Mutation scanning and genotyping by high-resolution DNA melting analysis in olive germplasm

Genome

Volumn 52, Issue 3, 2009, Pages 252-260

  Muleo, Rosario ^a   Colao, Maria Chiara ^a   Miano, Dario ^a   Cirilli, Marco ^a   Intrieri, Maria C ^a   Baldoni, Luciana ^b   Rugini, Eddo ^a  

^a UNIVERSITY OF TUSCIA   (Italy)

^b CNR   (Italy)

Author keywords

ARMS PCR; Genotyping; High resolution melting; HRM; Melting curve analysis; SNP

Indexed keywords

MICROSATELLITE DNA; PHYTOCHROME A; PLANT DNA;

ARTICLE; DNA DENATURATION; GENETICS; GENOTYPE; MUTATION; NUCLEOTIDE SEQUENCE; OLIVE TREE; POLYMERASE CHAIN REACTION; SINGLE NUCLEOTIDE POLYMORPHISM;

DNA MUTATIONAL ANALYSIS; DNA, PLANT; GENOTYPE; MICROSATELLITE REPEATS; MUTATION; NUCLEIC ACID DENATURATION; OLEA; PHYTOCHROME A; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE;

OLEA EUROPAEA;

EID: 65349139457     PISSN: 08312796     EISSN: None     Source Type: Journal    
DOI: 10.1139/G09-002     Document Type: Article

References (38)

