Efficiency of RFLP, RAPD, and AFLP markers for the construction of an intraspecific map of the tomato genome

Genome

Volumn 43, Issue 1, 2000, Pages 29-40

  Saliba Colombani, Vera ^a   Causse, Mathilde ^a   Gervais, Laurent ^a   Philouze, Jacqueline ^a  

^a CEMAGREF   (France)

Author keywords

AFLP; Intraspecific cross; Lycopersicon esculentum; Molecular linkage map; RFLP

Indexed keywords

AMPLIFIED FRAGMENT LENGTH POLYMORPHISM; GENE CLUSTER; GENE MAPPING; GENE SEGREGATION; GENETIC POLYMORPHISM; GENETIC RECOMBINATION; INBRED LINE; LINKAGE GROUP; LYCOPERSICON ESCULENTUM; PLANT GENOME; RANDOM AMPLIFIED POLYMORPHIC DNA; RESTRICTION FRAGMENT LENGTH POLYMORPHISM;

EMBRYOPHYTA; LYCOPERSICON; LYCOPERSICON ESCULENTUM; LYCOPERSICON ESCULENTUM VAR. CERASIFORME;

EID: 0034095037     PISSN: 08312796     EISSN: None     Source Type: Journal    
DOI: 10.1139/g99-096     Document Type: Article

References (55)

