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Lukens LN, Pires JC, Leon E, Vogelzang R, Oslach L, Osborn T.. Patterns of sequence loss and cytosine methylation within a population of newly resynthesized Brassica napus allopolyploids. Plant Physiol 140: 336-348

Department of Plant Agriculture, University of Guelph, Guelph, Ontario, Canada N1G 2W1.
Plant physiology (Impact Factor: 7.39). 02/2006; 140(1):336-48. DOI: 10.1104/pp.105.066308
Source: PubMed

ABSTRACT 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 S(1) 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 S(0) generation of resynthesized B. napus polyploids. In contrast, DNA methylation was altered extensively in a pattern that indicates tight regulation of epigenetic changes.

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    • "DNA methylation is restricted to CpG dinucleotides in many animal species, whereas in plants, the cytosine can be methylated at CpG, CpNpG and CpNpN sites (Feng et al. 2010). Sequence loss, gene duplication regulated by methylation, alteration of epigenetic silencing of transposons together with changes in regulatory networks are all genomic modifications commonly observed after polyploidization events in plants (Osborn et al. 2003; Wang et al. 2004; Adams & Wendel 2005; Lukens et al. 2006; Chen 2010; Kenan-Eichler et al. 2011; Xiao et al. 2013). Normal function and structure maintenance of the newly formed polyploid genome seems to have a close relationship with the epigenetic process (Matzke et al. 1999; Salmon et al. 2005; Wendel & Doyle 2005; Chen & Ni 2006). "
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    • "Accumulated evidence over the last two decades based on both molecular marker analysis of selected genomic loci (Feldman et al. 1997; Liu et al. 1998a; Ozkan et al. 2001; Shaked et al. 2001; Han et al. 2005) and recent whole genome and transcriptome sequencing (Saintenac et al. 2011; Pont et al. 2013; IWGSC 2014) have established that both single nucleotide polymorphisms (SNPs) and largereffect genetic changes including gene loss, copy number variations (CNVs), and chromosomal rearrangements are associated with genome evolution in tetraploid and hexaploid wheats. Epigenetic changes in the form of altered DNA methylation have also been shown to accompany allopolyploidization in newly formed wheat allopolyploids (Liu et al. 1998b; Shaked et al. 2001; Shitsukawa et al. 2007; Zhao et al. 2011), as in other studied allopolyploid plants (Madlung et al. 2002; Salmon et al. 2005; Lukens et al. 2006; Gaeta et al. 2007; Parisod et al. 2009; Xu et al. 2009; Mayfield et al. 2011; Hu et al. 2013; Madlung and Wendel 2013; Diez et al. 2014). Therefore, both genetic and epigenetic changes and their intertwined interactions should have underpinned genome evolution in polyploid wheat. "
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