1. Angiolillo, A., Mencuccini, M., and Baldoni, L. 1999. Olive genetic diversity assessed using amplified fragment length polymorphisms. Theor. Appl. Genet. 98(3-4): 411-421. doi:10. 1007/s001220051087.
2. Bartolini, G., Prevost, G., Messeri, C., and Carignani, G. 1998. Olive germplasm: cultivars and world-wide collections. Plant Production and Protection Div. 459, Accession No. 386185, Job No. X0724. FAO, Rome, Italy.
3. Belaj, A., Satovic, Z., Cipriani, G., Baldoni, L., Testolin, R., Rallo, L., and Trujillo, I. 2003. Comparative study of the discriminating capacity of RAPD, AFLP and SSR markers and of their effectiveness in establishing genetic relationships in olive. Theor. Appl. Genet. 107: 736-744. doi:10.1007/s00122-003-1301-5. PMID:12819908.
4. Besnard, G., Khadari, B., Baradat, P., and Bervillé, A. 2002. Olea europaea (Oleaceae) phylogeography based on chloroplast DNA polymorphism. Theor. Appl. Genet. 104: 1353-1361. doi:10. 1007/s00122-001-0832-x. PMID:12582591.
5. Bottero, M.T., Dalmasso, A., Cappelletti, M., Secchi, C., and Civera, T. 2007. Differentiation of five tuna species by a multiplex primer-extension assay. J. Biotechnol. 129: 575-580. doi:10. 1016/j.jbiotec.2007.01.032. PMID:17353060.
6. Chagné, D., Gasic, K., Crowhurst, R.N., Han, Y., Bassett, H.C., Bowatte, D.R., et al. 2008. Development of a set of SNP markers present in expressed genes of the apple. Genomics, 92: 353-358. doi:10.1016/j.ygeno. 2008.07.008. PMID:18721872.
7. Chateigner-Boutin, A.L., and Small, I. 2007. A rapid high-throughput method for the detection and quantification of RNA editing based on high-resolution melting of amplicons. Nucleic Acids Res. 35: e114. doi:10.1093/nar/gkm640. PMID:17726051.
8. Cipriani, G., Marrazzo, M.T., Marconi, R., Cimato, A., and Testolin, R. 2002. Microsatellite markers isolated in olive (Olea europaea L.) are suitable for individual fingerprinting and reveal polymorphism within ancient cultivars. Theor. Appl. Genet. 104: 223-228. doi:10.1007/s001220100685. PMID:12582690.
9. Corpet, F. 1988. Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res. 16: 10881-10890. Available from nar.oxfordjournals.org/cgi/reprint/16/22/10881. PMID:2849754.
10. Dahl, C., and Guldberg, P. 2007. High-resolution melting for accurate assessment of DNA methylation. Clin. Chem. 53: 1877- 1878. doi:10.1373/clinchem.2007.094854. PMID:17954495.
11. Doyle, J.J., and Doyle, J.L. 1990. Isolation of plant DNA from fresh tissue. Focus, 12: 13-15.
12. Fortini, D., Ciammaruconi, A., De Santis, R., Fasanella, A., Battisti, A., D'Amelio, R., et al. 2007. Optimization of high-resolution melting analysis for low-cost and rapid screening of allelic variants of Bacillus anthracis by multiple-locus variable-number tandem repeat analysis. Clin. Chem. 53: 1377-1380. doi:10. 1373/clinchem.2007.085993. PMID:17525105.
13. Gundry, C.N., Vandersteen, J.G., Reed, G.H., Pryor, R.J., Chen, J., and Wittwer, C.T. 2003. Amplicon melting analysis with labeled primers: a closed-tube method for differentiating homozygotes and heterozygotes. Clin. Chem. 49: 396-406. doi:10.1373/49.3. 396. PMID:12600951.
14. Herrmann, M.G., Durtschi, J.D., Bromley, L.K., Wittwer, C.T., and Voelkerding, K.V. 2006. Amplicon DNA melting analysis for mutation scanning and genotyping: cross platform comparison of instruments and dyes. Clin. Chem. 52: 494-503. doi:10.1373/ clinchem.2005.063438. PMID:16423901.
15. Hess, J., Kadereit, W., and Vargas, P. 2000. The colonization history of Olea europaea L. in Macaronesia based on internal transcribed spacer 1 (ITS-1) sequences, randomly amplified polymorphic DNAs (RAPD), and intersimple sequence repeats (ISSR). Mol. Ecol. 9: 857-868. doi:10.1046/j.1365-294x. 2000. 00942.x. PMID:10886649.
16. Intrieri, M.C., Muleo, R., and Buiatti, M. 2007. Chloroplast DNA polymorphisms as molecular markers to identify cultivars of Olea europaea L. J. Hortic. Sci. Biotechnol. 82: 109-113.
17. Jordan, E.T., Cherry, J.R., Walker, J.M., and Vierstra, R.D. 1996. The amino-terminus of phytochrome A contains two distinct functional domains. Plant J. 9: 243-257. doi:10.1046/j.1365-313X.1996.09020243.x. PMID:8820609.
18. Krypuy, M., Ahmed, A.A., Etemadmoghadam, D., Hyland, S.J., deFazio, A., Fox, S.B., et al. 2007. High resolution melting for mutation scanning of TP53 exons 5-8. BMC Cancer, 7(168): 16-17. doi:10.1186/1471-2407-7-168. PMID:17250773.
19. Laurie, A.D., Smith, M.P., and George, P.M. 2007. Detection of factor VIII gene mutations by high-resolution melting analysis. Clin. Chem. 53: 2211-2214. doi:10.1373/clinchem.2007.093781. PMID:17901109.
