Abstract
Bulked segregant analysis was used to identify random amplified polymorphic DNA (RAPD) markers linked to the Sw-5 gene for resistance to tomato spotted wilt virus (TSWV) in tomato. Using two pools of phenotyped individuals from one segregating population, we identified four RAPD markers linked to the gene of interest. Two of these appeared tightly linked to Sw-5, whereas another, linked in repulsion phase, enabled the identification of heterozygous and susceptible plants. After linkage analysis of an F2 population, the RAPD markers were shown to be linked to Sw-5 within a distance of 10.5 cM. One of the RAPD markers close to Sw-5 was used to develop a SCAR (sequence characterized amplified region) marker. Another RAPD marker was stabilized into a pseudo-SCAR marker by enhancing the specificity of its primer sequence without cloning and sequencing. RAPD markers were mapped to chromosome 9 on the RFLP tomato map developed by Tanksley et al. (1992). The analysis of 13 F3 families and eight BC2 populations segregating for resistance to TSWV confirmed the linkage of the RAPD markers found. These markers are presently being used in marker-assisted plant breeding.
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Adam-Blondon AF, Sévignac M, Bannerot H, Dron M (1994) SCAR, RAPD and RFLP markers linked to a dominant gene (Are) conferring resistance to anthracnose in common bean. Theor Appl Genet 88:865–870
Beek JG van der, Verkerk R, Zabel P, Linhout P (1992) Map** strategy for resistance genes in tomato based on RFLPs between cultivars: Cf-9 (resistance to Cladosporium fulvum) on chromosome 1. Theor Appl Genet 84:106–112
Beek JG van der, Pet F, Lindhout P (1994) Resistance to powdery mildew (Oidium lycopersicum) in Lycopersicon hirsutum is controlled by an incompletely dominant gene Ol-1 on chromosome 6. Theor Appl Genet 89:467–473
Behare J, Laterrot H, Safartii M, Zamir D (1991) RFLP map** of the Stemphylium resistance gene in tomato. Mol Plant Microbe Interact 4:489–492
Bernatzky R, Tanksley SD (1986) Toward a saturated linkage map in tomato based on isozymes and random cDNA sequences. Genetics 112:887–898
Biezen EA van der, Glagotskaya T, Overduin B, Nijkamp HJH, Hille J (1995) Inheritance and genetic map** of resistance to Alternaria alternata f. sp. lycopersici in Lycopersicon pennellii. Mol Gen Genet 247:453–461
Dellaporta SL, Wood J, Hicks JB (1983) A plant DNA minipreparation: version II. Plant Mol Biol Rep 1:19–21
Dickinson MJ, Jones DA, Jones JD (1993) Close linkage between the Cf-2/Cf-5 and Mi resistance loci in tomato. Mol Plant Microbe Interact 6: 341–347
Edwards K, Johnstone C, Thompson C (1991) A simple and rapid method for the preparation of plant genomic DNA for PCR analysis. Nucleic Acids Res 19:1349
Giovanni JJ, Wing RA, Ganal MW, Tanksley SD (1991) Isolation of molecular markers from specific chromosomal intervals using DNA pools from existing map** populations. Nuleic Acids Res 19:6553–6558
Hai Lu Y, Négre S (1993) Use of glycerol for enhanced efficiency and specificity of PCR amplification. Trends Genet 9:297
Haley SD, Miklas PN, Stavely JR, Byrum J, Kelly JD (1993) Identification of RAPD markers linked to a major rust resistance gene block in common bean. Theor Appl Genet 86:505–512
Jones DA, Dickinson MJ, Balint-Kurti PJ, Dixon MS (1993) Two complex resistance loci revealed in tomato by classical and RFLP map** of the Cf-2, Cf-4, Cf-5 and Cf9 genes for resistance to Cladosporium fulvum. Mol Plant Microbe Interact 6:348–355
Kosambi DD (1994) The estimation of map distances from recombination values. Ann Eugen 12:172–175
Lander ES, Green P, Abrahamson J, Barlow A, Daly M, Lincoln SE, Newburg L (1987) MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural population. Genomics 1:174–181
Levesque H, Vedel F, Mathieu C, de Courcel AGL (1990) Identification of a short DNA spacer sequence highly specific to a tomato line containing the Tm-1 gene introgressed from Lycopersicon hirsutum. Theor Appl Genet 80:602–608
