Marker Development for Erect versus Pendant-Orientated Fruit in Capsicum annuum L.

  • Lee, Heung-Ryul (Department of Plant Science, Seoul National University) ;
  • Cho, Myeong-Cheoul (National Horticultural Research Institute, Vegetable Research Division, Rural Development Administration) ;
  • Kim, Hyoun-Joung (Department of Plant Science, Seoul National University) ;
  • Park, Sung-Woo (Center for Plant Molecular Genetics and Breeding Research, Seoul National University) ;
  • Kim, Byung-Dong (Department of Plant Science, Seoul National University)
  • Received : 2008.05.22
  • Accepted : 2008.09.30
  • Published : 2008.12.31


The erect habit of fruit setting is a unique characteristic of ornamental peppers and wild pepper species. The erect habit is known to be controlled by the up locus on pepper (Capsicum annuum L.) chromosome 12. The result of a genetic analysis using Saengryeog 211 (pendant), Saengryeog 213 (erect), and their $F_1$ and $BC_1$ progeny demonstrated that up is a recessive gene. To develop an up-linked marker, bulked segregant analysis (BSA) and amplified fragment length polymorphism (AFLP) were employed using 108 $F_{2:3}$ individuals. The closest AFLP marker, $A2C7_{469}$, was located at a genetic distance of 1.7 cM from the up locus and was converted into a cleaved amplified polymorphic sequence (CAPS) marker. This marker was mapped at a genetic distance of 4.3 cM from the up locus. When the CAPS was applied to seven ornamental lines and 27 breeding lines with erect fruit, these genotypes of 28 lines were correctly predicted. Thus, the CAPS marker will be useful for marker-assisted selection (MAS) of pepper breeding lines with the up allele at the early seedling stage.


BSA -AFLP;CAPS;genetic marker;pepper;up gene


Supported by : Rural Development Administration


  1. Ben Chaim, A, Paran, I., Grube, R.C., Jahn, M., and Peleman, RW J. (2001). QTL mapping of fruit-related traits in pepper (Capsicum annuum). Theor. Appl. Genet. 102,1016-1028
  2. Lefebvre, V., Pflieger, S., Thabuis, A, Caranta, C., Blattes, A, Chauvet, J.C., Daubeze, AM., and Palloix, A (2002). Towards the saturation of the pepper linkage map by alignment of three intraspecific maps including known-function genes. Genome 45, 839-854
  3. Song, J., Bradeen, J.M., Naess, SK, Raasch, JA, Wielgus, S.M., Haberlach, G.T., Liu, J., Kuang, H., Austin-Phillips, S., Buell, C.R., et al. (2003). Gene RB cloned from Solanum bulbocasta-num confers broad Spectrum resistance to potato late blight. Proc. Natl. Acad. Sci. USA 100,9128-9133
  4. Vas, P., Hogers, R., Bleeker, M., Reijans, M., van de Lee, T., Homes, Me, Frijters, A., Pot, J., Peleman, J., Kuiper, M., et al. (1995). AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res. 23, 4407-4414
  5. Van der Vossen, E., Sikkema, A., Hekkert, B.L., Gros, J., Stevens, P., Muskens, M., Wouters, D., Pereira, A., Stiekema, W., and Allefs, S. (2003). An ancient R gene from the wild potato species Solanum bulbocastanum confers broad-spectrum resistance to Phytophthora infestans in cultivated potato and tomato. Plant J. 36,867-882
  6. Vi, G., Lee, J.M., Lee, S., Choi, D., and Kim, B.D. (2006). Exploitation of pepper EST-SSRs and an SSR-based linkage map. Theor. Appl. Genet. 114,113-130
  7. Kim, H.J., Lee, H.R., Han, J.H., Yeom, S.I., Ham, C.H., and Kim, B.D. (2008). Marker production by PCR amplification with primer pairs from conserved sequences of WRKY genes in the chili pepper. Mol. Cells 25, 196-204
  8. Lefebvre, V. (2004). Molecular markers for genetics and breeding: development and use in pepper (Capsicum spp.). In Molecular Marker Systems in Plant Breeding and Crop Improvement. H. Lorz and G. Wenzel, (eds.) Biotechnology in Agriculture and Forestry 55, 189-214
  9. Miller, J.C., and Fineman, Z.M. (1937). A genetic study of some qualitative and quantitative characters of the genus Capsicum. Proc. Am. Soc. Hort. Sci. 35, 544-550
  10. Ogundiwin, EA, Berke, 1.F., Massoudi, M., Black, L.L., Huestis, G., Choi, D., Lee, S., and Prince, J.P. (2005). Construction of 2 intraspecific linkage maps and identification of resistance QTLs for Phytophthora cepeici root-rot and foliar-blight diseases of pepper (Capsicum annuum L.). Genome 48, 698-711
  11. Meksem, K., Leister, D., Peleman, J., Zabeau, M., Salamini, F., and Gebhardt, C. (1995). A high-resolution map of the vicinity of the R1 locus on chromosome V of potato based on RFLP and AFLP markers. Mol. Gen. Genet. 249, 74-81
  12. Caranta, C., Thabuis, A, and Pallo ix, A (1999). Development of a CAPS marker for the Pvr4 locus: A tool for pyramiding potyvirus resistance genes in pepper. Genome 42, 1111-1116
  13. 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
  14. Andrews, J. (1995). Peppers, the domesticated Capsicums (Austin, USA; Universtiy of Texas Press)
  15. Iwai, K., and Watanabe, T. (2000). Red Peppers Science of Pungency. Saiwaishobo, Tokyo
  16. Kim, D.H., and Kim, B.D. (2005). Development of SCAR markers for early identification of cytoplasmic male sterility genotype in chili pepper (Capsicum annuum L.). Mol. Cells 20, 416-422
  17. Lee, M.H. (1994). Genetic analysis of determinate plant shape, fruit bearing habit and deciduous character of hot pepper (Capsicum annuum L.). Dissertation, Chungbuk National University
  18. Lippert, L.F., Bergh, B.O., and Smith, P.G. (1965). Gene list for the pepper. J. Hered. 56, 30-34
  19. Lee, C.J., Yoo, E.Y., Shin J.H., Lee J., Hwang H.S., and Kim B.D. (2005). Non-pungent Capsicum contains a deletion in the capsaicinoid synthetase gene, which allows early detection of pungency with SCAR markers. Mol. Cells 19,262-267
  20. Quirin, EA, Ogundiwin, EA, Prince, J.P., Mazourek, M., Briggs, M.O., Chlanda, 1.S., Kim, K.1., Falise, M., Kang, B.C., and Jahn, M.M. (2005). Development of sequence characterized amplified region (SCAR) primers for the detection of Phyto.5.2, a major QTL for resistance to Phytophthora cepsici Leon. in pepper. Theor. Appl. Genet. 110,605-612
  21. Lander, E.R., Green, P., Abrahamson, J., Barlow, A, Daly, M.J., Lioncoln, S.E., and Newburg, L. (1987). Mapmaker: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1,174-181
  22. Voorrips, RE., Finkers, R., Sanjaya, L., and Groenwold, R. (2004). QTL mapping of anthracnose (Colletotrichum spp.) resistance in a cross between Capsicum annuum and C. chinense. Theor. Appl. Genet. 109,1275-1282