Molecules and Cells

Korean Society for Molecular and Cellular Biology (한국분자세포생물학회)
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Construction of an Integrated Pepper Map Using RFLP, SSR, CAPS, AFLP, WRKY, rRAMP, and BAC End Sequences

  • Lee, Heung-Ryul (Department of Plant Science, Seoul National University) ;
  • Bae, Ik-Hyun (Department of Plant Science, Seoul National University) ;
  • Park, Soung-Woo (Department of Plant Science, Seoul National University) ;
  • Kim, Hyoun-Joung (Department of Plant Science, Seoul National University) ;
  • Min, Woong-Ki (Center for Plant Molecular Genetics and Breeding Research, Seoul National University) ;
  • Han, Jung-Heon (Center for Plant Molecular Genetics and Breeding Research, Seoul National University) ;
  • Kim, Ki-Taek (National Horticultural Research Institute) ;
  • Kim, Byung-Dong (Department of Plant Science, Seoul National University)
  • Received : 2008.05.22
  • Accepted : 2008.10.02
  • Published : 2009.01.31
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Abstract

Map-based cloning to find genes of interest, marker-assisted selection (MAS), and marker-assisted breeding (MAB) all require good genetic maps with high reproducible markers. For map construction as well as chromosome assignment, development of single copy PCR-based markers and map integration process are necessary. In this study, the 132 markers (57 STS from BAC-end sequences, 13 STS from RFLP, and 62 SSR) were newly developed as single copy type PCR-based markers. They were used together with 1830 markers previously developed in our lab to construct an integrated map with the Joinmap 3.0 program. This integrated map contained 169 SSR, 354 RFLP, 23 STS from BAC-end sequences, 6 STS from RFLP, 152 AFLP, 51 WRKY, and 99 rRAMP markers on 12 chromosomes. The integrated map contained four genetic maps of two interspecific (Capsicum annuum 'TF68' and C. chinense 'Habanero') and two intraspecific (C. annuum 'CM334' and C. annuum 'Chilsungcho') populations of peppers. This constructed integrated map consisted of 805 markers (map distance of 1858 cM) in interspecific populations and 745 markers (map distance of 1892 cM) in intraspecific populations. The used pepper STS were first developed from end sequences of BAC clones from Capsicum annuum 'CM334'. This integrated map will provide useful information for construction of future pepper genetic maps and for assignment of linkage groups to pepper chromosomes.

Keywords

Acknowledgement

Supported by : Rural Development Administration, Korea Science and Engineering Foundation

