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Acta Agron Sin ›› 2013, Vol. 39 ›› Issue (01): 50-59.doi: 10.3724/SP.J.1006.2013.00050

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

DNA Methylation Site Analysis of Haploid, Diploid and Hybrids in Twin-Seedling Rice

WU Shao-Hua1,2,ZHANG Hong-Yu1,XUE Jing-Jing1,XU Pei-Zhou1,WU Xian-Jun1,*   

  1. 1 Rice Research Institute, Key Laboratory of Southwest Crop Genetic Resources and Improvement, Ministry of Education, Sichuan Agricultural University, Chengdu 611130, China; 2 Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, China
  • Received:2012-03-07 Revised:2012-09-05 Online:2013-01-12 Published:2012-11-14
  • Contact: 吴先军, E-mail: wuxj@sicau.edu.cn, Tel: 028-86290906

Abstract:

Whole-genome duplication or polyploidy, followed by gene loss and diploidization has long been recognized as an important evolutionary force in plants. Epigenetic mechanism, such as DNA methylation and miRNA, plays an important role in plant growth and development, and may also change its regulation pattern to adapt genomic duplication in new species. In this study, the DNA cytosine methylation at the 5'-CpCpGpG sites was analyzed by MSAP (methylation-sensitive amplification polymorphism) method in haploid, diploid and their hybrids derived from twin-seedling rice. And also, the relationships between DNA methylation and miRNA were investigated by sequencing the methylated DNA fragments and predicting the targets of miRNA. A total of 462 DNA methylated sites were detected. The hybrid’s methylation level was 43.20% and a little different from that of its parents (haploid, 46.75%; diploid, 41.99%). TargetFinder was used to find that seven methylated genes matched in sequence of rice database had 1-4 binding sites of miRNAs. The annotation indicated that the genes might include retrotransposon protein, ras-related protein and core histone H2A/H2B/H3/H4 domain containing protein. Most of the genes were annotated as retrotransposons and their functions in evolution were discussed. The results might help us to understand the relationships between DNA methylation and miRNA in rice genome duplication.

Key words: Twin-seedling rice, Haploid, DNA methylation, MSAP, miRNA

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