Authentication of domestic Taiwan rice varieties based on fingerprinting analysis of microsatellite DNA markers

Botanical Studies

Volumn 52, Issue 4, 2011, Pages 393-405

  Chuang, Hsue Yu ^a   Lur, Huu Shen ^a   Hwu, Kae Kang ^a   Chang, Men Chi ^a  

^a NATIONAL TAIWAN UNIVERSITY   (Taiwan)

Author keywords

DNA fingerprinting analysis; Microsatellite markers; Polymorphism; Principle component analysis (PCA); Rice; Simple sequence repeat (SSR)

Indexed keywords

EID: 84255183189     PISSN: 1817406X     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (50)

1. Agrama, H.A., W.G. Yan, F. Lee, R. Fjellstrom, M.H. Chen, M. Jia, and A. McClung. 2009. Genetic assessment of a minicore subset developed from the USDA rice genebank. Crop Sci. 49: 1336-1346.
2. Anderson, J.A, G.A. Churchill, J.E. Autrique, S.D. Tanksley, and M.E. Sorreles. 1993. Optimizing parental selection for genetic linkage maps. Genomes 36: 181-186.
3. Archak, S., V. Lakshminarayanareddy, and J. Nagaraju. 2007. High-throughput multiplex microsatellite marker assay for detection and quantification of adulteration in Basmati rice (Oryza sativa). Electrophoresis 28: 2396-2405.
4. Bajracharya, J., K.A. Steele, D.J. Jarvis, B.R. Sthapti, and J.R. Witcombe. 2006. Rice landrace diversity in Nepal: variability of agro-morphological traits and SSR markers in landraces from a high-attitude site. Field Crops Res. 95: 327-335.
5. Bernardo, G.B., U. Galderisi, M. Cipollaro, and A. Cascino. 2005. Methods to improve the yield and quality of DNA from dried and processed figs. Biotechnol. Prog. 21: 546-549.
6. Bonow, S.W., E.V.R. Von Pinho., M.G.C. Vieira., and B. Vosman. 2009. Microsatellite markers in and around rice genes: application in variety identification and DUS testing. Crop Sci. 49: 880-886.
7. Botstein, D., R.L. White, M. Skolnick, and R.W. Davis. 1980. Construction of genetic linkage map in man using restriction fragment length polymorphism. Am. J. Hu. Genet. 32: 314-331.
8. Chen, H., M.S. Lin, and K.K. Hwu. 2008. A database of Taiwan rice pedigrees. Crop, Environment & Bioinformatics 5: 22-28, (Chinese in English Abstract)
9. Chen, X., S. Temnykh, Y. Xu, Y.G. Cho, and S.R. McCouch. 1997. Development of a microsatellite framework map providing genome-wide coverage in rice (Oryza sativa L.) Theor. Appl. Genet. 95: 553-567.
10. Cirillo, A., S.D. Gaudio, G.D. Bernardo, U. Galderisi, A. Cascino, and M. Cipollaro. 2009. Molecular characterization of Italian rice cultivars. Eur. Food Res. Technol. 228: 875-881
11. Colyer, A., R. Macarthur, J. Lloyd, and H. Hird. 2009. Comparison of calibration methods for the quantification of Basmati and non-Basmati rice using microsatellite analysis. Food Addit. Contam. (Part A) 25: 1189-1194.
12. Ebana, K., Y. Kojima, S. Fukuoka, T. Nagamine, and M. Kawase. 2008. Development of mini core collection of Japanese rice landrace. Breed. Sci. 58: 281-291.
13. Ganal, M.W., T. Altmann, and M.S. Roder. 2009. SNP identification in crop plants. Curr. Opin. Pl. Biol. 12: 211-217.
14. Giarrocco, L.E., M.A. Marassi, and G.L. Salerno. 2007. Assessment of the genetic diversity in Argentine rice cultivars with SSR Markers. Crop Sci. 47: 853-858.
15. Goodman, M.C. and C.W. Stuber. 1983. Races of maize. VI. Isozyme variation among races of maize in Bolivia. Maydica 28: 169-187.
