Analysis of distribution and proliferation of mPing family transposons in a wild rice (Oryza rufipogon Griff.)

Breeding Science

Volumn 59, Issue 3, 2009, Pages 297-307

  Karki, Shanta ^a   Tsukiyama, Takuji ^a   Okumoto, Yutaka ^a   Rizal, Govinda ^a   Naito, Ken ^b   Teraishi, Masayoshi ^a   Nakazaki, Tetsuya ^a   Tanisaka, Takatoshi ^a  

^a KYOTO UNIVERSITY   (Japan)

^b UNIVERSITY OF GEORGIA   (United States)

Author keywords

Elements; Mping; Oryza rufipogon; Transposable; Wild rice

Indexed keywords

ORYZA; ORYZA RUFIPOGON; ORYZA SATIVA; ZIZANIA;

EID: 70349486015     PISSN: 13447610     EISSN: 13473735     Source Type: Journal    
DOI: 10.1270/jsbbs.59.297     Document Type: Article

References (36)

1. Bennetzen, J.L. (2000) Transposable element contributions to plant gene and genome evolution. Plant Mol. Biol. 42: 251-269.
2. Biemont, C. and C. Vieira (2006) Genetics: Junk DNA as an evolution- ary force. Nature 443: 521-524.
3. Bureau, T.E., P.C. Ronald and S.R. Wessler (1996) A computer-based systematic survey reveals the predominance of small inverted- repeat elements in wild-type rice genes. Proc. Natl. Acad. Sci. USA 93: 8524-8529.
4. Casa, A.M., C. Brouwer, A. Nagel, L. Wang, Q. Zhang, S. Kresovich and S.R. Wessler (2000) The MITE family Heartbreaker (Hbr): Molec- ular markers in maize. Proc. Natl. Acad. Sci. USA 97: 10083- 10089.
5. Cheng, C., R. Motohashi, S. Tsuchimoto, Y. Fukuta, H. Ohtsubo and E. Ohtsubo (2003) Polyphyletic origin of cultivated rice: Based on the interspersion pattern of SINEs. Mol. Biol. Evol. 20: 67-75.
6. Feng, Q., Y. Zhang, P. Hao, S. Wang, G. Fu, Y. Huang, Y. Li, J. Zhu, Y.Liu, X.Hu et al. (2002) Sequence and analysis of rice chromosome 4. Nature 420: 316-320.
7. Feschotte, C., N. Jiang and S.R. Wessler (2002) Plant transposable ele- ments: where genetics meets genomics. Nat. Rev. Genet. 3: 329- 341.
8. Hu, H., J. Mu, H.J. Zhang, Y.Z. Tao and B. Han (2006) Differentiation of a miniature inverted transposable element (MITE) system in Asian rice cultivars and its inference for a diphyletic origin of two subspecies of Asian cultivated rice. J. Integr. Plant Biol. 48: 260- 267.
9. International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436: 793-799.
10. Iwamoto, M., H. Nagashima, T. Nagamine, H. Higo and K. Higo (1999) A Tourist element in the 5′-flanking region of the catalase gene CatA reveals evolutionary relationships among Oryza species with various genome types. Mol. Gen. Genet. 262: 493-500.
11. Jiang, N., Z. Bao, X. Zhang, H. Hirochika, S.R. Eddy, S.R. McCouch and S.R. Wessler (2003) An active DNA transposon family in rice. Nature 421: 163-167.
12. Jiang, N., C. Feschotte, X. Zhang and S.R. Wessler (2004) Using rice to understand the origin and amplification of MITEs. Curr. Opin. Plant Bio. l7: 115-119.
13. Kikuchi, K., K. Terauchi, M. Wada and H.Y. Hirano (2003) The plant MITE mPing is mobilized in anther culture. Nature 421: 167-170.
14. Kimura, M. (1980) A simple method for estimating evolutionary rate of base substitution through comparative studies of nucleotide se- quences. J. Mol. Evol. 16: 111-120.
15. Konishi, S., T. Izawa, S. Lin, K. Ebana, Y. Fukuta, T. Sasaki and M. Yano (2006) An SNP caused loss of seed shattering during rice domestication. Science 312: 1392-1396.
16. Kumar, S., K. Tamura and M. Nei (2004) MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence align- ment. Briefings in Bioinformatics 5: 150-163.
17. Le, Q.H., S. Wright, Z. Yu and T. Bureau (2000) Transposon diversity in Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 97: 7376- 7381.
