Molecular Genetics and Genomics

, Volume 282, Issue 6, pp 633–652 | Cite as

Diversity of the Ty-1 copia retrotransposon Tos17 in rice (Oryza sativa L.) and the AA genome of the Oryza genus

  • Julie Petit
  • Emmanuelle Bourgeois
  • Wilfried Stenger
  • Martine Bès
  • Gaétan Droc
  • Donaldo Meynard
  • Brigitte Courtois
  • Alain Ghesquière
  • François Sabot
  • Olivier Panaud
  • Emmanuel GuiderdoniEmail author
Original Paper


Retrotransposons are mobile genetic elements, ubiquitous in Eukaryotic genomes, which have proven to be major genetic tools in determining phylogeny and structuring genetic diversity, notably in plants. We investigate here the diversity of the Ty1-copia retrotransposon Tos17 in the cultivated rice of Asian origin (Oryza sativa L.) and related AA genome species of the Oryza genus, to contribute understanding of the complex evolutionary history in this group of species through that of the element in the lineages. In that aim, we used a combination of Southern hybridization with a reverse transcriptase (RT) probe and an adapter-PCR mediated amplification, which allowed the sequencing of the genomic regions flanking Tos17 insertions. This analysis was carried out in a collection of 47 A-genome Oryza species accessions and 202 accessions of a core collection of Oryza sativa L. representative of the diversity of the species. Our Southern hybridization results show that Tos17 is present in all the accessions of the A-genome Oryza species, except for the South American species O. glumaepatula and the African species O. glaberrima and O. breviligulata. In O. sativa, the number of putative copies of Tos17 per accession ranged from 1 to 11 and multivariate analysis based on presence/absence of putative copies yielded a varietal clustering which is consistent with the isozyme classification of rice. Adapter PCR amplification and sequencing of flanking regions of Tos17 insertions in A-genome species other than O. sativa, followed by anchoring on the Nipponbare genome sequence, revealed 13 insertion sites of Tos17 in the surveyed O. rufipogon and O. longistaminata accessions, including one shared by both species. In O. sativa, the same approach revealed 25 insertions in the 6 varietal groups. Four insertion sites located on chromosomes 1, 2, 10, and 11 were found orthologous in O. rufipogon and O. sativa. The chromosome 1 insertion was also shared between O. rufipogon and O. longistaminata. The presence of Tos17 at three insertion sites was confirmed by retrotransposon-based insertion polymorphism (RBIP) in a sample of O. sativa accessions. The first insertion, located on chromosome 3 was only found in two japonica accessions from the Bhutan region while the second insertion, located on chromosome 10 was specific to the varietal groups 1, 2, and 5. The third insertion located on chromosome 7 corresponds to the only insertion shown active in rice so far, notably in cv. Nipponbare, where it has been extensively used for insertion mutagenesis. This copy was only found in a few varieties of the japonica group 6 and in one group 5 accession. Taken together, these results confirm that Tos17 was probably present in the ancestor of A-genome species and that some copies of the element remained active in some Oryza lineages—notably in O. rufipogon and O. longistaminata—as well as in the indica and japonica O. sativa L. lineages.


Diversity Oryza sativa L. AA genome Tos17 Retrotransposon 



EB has benefited of a post doctoral grant from the French Genomics Initiative Génoplante. The authors warmly thank Dr M. Yano from NIAS for providing us with seeds of the Nipponbare/Kasalath BCIL population and of their parents.

