Korean Journal of Breeding Science (한국육종학회지)

The Korean Society of Breeding Science (한국육종학회)
권호 표지

A TILLING Rice Population Induced by Gamma-ray Irradiation and its Genetic Diversity

  • Cho, Hyun Yong (Plant Genomics Lab, Dept of Applied Plant Sciences, Kangwon Natl University) ;
  • Park, Seo Jung (Plant Genomics Lab, Dept of Applied Plant Sciences, Kangwon Natl University) ;
  • Kim, Dong Sub (Advaned Radiation Technology Institute, Korea Atomic Energy Research Institute) ;
  • Jang, Cheol Seong (Plant Genomics Lab, Dept of Applied Plant Sciences, Kangwon Natl University)
  • Received : 2010.09.16
  • Published : 2010.09.30
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Abstract

TILLING (Targeting Induced Local Lesions IN Genomes) is broadly regarded as an excellent methodology for reverse genetics applications. Approximately 15,000 $M_3$ TILLING lines have been developed via the application of gamma-ray irradiation to rice seeds (cv. Donganbyeo), followed by subsequent selections. In an effort to evaluate the genetic diversity of the TILLING population, we have employed the AFLP multiple dominant marker technique. A total of 96 (0.64%) TILLING lines as well as Donganbyeo were selected randomly and their genetic diversity was assessed based on AFLP marker polymorphisms using 5 primer combinations. An average of 100.4 loci in a range of 97 to 106 was detected using these primer combinations, yielding a total of 158 (31.4%) polymorphic loci between Donganbyeo and each of the 96 lines. A broad range of similarity from 80% to 96% with an average of 89.4% between Donganbyeo and each of the 96 lines was also observed, reflecting the genetic diversity of the TILLING population. Approximately 28 polymorphic loci have been cloned and their sequences were BLAST-searched against rice whole genome sequences, resulting in 20 matches to each of the gene bodies including exon, intron, 1 kb upstream and 1 kb downstream regions. Six polymorphic loci evidenced changes in the coding regions of genes as compared to the rice pseudomolecules, 4 loci of which exhibited missense mutations and 2 loci of which exhibited silent mutations. Therefore, the results of our study show that the TILLING rice population should prove to be a useful genetic material pool for functional genomics as well as mutation breeding applications.

Keywords

Acknowledgement

Supported by : Agriculture and Forestry, Ministry for Food, Agriculture, Forestry and Fisheries

