Chromosome Research

, 17:863 | Cite as

Unstable transmission of rice chromosomes without functional centromeric repeats in asexual propagation

  • Zhiyun Gong
  • Hengxiu Yu
  • Jian Huang
  • Chuandeng Yi
  • Minghong GuEmail author


During sexual propagation of primary trisomic 8, chromosome 8 breaks in some rice plants, resulting in a telotrisomic (2n+·8S) line. In this study, we observed that the extra short arm of chromosome 8 (·8S) can easily be lost in the telotrisomic, and we determined by fluorescence in-situ hybridization (FISH) analysis that the centromeric region of the extra ·8S did not contain the rice centromeric satellite repeat (CentO) and centromere-specific retrotransposon (CRR); however, the extra ·8S contained part of the CentO and CRR sequences in the initially preserved telotrisomic line. We confirmed by real-time quantitative PCR (RQ-PCR) analysis that the original functional centromere of the extra ·8S was lost. Using both FISH and RQ-PCR, the breakage point of the extra ·8S was found within the BAC clone a0070J19 sequence containing the first part of the short arm near the centromere region of chromosome 8 but without any CentO or CRR sequences. However, part of the DNA sequence within the a0070J19 BAC clone played a role in the new functional centromere, contributing to the morphological variations by asexually propagated plants of rice telotrisomics in the field. We conclude that CENH3, a key element in the eukaryotic kinetochore, may not always bind properly with the new functional centromere, resulting in loss of the extra ·8S during mitosis and the chromosome numbers returning to diploid levels in subsequent generations.


rice neocentromere CENH3 asexual propagation 



bacterial artificial chromosome


centromeric satellite repeat


centromere-specific retrotransposon




fluorescence in-situ hybridization


fluorescein isothiocyanate


pollen mother cell


real-time quantitative PCR



We are grateful to Zhukuan Cheng for critical reading of the manuscript and Yong Zhou for RQ-PCR analysis. This work was supported by grants from the National Natural Science Foundation of China (30600345 and 30770131).


