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First published online December 23, 2005; 10.1104/pp.105.066308 Plant Physiology 140:336-348 (2006) © 2006 American Society of Plant Biologists Patterns of Sequence Loss and Cytosine Methylation within a Population of Newly Resynthesized Brassica napus Allopolyploids1,[W]Department of Plant Agriculture, University of Guelph, Guelph, Ontario, Canada N1G 2W1 (L.N.L., L.O.); and Department of Agronomy, University of Wisconsin, Madison, Wisconsin 53706 (J.C.P., E.L., R.V., T.O.)
Allopolyploid formation requires the adaptation of two nuclear genomes within a single cytoplasm, which may involve programmed genetic and epigenetic changes during the initial generations following genome fusion. To study the dynamics of genome change, we synthesized 49 isogenic Brassica napus allopolyploids and surveyed them with 76 restriction fragment length polymorphism (RFLP) probes and 30 simple sequence repeat (SSR) primer pairs. Here, we report on the types and distribution of genetic and epigenetic changes within the S1 genotypes. We found that insertion/deletion (indel) events were rare, but not random. Of the 57,710 (54,383 RFLP and 3,327 SSR) parental fragments expected among the amphidiploids, we observed 56,676 or 99.9%. Three loci derived from Brassica rapa had indels, and one indel occurred repeatedly across 29% (14/49) of the lines. Loss of one parental fragment was due to the 400-bp reduction of a guanine-adenine dinucleotide repeat-rich sequence. In contrast to the 4% (3/76) RFLP probes that detected indels, 48% (35/73) detected changes in the CpG methylation status between parental genomes and the S1 lines. Some loci were far more likely than others to undergo epigenetic change, but the number of methylation changes within each synthetic polyploid was remarkably similar to others. Clear de novo methylation occurred at a much higher frequency than de novo demethylation within allopolyploid sequences derived from B. rapa. Our results suggest that there is little genetic change in the S0 generation of resynthesized B. napus polyploids. In contrast, DNA methylation was altered extensively in a pattern that indicates tight regulation of epigenetic changes.
1 This work was supported by the National Science Foundation Plant Genome Program (grant no. 0077774 to T.C.O.), and by the Natural Sciences and Engineering Research Council of Canada and the Ontario Ministry of Agriculture and Food (grants to L.L.). 2 These authors contributed equally to the paper. 3 Present address: Division of Biological Sciences, Life Sciences Center, University of Missouri, Columbia, MO 65211. 4 Present address: Seminis Vegetable Seeds, Inc., 37437 State Highway 16, Woodland, CA 95695. The authors responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) are: Lewis N. Lukens (llukens{at}uoguelph.ca) and J. Chris Pires (piresjc{at}missouri.edu). [W] The online version of this article contains Web-only data. Article, publication date, and citation information can be found at www.plantphysiol.org/cgi/doi/10.1104/pp.105.066308. * Corresponding author; e-mail llukens{at}uoguelph.ca; fax 519–763–8933. Received May 28, 2005; returned for revision September 21, 2005; accepted November 1, 2005. This article has been cited by other articles:
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