References

  1. Cooper JL, Till BJ, Laport RG, Darlow MC, Kleffner JM, Jamai A, El-Mellouki T, Liu S, Ritchie R, Nielsen N, Bilyeu KD, Meksem K, Comai L, Henikoff S. 2008. TILLING to detect induced mutations in soybean. BMC Plant Biol 8:9. https://doi.org/10.1186/1471-2229-8-9
  2. Delsney M. 2003. Towards an accurate sequence of the rice genome. Curr. Opin. Plant Biol. 6:101-105. https://doi.org/10.1016/S1369-5266(03)00010-4
  3. Devos KM. 2005 Updating the 'crop circle'. Curr. Opin. Plant Biol. 8:155–162.
  4. Dong C, Dalton-Morgan J, Vincent K, Sharp P. 2009. A Modified TILLING Method for Wheat Breeding. Plant Genome 2:1. https://doi.org/10.3835/plantgenome2009.02.0001ed
  5. Gorbunova V, Levy AA. 1997. How plants make ends meet: DNA double-strand break repair. Trends Plant Sci. 4:263–269.
  6. Greene EA, Codomo CA, Taylor NE, Henikoff JG, Till BJ, Reynolds SH, Enns LC, Burtner C, Johnson J E, Odden AR, Comai L, Henikoff S. 2003. Spectrum of chemically induced mutations from a large-scale reversegenetic screen in Arabidopsis. Genetics 164:731–740.
  7. International Rice Genome Sequencing Project. 2005. The map-based sequence of the rice genome. Nature 436:793-800. https://doi.org/10.1038/nature03895
  8. Kim DS, Lee IS, Jang CS, Hyun DY, Seo YW, Lee YI (2004a) Selection of radiation induced 5-methyltryptophan resistant rice mutants through embryo culture. Euphytica 135:9-19. https://doi.org/10.1023/B:EUPH.0000009509.78515.8e
  9. Kim DS, Lee IS, Jang CS, Lee SJ, Song HS, Lee YI, Seo YW (2004b) AEC resistant rice mutants induced by gamma-ray irradiation may include both elevated lysine production and increased activity of stress related enzymes. Plant Sci. 167:305-316. https://doi.org/10.1016/j.plantsci.2004.03.029
  10. Leela T, Wani SP, Kannan S, Beerelli N, Sreedevi TK, Hoisington DA, Devi P, Varshney RK. 2009. AFLP-based molecular characterization of an elite germplasm collection of Jatropha curcas L., a biofuel plant. Plant Sci.176:505-513. https://doi.org/10.1016/j.plantsci.2009.01.006
  11. McCallum CM, Comai L, Greene EA, Henikoff S. 2000. Targeted screening for induced mutations. Nat. Biotechnol. 18:455-457. https://doi.org/10.1038/74542
  12. Minoia S, Petrozza A, D'Onofrio O, Piron F, Mosca G, Sozio G, Cellini F, Bendahmane A, Carriero F. 2010. A new mutant genetic resource for tomato crop improvement by TILLING technology. BMC Research Notes 3:69. https://doi.org/10.1186/1756-0500-3-69
  13. Morita R, Kusaba M, Iida S, Yamaguchi H, Nishio T, Nishimura M. 2009. Molecular characterization of mutations induced by gamma irradiation in rice. Genes & Genetic Systems 84:361-370. https://doi.org/10.1266/ggs.84.361
  14. Saghai-Maroof MA, Soliman KM, Jorgensen RA, Allard RW. 1984. Ribosomal DNA spacer-length polymorphisms in barley: Mendelian inheritance, chromosomal location, and population dynamics. Proc. Natl. Acad. Sci. USA 81:8014-8018. https://doi.org/10.1073/pnas.81.24.8014
  15. Shibutani S, Takeshita M, Grollman AP. 1991. Insertion of specific bases during DNA synthesis past the oxidation -damaged base 8-oxodG. Nature 349:431-434. https://doi.org/10.1038/349431a0
  16. Shin YS, Jeon YH, Kang KH, Seo YW, Jeung JU. 2009. Variation of agronomic traits of rice mutant lines induced by sodium azide. Korean J. Breed. 41:92-100.
  17. Slade AJ, Fuerstenberg S I, Loeffler D, Steine MN, Facciotti D. 2005. A reverse genetic, nontransgenic approach to wheat crop improvement by TILLING. Nat. Biotechnol. 23:75-81. https://doi.org/10.1038/nbt1043
  18. Sokal RR, Sneath PHA. 1963. Principles of numeric taxonomy. Freeman Press, San Francisco, USA.
  19. Suzuki T, Eiguchi M, Kumamaru T, Satoh, H, Matsusaka H, Moriguchi K, Nagato Y. and Kurata, N. 2008. MNUinduced mutant pools and high performance TILLING enable finding of any gene mutation in rice. Mol. Genet. Genomics. 279:213-223. https://doi.org/10.1007/s00438-007-0293-2
  20. Tajiri T, Maki H, Sekiguchi M. 1995. Functional cooperation of MutT, MutM and MutY proteins in preventing mutations caused by spontaneous oxidation of guanine nucleotide in Escherichia coli. Mutat. Res. 336:257-267. https://doi.org/10.1016/0921-8777(94)00062-B
  21. Till BJ, Reynolds SH, Greene EA, Codomo CA, Enns LC, Johnson JE, Burtner C, Odden AR, Young K, Taylor NE, Heniko V JG, Comai L, HenikoVS. 2003. Large-scale discovery of induced point mutations with high-throughput TILLING. Genome Res. 13:524-530. https://doi.org/10.1101/gr.977903
  22. Till BJ, Reynolds SH, Weil C, Springer N, Burtner C, Young K, Bowers E, Codomo CA, Enns LC, Odden AR, Greene EA, Comai L, Henikoff S. 2004. Discovery of induced point mutations in maize genes by TILLING. BMC Plant Biol. 4:12. https://doi.org/10.1186/1471-2229-4-12
  23. Till BJ, Cooper J, Tai TH, Colowit P, Greene EA, Henikoff S, Comai L. 2007. Discovery of chemically induced mutations in rice by TILLING. BMC Plant Biol. 7:19. https://doi.org/10.1186/1471-2229-7-19
  24. Wu JL, Wu C, Lei C, Baraoidan M, Bordeos A, Madamba MR, Ramos-Pamplona M, Mauleon R, Portugal A, Ulat VJ, et al. 2005: Chemical- and Irradiation-induced Mutants of Indica Rice IR64 for Forward and Reverse Genetics. Plant Mol Biol. 59:85-97. https://doi.org/10.1007/s11103-004-5112-0
  25. Vos P, Hogers R, Bleeker M, Reijans M, Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M. 1995. AFLP: A new technique for DNA fingerprinting. Nucleic Acids Res. 23:4407-4414. https://doi.org/10.1093/nar/23.21.4407