Effect of male sterile and fertile cytoplasm on nuclear DNA methylation in hybrid rice

• Autorzy: Ali A. , Li Y. , Chen H. , Xu P. , Zhang H. , Chen X. , Yongxiang L. , Fu S. , Wu T. , Iqbal M.Z. , Farooq M.U. , Wu X.
• Języki publikacji: EN

Abstrakty

EN

Nucleus-controlled fertility restoration and cytoplasmic male sterility are important mechanisms to exploit heterosis. However, the effect of DNA methylation on cytoplasmic-nuclear interaction is not well understood yet. The current study used a methylation-sensitive amplified polymorphism to characterize polymorphism in nuclear DNA methylation among cytoplasmic male sterile line (D62A), corresponding maintainer line (D62B), and two F1 hybrids (D62A × R527 and D62B × R527). In results, 495 fragments were amplified between the parental D62A and D62B lines. The total methylation (double + single-stranded) and full methylation (double-stranded) rates of D62A (33.13%, 24.24%) both were found to be lower than that of corresponding maintainer D62B (33.94%, 24.85%). Analysis of methylation revealed that male sterile line D62A was less methylated than that of corresponding maintainer line D62B in all methylation types I, II and III. A total of 516 fragments were amplified between two F1 hybrids (D62A × R527 and D62B × R527). The total methylation in both hybrids (D62A × R527 and D62B × R527) was identical (34.69%). While full methylation rates for D62A × R527 and D62B × R527 were 25.78% and 25.58%, respectively, that is non-significant. Moreover, polymorphism in DNA methylation was found higher in F1 hybrids (5.43%) than parents (4.24%). These results implied that different cytoplasm leads to changes in nuclear DNA methylation and sterile cytoplasm has reduced the effect on nuclear methylation than non-sterile cytoplasm. Current study explains the interaction between cytoplasmic male sterility and DNA methylation which may contribute to further research.

• Wydawca: -
• Czasopismo: Acta Physiologiae Plantarum
• Rocznik: 2019
• Tom: 41
• Numer: 06
• Opis fizyczny: Article 81 [7p.], fig.,ref.

Twórcy

autor

Ali A.

• Key Laboratory of Southwest Crop Genetic Resources and Genetic Improvement, Rice Research institute, Ministry of Education, Sichuan Agricultural University, Chengdu, China

autor

Li Y.

• Chengdu Academy of Agriculture and Forestry Sciences, Chengdu, China

autor

Chen H.

• Key Laboratory of Southwest Crop Genetic Resources and Genetic Improvement, Rice Research institute, Ministry of Education, Sichuan Agricultural University, Chengdu, China

autor

Xu P.

• Key Laboratory of Southwest Crop Genetic Resources and Genetic Improvement, Rice Research institute, Ministry of Education, Sichuan Agricultural University, Chengdu, China

autor

Zhang H.

• Key Laboratory of Southwest Crop Genetic Resources and Genetic Improvement, Rice Research institute, Ministry of Education, Sichuan Agricultural University, Chengdu, China

autor

Chen X.

• Key Laboratory of Southwest Crop Genetic Resources and Genetic Improvement, Rice Research institute, Ministry of Education, Sichuan Agricultural University, Chengdu, China

autor

Yongxiang L.

• Key Laboratory of Southwest Crop Genetic Resources and Genetic Improvement, Rice Research institute, Ministry of Education, Sichuan Agricultural University, Chengdu, China

autor

Fu S.

• Chengdu Academy of Agriculture and Forestry Sciences, Chengdu, China

autor

Wu T.

• Key Laboratory of Southwest Crop Genetic Resources and Genetic Improvement, Rice Research institute, Ministry of Education, Sichuan Agricultural University, Chengdu, China

autor

Iqbal M.Z.

• Maize Research Institute, Sichuan Agricultural University, Chengdu, China

autor

Farooq M.U.

• Key Laboratory of Southwest Crop Genetic Resources and Genetic Improvement, Rice Research institute, Ministry of Education, Sichuan Agricultural University, Chengdu, China

autor

Wu X.

• Key Laboratory of Southwest Crop Genetic Resources and Genetic Improvement, Rice Research institute, Ministry of Education, Sichuan Agricultural University, Chengdu, China

