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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.

Allopolyploidy

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.

Aneuploidy

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.

More

See more research and publications at TILLING.

Publications

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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][2][3][4][5][6][7][8][9][10][11][12][13][14][15][16][17][18][19][20][21][22][23][24][25][26][27]

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