Supplementary material

438_2009_493_MOESM1_ESM.ppt (8.9 mb)
Figure 1: Location of Tos17 copies of Nipponbare, Kasalath, IR64 and Azucena and of QTLs related to germinal (He et al. 1998; Yamagishi et al. 1998) and somatic (Taguchi-Shiobara et al. 1997; Takeuchi et al. 2000)tissue culture abilities represented in the IR64/Azucena mapping framework (Huang et al. 1997), Figure 2: Southern hybridization of XbaI digests of DNA isolated from plants regenerated from 4 month-old, seed-embryo derived calli of cvs. Azucena (A) Nipponbare (B) and Kasalath (C) containing 4, 2 and 3 native copies of the retrotransposon Tos 17 respectively. Arrows point position of endogenous copies of Tos17 in the 3 cultivars. A reverse transcriptase probe of Tos17 was used for hybridization, Figure 3: Adapter PCR mediated amplification of regions flanking the 3’ LTR of Tos17 in Ssp1 and EcoRV digests of genomic DNA of O.sativa and O. rufipogon accessions. Supplementary material 1 (PPT 9094 kb)


  1. Aggarwal RK, Brar D, Nandi S, Huang N, Khush GS (1999) Phylogenetic relationships among Oryza species revealed by AFLP markers. Theor Appl Genet 98:1320–1328CrossRefGoogle Scholar
  2. Ammiraju JSS, Zuccolo A, Yu Y, Song X, Piegu B, Chevalier F, Walling JG, Ma J, Talag J, Brar DS, SanMiguel PJ, Jiang N, Jackson SA, Panaud O, Wing RA (2007) Evolutionary dynamics of an ancient retrotransposon family provides insights into evolution of genome size in the genus Oryza. Plant J 52:342–351CrossRefPubMedGoogle Scholar
  3. Balzergue S, Dubreucq B, Chauvin S, Le-Clainche I, Le Boulaire F, de Rose R, Samson F, Biaudet V, Lecharny A, Cruaud C, Weissenbach J, Caboche M, Lepiniec L (2001) Improved PCR-walking for large-scale isolation of plant T-DNA borders. Biotechniques 30:496–504PubMedGoogle Scholar
  4. Bennetzen JL (2000) Transposable element contributions to plant gene and genome evolution. Plant Mol Biol 42:251–269CrossRefPubMedGoogle Scholar
  5. Boissot N, Valdez M, Guiderdoni E (1990) Plant regeneration from leaf and seed-derived calli and suspension cultures of the African perennial wild rice, Oryza longistaminata. Plant Cell Rep 9:447–450CrossRefGoogle Scholar
  6. Caicedo AL, Williamson SH, Hernandez RD, Boyko A, Fledel-Alon A, York TL, Polato NR, Olsen KM, Nielsen R, McCouch SR, Bustamante CD, Purugganan MD (2007) Genome-wide patterns of nucleotide polymorphism in domesticated rice. PLoS Genet 3:e163CrossRefGoogle Scholar
  7. Cheng C, Tsuchimoto S, Ohtsubo H, Ohtsubo E (2002) Evolutionary relationships among rice species with AA genome based on SINE insertion analysis. Genes Genet Syst 77:323–334CrossRefPubMedGoogle Scholar
  8. Cheng C, Motohashi R, Tsuchimoto S, Fukuta Y, Ohtsubo H, Ohtsubo E (2003) Polyphyletic origin of cultivated rice: based on the interspersion pattern of SINEs. Mol Biol Evol 20:67–75CrossRefPubMedGoogle Scholar
  9. Cheng C, Daigen M, Hirochika H (2006) Epigenetic regulation of the rice retrotransposon Tos17. Mol Genet Genomics 276:378–390CrossRefPubMedGoogle Scholar
