iSNAP: A small RNA-based molecular marker technique

Plant Breeding

Volumn 130, Issue 5, 2011, Pages 515-520

  Gui, Yijie ^a   Yan, Guanghao ^a   Bo, Shiping ^a   Tong, Zhijun ^a   Wang, Yu ^a   Xiao, Bingguang ^b   Lu, Xiuping ^b   Li, Yongping ^b   Wu, Weiren ^a   Fan, Longjiang ^a  

^a ZHEJIANG UNIVERSITY   (China)

^b Yunnan Academy of Tobacco Agricultural Sciences   (China)

Author keywords

Inter small RNA polymorphism; Molecular marker technique; Small RNA; Tobacco

Indexed keywords

EUKARYOTA; NICOTIANA TABACUM;

EID: 80053898644     PISSN: 01799541     EISSN: 14390523     Source Type: Journal    
DOI: 10.1111/j.1439-0523.2011.01872.x     Document Type: Article

References (35)

1. Agarwal, M., N. Shrivastava, and H. Padh, 2008: Advances in molecular marker techniques and their applications in plant sciences. Plant Cell Rep. 27, 617-631.
2. Botstein, D., R. L. White, M. Skolnick, and R. W. Davis, 1980: Construction of a genetic-linkage map in man using restriction fragment length polymorphisms. Am. J. Hum Genet 32, 314-331.
3. Chang, R. Y., L. S. O'Donoughue, and T. E. Bureau, 2001: Inter-MITE polymorphisms (IMP): a high throughput transposon-based genome mapping and fingerprinting approach. Theor. Appl. Genet. 102, 773-781.
4. Chevreux, B., T. Pfisterer, B. Drescher, A. J. Driesel, W. E. G. Muller, T. Wetter, and S. Suhai, 2004: Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Res. 14, 1147-1159.
5. Crooks, G. E., G. Hon, J. M. Chandonia, and S. E. Brenner, 2004: WebLogo: a sequence logo generator. Genome Res. 14, 1188-1190.
6. Dugas, D. V., and B. Bartel, 2004: MicroRNA regulation of gene expression in plants. Curr. Opin. Plant Biol. 7, 512-520.
7. Julio, E., J. L. Verrier, and F. D. de Borne, 2006: Development of SCAR markers linked to three disease resistances based on AFLP within Nicotiana tabacum L. Theor. Appl. Genet. 112, 335-346.
8. Kalendar, R., T. Grob, M. Regina, A. Suoniemi, and A. Schulman, 1999: IRAP and REMAP: two new retrotransposon-based DNA fingerprinting techniques. Theor. Appl. Genet. 98, 704-711.
9. Kalendar, R., K. Antonius, P. Smykal, and A. H. Schulman, 2010: iPBS: a universal method for DNA fingerprinting and retrotransposon isolation. Theor. Appl. Genet. 121, 1419-1430.
10. Kasschau, K. D., N. Fahlgren, E. J. Chapman, C. M. Sullivan, J. S. Cumbie, S. A. Givan, and J. C. Carrington, 2007: Genome-wide profiling and analysis of Arabidopsis siRNAs. PLoS Biol. 5, 479-493.
11. Kuang, H. H., C. Padmanabhan, F. Li, A. Kamei, P. B. Bhaskar, O. Y. Shu, J. M. Jiang, C. R. Buell, and B. Baker, 2009: Identification of miniature inverted-repeat transposable elements (MITEs) and biogenesis of their siRNAs in the solanaceae: new functional implications for MITEs. Genome Res. 19, 42-56.
12. Lander, E., J. Abrahamson, A. Barlow, M. Daly, S. Lincoln, L. Newburg, and P. Green, 1987: Mapmaker a computer package for constructing genetic-linkage maps. Cytogenet. Cell Genet. 46, 642.
13. Leng, X. D., B. G. Xiao, S. Wang, Y. J. Gui, Y. Wang, X. P. Lu, J. H. Xie, Y. P. Li, and L. J. Fan, 2010: Identification of NBS-type resistance gene homologs in tobacco genome. Plant Mol. Biol. Rep. 28, 152-161.
14. Lister, R., B. D. Gregory, and J. R. Ecker, 2009: Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond. Curr. Opin. Plant Biol. 12, 107-118.
15. Litt, M., and J. A. Luty, 1989: A hypervariable microsatellite revealed by in vitro amplification of a dinucleotide repeat within the cardiac-muscle actin gene. Am. J. Hum. Genet. 44, 397-401.
16. Liu, R. H., and J. L. Meng, 2003: MapDraw: a Microsoft Excel macro for drawing genetic linkage maps based on given genetic linkage data. Hereditas 25, 317-321.