1. Baudracco-Arnas, S., and Pitrat, M. 1996. A genetic map of melon (Cucumis melo L) with RFLP, RAPD, isozyme, disease resistance and morphological markers. Theor. Appl. Genet. 93: 57-64.
2. Becker, J., Vos, P., Kuiper, M., Salamini, F., and Heun, M. 1995. Combined mapping of AFLP and RFLP markers in barley. Mol. Gen. Genet. 249: 65-73.
3. Burr, B., and Burr, F.A. 1991. Recombinant inbreds for molecular mapping in maize: Theoretical and practical considerations. Trends Genet. 7: 55-60.
4. Caranta, C., Palloix, A., Lefebvre, V., and Daubèze, A.M. 1997. QTLs for a component of partial resistance to cucumber mosaic virus in pepper: Restriction of virus installation in host-cells. Theor. Appl. Genet. 94: 431-438.
5. Causse, M., Fulton, T.M., Cho, Y.G., Ahn, S.N., Chunwongse, J., Wu, K., Xiao, J., Yu, Z., Ronald, P.C., Harringon, S.E., Second, G., McCouch, S.R., and Tanksley, S.D. 1994. Saturated molecular map of the rice genome based on an interspecific backcross population. Genetics, 138: 1251-1274.
6. Causse, M., Santoni, S., Damerval, C., Maurice, A., Charcosset, A., Deatrick, J., and de Vienne, D. 1996. A composite map of expressed sequences in maize. Genome, 39: 418-432.
7. Chevalier, C., Joubès, J., Petit, J., and Raymond, P. 1999. Isolation and characterization of a cDNA clone for Glutaredoxin from tomato (Lycopersicon esculentum Mill) developing fruits. Plant Physiol. 119: 363-367.
8. Cho, Y.G., McCouch, S.R., Kuiper, M., Kang, M.R., Pot, J., Groenen, J.T.M., and Eun, M.Y. 1998. Integrated map of AFLP, SSLP and RFLP markers using a recombinant inbred population of rice (Oryza sativa L). Theor. Appl. Genet. 97: 370-380.
9. de Vicente, M.C., and Tanksley, S.D. 1991. Genome-wide reduction in recombination of backcross progeny derived from male versus female gametes in an interspecific cross of tomato. Theor. Appl. Genet. 83: 173-178.
10. de Vicente, M.C., and Tanksley, S.D. 1993. QTL analysis of transgressive segregation in an interspecific tomato cross. Genetics, 134: 585-596.
11. Deruère, J., Bouvier, F., Steppuhn, J., Klein, A., Camara, B., and Kuntz, M. 1994. Structure and expression of two plant genes encoding chromoplast-specific proteins: Occurrence of partially spliced transcripts. Biochem. and Biophys. Res. Commun. 199: 1144-1150.
12. Eujayl, I., Baum, M., Powell, W., Erskine, W., and Pehu, E. 1998. A genetic linkage map of lentil (Lens sp.) based on RAPD and AFLP markers using recombinant inbred lines. Theor. Appl. Genet. 97: 83-89.
13. Foolad, M., Jones, R.A., and Rodriguez, R.L. 1993. RAPD markers for constructing intraspecific tomato genetic maps. Plant Cell Rep. 12: 293-297.
14. Fulton, T.M., Nelson, J.C., and Tanksley, S.D. 1997. Introgression and DNA marker analysis of Lycopersicon peruvianum, a wild relative of the cultivated tomato, into Lycopersicon esculentum, followed through three successive backcross generations. Theor. Appl. Genet. 95: 895-902.
15. Gebhardt, C., Ritter, E., Barone, A., Walkemeier, B., Schachtschabel, U., Kaufmann, H., Thompson, R.D., Bonierbale, M.W., Ganal, M.W., Tanksley, S.D., and Salamini, F. 1991. RFLP maps of potato and their alignment with the homoeologous tomato genome. Theor. Appl. Genet. 83: 49-57.
16. Germain, V., and Ricard, B. 1997. Two Ldh genes from tomato and their expression in different organs, during fruit ripening and in response to stress. Plant Mol. Biol. 35: 949-954.
17. Grandillo, S., and Tanksley, S.D. 1996. Genetic analysis of RFLPs, GATA, microsatellites and RAPDs in a cross between Lycopersicon esculentum and L. pimpinellifolium. Theor. Appl. Genet. 92: 957-965.
18. Hodgson, C.P., and Fisk, R.Z. 1987. Hybridization probe size control: Optimized 'oligolabelling.' Nucleic Acids Res. 15: 6295.
19. Kojima, T., Nagaok, T., Noda, K., and Ogihara, Y. 1998. Genetic linkage map of ISSR and RAPD markers in Einkorn wheat in relation to that of RFLP markers. Theor. Appl. Genet. 96: 37-45.
20. Kosambi, D.D. 1944. The estimation of map distances from recombination values. Ann. Eugen. 12: 172-175.
21. Lander, E.S., Green, P., Abrahamson, J., Barlow, A., Daly, M.J., Lincoln, S.E., Newburg, L. 1987. MAPMAKER: An interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics, 2: 174-181.
22. Lashbrook, C.C., Gonzales-Bosch, C., and Bennett, A.B. 1994. Two divergent endo-β-1,4-glucanase genes exhibit overlapping expression in ripening fruit and abscising flowers. Plant Cell, 6: 1485-1493.
23. Laurençon, A., Gay, F., Ducau, J., and Bregliano, J.C. 1997. Evidence for an inducible repair-recombination system in the female germ line of Drosophila melanogaster. III. Correlation between reactivity levels, crossover frequency and repair efficiency. Genetics, 146: 1333-1344.
24. Lefebvre, V., Palloix, A., and Rives, M. 1993. Nuclear RFLP between pepper cultivars (Capsicum annuum L). Euphytica, 71: 189-199.
25. Lefebvre, V., Palloix, A., Caranta, C., and Pochard, E. 1995. Construction of an intraspecific integrated linkage map of pepper using molecular markers and doubled haploid progenies. Genome, 38: 112-121.
26. Lincoln, S., Daly, M., and Lander, E. 1992. Constructing genetic maps with MAPMAKER/EXP version 3.0. Whitehead Institute Technical Report, 3rd ed.
27. Linthorst, H.J.M., Melchers, L.S., Mayer, A., Van Roeckel, J.S.C., Cornelissen, B.J.C., and Bol, J.F. 1990. Analysis of gene families encoding acidic and basic β-1,3-glucanases of tobacco. Proc. Natl. Acad. Sci. U.S.A. 87: 8756-8760.
28. Logan, D.C., Domergue, O., Teyssendier de la Serve, B., and Rossignol, M. 1997. A new family of plasma membrane polypeptides differentially regulated during plant development. Biochem. Mol. Biol. Int. 43: 1051-1062.