  10. Chu YE, Morishima H, Oka HI (1969) Reproductive barriers distributed in cultivated rice species and their wild relatives. Jpn J Genet 44:207–233CrossRefGoogle Scholar
  11. Dally AM, Second G (1990) Chloroplast DNA diversity in wild and cultivated species of rice (Genus Oryza, section Oryza). Cladistic-mutation and genetic distance analysis. Theor Appl Genet 80:209–222CrossRefGoogle Scholar
  12. Devic M, Albert S, Delseny M, Roscoe TJ (1997) Efficient PCR walking on plant genomic DNA. Plant Physiol Biochem 35:331–339Google Scholar
  13. Droc G, Ruiz M, Larmande P, Pereira A, Piffanelli P, Morel JB, Dievart A, Courtois B, Guiderdoni E, Perin C (2006) OryGenesDB: a database for rice reverse genetics. Nucl Acids Res 34:736–740CrossRefGoogle Scholar
  14. Gao L, McCarthy E, Ganko E, McDonald J (2004) Evolutionary history of Oryza sativa LTR retrotransposons: a preliminary survey of the rice genome sequences. BMC Genomics 5:18CrossRefPubMedGoogle Scholar
  15. Garris AJ, Tai TH, Coburn J, Kresovich S, McCouch S (2005) Genetic structure and diversity in Oryza sativa L. Genetics 169:1631–1638CrossRefPubMedGoogle Scholar
  16. Glaszmann JC (1987) Isozymes and classification of Asian rice varieties. Theor Appl Genet 74:21–30CrossRefGoogle Scholar
  17. Glaszmann JC, Mew T, Hibino H, Kim CK, Vergel de Dios-Mew TI, Vera Cruz CM, Notteghem JL, Bonman JM (1996) Molecular variation as a diverse source of disease resistance in cultivated rice. In: Khush GS (ed) Rice genetics III. Proceedings of 3rd international rice genetics symposium, Manila, Philippines, IRRI, pp 460–466Google Scholar
  18. Hayashi K, Yoshida H (2009) Refunctionalization of the ancient rice blast disease resistance gene Pit by the recruitment of a retrotransposon as a promoter. Plant J 57:413–425CrossRefPubMedGoogle Scholar
  19. He P, Shen L, Lu C, Chen Y, Zhu L (1998) Analysis of quantative trait loci which contribute to anther culturability in rice (Oryza sativa L.). Mol Breeding 4:165–172CrossRefGoogle Scholar
  20. Hirochika H (1997) Retrotransposons of rice: their regulation and use for genome analysis. Plant Mol Biol 35:231–240CrossRefPubMedGoogle Scholar
  21. Hirochika H (2001) Contribution of the Tos17 retrotransposon to rice functional genomics. Curr Opin Plant Biol 4:118–122CrossRefPubMedGoogle Scholar
  22. Hirochika H, Sugimoto K, Otsuki Y, Tsugawa H, Kanda M (1996) Retrotransposons of rice involved in mutations induced by tissue culture. Proc Natl Acad Sci USA 93:7783–7788CrossRefPubMedGoogle Scholar
  23. Huang N, Parco A, Mew T, Magpantay G, McCouch S, Guiderdoni E, Xu J, Subudhi P, Angeles ER, Khush GS (1997) RFLP mapping of isoenzymes, RAPD and QTLs for grain shape, brown planthopper resistance in a doubled haploid rice population. Mol Breeding 3:105–113CrossRefGoogle Scholar
  24. Izawa T (2008) The process of rice domestication: a new model based on recent data. Rice 1:127–134CrossRefGoogle Scholar
  25. Kawakami SI, Ebana K, Nishikawa T, Sato YI, Vaughan DA, Kadowaki K (2007) Genetic variation in the chloroplast genome suggests multiple domestication of cultivated Asian rice (Oryza sativa L.). Genome 50:180–187CrossRefPubMedGoogle Scholar
