Natural Homologous Triploidization and DNA Methylation in SARII-628, a Twin-seedling Line of Rice (Oryza sativa)

Abstract

Abstract: A total of five pairs of diploid-triploid twin-seedlings (a diploid seedling and a triploid seedling emerged from a grain) were selected out from 4500 pairs of seedlings from SARII-628, a twin-seedling rice line. SSR analysis indicated that no difference between the diploid seedling and corresponding triploid seedling in a twin-seedling was found at the 310 loci, indicating that there was no obvious change in DNA primary structure. A modified AFLP technique ‘MSAP (methylation-sensitive AFLP)’ was used to analyze methylation mutation. Although no methylation mutation was noted among the five diploids, 29 methylation mutation loci were found from the corresponding triploids. This suggested that methylation mutation happened rapidly on M₀generation after natural homologous triploidization. The mutations were classified into 10 types, including 3 increased types, 3 decreased types and 4 undecided types of methylation-degrees. The bands of 22 loci were sequenced and then those sequences were searched through website. The result showed that the methylation mutation involved into the whole rice genome and the 12 pairs of chromosomes. The mutation trend was site-related and there were different mutation loci for different triploids, which foretold that SARII-628 would have different evolution fates after natural homologous triploidization.

Key words: twin-seedling, diploid, triploidization, DNA methylation, rice (Oryza sativa)

PENG Hai, ZHANG Hong-yu, LI Yun, XU Pei-zhou, WANG Xu-dong, WU Xian-jun. Natural Homologous Triploidization and DNA Methylation in SARII-628, a Twin-seedling Line of Rice (Oryza sativa)[J]. RICE SCIENCE, 2007, 14(4): 265-271 .