Martin GB, Williams JGK, Tanksley SD (1991) Rapid identification of markers linked to a Pseudomonas resistance gene in tomato by using random primers and near-isogenic lines. Proc Natl Acad Sci USA 88:2336–2340
Messeguer R, Ganal MW, de Vicente MC, Young ND, Bolkan H, Tanksley SD (1991) High resolution RFLP map around the root knot nematode resistance gene (Mi) in tomato. Theor Appl Genet 82:529–536
Michelmore RW, Paran I, Kesseli RV (1991) Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proc Natl Acad Sci USA 88: 9828–9832
Miklas PN, Stavely JR, Kelly JD (1993) Identification and potential use of molecular marker for rust resistance in common bean. Theor Appl Genet 85:745–749
Paran I, Kesseli R, Michelmore R (1991) Identification of restriction fragment length polymorphism and random amplified polymorphic DNA markers linked to downy mildew resistance genes in lettuce, using near-isogenic lines. Genome 34:1021–1027
Paran I, Michelmore RW (1993) Development of reliable PCR-based markers linked to downy mildew resistance genes in lettuce. Theor Appl Genet 85:985–993
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
Sambrook L, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
Sarfatti M, Katan J, Fluhr R, Zamir D (1989) An RFLP marker in tomato linked to the Fusarium oxysporum resistance gene I-2. Theor Appl Genet 78:755–759
Sarfatti M, Abu-Abied M, Katan J, Zamir D (1991) RFLP map** of I1, a new locus in tomato conferring resistance against Fusarium oxysporum f. sp. lycopersici race 1. Theor Appl Genet 82:22–26
Schierwater B, Ender A (1993) Different thermostable DNA polymerases may amplify different RAPD products. Nucleic Acids Res 21:4647–4648
Stevens JM (1964) Tomato breeding. Project report W-Vv1, Dept Agric Tech Serv.
Stevens MR, Scott SJ, Gergerich RC, (1992) Inheritance of a gene for resistance to tomato spotted wilt virus (TSWV) from Lycopersicon peruvianum Mill. Euphytica 59:9–17
Stevens MR, Lamb EM, Rhoad DD (1995) Map** the Sw-5 locus for tomato spotted wilt virus resistance in tomatoes using RAPD and RFLP analyses. Theor Appl Genet 90:451–456
Tanksley SD, Ganal MW, Prince JP, de Vicente MC, Bonierbale MW, Broun P, Fulton TM, Giovanni JJ, Grandillo S, Martin GB, Messeguer R, Miller L, Paterson AH, Pineda O, Röder MS, Wing RA, Wu W, Young ND (1992) High density molecular linkage maps of the tomato and potato genomes. Genetics 132: 1141–1160
Vries J, de Jongerius R, Sandbrink H, Lindhout P (1992) RAPD markers assist in resistance breeding. Prophyta 2:50–51
Welsh J, McClelland M (1990) Fingerprinting genomes using PCR with arbitrary primer. Nucleic Acids Res 24:7213–7218
Williams JGK, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic makers. Nucleic Acids Res 18:6531–6535
Witsenboer HMA. van de Griend EG, Tiersma JB, Nijkamp HJJ, Hille J (1989) Tomato resistance to Alternaria stem canker: localisation in host genotypes and functionnal expression compared to non-host resistance. Theor Appl Genet 78:457–462
Wolf K, Schoen ED, Peters-Van Rijn J (1993) Optimizing the generation of random amplified polymorphic DNAs in chrysanthemum. Theor Appl Genet 86:1033–1037
Young ND, Zamir D, Ganal MW, Tanksley SD (1988) Use of isogenic lines and simultaneous probing to identify DNA markers tightly linked to the Tm-2a gene in tomato. Genetics 120:579–585
Zamir D, Bolkan H, Juvik JA, Watterson JC, Tanksley SD (1993) New evidence for placement of Ve the gene for resistance to Verticillium race 1. Tomato Genet Coop Rep 43:51–52
Zamir D, Ekstein-Michelson J, Zakay Y, Navot N, Zeidan M, Safartii M, Eshed Y, Harez E, Pleban T, van Oss H, Kedar N, Rabinowitch HD, Czosnek H (1994) Map** and introgression of a yellow leaf curl virus tolerance gene, Ty-1. Theor Appl Genet 88:141–146
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Chagué, V., Mercier, J.C., Guénard, M. et al. Identification and map** on chromosome 9 of RAPD markers linked to Sw-5 in tomato by bulked segregant analysis. Theoret. Appl. Genetics 92, 1045–1051 (1996). https://doi.org/10.1007/BF00224047
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DOI: https://doi.org/10.1007/BF00224047