Polyploidy

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 vigor 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 A Gene Expression Map of the Arabidopsis Root 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

  1. Diana Burkar-Waco et al. describe a network of quantitative loci regulating response to interspecific hybridization. The paper appeared in Plant Physiology.
  2. 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.
  3. Isabelle Henry et al. describe the inheritance of chromosomes in aneuploids of Arabidopsis thaliana. The paper appeared in Heredity.
  1. Burkart-Waco D, Josefsson C, Dilkes B, et al. Hybrid incompatibility in Arabidopsis is determined by a multiple-locus genetic network. Plant Physiol. 2012;158(2):801‐812. doi:10.1104/pp.111.188706
  2. Henry IM, Dilkes BP, Miller ES, Burkart-Waco D, Comai L. Phenotypic consequences of aneuploidy in Arabidopsis thaliana. Genetics. 2010;186(4):1231‐1245. doi:10.1534/genetics.110.121079
  3. Henry IM, Dilkes BP, Tyagi AP, Lin HY, Comai L. Dosage and parent-of-origin effects shaping aneuploid swarms in A. thaliana. Heredity (Edinb). 2009;103(6):458‐468. doi:10.1038/hdy.2009.81
  4. Pignatta D, Comai L. Parental squabbles and genome expression: lessons from the polyploids. J Biol. 2009;8(4):43. doi:10.1186/jbiol140
  5. Walia H, Josefsson C, Dilkes B, Kirkbride R, Harada J, Comai L. Dosage-dependent deregulation of an AGAMOUS-LIKE gene cluster contributes to interspecific incompatibility. Curr Biol. 2009;19(13):1128‐1132. doi:10.1016/j.cub.2009.05.068
  6. Dilkes BP, Spielman M, Weizbauer R, et al. The maternally expressed WRKY transcription factor TTG2 controls lethality in interploidy crosses of Arabidopsis. PLoS Biol. 2008;6(12):2707‐2720. doi:10.1371/journal.pbio.0060308
  7. Pignatta D, Dilkes B, Wroblewski T, Michelmore RW, Comai L. Transgene-induced gene silencing is not affected by a change in ploidy level. PLoS One. 2008;3(8):e3061. Published 2008 Aug 26. doi:10.1371/journal.pone.0003061
  8. Henry IM, Dilkes BP, Comai L. Genetic basis for dosage sensitivity in Arabidopsis thaliana. PLoS Genet. 2007;3(4):e70. doi:10.1371/journal.pgen.0030070
  9. Henry IM, Dilkes BP, Comai L. Molecular karyotyping and aneuploidy detection in Arabidopsis thaliana using quantitative fluorescent polymerase chain reaction. Plant J. 2006;48(2):307‐319. doi:10.1111/j.1365-313X.2006.02871.x
  10. Josefsson C, Dilkes B, Comai L. Parent-dependent loss of gene silencing during interspecies hybridization. Curr Biol. 2006;16(13):1322‐1328. doi:10.1016/j.cub.2006.05.045
  11. Wang J, Tian L, Lee HS, et al. Genomewide nonadditive gene regulation in Arabidopsis allotetraploids. Genetics. 2006;172(1):507‐517. doi:10.1534/genetics.105.047894
  12. Comai L. The advantages and disadvantages of being polyploid. Nat Rev Genet. 2005;6(11):836‐846. doi:10.1038/nrg1711
  13. Henry IM, Dilkes BP, Young K, Watson B, Wu H, Comai L. Aneuploidy and genetic variation in the Arabidopsis thaliana triploid response. Genetics. 2005;170(4):1979‐1988. doi:10.1534/genetics.104.037788
  14. Wang J, Lee JJ, Tian L, et al. Methods for genome-wide analysis of gene expression changes in polyploids. Methods Enzymol. 2005;395:570‐596. doi:10.1016/S0076-6879(05)95030-1
  15. Madlung A, Tyagi AP, Watson B, et al. Genomic changes in synthetic Arabidopsis polyploids. Plant J. 2005;41(2):221‐230. doi:10.1111/j.1365-313X.2004.02297.x
  16. Pontes O, Neves N, Silva M, et al. Chromosomal locus rearrangements are a rapid response to formation of the allotetraploid Arabidopsis suecica genome. Proc Natl Acad Sci U S A. 2004;101(52):18240‐18245. doi:10.1073/pnas.0407258102
  17. Dilkes BP, Comai L. A differential dosage hypothesis for parental effects in seed development. Plant Cell. 2004;16(12):3174‐3180. doi:10.1105/tpc.104.161230
  18. Madlung A, Comai L. The effect of stress on genome regulation and structure. Ann Bot. 2004;94(4):481‐495. doi:10.1093/aob/mch172
  19. Wang J, Tian L, Madlung A, et al. Stochastic and epigenetic changes of gene expression in Arabidopsis polyploids. Genetics. 2004;167(4):1961‐1973. doi:10.1534/genetics.104.027896
  20. Comai L, Madlung A, Josefsson C, Tyagi A. Do the different parental ‘heteromes’ cause genomic shock in newly formed allopolyploids?. Philos Trans R Soc Lond B Biol Sci. 2003;358(1434):1149‐1155. doi:10.1098/rstb.2003.1305
  21. Osborn TC, Pires JC, Birchler JA, et al. Understanding mechanisms of novel gene expression in polyploids. Trends Genet. 2003;19(3):141‐147. doi:10.1016/s0168-9525(03)00015-5
  22. Comai L, Tyagi AP, Lysak MA. FISH analysis of meiosis in Arabidopsis allopolyploids. Chromosome Res. 2003;11(3):217‐226. doi:10.1023/a:1022883709060
  23. Madlung A, Masuelli RW, Watson B, Reynolds SH, Davison J, Comai L. Remodeling of DNA methylation and phenotypic and transcriptional changes in synthetic Arabidopsis allotetraploids. Plant Physiol. 2002;129(2):733‐746. doi:10.1104/pp.003095
  24. Talbert PB, Masuelli R, Tyagi AP, Comai L, Henikoff S. Centromeric localization and adaptive evolution of an Arabidopsis histone H3 variant. Plant Cell. 2002;14(5):1053‐1066. doi:10.1105/tpc.010425
  25. Comai L, Tyagi AP, Winter K, et al. Phenotypic instability and rapid gene silencing in newly formed arabidopsis allotetraploids. Plant Cell. 2000;12(9):1551‐1568. doi:10.1105/tpc.12.9.1551
  26. Comai L. Genetic and epigenetic interactions in allopolyploid plants. Plant Mol Biol. 2000;43(2-3):387‐399. doi:10.1023/a:1006480722854
  27. Chen ZJ, Comai L, Pikaard CS. 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. 1998;95(25):14891‐14896. doi:10.1073/pnas.95.25.14891
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