References

1 Otto S P, Whitton J. Polyploid incidence and evolution. Annu Rev Genet, 2000, 34: 401−437.
2 Huang R F, Guo P Y, Huang D F. DNA methylation in plants. Biotech Bull, 2001, 5: 1−3.
3 Grant-Downton R T, Dickinson H G. Epigenetics and its implications for plant biology: II. The 'epigenetic epiphany': epigenetics evolution and beyond. Ann Bot, 2006, 97(1): 11−27.
4 Kashkush K, Feldman M, Levy A A. Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat. Nat Genet, 2003, 33(1): 102−106.
5 Madlung A, Masuelli R W, Watson B, Reynolds S H, Davison J, Comai L. Remodeling of DNA methylation and phenotypic and transcriptional changes in synthetic Arabidopsis allotetraploids. Plant Physiol, 2002, l29: 733−746.
6 Adams K L, Percifield R, Wendel J F. Organ-specific silencing of duplicated genes in a newly synthesized cotton allotetraploid. Genetics, 2004, 168(4): 2217−2226.
7 Wang J, Tian L, Madlung A, Lee H S, Chen M, Lee J J, Watson B, Kagochi T, Comai L, Chen Z J. Stochastic and epigenetic changes of gene expression in Arabidopsis polyploids. Genetics, 2004, 167(4): 1961−1973.
8 Chen Z J, Pikaard C S. Epigenetic silencing of RNA polymerase I transcription: A role for DNA methylation and histone modification in nucleolar dominance. Genes Dev, 1997, 11(16): 2124−2136.
9 Lawrence R J, Earley K, Pontes O, Silva M, Chen Z J, Neves N, Viegas W, Pikaard C S. A concerted DNA methylation/ histone methylation switch regulates rRNA gene dosage control and nucleolar dominance. Mol Cell, 2004, 13(4): 599−609.
10 Wu X J, Wang X D, Zhou K D, Zhu L H. A non-segregating F2 population derived from the cross of triploid×diploid in rice. Acta Bot Sin, 1999, 41(10): 1067−1071. (in Chinese with English abstract)
11 Li Y, Zhang H Y, Wang X Z, Zhang P, Wang X D, Wu X J. Identification and analysis of F2 stable population derived from the cross of triploid×diploid in rice. Acta Genet Sin, 2004, 31(6): 604−608. (in Chinese with English abstract)
12 Zhang S Q, Tong H H, Xue R, Hua Z H, Wang X L, Huang D N, Xie X B. Tests on improving purity in hybrid rice seed production by introducing bar gene to restorers. Sci Agric Sin, 1998, 31(6): 33−37. (in Chinese with English abstract)
13 Panaud O, Chen X, McCouch S R. Development of microsatellite markers and characterization of simple sequence length polymorphism (SSLP) in rice (Oryza sativa L.). Mol Gen Genet, 1996, 252(5): 597−607.
14 Xiong L Z, Xu C G, Saghai Maroof M A, Zhang Q. Patterns of cytosine methylation in an elite rice hybrid and its parental lines, detected by a methylation-sensitive amplification poly- morphism technique. Mol Gen Genet, 1999, 261(3): 439−446.
15 McClelland M, Nelson M, Raschke E. Effect of site-specific modification on restriction endonucleases and DNA modification methyltransferases. Nucl Acids Res, 1994, 22 (17): 3640−3659.
16 Song K, Lu P, Tang K, Osborn T C. Rapid genome changes in synthetic polyploids of Brassica and its importance for polyploidy evolution. Proc Natl Acad Sci, USA, 1995, 92: 7719−7723.
17 Feldman M, Liu B, Segal G, Abbo S, Levy A A, Vega J M. Rapid elimination of low-copy DNA sequences in polyploid wheat: A possible mechanism for differentiation of homoeologous chromosomes. Genetics, 1997, 147(3): 1381−1387.
18 Liu B, Vega J M, Feldman M. Rapid genomic changes in newly synthesized amphiploids of Triticum and Aegilops: II. Changes in low-copy coding DNA sequences. Genome, 1998, 41(4): 535−542.
19 Wendel J F, Schnabel A, Seelanan T. Bidirectional interlocus concerted evolution following allopolyploid speciation in cotton (Gossypium). Proc Natl Acad Sci, USA, 1995, 92(1): 280−284.
20 Shaked H, Kashkush K, Ozkan H, Feldman M, Levy A A. Sequence elimination and cytosine methylation are rapid and reproducible responses of the genome to wide hybridization and allopolyploidy in wheat. Plant Cell, 2001, 13(8): 1749−1759.
21 Ruiz-Garcia L, Cervera M T, Martinez-Zapater J M. DNA methylation increases throughout Arabidopsis development. Planta, 2005, 222(2): 301−306.
22 Bastow R, Mylne J S, Lister C, Lippman Z, Martienssen R A. Vernalization requires epigenetic silencing of FLC by histone methylation. Nature, 2004, 427(6970): 164−167.
23 Sung S, Amasino R M. Vernalization in Arabidopsis thaliana is mediated by the PHD finger protein VIN3. Nature, 2004, 427: 159−164.
24 Cheng Z J, Qin R Z, Zhang X, Lei C L, Guo X P, Wan J M. Molecular mechanism for phenotypic mutation arisen from polyploidization in plant. Acta Agron Sin, 2005, 31(7): 940−943. (in Chinese with English abstract)
25 Soltis D E, Soltis P S. Molecular data and the dynamic nature of polyploidy. Crit Rev Plant Sci, 1993, 12(3): 243−273.
26 Liu B, Wendel J F. Epigenetic phenomena and the evolution of plant allopolyploids. Mol Phylogenet Evol, 2003, 29(3): 365−379.

