Research article
Molecular characterization of a rice mutator-phenotype derived from an incompatible cross-pollination reveals transgenerational mobilization of multiple transposable elements and extensive epigenetic instability
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* Corresponding authors: Chunming Xu xucm848@nenu.edu.cn - Bao Liu baoliu@nenu.edu.cn
- † Equal contributors
1 Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun 130024, PR China
2 Tonghua Academy of Agricultural Sciences, Hailong 135007, Jilin Province, PR China
3 Key Laboratory of Applied Statistics of MOE, Northeast Normal University, Changchun 130024, PR China
BMC Plant Biology 2009, 9:63 doi:10.1186/1471-2229-9-63
Published: 29 May 2009Additional files
Additional file 1:
Characterization of mPing excisions. A total of 16 loci that were excised from one or more of the 8 studied progeny individuals (from S1-1 to S1 – 8) of the mutator-phenotype Tong211-LP (S0) were identified by mPing-specific transposon-display (TD) and validated by cloning, sequencing, and locus-specific PCR amplification.
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Additional file 2:
Characterization of mPing de novo insertions. A total of 14 mPing de novo insertion events which occurred in some of the selfed progeny individuals (from S1-1 to S1 – 8) of the mutator-phenotype Tong211-LP(S0) were identified by mPing-specific transposons-display (TD) and validated by cloning, sequencing and locus-specific PCR amplification.
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Additional file 3:
Characterization of variant AFLP and MSAP bands. Chromosomal location and functional homology of isolated variant AFLP and MSAP fragments from the mutator phenotype Tong211-LP (S0) and/or its 8 selfed progeny individuals (from S1-1 to S1 – 8) were determined based on the reference genome sequence of cv. Nipponbare.
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Additional file 4:
Primers used to amplify the probe fragments of 12 low-copy and potentially active transposable elements (TEs) endogenous to the rice genome. Authenticity of the amplicons were verified by sequencing.
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Additional file 5:
Real-time q-RT PCR primers used to measure the transcript quantity of a set of genes related to the chromatin epigenetic maintenance machinery. Primers of a set of 13 genes encoding for the putative DNA methyltransferases, 5-methylcytosine DNA glycosylases and siRNA-related proteins were designed by the Primer 5 software, based on the sequence information deposited at the Chromatin database http://www.chromdb.org/ webcite.
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