Abstract
Random amplified polymorphism DNA (RAPD) and bulk segregant analysis (BSA) approaches were used to characterize the molecular marker linked to the Phytophthora infestans resistance gene Ph-3 in tomato. A total of 800 RAPD primers were screened. One RAPD marker UBC#602 was identified to be tightly linked to the Ph-3 gene. The marker was successfully converted into a co-dominant sequence characterized amplified region (SCAR) marker. The SCAR marker SCU602 was used to analyze 96 F2 progenies and fitted the expected 1:2:1 Mendelian segregation ratio. Forty one tomato inbred lines were screened using the SCAR marker in comparison with a reference marker linked to the Ph-3 gene and both markers gave the same results. SCU602 was further validated for association to resistance and its potential in MAS in 72 tomato lines and cultivars. The marker identified three genotypes harbouring the resistance allele. This SCAR marker can be used in breeding programs for the selection of the Ph-3 gene for Phytophthora infestans resistance.
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Adam-Blondon, A. F., Sevignac, M., Bannerot, H., & Dron, M. (1994). SCAR, RAPD and RFLP markers linked to a dominant gene (Are) conferring resistance to anthracnose in common bean. Theoretical and Applied Genetics, 88, 865–870.
AVRDC. (1994). 1993 Progress Report 201–203. Tainan: Asian Vegetable Research and Development Center.
Bartoszewski, G., Waszczak, C., Gawronski, P., Stepien, I., Bolibok-Bragoszewska, H., Palloix, A., et al. (2012). Mapping of the ms8 male sterility gene in sweet pepper (Capsicum annuum L.) on the chromosome P4 using PCR-based markers useful for breeding programmes. Euphytica, 186, 453–461.
Barua, U. M., Chalmers, K. J., Hackett, C. A., Thomas, W. T. B., Powell, W., & Waugh, R. (1993). Identification of RAPD markers linked to a Rhynchosporium secalis resistance locus in barley using near-isogenic lines and bulked segregant analysis. Heredity, 71, 177–184.
Chunwongse, J., Chunwongse, C., Black, L., & Hanson, P. (2002). Molecular mapping of the Ph-3 gene for late blight resistance in tomato. The Journal of Horticultural Science and Biotechnology, 77, 281–286.
Du, Z., Hou, R., Zhu, Y., Li, X., Zhu, H., & Wang, Z. (2011). A random amplified polymorphic DNA (RAPD) molecular marker linked to late-bolting gene in pak-choi (Brassica campestris ssp. chinensis Makino L.). African Journal of Biotechnology, 10, 7962–7968.
Eagles, H. A., Bariana, H. S., Ogbonnaya, F. C., Rebetzke, G. J., Hollamby, G. J., Henry, R. J., et al. (2001). Implementation of markers in Australian wheat breeding. Australian Journal of Agricultural Research, 52, 1349–1356.
Foolad, M. R., Merk, H. L., & Ashrafi, H. (2008). Genetics, genomics and breeding of late blight and early blight resistance in tomato. Critical Reviews in Plant Sciences, 27, 75–107.
Fry, W. E., & Goodwin, S. B. (1997). Resurgence of the Irish potato famine fungus. BioScience, 47, 363–371.
Gisi, U., & Cohen, Y. (1996). Resistance to phenylamide fungicides: a case study with Phytophthora infestans involving mating type and race structure. Annual Review of Phytopathology, 34, 549–572.
Hall, T. A. (1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series, 41, 95–98.
Irzhansky, I., & Cohen, Y. (2006). Inheritance of resistance against Phytophtora infestans in Lycopersicon pimpinellifolium L3707. Euphytica, 149, 309–316.
Kaplan, D. T., Vanderspool, M. C., Garrett, C., Chang, S., & Opperman, C. H. (1996). Molecular polymorphisms associated with host range in the highly conserved genomes of burrowing nematodes, Radopholus spp. Molecular Plant–Microbe. Interactions, 9, 32–38.