  26. Khush GS (1997) Origin, dispersal, cultivation and variation of rice. Plant Mol Biol 35:25–34CrossRefPubMedGoogle Scholar
  27. Kovach MJ, Sweeney M, McCouch SR (2007) New insights into the history of rice domestication. Trends Genet 23:578–587CrossRefPubMedGoogle Scholar
  28. Kumar A, Hirochika H (2001) Applications of retrotransposons as genetic tools in plant biology. Trends Plant Sci 6:127–134CrossRefPubMedGoogle Scholar
  29. Lander ES, Green P, Abrahamson J, Barlow A, Daly MJ, Lincoln SE, Newberg L (1987) MAPMAKER : an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–181CrossRefPubMedGoogle Scholar
  30. Li C, Zhou A, Sang T (2006) Genetic analysis of rice domestication syndrome with the wild annual species, Oryza nivara. New Phytol 170Google Scholar
  31. Lin SY, Sasaki T, Yano M (1998) Mapping quantitative trait loci controlling seed dormancy and heading date in rice, Oryza sativa L., using backcross inbred lines. Theor Appl Genet 96:997–1003CrossRefGoogle Scholar
  32. Liu ZL, Han FP, Tan M, Shan XH, Dong YZ, Wang XZ, Fedak G, Hao S, Liu B (2004) Activation of a rice endogenous retrotransposon Tos17 in tissue culture is accompanied by cytosine demethylation and causes heritable alteration in methylation pattern of flanking genomic regions. TAG Theor and Appl Genet 109:200–209CrossRefGoogle Scholar
  33. Londo JP, Chiang Y-C, Hung K-H, Chiang T-Y, Schaal BA (2006) Phylogeography of Asian wild rice, Oryza rufipogon, reveals multiple independent domestications of cultivated rice, Oryza sativa. Proc Natl Acad Sci USA 103:9578–9583CrossRefPubMedGoogle Scholar
  34. Ma J, Devos KM, Bennetzen JL (2004) Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice. Genome Res 14:860–869CrossRefPubMedGoogle Scholar
  35. Matsumoto T, Wu JZ, Kanamori H, Katayose Y, Fujisawa M, Namiki N, Mizuno H, Yamamoto K, Antonio BA, Baba T, Sakata K, Nagamura Y, Aoki H, Arikawa K, Arita K, Bito T, Chiden Y, Fujitsuka N, Fukunaka R, Hamada M, Harada C, Hayashi A, Hijishita S, Honda M, Hosokawa S, Ichikawa Y, Idonuma A, Iijima M, Ikeda M, Ikeno M, Ito K, Ito S, Ito T, Ito Y, Ito Y, Iwabuchi A, Kamiya K, Karasawa W, Kurita K, Katagiri S, Kikuta A, Kobayashi H, Kobayashi N, Machita K, Maehara T, Masukawa M, Mizubayashi T, Mukai Y, Nagasaki H, Nagata Y, Naito S, Nakashima M, Nakama Y, Nakamichi Y, Nakamura M, Meguro A, Negishi M, Ohta I, Ohta T, Okamoto M, Ono N, Saji S, Sakaguchi M, Sakai K, Shibata M, Shimokawa T, Song JY, Takazaki Y, Terasawa K, Tsugane M, Tsuji K, Ueda S, Waki K, Yamagata H, Yamamoto M, Yamamoto S, Yamane H, Yoshiki S, Yoshihara R, Yukawa K, Zhong HS, Yano M, Sasaki T, Yuan QP, Shu OT, Liu J, Jones KM, Gansberger K, Moffat K, Hill J, Bera J, Fadrosh D, Jin SH, Johri S, Kim M, Overton L, Reardon M, Tsitrin T, Vuong H, Weaver B, Ciecko A, Tallon L, Jackson J, Pai G, Van Aken S, Utterback T, Reidmuller S, Feldblyum T, Hsiao J, Zismann V, Iobst S, de Vazeille AR, Buell CR, Ying K, Li Y, Lu TT, Huang YC, Zhao Q, Feng Q, Zhang L, Zhu JJ, Weng QJ, Mu J, Lu YQ, Fan DL, Liu YL, Guan JP, Zhang YJ, Yu SL, Liu XH, Zhang