[1]	ZHENG Xiao-guo, CHEN Liang, LOU Qiao-jun, XIA Hui, LI Ming-shou, LUO Li-jun. Changes in DNA Methylation Pattern at Two Seedling Stages in Water Saving and Drought-Resistant Rice Variety after Drought Stress Domestication [J]. RICE SCIENCE, 2014, 21(5): 262-270.
[2]	WU Shao-hua, XUE Jing-jing, ZHANG Hong-yu, XU Pei-zhou, WU Xian-jun. Special DNA Methylated Sites Between Haploid of Twin-Seedling and Its Hybrids in Rice (Oryza sativa) [J]. RICE SCIENCE, 2012, 19(2): 94-99.
[3]	WANG Yang, GUO Yuan, HONG De-lin . QTL Analysis of Anoxic Tolerance at Seedling Stage in Rice [J]. RICE SCIENCE, 2010, 17(3): 192-198 .
[4]	WU Ji-rong, FAN Fang-jun, DU Jing-hong, FAN Ye-yang, ZHUANG Jie-yun. Dissection of QTLs for Hull Silicon Content on the Short Arm of Rice Chromosome 6 [J]. RICE SCIENCE, 2010, 17(2): 99-104 .
[5]	MA Hao-li, ZHOU Han-lin, ZHANG Huai-yu, ZHAO Jie. Cloning and Expression Analysis of an AP2/ERF Gene and Its Responses to Phytohormones and Abiotic Stresses in Rice [J]. RICE SCIENCE, 2010, 17(1): 1-9 .
[6]	DU Qin, CHEN Ming-xue, ZHOU Rong, CHAO Zhao-yun, ZHU Zhi-wei, SHAO Guo-sheng, WANG Guang-ming . Cd Toxicity and Accumulation in Rice Plants Vary with Soil Nitrogen Status and Their Genotypic Difference can be Partly Attributed to Nitrogen Uptake Capacity [J]. RICE SCIENCE, 2009, 16(4): 283-291 .
[7]	WU Kun , RAO Yu-chun , HU Jiang , ZHU Guan-lin , ZHANG Guang-hen , HU Xin-ming , GUO Long-biao , WANG Yong-hong , QIAN Qian , ZENG Da-li . Characterization and Fine Mapping of Non-panicle Mutant (nop) in Rice [J]. RICE SCIENCE, 2009, 16(3): 165-172 .
[8]	QI Yong-bin , YE Sheng-hai , LU Yan-ting , JIN Qing-sheng , ZHANG Xiao-ming . Development of Marker-Free Transgenic Cry1Ab Rice with Lepidopteran Pest Resistance by Agrobacterium Mixture-Mediated Co-transformation [J]. RICE SCIENCE, 2009, 16(3): 181-186 .
[9]	Liu Wen-qiang, Fan Ye-yang, Chen Jie, Shi Yong-feng, Wu Jian-li. Avoidance of Linkage Drag Between Blast Resistance Gene and the QTL Conditioning Spikelet Fertility Based on Genotype Selection Against Heading Date in Rice [J]. RICE SCIENCE, 2009, 16(1): 21-26 .
[10]	FU Xue-lin, LU Yong-gen, LIU Xiang-dong, LI Jin-quan, ZHAO Xing-juan. Comparative Embryological Studies on Infertility of Interspecific Hybridizations Between Oryza sativa with Different Ploidy Levels and O. officinalis [J]. RICE SCIENCE, 2009, 16(1): 58-64 .
[11]	Hossein SABOURI, Babak RABIEI, Maryam FAZLALIPOUR. Use of Selection Indices Based on Multivariate Analysis for Improving Grain Yield in Rice [J]. RICE SCIENCE, 2008, 15(4): 303-310 .
[12]	WAN Jia, XI Jiang, DU Zhi-ru, XU Zheng-jun, . A Rice CaMBP Gene is Induced in Organ-Specific Manner by Both Chilling and Heat-Shock Treatments [J]. RICE SCIENCE, 2008, 15(3): 166-172 .
[13]	XIAO Hui-hai, WANG Wen-long. Elongation of the Uppermost Internode for Changxuan 3S, a Thermo- Sensitive Genic Male Sterile Rice Line [J]. RICE SCIENCE, 2008, 15(3): 209-214 .
[14]	HUANG Ting-you, WANG Zhi, HU Yun-gao, SHI Shou-pei, PENG Tao, CHU Xu-dong, SHI Jun, XIANG Zu-fen, LIU Ding-you . Genetic Analysis and Primary Mapping of pms4, a Photoperiod-Sensitive Genic Male Sterility Gene in Rice (Oryza sativa) [J]. RICE SCIENCE, 2008, 15(2): 153-156 .
[15]	YING Jie-zheng, SHI Yong-feng, E Zhi-guo, ZENG Rui-zhen, CHEN Jie, ZHU Zhi-wei, ZHUANG Jie-yun . Construction and Testing of a Primary Microsatellite Database of Major Rice Varieties in China [J]. RICE SCIENCE, 2007, 14(4): 247-255 .