • 4Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
  • 5Divisions of Plant Science and Biochemistry, University of Missouri, Columbia, MO, 65211, USA.
  • 6Department of Botany and Microbiology, University of Oklahoma, Norman, OK, 73019, USA.
  • 7College of Computing and Informatics, University of North Carolina Charlotte, Charlotte, NC, 28223, USA.
  • 8National Center for Genome Resources, Santa Fe, NM, USA.


Polyploidy is generally not tolerated in animals, but is widespread in plant genomes and may result in extensive genetic redundancy. The fate of duplicated genes is poorly understood, both functionally and evolutionarily. Soybean (Glycine max L.) has undergone two separate polyploidy events (13 and 59 million years ago) that have resulted in 75% of its genes being present in multiple copies. It therefore constitutes a good model to study the impact of whole-genome duplication on gene expression. Using RNA-seq, we tested the functional fate of a set of approximately 18 000 duplicated genes. Across seven tissues tested, approximately 50% of paralogs were differentially expressed and thus had undergone expression sub-functionalization. Based on gene ontology and expression data, our analysis also revealed that only a small proportion of the duplicated genes have been neo-functionalized or non-functionalized. In addition, duplicated genes were often found in collinear blocks, and several blocks of duplicated genes were co-regulated, suggesting some type of epigenetic or positional regulation. We also found that transcription factors and ribosomal protein genes were differentially expressed in many tissues, suggesting that the main consequence of polyploidy in soybean may be at the regulatory level.

© 2012 The Authors The Plant Journal © 2012 Blackwell Publishing Ltd.


Glycine max; RNA-seq; duplicated gene expression; genome evolution; polyploidy; sub-functionalization

[PubMed - in process]
PubMed Commons home

PubMed Commons

How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for Wiley
    Loading ...
    Write to the Help Desk