Y, Hong GF, Han B, Choisne N, Demange N, Orjeda G, Samain S, Cattolico L, Pelletier E, Couloux A, Segurens B, Wincker P, D’Hont A, Scarpelli C, Weissenbach J, Salanoubat M, Quetier F, Yu Y, Kim HR, Rambo T, Currie J, Collura K, Luo MZ, Yang TJ, Ammiraju JSS, Engler F, Soderlund C, Wing RA, Palmer LE, de la Bastide M, Spiegel L, Nascimento L, Zutavern T, O’Shaughnessy A, Dike S, Dedhia N, Preston R, Balija V, McCombie WR, Chow TY, Chen HH, Chung MC, Chen CS, Shaw JF, Wu HP, Hsiao KJ, Chao YT, Chu MK, Cheng CH, Hour AL, Lee PF, Lin SJ, Lin YC, Liou JY, Liu SM, Hsing YI, Raghuvanshi S, Mohanty A, Bharti AK, Gaur A, Gupta V, Kumar D, Ravi V, Vij S, Kapur A, Khurana P, Khurana P, Khurana JP, Tyagi AK, Gaikwad K, Singh A, Dalal V, Srivastava S, Dixit A, Pal AK, Ghazi IA, Yadav M, Pandit A, Bhargava A, Sureshbabu K, Batra K, Sharma TR, Mohapatra T, Singh NK, Messing J, Nelson AB, Fuks G, Kavchok S, Keizer G, Llaca ELV, Song RT, Tanyolac B, Young S, Il KH, Hahn JH, Sangsakoo G, Vanavichit A, de Mattos LAT, Zimmer PD, Malone G, Dellagostin O, de Oliveira AC, Bevan M, Bancroft I, Minx P, Cordum H, Wilson R, Cheng ZK, Jin WW, Jiang JM, Leong SA, Iwama H, Gojobori T, Itoh T, Niimura Y, Fujii Y, Habara T, Sakai H, Sato Y, Wilson G, Kumar K, McCouch S, Juretic N, Hoen D, Wright S, Bruskiewich R, Bureau T, Miyao A, Hirochika H, Nishikawa T, Kadowaki K, Sugiura M, Project IRGS (2005) The map-based sequence of the rice genome. Nature 436:793–800CrossRefGoogle Scholar
  36. McCarthy EM, Liu J, Lizhi G, McDonald JF (2002) Long terminal repeat retrotransposons of Oryza sativa. Genome Biol 3:research0053.0051 - research0053.0011Google Scholar
  37. Miyao A, Tanaka K, Murata K, Sawaki H, Takeda S, Abe K, Shinozuka Y, Onosato K, Hirochika H (2003) Target site specificity of the Tos17 retrotransposon shows a preference for insertion within genes and against insertion in retrotransposon-rich regions of the genome. Plant Cell 15:1771–1780CrossRefPubMedGoogle Scholar
  38. Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89:583–590PubMedGoogle Scholar
  39. Perrier X, Jacquemoud-Collet JP (2006) DARwin softwareGoogle Scholar
  40. Picault N, Chaparro C, Piegu B, Stenger W, Formey D, Llauro C, Descombin J, Sabot F, Lasserre E, Meynard D, Guiderdoni E, Panaud O (2009) Identification of an active LTR retrotransposon in rice. Plant J 58:754–765CrossRefPubMedGoogle Scholar
  41. Piegu B, Guyot R, Picault N, Roulin A, Saniyal A, Kim H, Collura K, Brar DS, Jackson S, Wing RA, Panaud O (2006) Doubling genome size without polyploidization: dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice. Genome Res 16:1262–1269CrossRefPubMedGoogle Scholar
  42. Piffanelli P, Droc G, Mieulet D, Lanau N, Bès M, Bourgeois E, Rouvière C, Gavory F, Cruaud C, Ghesquière A, Guiderdoni E (2007) Large-scale characterization of Tos17 insertion sites in a rice T-DNA mutant library. Plant Mol Biol 65:587–601CrossRefPubMedGoogle Scholar
  43. R Development Team (2005) A language and environment for statistical computing. R foundation for statistical computing, Vienna, Austria. ISBN 3-900051-07-0Google Scholar
