CEL I nuclease digestion for SNP discovery and marker development in common bean (Phaseolus vulgaris L.)

Crop Science

Volumn 49, Issue 2, 2009, Pages 381-394

  Galeano, Carlos H ^a   Gomez, Marcela ^a   Rodriguez, Lina M ^a   Blair, Matthew W ^a  

^a INTERNATIONAL CENTER FOR TROPICAL AGRICULTURE CIAT   (Colombia)

Author keywords

[No Author keywords available]

Indexed keywords

PHASEOLUS VULGARIS;

EID: 63149104088     PISSN: 0011183X     EISSN: None     Source Type: Journal    
DOI: 10.2135/cropsci2008.07.0413     Document Type: Article

References (44)

1. Abreu, E.F.M., and F.J.L. Aragao. 2007. Isolation and characterization of a myo-inositol-1-phosphate synthase gene from yellow passion fruit (Passiflora edulis f. flavicarpa) expressed during seed development and environmental stress. Ann. Bot. (Lond.) 99:285-292.
2. Andersen, J.R., and T. Lubberstedt. 2003. Functional markers in plants. Trends Plant Sci. 8:554-560.
3. Bertin, I., J. Zhu, and M. Gale. 2005. SSCP-SNP in pearl millet: A new marker system for comparative genetics. Theor. Appl. Genet. 110:1467-1472.
4. Blair, M.W., F. Pedraza, H.F. Buendia, E. Gaitán-Solís, S.E. Beebe, P. Gepts, and J. Tohme. 2003. Development of a genome-wide anchored microsatellite map for common bean (Phaseolus vulgaris L.). Theor. Appl. Genet. 107:1362-1374.
5. Blair, M.W., L. Rodriguez, F. Pedraza, F. Morales, and S. Beebe. 2007. Genetic mapping of the bean golden yellow mosaic geminivirus resistance gene bgm-1 and linkage with potyvirus resistance in common bean (Phaseolus vulgaris L.). Theor. Appl. Genet. 114:261-271.
6. Castelblanco, W., and M. Fregene. 2006. SSCP-SNP-based conserved ortholog set (COS) markers for comparative genomics in cassava (Manihot esculenta Crantz). Plant Mol. Biol. Rep. 24:229-236.
7. Ching, A., K. Caldwell, M. Jung, M. Dolan, O. Smith, S. Tingey, M. Morgante, and A. Rafalski. 2002. SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines. BMC Genet. 3:19.
8. Choi, H.-K., M. Luckow, J. Doyle, and D. Cook. 2006. Development of nuclear gene-derived molecular markers linked to legume genetic maps. Mol. Genet. Genomics 276:56-70.
9. Comai, L., and S. Henikoff. 2006. TILLING: Practical single-nucleotide mutation discovery. Plant J. 45:684-694.
10. Comai, L., K. Young, B.J. Till, S.H. Reynolds, E.A. Greene, C.A. Codomo, L.C. Enns, J.E. Johnson, C. Burtner, A.R. Odden, and S. Henikoff. 2004. Efficient discovery of DNA polymorphisms in natural populations by EcoTILLING. Plant J. 37:778-786.
11. Ewing, B., L. Hillier, M.C. Wendl, and P. Green. 1998. Base-calling of automated sequencer traces using Phred: I. Accuracy assessment. Genome Res. 8:175-185.
12. FAOSTAT. 2008. FAO statistical databases. Available at http://faostat.fao.org/ (verified 19 January 2009). FAO, Rome.
13. Gepts, P., F.J.L. Aragão, E.D. Barros, M.W. Blair, R. Brondani, W. Broughton, I. Galasso, G. Hernández, J. Kami, P. Lariguet, P. McClean, M. Melotto, P. Miklas, P. Pauls, A. Pedrosa-Harand, T. Porch, F. Sánchez, F. Sparvoli, and K. Yu. 2008. Genomics of Phaseolus beans, a major source of dietary protein and micronutrients in the tropics, p. 113-143. In P. H. Moore and R. Ming (ed.) Genomics of tropical crop plants. Springer-Verlag, New York.