Bibliografia

• Ahmadikhah A, Karlov GI (2006) Molecular mapping of the fertility-restoration gene Rf4 for WA-cytoplasmic male sterility in rice. Plant Breed 125:363–367
• Ba Q, Zhang G, Niu N, Ma S, Wang J (2014) Cytoplasmic effects on DNA methylation between male sterile lines and the maintainer in wheat (Triticum aestivum L.). Gene 549:192–197
• Cervera MT, Ruizgarcia L, Martinezzapater JM (2002) Analysis of DNA methylation in Arabidopsis thaliana based on methylation-sensitive AFLP markers. Mol Genet Genomics 268:543–552
• Chakrabarty D, Yu K, Paek KY (2003) Detection of DNA methylation changes during somatic embryogenesis of Siberian ginseng (Eleuterococcus senticosus). Plant Sci 165:61–68
• Chen L, Liu Y (2014) Male sterility and fertility restoration in crops. Annu Rev Plant Biol 65:579–606
• Dong Z et al (2006) Extent and pattern of DNA methylation alteration in rice lines derived from introgressive hybridization of rice and Zizania latifolia Griseb. Theor Appl Genet 113:196–205
• Dowen RH et al (2012) Widespread dynamic DNA methylation in response to biotic stress. Pro Natl Acad Sci US Am 109:12858–12859
• Du J, Johnson LM, Jacobsen SE, Patel DJ (2015) DNA methylation pathways and their crosstalk with histone methylation. Nat Rev Mol Cell Bio 16:519–532
• Fujii S, Toriyama K (2008) Genome barriers between nuclei and mitochondria exemplified by cytoplasmic male sterility. Plant Cell Physiol 49:1484–1494
• Gazzani S, Gendall AR, Lister C, Dean C (2003) Analysis of the molecular basis of flowering time variation in Arabidopsis accessions. Plant Physiol 132:1107–1114
• Guzywrobelska J, Filek M, Kaliciak A, Szarejko I, Machackova I, Krekule J, Barciszewska MZ (2013) Vernalization and photoperiod-related changes in the DNA methylation state in winter and spring rapeseed. Acta Physiol Plant 35:817–827
• He G et al (2010) Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids. Plant Cell 22:17–33
• Hongyu Z, Hai P, Yun L, Peizhou X, Xudong W, Wu X (2006) Patterns of DNA cytosine methylation between haploids and corresponding diploids in rice. Chinese Sci Bull 51:1721–1728
• Jing R, Li X, Yi P, Zhu Y (2001) Mapping fertility-restoring genes of rice WA cytoplasmic male sterility using SSLP markers. Bot Bull Acad Sin 42:167–171
• Law JA, Jacobsen SE (2010) Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet 11:204–220
• Li Y, Shan X, Liu X, Hu L, Guo W, Liu B (2008) Utility of the methylation-sensitive amplified polymorphism (MSAP) marker for detection of DNA methylation polymorphism and epigenetic population structure in a wild barley species (Hordeum brevisubulatum). Ecol Res 23:927–930
• Li Y, Zhang M, Yang X, Lin C, Duan Y, Wang N (2016) Fine mapping of a fertility restoring gene for a new CMS hybrid rice system. Mol Breed 36:141
• Miyashita NT, Mori N, Tsunewaki K (1994) Molecular variation in chloroplast DNA regions in ancestral species of wheat. Genetics 137:883–889
• Murray MG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 8:4321–4325
• Ng H, Adrian B (1999) DNA methylation and chromatin modification. Curr Opin Genet Dev 9:158–163
• Schmitz RJ et al (2013) Patterns of population epigenomic diversity. Nature 495:193–198
• Sha AH, Lin XH, Huang JB, Zhang DP (2005) Analysis of DNA methylation related to rice adult plant resistance to bacterial blight based on methylation-sensitive AFLP (MSAP) analysis. Mol Genet and Genomics 273:484–490
• Shi J, Dong A, Shen W (2015) Epigenetic regulation of rice flowering and reproduction. Front Plant Sci 5:803
• Tao D et al (2004) Cytoplasm and cytoplasm–nucleus interactions affect agronomic traits in japonica rice. Euphytica 135:129–134
• Tao D et al (2011) Cytoplasm affects grain weight and filled-grain ratio in indica rice. BMC Genet 12:53
• Traven A, Wong JMS, Xu D, Sopta M, Ingles CJ (2001) Interorganellar communication altered nuclear gene expression profiles in a yeast mitochondrial DNA mutant. J Biol Chem 276:4020–4027
• Wang W et al (2011) Drought-induced site-specific DNA methylation and its association with drought tolerance in rice (Oryza sativa L.). J Exp Bot 62:1951–1960
• Xiong L, Xu CG, Maroof MAS, Zhang Q (1999) Patterns of cytosine methylation in an elite rice hybrid and its parental lines, detected by a methylation-sensitive amplification polymorphism technique. Mol Genet Genomics 261:439–446
• Xu M, Li X, Korban SS (2000) AFLP-based detection of DNA methylation. Plant Mol Biol Rep 18:361–368
• Xu P, Yan W, He J, Li Y, Zhang H, Peng H, Wu X (2013) DNA methylation affected by male sterile cytoplasm in rice (Oryza sativa L.). Mol Breed 31:719–727
• Yan H, Kikuchi S, Neumann P, Zhang W, Wu Y, Chen F, Jiang J (2010) Genome-wide mapping of cytosine methylation revealed dynamic DNA methylation patterns associated with genes and centromeres in rice. Plant J 63:353–365
• Yinging C, Daming Z (2010) Surveying DNA methylation diversity in the wild rice, Oryza nivara and O. rufipogon. Biodiversity Sci 18:227–232
• Zemach A, Kim MY, Silva P, Rodrigues JA, Dotson B, Brooks MD, Zilberman D (2010) Local DNA hypomethylation activates genes in rice endosperm. Pro Natl Acad Sci US Am 107:18729–18734
• Zhang et al (2006) Patterns of DNA cytosine methylation between haploids and corresponding diploids in rice. Chinese Sci Bull 51:1721–1728
• Zhang C, Qi L, Hou X, Shi G, Zhang J (2010) Differential gene expression analysis of a new ogura CMS line and its maintainer in non-heading Chinese cabbage by cDNA-AFLP. Acta Physiol Plant 32:781–787

Identyfikatory

DOI

10.1007/s11738-019-2874-1