  44. Risterucci AM, Grivet L, N’Goran JAK, Pieretti I, Flament MH, Lanaud C (2000) A high-density linkage map of Theobroma cacao L. Theor Appl Genet 101:948–955CrossRefGoogle Scholar
  45. Second G (1985) Evolutionary relationships in the Sativa group of Oryza based on isozyme data. Genét Sél Evol 17:89–114CrossRefGoogle Scholar
  46. Shirasu K, Schulman AH, Lahaye T, Schulze-Lefert P (2000) A contiguous 66-kb barley DNA sequence provides evidence for reversible genome expansion. Genome Res 10:908–915CrossRefPubMedGoogle Scholar
  47. Siebert PD, Chenchik A, Kellogg DE, Lukyanov KA, Lukyanov SA (1995) An improved PCR method for walking in uncloned genomic DNA. Nucl Acids Res 23:1087–1088CrossRefPubMedGoogle Scholar
  48. Sweeney M, McCouch S (2007) The complex history of the domestication of rice. Ann Bot 100:951–957CrossRefPubMedGoogle Scholar
  49. Taguchi-Shiobara F, Lin SY, Tanno K, Komatsuda T, Yano M, Sasaki T, Oka S (1997) Mapping quantitative trait loci associated with regeneration ability of seed callus in rice, Oryza sativa L. Theor Appl Genet 95:828–833CrossRefGoogle Scholar
  50. Takeuchi Y, Abe T, Sasahara T (2000) RFLP mapping of QTLs influencing shoot regeneration from mature seed-derived calli in rice. Crop Sci 40:245–247CrossRefGoogle Scholar
  51. Vaughan DA, Morishima H, Kadowaki K (2003) Diversity in the Oryza genus. Curr Opin Plant Biol 6:139–146CrossRefPubMedGoogle Scholar
  52. Vicient CM, Jääskeläinen M, Kalendar R, Schulman AH (2001) Active retrotransposons are a common feature of grass genomes. Plant Physiol 125:1283–1292CrossRefPubMedGoogle Scholar
  53. Vitte C, Ishii T, Lamy F, Brar D, Panaud O (2004) Genomic paleontology provides evidence for two distinct origins of Asian rice (Oryza sativa L.). Mol Genet Genomics 272:504–511CrossRefPubMedGoogle Scholar
  54. Wang ZY, Second G, Tanksley SD (1992) Polymorphism and phylogenetic relationships among species in the genus Oryza as determined by analysis of nuclear RFLPs. Theor Appl Genet 83:565–581CrossRefGoogle Scholar
  55. Yamagishi M, Otani M, Higashi M, Fukuta Y, Fukui K, Yano M, Shimada T (1998) Chromosomal regions controlling anther culturability in rice (Oryza sativa L.). Euphytica 103:227–234CrossRefGoogle Scholar
  56. Yamazaki M, Tsugawa H, Miyao A, Yano M, Wu J, Yamamoto S, Matsumoto T, Sasaki T, Hirochika H (2001) The rice retrotransposon Tos17 prefers low-copy-number sequences as integration targets. Mol Genet Genomics 265:336–344CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag 2009

Authors and Affiliations

  • Julie Petit
    • 1
  • Emmanuelle Bourgeois
    • 1
  • Wilfried Stenger
    • 2
  • Martine Bès
    • 1
  • Gaétan Droc
    • 1
  • Donaldo Meynard
    • 1
  • Brigitte Courtois
    • 1
  • Alain Ghesquière
    • 3
  • François Sabot
    • 3
  • Olivier Panaud
    • 2
  • Emmanuel Guiderdoni
    • 1
    Email author
  1. 1.CIRAD, UMR DAP, TAA96/03Montpellier Cedex 5France
  2. 2.Université de Perpignan-CNRS, UMR GDPPerpignanFrance
  3. 3.IRD, UMR GDPMontpellier Cedex 5France

Personalised recommendations