14. Gilchrist, E.J., G.W. Haughn, C.C. Ying, S.P. Otto, J.U.N. Zhuang, D. Cheung, B. Hamberger, F. Aboutorabi, T. Kalynyak, L.E.E. Johnson, J. Bohlmann, B.E. Ellis, C.J. Douglas, and Q.C.B. Cronk. 2006. Use of EcoTILLING as an efficient SNP discovery tool to survey genetic variation in wild populations of Populus trichocarpa. Mol. Ecol. 15:1367-1378.
15. Hu, W.-W., H. Gong, and E.C. Pua. 2005. The pivotal roles of the plant S-adenosylmethionine decarboxylase 5′ untranslated leader sequence in regulation of gene expression at the transcriptional and posttranscriptional levels. Plant Physiol. 138:276-286.
16. Kadaru, S., A. Yadav, R. Fjellstrom, and J. Oard. 2006. Alternative EcoTILLING protocol for rapid, cost-effective single-nucleotide polymorphism discovery and genotyping in rice (Oryza sativa L.). Plant Mol. Biol. Rep. 24:3-22.
17. Kim, M., B.-K. Ha, T.-H. Jun, E.-Y. Hwang, K. Van, Y. Kuk, and S.-H. Lee. 2004. Single nucleotide polymorphism discovery and linkage mapping of lipoxygenase-2 gene (Lx2) in soybean. Euphytica 135:169-177.
18. Lai, Z., K. Livingstone, Y. Zou, S. Church, S. Knapp, J. Andrews, and L. Rieseberg. 2005. Identification and mapping of SNPs from ESTs in sunflower. Theor. Appl. Genet. 111:1532-1544.
19. Lander, E.S., P. Green, J. Abrahamson, A. Barlow, M.J. Daly, S.E. Lincoln, and L. Newburg. 1987. MAPMAKER: An interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174-181.
20. Lis, J.T., G. Lawrence, and M. Kivie. 1980. Fractionation of DNA fragments by polyethylene glycol induced precipitation. Methods Enzymol. 65:347-353.
21. Meksem, K., E. Ruben, D.L. Hyten, M.E. Schmidt, and D.A. Lightfoot. 2001. High-throughput genotyping for a polymorphism linked to soybean cyst nematode resistance gene Rhg4 by using Taqman™ probes. Mol. Breed. 7:63-71.
22. Micheletto, S., L. Rodriguez-Uribe, R. Hernandez, R.D. Richins, J. Curry, and M.A. O'Connell. 2007. Comparative transcript profiling in roots of Phaseolus acutifolius and P. vulgaris under water deficit stress. Plant Sci. 173:510-520.
23. Miklas, P., J. Kelly, S. Beebe, and M.W. Blair. 2006. Common bean breeding for resistance against biotic and abiotic stresses: From classical to MAS breeding. Euphytica 147:105-131.
24. 2 resistance to bean common mosaic potyvirus in common bean. Euphytica 116:211-219.
25. Nasu, S., J. Suzuki, R. Ohta, K. Hasegawa, R. Yui, N. Kitazawa, L. Monna, and Y. Minobe. 2002. Search for and analysis of single nucleotide polymorphisms (SNPs) in rice (Oryza sativa, Oryza rufipogon) and establishment of SNP markers. DNA Res. 9:163-171.
26. Nordstrom, T., K. Nourizad, M. Ronaghi, and P. Nyren. 2000. Method enabling pyrosequencing on double-stranded DNA. Anal. Biochem. 282:186-193.
27. Oleykowski, C.A., C.R. Bronson Mullins, A.K. Godwin, and A.T. Yeung. 1998. Mutation detection using a novel plant endonuclease. Nucleic Acids Res. 26:4597-4602.
28. Qiu, P., H. Shandilya, J. D'Alessio, K. O'Connor, J. Durocher, and F. Gerard. 2004. Mutation detection using Surveyor nuclease. Biotechniques 36:702-707.
29. Raghavan, C., M. Naredo, H. Wang, G. Atienza, B. Liu, F. Qiu, K. McNally, and H. Leung. 2007. Rapid method for detecting SNPs on agarose gels and its application in candidate gene mapping. Mol. Breed. 19:87-101.