  1. Amor DJ, Choo KH (2002) Neocentromeres: role in human disease, evolution, and centromere study. Am J Hum Genet 71:695–714CrossRefPubMedGoogle Scholar
  2. Amor DJ, Kalitsis P, Sumer H, Choo KH (2004) Building the centromere: from foundation proteins to 3D organization. Trends Cell Biol 14:359–368CrossRefPubMedGoogle Scholar
  3. Ananiev EV, Phillips RL, Rines HW (1998) Chromosome-specific molecular organization of maize (Zea mays L.) centromeric regions. Proc Natl Acad Sci USA 95:13073–13078CrossRefPubMedGoogle Scholar
  4. Blower MD, Karpen GH (2001) The role of Drosophila CID in kinetochore formation, cell-cycle progression and heterochromatin interactions. Nat Cell Biol 3:730–739CrossRefPubMedGoogle Scholar
  5. Cheeseman IM, Drubin DG, Barnes G (2002) Simple centromere, complex kinetochore: linking spindle microtubules and centromeric DNA in budding yeast. J Cell Biol 157:199–203CrossRefPubMedGoogle Scholar
  6. Cheng Z, Presting GG, Buell CR, Wing RA, Jiang J (2001a) High-resolution pachytene chromosome mapping of bacterial artificial chromosomes anchored by genetic markers reveals the centromere location and the distribution of genetic recombination along chromosome 10 of rice. Genetics 157:1749–1757PubMedGoogle Scholar
  7. Cheng Z, Yan H, Yu H et al (2001b) Development and applications of a complete set of rice telotrisomics. Genetics 157:361–368PubMedGoogle Scholar
  8. Cheng Z, Dong F, Langdon T et al (2002) Functional rice centromeres are marked by a satellite repeat and a centromere-specific retrotransposon. Plant Cell 14:1691–1704CrossRefPubMedGoogle Scholar
  9. Choo KH (2001) Domain organization at the centromere and neocentromere. Dev Cell 1:165–177CrossRefPubMedGoogle Scholar
  10. Clarke L, Carbon J (1983) Genomic substitutions of centromeres in Saccharomyces cerevisiae. Nature 305:23–28CrossRefPubMedGoogle Scholar
  11. Henikoff S, Ahmad K, Malik HS (2001) The centromere paradox: stable inheritance with rapidly evolving DNA. Science 293:1098–1102CrossRefPubMedGoogle Scholar
  12. Hosouchi T, Kumekawa N, Tsuruoka H, Kotani H (2002) Physical map-based sizes of the centromeric regions of Arabidopsis thaliana chromosomes 1, 2, and 3. DNA Res 9:117–121CrossRefPubMedGoogle Scholar
  13. Houben A, Schubert I (2003) DNA and proteins of plant centromeres. Curr Opin Plant Biol 6:554–560CrossRefPubMedGoogle Scholar
  14. Howman EV, Fowler KJ, Newson AJ et al (2000) Early disruption of centromeric chromatin organization in centromere protein A (Cenpa) null mice. Proc Natl Acad Sci USA 97:1148–1153CrossRefPubMedGoogle Scholar
  15. Jiang J, Gill BS, Wang GL, Ronald PC, Ward DC (1995) Metaphase and interphase fluorescence in situ hybridization mapping of the rice genome with bacterial artificial chromosomes. Proc Natl Acad Sci USA 92:4487–4491CrossRefPubMedGoogle Scholar
  16. Kamm A, Galasso I, Schmidt T, Heslop-Harrison JS (1995) Analysis of a repetitive DNA family from Arabidopsis arenosa and relationships between Arabidopsis species. Plant Mol Biol 27:853–862CrossRefPubMedGoogle Scholar
  17. Kumekawa N, Hosouchi T, Tsuruoka H, Kotani H (2000) The size and sequence organization of the centromeric region of Arabidopsis thaliana chromosome 5. DNA Res 7:315–321CrossRefPubMedGoogle Scholar
  18. Kumekawa N, Hosouchi T, Tsuruoka H, Kotani H (2001) The size and sequence organization of the centromeric region of Arabidopsis thaliana chromosome 4. DNA Res 8:285–290CrossRefPubMedGoogle Scholar
  19. Kurata N, Omura T (1978) Karyotype analysis in rice I. A new method for identifying all chromosome pairs. Jpn J Genet 53:251–255.Google Scholar
  20. Larkin PJ, Scowcroft WP (1981) Somaclonal variation novel source of variability from cell culture for plant improvement. Theor Appl Genet 60:197–214CrossRefGoogle Scholar
  21. Lermontova I, Schubert V, Fuchs J, Klatte S, Macas J et al (2006) Loading of Arabidopsis centromeric histone CENH3 occurs mainly during G2 and requires the presence of the histone fold domain. Plant Cell 18:2443–2451CrossRefPubMedGoogle Scholar
  22. Ma J, Jackson SA (2006) Retrotransposon accumulation and satellite amplification mediated by segmental duplication facilitate centromere expansion in rice. Genome Res 16:251–259CrossRefPubMedGoogle Scholar
  23. Maggert KA, Karpen GH (2001) The activation of a neocentromere in Drosophila requires proximity to an endogenous centromere. Genetics 158:1615–1628PubMedGoogle Scholar
  24. Malik HS, Henikoff S (2002) Conflict begets complexity: the evolution of centromeres. Curr Opin Genet Dev 12:711–718CrossRefPubMedGoogle Scholar
