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Molecular and cytogenetic characterization of an Oryza officinalis–O. sativa chromosome 4 addition line and its progenies

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Abstract

The wild species Oryza officinalis Wall. ex Watt (2n = 24, CC) is a valuable genetic resource for rice (O. sativa L., 2n = 24, AA) breeding and genomics research. Genomic in situ hybridization (GISH) and molecular approaches were used to determine the nature and composition of the additional chromosome in a monosomic alien addition line (MAAL) of O. officinalis and its backcross progenies. The extra wild species chromosome in the MAAL (2n = 2x = 25) was a mosaic one, comprising of the long arm of chromosome 4 from O. officinalis and the short arm from O. sativa. Comparative analysis showed that O. sativa and O. officinalis shared high synteny of restriction fragment length polymorphism (RFLP) markers and low synteny of simple sequence repeat (SSR) markers. A DNA methylation alteration was revealed at C619 in the MAAL and progenies. Analysis of progenies of the MAAL indicated that introgression segments were small in size and introgression was not evenly distributed along the long arm. One recombination hot spot between C513 and RG177 was identified, which is in a gene-rich region.

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References

  • Aggarwal RK, Brar DS, Khush GS (1997) Two new genomes in the Oryza complex identified on the basis of molecular divergence analysis using total genomic DNA hybridization. Mol Gen Genet 254:1–12

    Article  PubMed  CAS  Google Scholar 

  • Brar DS, Khush GS (1997) Alien introgression in rice. Plant Mol Biol 35:35–47

    Article  PubMed  CAS  Google Scholar 

  • Brar DS, Dalmacio R, Elloran R, Aggarwal R, Angeles R, Khush GS (1996) Gene transfer and molecular characterization of introgression from wild Oryza species into rice. In: Rice Genetics III. IRRI, Manila, Philippines, pp 477–486

  • Chen X, Temnykh S, Xu Y, Cho YG, McCouch SR (1997) Development of a microsatellite framework map providing genome-wide coverage in rice (Oryza sativa L.). Theor Appl Genet 95:553–567

    Article  CAS  Google Scholar 

  • Cheng Z, Dong F, Langdon T, Ouyang S, Buell CR, Gu M, Blattner FR, Jiang J (2002) Functional rice centromeres are marked by a satellite repeat and a centromere-specific retrotransposon. Plant Cell 14:1691–1704

    Article  PubMed  CAS  Google Scholar 

  • Dong YZ, Liu ZL, Shan XH, Qiu T, He MY, Liu B (2005) Allopolyploidy in wheat induces rapid and heritable alterations in DNA methylation patterns of cellular genes and mobile elements. Genetika 41:1089–1095

    PubMed  CAS  Google Scholar 

  • Ge S, Sang T, Lu BR, Hong DY (1999) Phylogeny of rice genomes with emphasis on origins of allotetraploid species. Proc Natl Acad Sci USA 96:14400–14405

    Article  PubMed  CAS  Google Scholar 

  • Huang Z, He GC, Shu LH, Li XH, Zhang QF (2001) Identification and mapping of two brown planthopper genes in rice. Theor Appl Genet 102:929–934

    Article  CAS  Google Scholar 

  • International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436:793–800

    Google Scholar 

  • Ishii T, Brar DS, Multani DS, Khush GS (1994) Molecular tagging of genes for brown planthopper resistance and earliness introgressed from Oryza australiensis into cultivated rice, O. sativa. Genome 37:217–221

    CAS  Google Scholar 

  • Jena KK, Khush GS (1989) Monosomic alien lines of rice: production, morphology, cytology, and breeding behavior. Genome 32:449–455

    Google Scholar 

  • Jena KK, Khush GS (1990) Introgression of genes from Oryza officinalis Well ex Watt to cultivated rice, O. sativa L. Theor Appl Genet 80:737–745

    Article  Google Scholar 

  • Jena KK, Khush GS, Kochert G (1992) RFLP analysis of rice (Oryza sativa L.) introgression lines. Theor Appl Genet 84:608–616

    Article  Google Scholar 

  • Jena KK, Khush GS, Kochert G (1994) Comparative RFLP mapping of a wild rice, Oryza officinalis, and cultivated rice, O. sativa. Genome 37:382–389

    PubMed  CAS  Google Scholar 

  • Ji Y, Chetelat RT (2003) Homoeologous pairing and recombination in Solanum lycopersicoides monosomic addition and substitution lines of tomato. Theor Appl Genet 106:979– 989

    PubMed  CAS  Google Scholar 

  • Liu ZL, Wang YM, Shen Y, Guo WL, Hao S, Liu B (2004) Extensive alterations in DNA methylation and transcription in rice caused by introgression from Zizania latifolia. Plant Mol Biol 54:571–582

    Article  PubMed  CAS  Google Scholar 

  • Madlung A, Masuelli R, Watson B, Reynolds S, Davison J, Comai L (2002) Remodeling of DNA methylation and phenotypic and transcriptional changes in synthetic Arabidopsis allotetraploids. Plant Physiol 129:733–746