Kim, M. J., & Mutschler, M. A. (2005). Transfer to processing tomato and characterization of late blight resistance derived from Solanum pimpinellifolium L. L3708. Journal of the American Society for Horticultural Science, 130, 877–884.
Klein-Lankhorst, R. M., Vermut, A., Weide, R., Liharska, T., & Zabel, P. (1991). Isolation of molecular markers for tomato (L. esculentum) using random amplified polymorphic DNA (RAPD). Theoretical and Applied Genetics, 83, 108–114.
Legard, D. E., Lee, T. Y., & Fry, W. E. (1995). Pathogenic specialization in Phytophthora infestans: aggressiveness on tomato. Phytopathology, 85, 1355–1361.
Li, Y., He, Y. M., Zu, Y. Q., & Zhan, F. D. (2011). Identification and cloning of molecular markers for UV-B tolerant gene in wild sugarcane (Saccharum spontaneum L.). Journal of Photochemistry and Photobiology B: Biology, 105, 119–125.
Liu, F., Yao, J., Wang, X., Hu, Z., & Duan, D. (2011). Identification of SCAR marker linking to longer frond length of Saccharina japonica (Laminariales, Phaeophyta) using bulked-segregant analysis. Journal of Applied Phycology, 23, 709–713.
Martin, G. B., Williams, J. G. K., & Tanksley, S. D. (1991). Rapid identification of markers linked to a Pseudomonas resistance gene in tomato by using random primers and near-isogenic lines. Proceedings of the National Academy of Sciences, 88, 2336–2340.
Michelmore, R., Paran, I., & Kesseli, R. V. (1991). Identification of marker linked to disease resistance gene by bulk segregant analysis: a rapid method to detect markers in specific genomic regions using segregating populations. Proceedings of the National Academy of Sciences, 88, 9828–9832.
Panthee, D. R., & Foolad, M. R. (2012). A reexamination of molecular markers for use in marker-assisted breeding in tomato. Euphytica, 184, 165–179.
Paran, I., & Michelmore, R. W. (1993). Development of reliable PCR-based markers linked to downy mildew resistance genes in lettuce. Theoretical and Applied Genetics, 85, 985–993.
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.
Park, P. H., Kim, H. R., Chung, K. H., Oh, D. G., & Kim, K. T. (2010). Development of a SCAR marker linked to Ph-3 in Solanum ssp. Korean Journal of Breed Science, 42, 308–312.
Robbins, M. D., Masud, M. A. T., Panthee, D. R., Gardner, C. O., Francis, D., & Stevens, M. A. (2010). Marker-assisted selection for coupling phase resistance to tomato spotted wilt virus and Phytophthora infestans (late blight) in tomato. HortScience, 45, 1424–1428.
Rozen, S., & Skaletsky, H. J. (2000). Primer3 on the SSS for general users and for biologist programmers. Methods in Molecular Biology, 132, 365–386.
Shobha, D., & Thimmappaiah. (2011). Identification of RAPD markers linked to nut weight and plant stature in cashew. Scientia Horticulturae, 129, 637–641.
Thormann, C. E., Ferreira, M. E., Camargo, L. E. A., Tivang, J. G., & Osborn, T. C. (1994). Comparison of RFLP and RAPD markers for estimating genetic relationships within and among cruciferous species. Theoretical and Applied Genetics, 88, 973–980.
Williams, J. G. K., Kubelik, A. R., Livak, K. J., Rafalski, J. A., & Tingey, S. V. (1990). DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Research, 18, 6531–6535.
Zhang, X. Z., & Kim, B. S. (2007). Physiological races of Phytophthora infestans in Korea. Plant Pathology Journal, 23, 219–222.
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Truong, H.T.H., Tran, H.N., Choi, H.S. et al. Development of a co-dominant SCAR marker linked to the Ph-3 gene for Phytophthora infestans resistance in tomato (Solanum lycopersicum). Eur J Plant Pathol 136, 237–245 (2013). https://doi.org/10.1007/s10658-012-0157-4
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DOI: https://doi.org/10.1007/s10658-012-0157-4