16. Hashimoto, Z., N. Mori, M. Kawamura, T. Ishii, S. Yoshida, M. Ikegami, S. Takumi, and C. Nakamura. 2004. Genetic diversity and phylogeny of Japanese sake-brewing rice as revealed by AFLP and nuclear and chloroplast SSR markers. Theor. Appl. Genet. 109: 1586-1596.
17. Hour, A.L., Y.C. Lin, P.F. Li, T.Y. Chow, W.F. Lu, F. Wei, and Y.I. Hsing. 2007. Detection of SNPs between Tainung 67 and Niponbare rice cultivars. Bot. Stud. 48: 243-253
18. Hsieh, L.Y., D.R. Wu, and K.K. Hu. 2007. Variety identification among major Japonica rice cultivars of Taiwan based on simple sequence repeat markers. Seed & Nursery (Taiwan) 9: 25-39.
19. Huang, S. 2001. Taiwan's rice import market to open with WTO accession. Rice Situation and Outlook Yearbook. Market and Trade Economics Division, ERS. USDA. November 2-1. RCS-2001, pp. 33-36.
20. Jain, S., R.K. Jain, and S.R. McCouch. 2004. Genetic analysis of Indian aromatic and quality rice (Oryza sativa L.) germplasm using panels of fluorescent-labeled microsatellite markers. Theor. Appl. Genet. 109: 965-977.
21. Jayamani, P., S. Negrao, M. Martins, B. Macas, and M.M. Oliveira. 2007. Genetic relatedness of Portuguese rice accessions from diverse origins as assessed by microsatellite markers. Crop Sci. 47: 879-884.
22. Lin, M.S. 1991. Genetic base of Japonica rice varieties released in Taiwan. Euphytica 56: 43-46.
23. Lu, C.Y. and H.Y. Lu. 2010. Establishment and application of Taiwan Rice Information System. J. Taiwan Agric. Res. 59: 61-69
24. Lu, H., M.A. Redus, J.R. Coburn, J. N. Rutger, S.R. MuCouch, and H.T. Tai. 2005 Population structure and breeding patterns of 145 U.S. rice cultivars based on SSR marker analysis. Crop Sci. 45: 66-76.
25. McCouch, S.R., L. Teytelman, Y. Xu, K.B. Lobos, K. Clare, M. Walton, B. Fu, R. Maghirang, Z. Li, Y. Xing, Q. Zhang, I. Kono, M. Yano, R. Fjellstrom, G. DeClerck, D. Schneider, S. Cartinhour, D. Ware, and L. Stein. 2002. Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Res. 9: 199-207.
26. Pal, S., S. Jain, N. Saini Aarti, and R.K. Jain. 2004. Identification of microsatellite markers for differentiating some Basmati and non-Basmati rice varieties. Indian J. Biotech. 3: 519-526.
27. Pervaiz, Z.H., M.A. Rabbani, S.R. Pearce, and S.A. Malik. 2009. Determination of genetic variability of Asian rice (Oryza sativa L.) varieties using microsatellite markers. African J. Biotech. 8: 5641-5651.
28. Pessoa-Filho, M., A. Beló, AN.A. António, P.H.N. Rangel, and M.F. Ferreira. 2007. A set of multiplex panels of microsatellite markers for rapid molecular characterization of rice accessions. BMC Plant Biol. 7: 23.
29. Popping, B. 2002. The application of biotechnological methods in authenticity testing. J. Biotech. 98: 107-112.
30. Primrose, S., M. Woolfe, and S. Rollinson. 2010. Food forensics: methods for determing the authenticity of foodstuffs. Trends Food Sci. Tech. 21: 582-590.
31. Rahman, M.S., Md. R. Molla, Md. S. Alam, and L. Rahman. 2009. DNA fingerprinting of rice (Oryza sativa L.) cultivars using microsatellite markers. Aust. J. Crop Sci. 3: 122-128
32. Reif, J.C, A.E. Melchinger, X.C. Xia, M.L. Warburton, D.A. Hoisington, K. Vasal, G. Srinivasan, M. Bohn, and M. Fisch. 2003. Genetic distance based on simple sequence repeats and heterosis in tropical maize populations. Crop Sci. 43: 1275-1282.
33. Reif, J.C., A.E. Melchinger, and M. Fisch. 2005. Genetical and mathematical properties of similarity and dissimilarity coefficients applied in plant breeding and seed bank management. Crop Sci. 45: 1-7.