29. Lyttle, T.W. 1991. Segregation distorters. Annu. Rev. Genet. 25: 511-557.
30. Marques, C.M., Araújo, J.A., Ferreira, J.G., Whetten, R., O'Malley, D.M., Liu, B-H., and Sederoff, R. 1998. AFLP genetic maps of Eucalyptus globulus and E. tereticornis. Theor. Appl. Genet. 96: 727-737.
31. McCouch, S.R., Kochert, G., Yu, Z.H., Wang, Z.Y., Khush, G.S., Coffman, W.R., and Tanksley, S.D. 1988. Molecular mapping of rice chromosomes. Theor. Appl. Genet. 76: 815-829.
32. Menéndez, C.M., Hall, A.E., and Gepts, P. 1997. A genetic linkage map of cowpea (Vigna unguiculata) developed from a cross between two inbred, domesticated lines. Theor. Appl. Genet. 95: 1210-1217.
33. Messeguer, R., Ganal, M.W., Steffens, J.C., and Tanksley, S.D. 1991. Characterization of the level, target sites and inheritance of cytosine methylation in tomato nuclear DNA. Plant Mol. Biol. 16: 753-770.
34. Miller, J.C., and Tanksley, S.D. 1990. RFLP analysis of phylogenetic relationships and genetic variation in the genus Lycopersicon. Theor. Appl. Genet. 80: 437-448.
35. Mutschler, M.A., Doerge, R.W., Liu, S.C., Kuai, J.P., Liedl, B.E., and Shapiro, J.A. 1996. QTL analysis of pest resistance in the wild tomato Lycopersicon pennellii: QTLs controlling acylsugar level and composition. Theor. Appl. Genet. 92: 709-718.
36. Paillard, M., Lashermes, P., and Pétiard, V. 1996. Construction of a molecular linkage map in coffee. Theor. Appl. Genet. 93: 41-47.
37. Paran, I., Goldman, I., Tanksley, S.D., and Zamir, D. 1995. Recombinant inbred lines for genetic mapping in tomato. Theor. Appl. Genet. 90: 542-548.
38. Paterson, A.H., Lander, E.S., Hewitt, J.D., Peterson, S., Lincoln, S.E., and Tanksley, S.D. 1988. Resolution of quantitative traits into Mendelian factors by using a complete linkage map of restriction fragment length polymorphisms. Nature, 335: 721-726.
39. Paterson, A.H., Damon, S., Hewitt, J.D., Zamir, D., Rabinowitch, H.D., Lincoln, S.E., Lander, E.S., and Tanksley, S.D. 1991. Mendelian factors underlying quantitative traits in tomato: Comparison across species generations and environments. Genetics, 127: 181-197.
40. Pellegrini, L., Geoffroy, P., Fritig, B., and Legrand, M. 1993. Molecular cloning and expression of a new class of ortho-diphenol-O-methyltransferases induced in tobacco (Nicotiana tabacum L.) leaves by infection or elicitor treatment. Plant Physiol. 103: 509-517.
41. Reiter, R.S., Williams, J.G.K., Feldmann, K.A., Rafalsky, J.A., Tingey, S.V., and Scolnik, P.A. 1992. Global and local genome mapping in Arabidopsis thaliana by using recombinant inbred lines and random amplified polymorphic DNAs. Proc. Natl. Acad. Sci. U.S.A. 89: 1477-1481.
42. Rouppe van der Voort, J.N.A.M., van Zandvoort, P., van Eck, H.J., Folkertsma, R., Hutten, R.C.B., Draaistra, J., Gommers, F.J., Jacobsen, E., Helder, J., and Bakker, J. 1997. Use of allele specificity of comigrating AFLP markers used to align genetic maps from different potato genotypes. Mol. Gen. Genet. 255: 438-447.
43. Saliba, V., Duffé, P., Gervais, L., and Causse, M. 1998. Efficiency of AFLP markers to saturate a tomato intraspecific map. Report of the Tomato Genetics Cooperative, 48: 44-45.
44. Schwarz-Sommer, Z., Gierl, A., Cuypers, H., Peterson, P.A., and Saedler, H. 1985. Plant transposable elements generate the DNA sequence diversity needed in evolution. EMBO J. 4: 591-597.
45. Shattuck-Eidens, D.M., Bell, R.N., Neuhausen, S.L., and Helentjaris, T. 1990. DNA sequence variation within maize and melon: Observations from polymerase chain reaction amplification and direct sequencing. Genetics, 126: 207-217.
46. Shi, L., Gast, R.T., Gopalraj, M., and Olzewski, N.E. 1992. Characterization of a shoot-specific, GA3-and ABA-regulated gene from tomato. Plant J. 2: 153-159.
47. Song, W.Y., Wang, G.L., Chen, L.L., Kim, H.S., Pi, L.Y., Holsten, T., Gardner, J., Wang, B., Zhai, W.X., Zhu, L.H., Fauquet, C., and Ronald, P. 1995. A receptor kinase-like protein encoded by the rice disease resistance gene, Xa21. Science, 270: 1804-1806.
48. Tanksley, S.D., and Nelson, J.C. 1996. Advanced backcross QTL analysis: A method for the simultaneous discovery and transfer of valuable QTLs from unadapted germplasm into elite breeding lines. Theor. Appl. Genet. 92: 191-203.
49. Tanksley, S.D., Bernatzky, R., Lapitan, N.L., and Prince, J.P. 1988a. Conservation of gene repertoire but not gene order in pepper and tomato. Proc. Natl. Acad. Sci. U.S.A. 85: 6419-6423.
50. Tanksley, S.D., Miller, J., Paterson, A., and Bernatzky, R., 1988b. Molecular mapping of plant chromosomes. In Proceedings of the 18th Stadler Genetics Symposium, New York. Plenum Press, pp. 157-173.
51. Tanksley, S.D., Ganal, M.W., Prince, J.P., de Vicente, M.C., Bonierbale, M.W., Broun, P., Fulton, T.M., Giovannoni, J.J., Grandillo, S., Martin, J.C., Messeguer, R., Miller, J.C., Miller, A.H., and Fulton, T.W. 1992. High density molecular linkage maps of the tomato and potato genomes. Genetics, 132: 1141-1160.
52. Vos, P., Hogers, R., Bleeker, M., Reijans, M., Van Delee, T., Hornes, M., Frijters, A., Pot, J., Peleman, J., Kuiper, M., and Zabeau, M. 1995. AFLP: A new technique for DNA fingerprinting. Nucleic Acids Res. 23: 4407-4414.
53. Wang, F., Smith, A.G., and Brenner, M.L. 1993. Isolation and sequencing of tomato fruit sucrose synthase cDNA. Plant Physiol. 103: 1463-1464.
54. Wang, Y.-H., Thomas, C.E., and Dean, R.A. 1997. A genetic map of melon (Cucumis melo L) based on amplified fragment length polymorphism (AFLP) markers. Theor. Appl. Genet. 95: 791-798.
55. Williams, J.G.K., Kubelik, A.R., Livak, K.J., Rafalski, J.A., and Tingey, S.V. 1990. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res. 18: 6531-6535.