30. Ramirez, M., M.A. Graham, L. Blanco-Lopez, S. Silvente, A. Medrano-Soto, M.W. Blair, G. Hernandez, C.P. Vance, and M. Lara. 2005. Sequencing and analysis of common bean ESTs. Building a foundation for functional genomics. Plant Physiol. 137:1211-1227.
31. Rozen, S., and H.J. Skaletsky. 2000. PRIMER 3 on the WWW for general users and for biologist programmers. p. 365-386. In S. Krawetz and S. Misener (ed.) Bioinformatics methods and protocols: Methods in molecular biology. Humana Press, Totowa, NJ.
32. Rungis, D., B. Hamberger, Y. Bérubé, J. Wilkin, J. Bohlmann, and K. Ritland. 2005. Efficient genetic mapping of single nucleotide polymorphisms based upon DNA mismatch digestion. Mol. Breed. 16:261-270.
33. Shirasawa, K., S. Shiokai, M. Yamaguchi, S. Kishitani, and T. Nishio. 2006. Dot-blot-SNP analysis for practical plant breeding and cultivar identification in rice. Theor. Appl. Genet. 113:147-155.
34. Soleimani, V., B. Baum, and D. Johnson. 2003. Efficient validation of single nucleotide polymorphisms in plants by allele-specific PCR, with an example from barley. Plant Mol. Biol. Rep. 21:281-288.
35. Thiel, T., R. Kota, I. Grosse, N. Stein, and A. Graner. 2004. SNP2CAPS: A SNP and INDEL analysis tool for CAPS marker development. Nucleic Acids Res. 32:e5.
36. Till, B.J., C. Burtner, L. Comai, and S. Henikoff. 2004. Mismatch cleavage by single-strand specific nucleases. Nucleic Acids Res. 32:2632-2641.
37. Till, B.J., T. Colbert, R. Tompa, L. Enns, C. Codomo, J. Johnson, S.H. Reynolds, J.G. Henikoff, E.A. Greene, M.N. Steine, L. Comai, and S. Henikoff. 2003. High-throughput TILLING for functional genomics. p. 205-220. In E. Grotewald (ed.) Plant functional genomics: Methods and protocols. Humana Press, Totowa, NJ.
38. Tondelli, A., E. Francia, D. Barabaschi, A. Aprile, J. Skinner, E. Stockinger, A. Stanca, and N. Pecchioni. 2006. Mapping regulatory genes as candidates for cold and drought stress tolerance in barley. Theor. Appl. Genet. 112:445-454.
39. Van, K., E.Y. Hwang, M.Y. Kim, H.J. Park, S.H. Lee, and P.B. Cregan. 2005. Discovery of SNPs in soybean genotypes frequently used as the parents of mapping populations in the United States and Korea. J. Hered. 96:529-535.
40. 2 in common bean. Mol. Breed. 10:193-201.
41. Yamanaka, S., I. Nakamura, K. Watanabe, and Y.-I. Sato. 2004. Identification of SNPs in the waxy gene among glutinous rice cultivars and their evolutionary significance during the domestication process of rice. Theor. Appl. Genet. 108:1200-1204.
42. Yang, W., X. Bai, E. Kabelka, C. Eaton, S. Kamoun, E. van der Knaap, and F. David. 2004. Discovery of single nucleotide polymorphisms in Lycopersicon esculentum by computer aided analysis of expressed sequence tags. Mol. Breed. 14:21-34.
43. Zhang, W.K., Y.J. Wang, G.Z. Luo, J.S. Zhang, C.Y. He, X.L. Wu, J.Y. Gai, and S.Y. Chen. 2004. QTL mapping of ten agronomic traits on the soybean (Glycine max L. Merr.) genetic map and their association with EST markers. Theor. Appl. Genet. 108:1131-1139.
44. Zhu, Y.L., Q.J. Song, D.L. Hyten, C.P. Van Tassell, L.K. Matukumalli, D.R. Grimm, S.M. Hyatt, E.W. Fickus, N.D. Young, and P.B. Cregan. 2003. Single-nucleotide polymorphisms in soybean. Genetics 163:1123-1134.