References

  1. Bao, J.S., Corke, H., and Sun, M. (2006). Microsatellites, single nucleotide polymorphisms and a sequence tagged site in starchsynthesizing genes in relation to starch physicochemical properties in nonwaxy rice(Oryza sativa L.). Theor. Appl. Genet. 113, 1185-1196 https://doi.org/10.1007/s00122-006-0394-z
  2. Barchi, L., Bonnet, J., Boudet, C., Signoret, P., Nagy, I., Lanteri, S., Palloix, A., and Lefebvre, V. (2007). A high-resolution , intraspecific linkage map of pepper (Capsicum annuum L.) and selection of reduced recombinant inbred line subsets for fast mapping. Mol. Breed. 13, 251-261 https://doi.org/10.1139/G06-140
  3. Ben Chaim, A., Paran, I., Grube, R.C., Jahn, M., Wijk, Rv., and Peleman, J. (2001). QTL mapping of fruit-related traits in pepper (Capsicum annuum). Theor. Appl. Genet. 102, 1016-1028 https://doi.org/10.1007/s001220000461
  4. Bowers, J.E., Abbey, C., Anderson, S., Chang, C., Draye, X., Hoppe, A.H., Jessup, R., Lemke, C., Lennington, J., Li, Z., et al. (2003). A high-density genetic recombination map of sequencetagged sites for sorghum, as a framework for comparative structural and evolutionary genomics of tropical grains and grasses. Genteics 165, 367-386
  5. Bradeen, J.M., Staub, J.E., Wye, C., Antonise, R., and Peleman, J. (2001). Towards an expanded and integrated linkage map of cucumber (Cucumis sativus L.). Genomes 44, 111-119 https://doi.org/10.1139/gen-44-1-111
  6. Bruce, B., Eric, D.G., Sue, K., Richard, M.M., and Jane, R. (1997). Genome Analysis. 1, Cold Spring Harbor, Cold Spring Harbor Laboratory Press, pp. 24-25
  7. Chen, C., Yu, Q., Hou, S., Li, Y., Eustice, M., Skelton, R.L., Veatch, O., Herdes, R.E., Diebold, L., Saw, J., et al. (2007). Construction of a sequence-tagged high-density genetic map of papaya for comparatives structural and evolutionary genomics in brassicales. Genetics 177, 2481-2491 https://doi.org/10.1534/genetics.107.081463
  8. Chiba, N., Suwabe, K., Nunome, R., and Hirai, M. (2003). Develoment of microsatellite markers in melon (Cucumis melo L.) and their application to major cucurbit crops. Breed. Sci. 53, 21-27 https://doi.org/10.1270/jsbbs.53.21
  9. Collins, A., Milbourne, D., Ramsay, L., Meyer, C., Chatot-Balandras, C., Overhagemann, P., De Jong, W., Gebhardt, C., Connel, E., and Waugh, R. (1999). QTL for field resistance to late blight in potato are strongly correlated with maurity and vigour. Mol. Breed. 5, 387-398 https://doi.org/10.1023/A:1009601427062
  10. Doligez, A., Adam-Blondon, A.F., Cipriani, G., Di Gaspero, G., Laucou, V., Merdinoglu, D., Meredith, C.P., Riaz, S., Roux, C., and This, P. (2006). An integrated SSR map of grapevine based on five mapping populations. Theor. Appl. Genet. 113, 369-382 https://doi.org/10.1007/s00122-006-0295-1
  11. Frelichowski Jr, J.E., Palmer. M.B., Main, D., Tomkins, J.P., Cantrell, R.G., Stelly, D.M., Yu, J., Kohel, R.J., and Ulloa, M. (2006). Cotton genome mapping with new microsatellites from Acala 'Maxxa' BAC-ends. Mol. Gen. Genomics 275, 479-491 https://doi.org/10.1007/s00438-006-0106-z
  12. Guo, Y., Saha, S., Yu, J.Z., Jenkins, J.N., Kohel, R.J., Scheffler, B.E., and Stelly, D.M. (2008). BAC-derived SSR markers chro mosome locations in cotton. Euphytica 161, 361-370 https://doi.org/10.1007/s10681-007-9585-1
  13. Han, Z., Wang, C., Song, X., Guo, W., Guo, J., Li, C., Chen, X., and Zhang, T. (2006). Characteristics, development and mapping of Gossypium hirsutum derived EST-SSRs in allotetraploid cotton. Theor. Appl. Genet. 112, 430-439 https://doi.org/10.1007/s00122-005-0142-9