    Article  PubMed  CAS  Google Scholar 

  • Mao L, Zhou Q, Wang XP, Hu H, Zhu LH (1995) RFLP analysis of the progeny from Oryza alta Swallen × Oryza sativa L. Genome 38:913–918

    CAS  Google Scholar 

  • Muller K, Heller H, Doerfler W (2001) Foreign DNA integration. Genome-wide perturbations of methylation and transcription in the recipient genomes. J Biol Chem 276:14271–14278

    Article  PubMed  CAS  Google Scholar 

  • Murray MG, Thompson WF (1980) Rapid isolation of high-molecular-weight plant DNA. Nucleic Acids Res 8:4321–4325

    PubMed  CAS  Google Scholar 

  • Roberts RJ, Macelis D (2001) REBASE-restriction enzymes and methylases. Nucleic Acids Res 29:268–269

    Article  PubMed  CAS  Google Scholar 

  • Shaked H, Kashkush K, Ozkan H, Feldman M, Levy AA (2001) Sequence elimination and cytosine methylation are rapid and reproducible responses of the genome to wide hybridization and allopolyploidy in wheat. Plant Cell 13:1749–1759

    Article  PubMed  CAS  Google Scholar 

  • Tan GX, Huang Z, Weng QM, Ren X, Zhu LL, He GC (2004a) Two whitebacked planthopper resistance genes shared the same genomic intervals with brown planthopper resistance genes. Heredity 92:212–217

    Article  CAS  Google Scholar 

  • Tan GX, Weng QM, Ren X, Shi ZY, Zhu LL, He GC (2004b) Mapping of a new resistance gene to bacterial blight in rice line introgressed from Oryza officinalis. Acta Genet Sin 31:724–729

    CAS  Google Scholar 

  • Tan GX, Jin HJ, Li G, He RF, Zhu LL, He GC (2005) Production and characterization of a complete set of individual chromosome additions from Oryza officinalis to Oryza sativa using RFLP and GISH analyses. Theor Appl Genet 111:1585–1595

    Article  PubMed  CAS  Google Scholar 

  • Tang M, Jin HJ, Tan GX, Zhu LL, He GC (2005) Analysis of a mosaic monosomic alien addition line of rice with chromosome 7 of Oryza Officinalis C-genome and its backcross progeny. Wuhan Bot Res 23:221–226

    CAS  Google Scholar 

  • Tian F, Li DJ, Fu Q, Zhu ZF, Fu YC, Wang XK, Sun CQ (2006) Construction of introgression lines carrying wild rice (Oryza rufipogon Griff.) segments in cultivated rice (Oryza sativa L.) background and characterization of introgressed segments associated with yield-related traits. Theor Appl Genet 112:570–580

    Article  PubMed  CAS  Google Scholar 

  • Uozu S, Ikehashi H, Ohmido N, Ohtsubo H, Ohtsubo E, Fukui K (1997) Repetitive sequences: cause for variation in genome size and chromosome morphology in the genus Oryza. Plant Mol Biol 35:791–799

    Article  PubMed  CAS  Google Scholar 

  • Vaughan DA, Morishima H, Kadowaki K (2003) Diversity in the Oryza genus. Curr Opin Plant Biol 6:139–146

    Article  PubMed  CAS  Google Scholar 

  • Wang YM, Dong ZY, Zhang ZJ, Lin XY, Shen Y, Zhou DW, Liu B (2005) Extensive de novo genomic variation in rice induced by introgression from wild rice (Zizania latifolia Griseb.). Genetics 170:1945–1956

    Article  PubMed  CAS  Google Scholar 

  • Yan HH, Min SK, Zhu LH (1999) Visualization of Oryza eichingeri chromosomes in intergenomic hybrid plants from O. sativa × O. eichingeri via fluorescent in situ hybridization. Genome 42:48–51

    Article  Google Scholar 

  • Yan HH, Liu GQ, Cheng ZK, Min SK, Zhu LH (2001) Characterization of euploid backcross progenies derived from interspecific hybrids between Oryza sativa and O. eichingeri by restriction fragment length polymorphism (RFLP) analysis and genomic in situ hybridizatoin (GISH). Genome 44:86–95

    Article  PubMed  CAS  Google Scholar 

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Acknowledgements

We sincerely thank Dr. T Sasaki providing the RFLP probes. This study was supported by grants from the National Program of High Technology Development and National Special Program for Research and Industrialization of Transgenic Plants of China.

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Correspondence to Guangcun He.

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Jin, H., Tan, G., Brar, D.S. et al. Molecular and cytogenetic characterization of an Oryza officinalis–O. sativa chromosome 4 addition line and its progenies. Plant Mol Biol 62, 769–777 (2006). https://doi.org/10.1007/s11103-006-9056-4

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  • DOI: https://doi.org/10.1007/s11103-006-9056-4

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