18. Mao, L., T.C. Wood, Y. Yu, M.A. Budiman, J. Tomkins, S.S. Woo, M. Sasinowski, G. Presting, D. Frisch, S. Goff, R.A. Dean and R.A. Wing (2000) Rice transposable elements: a survey of 73,000 sequence-tagged-connectors. Genome Res. 10: 982-990.
19. Morishima, H. and P. Barbier (1990) Mating system and genetic struc- ture of natural populations in wild rice, Oryza rufipogon. Plant Spec. Biol. 5: 31-39.
20. Murray, M. and W.F. Thompson (1980) Rapid isolation of high-molecular weight plant DNA. Nucleic Acids Res. 8: 4321-4325.
21. Naito, K., E.Y. Cho, G. Yang, M. Campbell, K. Yano, Y. Okumoto, T. Tanisaka and S.R. Wessler (2006) Dramatic amplification of a rice transposable element during recent domestication. Proc. Natl. Acad. Sci. USA 103: 17620-17625.
22. Nakazaki, T., Y. Okumoto, A. Horibata, S. Yamahira, M. Teraishi, H. Nishida, H. Inoue and T. Tanisaka (2003) Mobilization of a transposon in the rice genome. Nature 421: 170-172.
23. Ohtsubo, H., C. Cheng, I. Ohsawa, S. Tsuchimoto and E. Ohtsubo (2004) Rice retroposon p-SINE1 and origin of cultivated rice. Breed. Sci. 54: 1-11.
24. Oki, N., K. Yano, Y. Okumoto, T. Tsukiyama, M. Teraishi and T. Tanisaka (2008) A genome-wide view of miniature inverted-repeat trans- posable elements (MITEs) in rice, Oryza sativa ssp. japonica. Genes Genet. Syst. 83: 321-329.
25. Onishi, K., K. Takagi, M. Kontani, T. Tanaka and Y. Sano (2007) Differ- ent patterns of genealogical relationships found in the two major QTLs causing reduction of seed shattering during rice domestica- tion. Genome 50: 757-766.
26. Park, K.C., N.H. Kim, Y.S. Cho, K.H. Kang, J.K. Lee and N.S. Kim (2003a) Genetic variations of AA genome Oryza species measured by MITE-AFLP. Theor. Appl. Genet. 107: 203-209.
27. Park, K.C., J.K. Lee, N.H. Kim, Y.B. Shin, J.H. Lee and N.S. Kim (2003b) Genetic variation in Oryza species detected by MITE- AFLP. Genes Genet. Syst. 78: 235-243.
28. Saitou, N. and M. Nei (1987) The neighbor-joining method: A new.method for reconstruction phylogenetic trees. Mol. Biol. Evol. 4: 406-425.
29. Takata, M., Y. Kishima and Y. Sano (2005) DNA methylation polymor- phisms in rice and wild rice strains: Detection of epigenetic mark- ers. Breed. Sci. 55: 57-63.
30. Takata, M., A. Kiyohara, A. Takasu, Y. Kishima, H. Ohtsubo and Y. Sano (2007) Rice transposable elements are characterized by various methylation environments in the genome. BMC Genomics 8: 469.
31. Turcotte, K., S. Srinivasan and T. Bureau (2001) Survey of transposable elements from rice genomic sequences. Plant J. 25: 169-180.
32. Vaughan, A.D., K. Kadowaki, A. Kaga and N. Tamooka (2005) On the phylogeny and biogeography of the genus Oryza. Breed. Sci. 55: 113-122.
33. Xu, J.H., C. Cheng, S. Tsuchimoto, H. Ohtsubo and E. Ohtsubo (2007) Phylogenetic analysis of Oryza rufipogon strains and their relations to Oryza sativa strains by insertion polymorphism of rice SINEs. Genes Genet. Syst. 82: 217-229.
34. Yang, G., J. Dong, M.B. Chandrasekharan and T.C. Hall (2001) Kiddo, a new transposable element family closely associated with rice genes. Mol. Genet. Genomics 266: 417-424.
35. Yang, G., Y.H. Lee, X. Shi, S. Kertbundit and T.C. Hall (2005) A two- edged role for the transposable element Kiddo in the rice ubiquitin 2 promoter. Plant Cell 17: 1559-1568.
36. Yang, G., F. Zhang, C.N. Hancock and S.R. Wessler (2007) Transposi- tion of the rice miniature inverted repeat transposable element mPing in Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 104: 10962-10967.