  14. Hayashi, K., Hashimoto, N., Daigen, M., and Ashikawa, I. (2004). Development of PCR-based SNP markers for rice blast resistance genes at the Piz locus. Theor. Appl. Genet. 108, 1212-1220 https://doi.org/10.1007/s00122-003-1553-0
  15. Hearnden, P.R., Eckermann, P.J., McMichael, G.L., Hayden, M.J., Eglinton, J.K., and Chalmers, K.J. (2007). A genetic map of 1,000 SSR and DArT markers in a wide barley cross. Theor. Appl. Genet. 115, 383-391 https://doi.org/10.1007/s00122-007-0572-7
  16. Kanazin, V., Marex, L.F., and Shoemaker, R.C. (1996). Resistance gene analogs are conserved and clustered in soybean. Proc. Natl. Acad. Sci. USA 93, 11746-50 https://doi.org/10.1073/pnas.93.21.11746
  17. Kang, B.C., Nahm, S.H., Huh, J.H., Yoo, H.S., Yu, J.W., Lee, J.M., and Kim, B.D. (2001). An interspecific (Capsicum annuum $\times$ C. chinese) $F_{2}$ linkage map in pepper using RFLP and AFLP markers. Theor. Appl. Genet. 102, 531-539 https://doi.org/10.1007/s001220051678
  18. Kim, H.J., Nahm, S.H., Lee, H.R., Yoon, G.B., Kim, K.T., Kang, B.C., Choi, D., Kweon, O.Y., Cho, M.C., Kwon, J.K., et al. (2008a). BAC-derived markers converted from RFLP related to Phytophthora capsici resistance in pepper (Capsicum L.) Theor. Appl. Genet. 118, 15-27 https://doi.org/10.1007/s00122-008-0873-5
  19. Kim, H.J., Lee, H.R., Han, J.H., Yeom, S.I., Harn, C.H., and Kim, B.D. (2008b). Marker production by PCR amplification with primer pairs from conserved sequences of WRKY genes in the chili pepper. Mol. Cells 25, 196-204
  20. Kosambi, D.D. (1944). The estimation of map distance from recombination values. Ann. Eugenics 12, 172-175
  21. Lee, J.M., Nahm, S.H., Kim, Y.M., and Kim, B.D. (2004). Characterization and molecular genetic mapping of microsatellite loci in pepper. Theor. Appl. Genet. 108, 619-627 https://doi.org/10.1007/s00122-003-1467-x
  22. Lefebvre, V., Palloix, A., Caranta, C., and Pochard, E. (1995). Construction of an intra-specific integrated linkage map of pepper using molecular markers and doubled-haploid progenies. Genome 38, 112-121 https://doi.org/10.1139/g95-014
  23. Lefebvre, V., Pflieger, S., Habuis, A., Caranta, C., Blattes, C., Chauvet, J.C., Caubeze, A.M., 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 https://doi.org/10.1139/g02-053
  24. Livingstone, K.D., Lackney, V.K., Blauth, J.R., van Wijk, R., and Jahn, M.K. (1999). Genome mapping in capsicum and the evolution of genome structure in the solanaceae. Genetics 152, 1183-1202
  25. Minamiyama, Y., Tsuro, M., and Hirai, M. (2006). An SSR-based linkage map of Capsicum annuum. Mol. Breed. 18, 157-169 https://doi.org/10.1007/s11032-006-9024-3
  26. Minamiyama Y., Tsuro, M., Kubo, T., and Hirai, M. (2007). QTL analysis for resistance to Phytophthora Capsici in pepper using high density SSR-based map. Breed. Sci. 57, 129-134 https://doi.org/10.1270/jsbbs.57.129
  27. Min, W.K., Han, J.H., Kang, W.H., Lee, H.R., and Kim, B.D. (2008). Reverse random amplified microsatellite polymorphism reveals enhanced olymorphisms in the 3' end of simple sequence repeats on pepper genome. Mol. Cells 26, 250-257
  28. Oberhagemann, P., Chatot-Balandras, C., Schafer-Pregl, R., Wegener, D., Palomino, C., Salamini, F., Bonnel, E., and Gebhardt, C. (1999). A genetic analysis of quantitative resistance to late blight in potato, towards marker-assisted selection. Mol. Breed. 5, 399-415 https://doi.org/10.1023/A:1009623212180