34. Shu, A.P., K.J. Hwan, S.Y. Zhang, G.L. Cao, Z.H. Nan, K.S. Lee, M.Q. Lu, and L.Z. An. 2009. Analysis on genetic similarity of japonica rice variety from different origins of geography in the world. Agricultural Sciences in China 8: 513-320.
35. Singh, R.K., R.K. Sharma, A.K. Singh, V.P. Singh, S.P. Tiwari, and T. Mohapatra. 2004. Suitability of mapped sequence tagged microsatellite site markers for establishing distinctness, uniformity and stability in aromatic rice. Euphytica 135: 135-143.
36. Steele, K.A., R. Ogden, R. McEwing, H. Briggs, and J. Gorham. 2008. InDel markers distinguish Basmatis from other fragrant rice varieties. Field Crops Res. 105: 81-87
37. Tautz, D. 1989. Hypervariability of simple sequences as a general source of polymorphic DNA markers. Nucleic. Acids. Res. 17: 6463-6471.
38. Terzi, V., C. Morcia, A. Gorrini, A.M. Stanca, P.R. Shewry, and P. Faccioli. 2005. DNA-based methods for identification and quantification of small grain cereal mixtures and fingerprinting of varieties. J. Cereal Sci. 41: 213-220.
39. Thomposon, M.J., E.M. Septiningsih, F. Suwardjo, T.J. Santoso, T.S. Silitonga, and S.R. McCoush. 2007. Genetic diversity analysis of traditional and improved Indonesian rice (Oryza sativa L.) germplasm using microsatellite markers. Theor. Appl. Genet. 114: 559-568.
40. Vlachos, A. and L.S. Arvanitoyannis. 2009. A review of rice authenticity/adulteration methods and results. Crit. Rev. Food Sci. Nut. 48: 553-598.
41. Vemireddy, L., S. Archak, and J. Nagarju. 2007. Capillary electrophoresis is essential for microsatellite marker based detection and quantification of adulteration of basmati rice (Oryza sativa L.). J. Agric. Food Chem. 55: 8112-8117.
42. Vos, P., R. Hogers, M. Bleeker, M. Reijans, V.D. Lee, and M. Hornes. 1995. AFLP: a new concept for DNA fingerprinting. Nucleic. Acids. Res. 23: 4407-4414.
43. Wang, X.W., A.T. Rinehart, P.A. Wadl, J.M. Spiers, D. Hadziabdic, M.T. Windham, and R.N. Trigiano. 2009. A new electrophoresis technique to separate microsatellite alleles African. J. Biotech. 8: 2432-2436.
44. Williams, J.G.K., A.R. Kubelik, K.J. Livak, J.A. Rafalski, and S.V. Tingey. 1990. DNA polymorphism amplified by arbitrary primers are useful as genetic markers. Nucleic. Acids. Res. 18: 6531-6535.
45. Woolfe, M. and S. Primrose. 2004. Food Forensics: using DNA technology to combat misdescription and fraud. Trends Biotechnol. 22: 222-226.
46. Wu, W.C. and M.S. Lin. 2008. Pedigree analysis of rice varieties of Taiwan: I. relationships among Japanese introductions. Crop Environ. Bioinformatics 5: 248-257. (Chinese in English Abstract)
47. Wu, Y.J., Z.M. Zhang, Y. Chen, B. Wang, G.U. Yang, and W.Y. Yang. 2009. Authentication of Thailand jasmine rice using RAPD and SCAR methods. Eur. Food Res. Technol. 229: 515-521.
48. Xu, Y.B., H. Beachell, and S.R. McCouch. 2004. A marker-based approach to broadening the genetic base of rice in the USA. Crop Sci. 44: 1947-1959.
49. Yuan, X.P., X.H. Wei, H. Lei, H.Y. Yu, Y.P. Wang, Q. Xu, and S.X. Tang. 2007. A comparative study of SSR diversity in Chinese major rice varieties planted in 1950s and in the recent ten years (1995-2004). Rice Sci. 14: 78-84.
50. Zhang, Y. and J.R. Stommel. 2001. Development of SCAR and CAPS markers linked to the Beta gene in tomato. Crop Sci. 41: 1602-1608.