Construction of an integrated pepper map using RFLP, SSR, CAPS, AFLP, WRKY, rRAMP, and BAC end sequences

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• 作者：Heung-Ryul Lee (1)
  Ik-Hyun Bae (1)
  Soung-Woo Park (1)
  Hyoun-Joung Kim (1)
  Woong-Ki Min (2)
  Jung-Heon Han (2)
  Ki-Taek Kim (3)
  Byung-Dong Kim (1) (2) (4)
  
• 关键词：BAC ; integrated map ; marker ; pepper ; SSR
• 刊名：Molecules and Cells
• 出版年：2009
• 出版时间：January 2009
• 年：2009
• 卷：27
• 期：1
• 页码：21-37
• 全文大小：1959KB
• 参考文献：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, 1185-196. CrossRef
  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, 251-61.
  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, 1016-028. CrossRef
  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, 367-86.
  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, 111-19. CrossRef
  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. 24-5.
  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, 2481-491. CrossRef
  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, 21-7. CrossRef
  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, 387-98. CrossRef
  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, 369-82. CrossRef
  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, 479-91. CrossRef
  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 chromosome locations in cotton. Euphytica / 161, 361-70. CrossRef
  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, 430-39. CrossRef
  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, 1212-220. CrossRef
  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, 383-91. CrossRef
  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, 11746-1750. CrossRef
  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 × C. chinese) F₂ linkage map in pepper using RFLP and AFLP markers. Theor. Appl. Genet. / 102, 531-39. CrossRef
  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 annuum L.) Theor. Appl. Genet. / 118, 15-7. CrossRef
  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, 196-04.
  20. Kosambi, D.D. (1944). The estimation of map distance from recombination values. Ann. Eugenics / 12, 172-75.
  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, 619-27. CrossRef
  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, 112-21.
  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, 839-54. CrossRef
  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, 1183-202.
  25. Minamiyama, Y., Tsuro, M., and Hirai, M. (2006). An SSR-based linkage map of / Capsicum annuum. Mol. Breed. / 18, 157-69. CrossRef
  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, 129-34. CrossRef
  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 polymorphisms in the 3-end of simple sequence repeats on pepper genome. Mol. Cells / 26, 250-57.
  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, 399-15. CrossRef
  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, 698-11. CrossRef
  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, 251-61. CrossRef
  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, 1457-466.
  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, 1305-317. CrossRef
  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, 1141-160.
  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, 2637-650. CrossRef
  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, 735-46. CrossRef
  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, 77-8. CrossRef
  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, 4407-414. CrossRef
  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, 63-2. CrossRef
  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, 766-77. CrossRef
  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, 113-30. CrossRef
  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, 540-43. CrossRef
  
• 作者单位：Heung-Ryul Lee (1)
  Ik-Hyun Bae (1)
  Soung-Woo Park (1)
  Hyoun-Joung Kim (1)
  Woong-Ki Min (2)
  Jung-Heon Han (2)
  Ki-Taek Kim (3)
  Byung-Dong Kim (1) (2) (4)
  
  1. Department of Plant Science, Seoul National University, Seoul, 151-921, Korea
  2. Center for Plant Molecular Genetics and Breeding Research, Seoul National University, Seoul, 151-921, Korea
  3. National Horticultural Research Institute, Suwon, 440-706, Korea
  4. Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Korea
  
• ISSN：0219-1032

文摘

Map-based cloning to find genes of interest, markerassisted 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.