  29. Ogundiwin, E.A., Berke, T.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 capsici root-rot and foliar-blight diseases of pepper (Capsicum annuum L.). Genome 48, 698-711 https://doi.org/10.1139/g05-028
  30. Paran, I., van der Voort, J.R., Lefebvre, V., Jahn, M., Landry, L., van Schriek, M., Tanyolac, B., Caranta, C., Ben Chaim, A., Livingstone, K., et al. (2004). An integrated genetic linkage map of pepper (Capsicum spp.). Mol. Breed. 13, 251-261 https://doi.org/10.1023/B:MOLB.0000022526.30914.31
  31. Rao, G.U., Ben Chaim, A., Borovsky, Y., and Paran, I. (2003). Mapping of yield-related QTLs in pepper in an interspecific cross of Capsicum annuum and C. frutescens. Theor. Appl. Genet. 106, 1457-1466 https://doi.org/10.1007/s00122-003-1204-5
  32. Sambrook, J., Fritsch, E.F., and Maniatis, T. (1989). Molecular Cloning: A Laboratory Manual, (NY, USA; Cold Spring Harbor, Laboratory Press)
  33. Sun, Z., Wang, Z., Tu, J., Zhang, J., Yu, F., McVetty, P.B.E., and Li, G. (2007). An ultradense genetic recombination map for Brassica napus, consistingof 13551 SRAP markers. Theor. Appl. Genet. 114, 1305-1317 https://doi.org/10.1007/s00122-006-0483-z
  34. 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. G.B., et al. (1992). High density molecular linkage maps of the tomato and potato genomes; biological inferences and practical applications. Genetics 132, 1141-1160
  35. Troggio, M., Malacarne, G., Coppola, C., Segala, C., Gartwright, D.A., Pindo, M., Stefanini, M., Mank, R., Moroldo, M., Morgante, M., et al. (2007). A dense single-nucleotied polymorphismbased genetic linkage map of grapevine (Vitis vinifera L.) anchoring pinot noir bacterial artificial chromosome contigs. Genetics 176, 2637-2650 https://doi.org/10.1534/genetics.106.067462
  36. Truco, M.J., Antonise, R., Lavelle, D., Ochoa, O., Kozik, A., Witsenboer, H., Fort, S.B., Jeuken, M.J.W., Kesseli, R.V., Lindhout, P., et al. (2007). A high-density, integrated genetic linkage map of lettuce (Lactuca spp.). Theor. Appl. Genet. 115, 735-746 https://doi.org/10.1007/s00122-007-0599-9
  37. Van Ooijen, J.W., and Voorrips, R.E. (2001). JoinMap 3.0, Software for the calculation of genetic linkage maps. Plant Research International, Wageningen, The Netherlands
  38. Voorrips, R.E. (2002). MapChart, Software for the graphical presentation of linkage maps and QTLs. J. Hered. 93, 77-78 https://doi.org/10.1093/jhered/93.1.77
  39. Vos, P., Hogers, R., Bleeker, M., Reijans, M., van de Lee, T., Hornes, M., Frijters, A., Pot, J., Peleman, J., Kuiper, M., et al. (1995). AFLP, a new technique for DNA fingerprinting. Nucleic Acids Res. 23, 4407-4414 https://doi.org/10.1093/nar/23.21.4407
  40. Wenkai, X., Mingliang, X., Jiuren, Z., Fengge, W., Jiansheng, L., and Jingrui, D. (2006). Genome-wide isolation of resistance gene analogs in maize (Zea mays L.). Theor. Appl. Genet. 113, 63-72 https://doi.org/10.1007/s00122-006-0272-8
  41. Yan, Z., Denneboom, C., Hattendorf, A., Dolstra, O., Debener, T., Stam, P., and Visser, P.B. (2005). Construction of an integrated map of rose with AFLP, SSR, PK, RGA, RFLP, SCAR and morphological markers. Theor. Appl. Genet. 110, 766-777 https://doi.org/10.1007/s00122-004-1903-6
  42. Yi, 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 https://doi.org/10.1007/s00122-006-0415-y
  43. Yoo, E.Y., Kim, S., Kim, Y.H., Lee, C.J., and Kim, B.D. (2003). Construction of a deep coverage BAC library from Capsicum annuum 'CM334'. Theor. Appl. Genet. 107, 540-543 https://doi.org/10.1007/s00122-003-1279-z

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