17. Meyer, W., T. G. Mitchell, E. Z. Freedman, and R. Vilgalys, 1993: Hybridization probes for conventional DNA-fingerprinting used as single primers in the polymerase chain-reaction to distinguish strains of cryptococcus-neoformans. J. Clin. Microbiol. 31, 2274-2280.
18. Nei, M., and W. H. Li, 1979: Mathematical-model for studying genetic-variation in terms of restriction endonucleases. Proc. Natl Acad. Sci. USA 76, 5269-5273.
19. Oki, N., K. Yano, Y. Okumoto, T. Tsukiyama, M. Teraishi, and T. Tanisaka, 2008: A genome-wide view of miniature inverted-repeat transposable elements (MITEs) in rice, Oryza sativa ssp japonica. Genes Genet. Syst. 83, 321-329.
20. Rafalski, A., 2002: Applications of single nucleotide polymorphisms in crop genetics. Curr. Opin. Plant Biol. 5, 94-100.
21. Ren, N., and M. P. Timko, 2001: AFLP analysis of genetic polymorphism and evolutionary relationships among cultivated and wild Nicotiana species. Genome 44, 559-571.
22. Rohlf, F. J., 2000: NTSYS-pc: Numerical Taxonomy and Multivariate Analysis System, 2.1 Ed. Exeter Software, Setauket, NY.
23. Sambrook, J., and D. W. Russell, 2001: Molecular Cloning a Laboratory Manual, 3rd edn. Cold Spring Harbor, New York.
24. Syvanen, A. C., 2001: Accessing genetic variation: genotyping single nucleotide polymorphisms. Nat. Rev. Gen. 2, 930-942.
25. Taft, R. J., E. A. Glazov, N. Cloonan, C. Simons, S. Stephen, G. J. Faulkner, T. Lassmann, A. R. R. Forrest, S. M. Grimmond, K. Schroder, K. Irvine, T. Arakawa, M. Nakamura, A. Kubosaki, K. Hayashida, C. Kawazu, M. Murata, H. Nishiyori, S. Fukuda, J. Kawai, C. O. Daub, D. A. Hume, H. Suzuki, V. Orlando, P. Carninci, Y. Hayashizaki, and J. S. Mattick, 2009: Tiny RNAs associated with transcription start sites in animals. Nat. Genet. 41, 572-578.
26. Tang, D., W. Wu, W. Li, H. Lu, and A. J. Worland, 2000: Mapping of QTLs conferring resistance to bacterial leaf streak in rice. Theor. Appl. Genet. 101, 286-291.
27. Tautz, D., 1989: Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Res. 17, 6463-6471.
28. Vos, P., R. Hogers, M. Bleeker, M. Reijans, T. Vandelee, M. Hornes, A. Frijters, J. Pot, J. Peleman, M. Kuiper, and M. Zabeau, 1995: AFLP - a new technique for DNA-fingerprinting. Nucleic Acids Res. 23, 4407-4414.
29. Wang, Z., J. L. Weber, G. Zhong, and S. D. Tanksley, 1994: Survey of plant short tandem DNA repeats. Theor. Appl. Genet. 88, 1-6.
30. Wang, Y., D. Shen, S. P. Bo, H. A. Chen, J. A. Zheng, Q. H. Zhu, D. G. Cai, C. Helliwell, and L. J. Fan, 2010: Sequence variation and selection of small RNAs in domesticated rice. BMC Evol. Biol. 10, 119.
31. Waugh, R., K. McLean, A. J. Flavell, S. R. Pearce, A. Kumar, B. B. T. Thomas, and W. Powell, 1997: Genetic distribution of Bare-1-like retrotransposable elements in the barley genome revealed by sequence-specific amplification polymorphisms (S-SAP). Mol. Gen. Genet. 253, 687-694.
32. Wernsman, E. A., 1999: An overview of tobacco breeding - past, present and future. Recent Adv. Tob. Sci. 25, 5-35.
33. Williams, J. G. K., A. R. Kubelik, K. J. Livak, J. A. Rafalski, and S. V. Tingey, 1990: DNA polymorphisms amplified by arbitrary primers are useful as genetic-markers. Nucleic Acids Res. 18, 6531-6535.
34. Zhu, Q. H., A. Spriggs, L. Matthew, L. J. Fan, G. Kennedy, F. Gubler, and C. Helliwell, 2008: A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains. Genome Res. 18, 1456-1465.
35. Zietkiewicz, E., A. Rafalski, and D. Labuda, 1994: Genome fingerprinting by simple sequence repeat (ssr)-anchored polymerase chain-reaction amplification. Genomics 20, 176-183.