20. Liew, M., Pryor, R., Palais, R., Meadows, C., Erali, M., Lyon, E., and Wittwer, C.T. 2004. Genotyping of single-nucleotide polymorphisms by high-resolution melting of small amplicons. Clin. Chem. 50: 1156-1165. doi:10.1373/clinchem.2004.032136. PMID:15229148.
21. Lumaret, R., Ouazzani, N., Michaud, H., Vivier, G., Deguilloux, M.F., and Di Giusto, F. 2004. Allozyme variation of oleaster populations (wild olive tree) (Olea europaea L.) in the Mediterranean Basin. Heredity, 92: 343-351. doi:10.1038/sj.hdy.6800430. PMID:14985782.
22. Mackay, J.F., Wright, C.D., and Bonfiglioli, R.G. 2008. A new approach to varietal identification in plants by microsatellite high resolution melting analysis: application to the verification of grapevine and olive cultivars. Plant Methods, 4: 8. doi:10.1186/ 1746-4811-4-8. PMID:18489740.
23. Margraf, R.L., Mao, R., Highsmith, W.E., Holtegaard, L.M., and Wittwer, C.T. 2007. RET proto-oncogene genotyping using un-labeled probes, the masking technique, and amplicon high-resolution melting analysis. J. Mol. Diagnostics, 9: 184-196. doi:10. 2353/jmoldx.2007.060091.
24. Muleo, R., Miano, D., Latini, P., Nesta, M., Cirilli, M., Intrieri, M.C., et al. 2006. High-resolution DNA melting analysis to simultaneously scan mutations and genotype olive germoplasm. In Proceedings of the Biotechnology and Quality of Olive Tree Products Around the Mediterranean Basin. OLIVEBIOTEQ 2006, 2nd International Seminar, Marsala-Mazara del Vallo, Italy, 5-10 November 2006. Vol. 1. DCA-Università degli Studi di Palermo, Mazara del Vallo (TP), Sicily. pp. 109-116.
25. Quail, P.H., Boylan, M.T., Parks, B.M., Short, T.W., Xu, Y., and Wagner, D. 1995. Phytochromes: photosensory perception and signal transduction. Science (Washington, D.C.), 268(5211): 675-680. doi:10.1126/science.7732376. PMID:7732376.
26. Rafalski, A. 2002. Applications of single nucleotide polymorphisms in crop genetics. Curr. Opin. Plant Biol. 5: 94-100. doi:10.1016/ S1369-5266(02)00240-6. PMID:11856602.
27. Rallo, P., Dorado, G., and Martin, A. 2000. Development of simple sequence repeats (SSRs) in the olive tree (Olea europaea L.). Theor. Appl. Genet. 101: 984-989. doi:10.1007/s001220051571.
28. Reale, S., Doveri, S., Díaz, A., Angiolillo, A., Lucentini, L., Pilla, F., et al. 2006. SNP-based markers for discriminating olive (Olea europaea L.) cultivars. Genome, 49: 1193-1205. doi:10. 1139/G06-068. PMID:17110999.
29. Remberg, A., Schmidt, P., Braslavsky, S.E., Gartner, W., and Schaffner, K. 1999. Differential effects of mutations in the chromophore pocket of recombinant phytochrome on chromoprotein assembly and Pr-to-Pfr photoconversion. Eur. J. Biochem. 266: 201-208. doi:10.1046/j.1432-1327.1999.00844.x. PMID:10542065.
30. Ritter, E., Ruiz de Galarreta, J.I., van Eck, H.J., and Sánchez, I. 2008. Construction of a potato transcriptome map based on the cDNA-AFLP technique. Theor. Appl. Genet. 116: 1003-1013. doi:10.1007/s00122-008- 0731-5. PMID:18317719.
31. Salmaso, M., Malacarne, G., Troggio, M., Faes, G., Stefanini, M., Grando, M.S., and Velasco, R. 2008. A grapevine (Vitis vinifera L.) genetic map integrating the position of 139 expressed genes. Theor. Appl. Genet. 116: 1129-1143. doi:10.1007/s00122-008-0741-3.
32. Sefc, K.M., Lopes, M.S., Mendonica, D., Rodrigues Dos Santos, M., Laimer Da Câmara Machado, M., and Da Câmara Machado, A. 2000. Identification of microsatellite loci in olive (Olea europaea) and their characterization in Italian and Iberian olive trees. Mol. Ecol. 9: 1171-1173. doi:10.1046/j.1365-294x.2000.00954. x. PMID:10964237.
33. Vierstra, R.D., and Quail, P.H. 1982. Proteolysis alters the spectral properties of 124 kdalton phytochrome from Avena. Planta, 156: 158-165. doi:10.1007/BF00395430.
34. Vierstra, R.D., and Quail, P.H. 1983. Purification and initial characterization of 124-kilodalton phytochrome from Avena. Biochemistry, 22: 2498-2505. doi:10.1021/bi00279a029.
35. von Ahsen, N., Oellerich, M., and Schutz, E. 2001. Limitations of genotyping based on amplicons melting temperature. Clin. Chem. 47: 1331-1332. Available from www.clinchem.org/cgi/reprint/47/11/1956.
36. Wu, S.B., Wirthensohn, M.G., Hunt, P., Gibson, J.P., and Sedgley, M. 2008. High resolution melting analysis of almond SNPs derived from ESTs. Theor. Appl. Genet. 118: 1-14. doi:10.1007/ s00122-008-0870-8. PMID:18781291.
37. Wu, S.H., and Lagarias, J.C. 2000. Defining the billin lyase domain: lessons from the extended phytochrome superfamily. Biochemistry, 39: 13487-13495. doi:10.1021/bi001123z. PMID:11063585.
38. Zhou, L., Myers, A.N., Vandersteen, J.G., Wang, L., and Wittwer, C.T. 2004. Closed-tube genotyping with unlabeled oligonucleotide probes and a saturating DNA dye. Clin. Chem. 50: 1328- 1335. doi:10.1373/clinchem. 2004.034322. PMID:15166111.