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Current Research Topics

We study three aspects of polyploidy, focusing on members of the genus Arabidopsis. The small and completely sequenced genome, substantial genetic resources, and short generation time allows us to determine the effects of gene and genome-level duplication.


We are investigating the roles of non-additive gene regulation in allopolyploid fitness and vigour using genomics and quantitative genetics. Our goal is to identify the genetic mechanisms for adaptation to allopolyploidy using the naturally occurring allopolyploid Arabidopsis suecica and Arabidopsis thaliana X Arabidopsis arenosa species hybrids produced in the lab. This is part of the collaborative NSF project Functional Genomics of Plant Polyploids.

Effect of polyploidy on gene expression

A second component of the Functional Genomics of Plant Polyploids project, a collaborative project funded by the NSF Plant Genome Research Program, is focused on determining the molecular basis of changes in gene expression that occur following genome duplication. During the previous funding cycle, we and our collaborators (as well as other groups) demonstrated that many genes exhibit altered regulation when moved from the diploid to either the autopolyploid or allopolyploid condition. In this work, we used microarrays which are inexpensive on a per gene basis and capable of surveying the whole genome to describe the global patterns of changes in gene expression following a shift in ploidy. Unfortunately, microarrays are expensive on a per-sample basis and relatively insensitive to changes in spatial distribution of gene expression within an organism (but see this paper for the results of another NSF funded collaborative project). We are in the process of generating new tools that will overcome these challenges and will investigate the molecular and developmental mechanisms for non-additive gene regulation in polyploids.

Postzygotic incompatibility

One dramatic feature of polyploids is the lethality of intercrosses between a newly formed polyploid and its diploid progenitors. This can serve to isolate newly formed auto or allopolyploids and potentiate speciation. Using multiple species of Arabidopsis we are investigating the basis of seed failure in inter-ploidy and inter-species crosses.


Changes in the balance of chromosomes can also have dramatic effects on plant development and fitness. The dosage-balance hypothesis, articulated by Bridges at the beginning of the 20th century, proposes that this is due to a disruption in the quantity of genes and gene products that function via stoichiometric interaction. While this would seem to affect all eukaryotes similarly, this is not the case. Plants appear far less susceptible to the negative consequences than large animals, and even within plants there is substantial variation between species for the effects of aneuploidy on viability. Given such variation it is not surprising that within species there is even variation for tolerance to genomic imbalance. We have identified variation between ecotypes of Arabidopsis thaliana for their tolerance to changes in chromosome number. We are currently characterizing the variation at the genetic level and investigating the molecular basis of this genetically-determined aneuploidy tolerance.


See more research and publications at TILLING.


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  • Diana Burkar-Waco et al. describe a network of quantitative loci regulating response to interspecific hybridization. The paper appeared in Plant Physiology.
  • Harkamal Walia et al. describe the contribution of AGAMOUS LIKE GENES to interspecific incompatibility between Arabidopsis thaliana and Arabidopsis arenosa. The paper appeared in Current Biology.
  • Isabelle Henry et al. describe the inheritance of chromosomes in aneuploids of Arabidopsis thaliana. The paper appeared in Heredity.


  1. Burkart-Waco D et al. (2011) Hybrid incompatibility in Arabidopsis is determined by a multi-locus genetic network. Plant Physiol ': PubMed
  2. Henry IM et al. (2010) Phenotypic Consequences of Aneuploidy in Arabidopsis thaliana. Genetics ': PubMed
  3. Henry IM et al. (2009) Dosage and parent-of-origin effects shaping aneuploid swarms in A. thaliana. Heredity 103: 458-68 PubMed
  4. Pignatta D & Comai L (2009) Parental squabbles and genome expression: lessons from the polyploids. J Biol 8: 43 PubMed
  5. Walia H et al. (2009) Dosage-dependent deregulation of an AGAMOUS-LIKE gene cluster contributes to interspecific incompatibility. Curr Biol 19: 1128-32 PubMed
  6. Dilkes BP et al. (2008) The maternally expressed WRKY transcription factor TTG2 controls lethality in interploidy crosses of Arabidopsis. PLoS Biol 6: 2707-20 PubMed
  7. Pignatta D et al. (2008) Transgene-induced gene silencing is not affected by a change in ploidy level. PLoS ONE 3: e3061 PubMed
  8. Henry IM et al. (2007) Genetic basis for dosage sensitivity in Arabidopsis thaliana. PLoS Genet 3: e70 PubMed
  9. Henry IM et al. (2006) Molecular karyotyping and aneuploidy detection in Arabidopsis thaliana using quantitative fluorescent polymerase chain reaction. Plant J 48: 307-19 PubMed
  10. Josefsson C et al. (2006) Parent-dependent loss of gene silencing during interspecies hybridization. Curr Biol 16: 1322-8 PubMed
  11. Wang J et al. (2006) Genomewide nonadditive gene regulation in Arabidopsis allotetraploids. Genetics 172: 507-17 PubMed
  12. Comai L (2005) The advantages and disadvantages of being polyploid. Nat Rev Genet 6: 836-46 PubMed
  13. Henry IM et al. (2005) Aneuploidy and genetic variation in the Arabidopsis thaliana triploid response. Genetics 170: 1979-88 PubMed
  14. Wang J et al. (2005) Methods for genome-wide analysis of gene expression changes in polyploids. Methods Enzymol 395: 570-96 PubMed
  15. Madlung A et al. (2005) Genomic changes in synthetic Arabidopsis polyploids. Plant J 41: 221-30 PubMed
  16. Pontes O et al. (2004) Chromosomal locus rearrangements are a rapid response to formation of the allotetraploid Arabidopsis suecica genome. Proc Natl Acad Sci U S A 101: 18240-5 PubMed
  17. Dilkes BP & Comai L (2004) A differential dosage hypothesis for parental effects in seed development. Plant Cell 16: 3174-80 PubMed
  18. Madlung A & Comai L (2004) The effect of stress on genome regulation and structure. Ann Bot (Lond) 94: 481-95 PubMed
  19. Wang J et al. (2004) Stochastic and epigenetic changes of gene expression in Arabidopsis polyploids. Genetics 167: 1961-73 PubMed
  20. Comai L et al. (2003) Do the different parental 'heteromes' cause genomic shock in newly formed allopolyploids? Philos Trans R Soc Lond B Biol Sci 358: 1149-55 PubMed
  21. Osborn TC et al. (2003) Understanding mechanisms of novel gene expression in polyploids. Trends Genet 19: 141-7 PubMed
  22. Comai L et al. (2003) FISH analysis of meiosis in Arabidopsis allopolyploids. Chromosome Res 11: 217-26 PubMed
  23. Madlung A et al. (2002) Remodeling of DNA methylation and phenotypic and transcriptional changes in synthetic Arabidopsis allotetraploids. Plant Physiol 129: 733-46 PubMed
  24. Talbert PB et al. (2002) Centromeric localization and adaptive evolution of an Arabidopsis histone H3 variant. Plant Cell 14: 1053-66 PubMed
  25. Comai L et al. (2000) Phenotypic instability and rapid gene silencing in newly formed arabidopsis allotetraploids. Plant Cell 12: 1551-68 PubMed
  26. Comai L (2000) Genetic and epigenetic interactions in allopolyploid plants. Plant Mol Biol 43: 387-99 PubMed
  27. Chen ZJ et al. (1998) Gene dosage and stochastic effects determine the severity and direction of uniparental ribosomal RNA gene silencing (nucleolar dominance) in Arabidopsis allopolyploids. Proc Natl Acad Sci U S A 95: 14891-6 PubMed

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