  25. Nagaki K, Cheng Z, Ouyang S et al (2004) Sequencing of a rice centromere uncovers active genes. Nat Genet 36:138–145CrossRefPubMedGoogle Scholar
  26. Nagaki K, Kashihara K, Murata M (2009) A centromeric DNA sequence colocalized with a centromere-specific histone H3 in tobacco. Chromosoma 118:249–257CrossRefPubMedGoogle Scholar
  27. Nasuda S, Hudakova S, Schubert I, Houben A, Endo TR (2005) Stable barley chromosomes without centromeric repeats. Proc Natl Acad Sci USA 102:9842–9847CrossRefPubMedGoogle Scholar
  28. Ngezahayo F, Dong Y, Liu B (2007) Somaclonal variation at the nucleotide sequence level in rice (Oryza sativa L.) as revealed by RAPD and ISSR markers, and by pairwise sequence analysis. J Appl Genet 48:329–336PubMedGoogle Scholar
  29. Palmer DK, O’Day K, Wener MH, Andrews BS, Margolis RL (1987) A 17-kD centromere protein (CENP-A) copurifies with nucleosome core particles and with histones. J Cell Biol 104:805–815CrossRefPubMedGoogle Scholar
  30. Palmer DK, O’Day K, Trong HL, Charbonneau H, Margolis RL (1991) Purification of the centromere-specific protein CENP-A and demonstration that it is a distinctive histone. Proc Natl Acad Sci USA 88:3734–3738CrossRefPubMedGoogle Scholar
  31. Richards EJ, Ausubel FM (1988) Isolation of a higher eukaryotic telomere from Arabidopsis thaliana. Cell 53:127–136CrossRefPubMedGoogle Scholar
  32. Schueler MG, Higgins AW, Rudd MK, Gustashaw K, Willard HF (2001) Genomic and genetic definition of a functional human centromere. Science 294:109–115CrossRefPubMedGoogle Scholar
  33. Sullivan BA, Blower MD, Karpen GH (2001) Determining centromere identity: cyclical stories and forking paths. Nat Rev Genet 2:584–596CrossRefPubMedGoogle Scholar
  34. Sun X, Wahlstrom J, Karpen G (1997) Molecular structure of a functional Drosophila centromere. Cell 91:1007–1019CrossRefPubMedGoogle Scholar
  35. Talbert PB, Masuelli R, Tyagi AP, Comai L, Henikoff S (2002) Centromeric localization and adaptive evolution of an Arabidopsis histone H3 variant. Plant Cell 14:1053–1066CrossRefPubMedGoogle Scholar
  36. Tanaka TU (2008) Bi-orienting chromosomes: acrobatics on the mitotic spindle. Chromosoma 117:521–533CrossRefPubMedGoogle Scholar
  37. Thomas JW, Schueler MG, Summers TJ et al (2003) Pericentromeric duplications in the laboratory mouse. Genome Res 13:55–63CrossRefPubMedGoogle Scholar
  38. Vafa O, Sullivan KF (1997) Chromatin containing CENP-A and alpha-satellite DNA is a major component of the inner kinetochore plate. Curr Biol 7:897–900CrossRefPubMedGoogle Scholar
  39. Warburton PE (2004) Chromosomal dynamics of human neocentromere formation. Chromosome Res 12:617–626CrossRefPubMedGoogle Scholar
  40. Warburton PE, Cooke CA, Bourassa S et al (1997) Immunolocalization of CENP-A suggests a distinct nucleosome structure at the inner kinetochore plate of active centromeres. Curr Biol 7:901–904CrossRefPubMedGoogle Scholar
  41. Wevrick R, Willard HF (1989) Long-range organization of tandem arrays of alpha satellite DNA at the centromeres of human chromosomes: high-frequency array-length polymorphism and meiotic stability. Proc Natl Acad Sci USA 86:9394–9398CrossRefPubMedGoogle Scholar
  42. Wu HK (1967) Note on preparing of pachytene chromosomes by double mordant. Sci Agric 15:40–44Google Scholar
  43. Yan H, Jin W, Nagaki K et al (2005) Transcription and histone modifications in the recombination-free region spanning a rice centromere. Plant Cell 17:3227–3238CrossRefPubMedGoogle Scholar
  44. Yang H, Tabei Y, Kamada H, Kayano T, Takaiwa F (1999) Detection of somaclonal variation in cultured rice cells using digoxigenin-based random amplified polymorphic DNA. Plant Cell Rep 18:520–526CrossRefGoogle Scholar
  45. Yu HX, Wang X, Gong ZY et al (2008) Generating of rice OsCENH3-GFP transgenic plants and their genetic applications. Chin Sci Bull 53:2981–2988CrossRefGoogle Scholar
  46. Zhang W, Yi C, Bao W et al (2005) The transcribed 165-bp CentO satellite is the major functional centromeric element in the wild rice species Oryza punctata. Plant Physiol 139:306–315CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2009

Authors and Affiliations

  • Zhiyun Gong
    • 1
  • Hengxiu Yu
    • 1
  • Jian Huang
    • 2
  • Chuandeng Yi
    • 1
  • Minghong Gu
    • 1
    Email author
  1. 1.Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of Ministry of EducationYangzhou UniversityYangzhouChina
  2. 2.Laboratory of Genetics, School of Basic Medicine & Biological SciencesSuzhou UniversitySuzhouChina

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