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

Molecules and Cells

Volumn 27, Issue 1, 2009, Pages 21-37

  Lee, Heung Ryul ^a   Bae, Ik Hyun ^a   Park, Soung Woo ^a   Kim, Hyoun Joung ^a   Min, Woong Ki ^b   Han, Jung Heon ^b   Kim, Ki Taek ^c   Kim, Byung Dong ^a,b  

^a Seoul National University   (South Korea)

^b School of Agricultural Biotechnology Center for Plant Molecular Genetics and Breeding Research   (South Korea)

^c National Institute of Animal Science   (South Korea)

Author keywords

BAC; Integrated map; Marker; Pepper; SSR

Indexed keywords

AMPLIFIED FRAGMENT LENGTH POLYMORPHISM; ARTICLE; CHROMOSOME 12; EXPRESSED SEQUENCE TAG; GENE FUNCTION; GENE MAPPING; GENE SEQUENCE; GENETIC LINKAGE; NONHUMAN; PEPPER; PROTEIN MOTIF; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; SEQUENCE ANALYSIS; SEQUENCE TAGGED SITE; SIMPLE SEQUENCE REPEAT; SINGLE NUCLEOTIDE POLYMORPHISM; BACTERIAL ARTIFICIAL CHROMOSOME; CHROMOSOME MAP; DNA SEQUENCE; GENETIC MARKER; GENETICS; SPECIES DIFFERENCE; VARIABLE NUMBER OF TANDEM REPEAT;

CAPSICUM; CAPSICUM ANNUUM; CAPSICUM CHINENSE;

MICROSATELLITE DNA;

AMPLIFIED FRAGMENT LENGTH POLYMORPHISM ANALYSIS; CAPSICUM; CHROMOSOMES, ARTIFICIAL, BACTERIAL; GENETIC MARKERS; MICROSATELLITE REPEATS; MINISATELLITE REPEATS; PHYSICAL CHROMOSOME MAPPING; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

EID: 62849085192     PISSN: 10168478     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10059-009-0002-6     Document Type: Article

References (43)

1. J.S. Bao H. Corke M. Sun 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 16964521 1:CAS:528:DC%2BD28XhtVOmu7vO 10.1007/s00122-006-0394-z (Pubitemid 44581683)
2. L. Barchi J. Bonnet C. Boudet P. Signoret I. Nagy S. Lanteri A. Palloix V. Lefebvre 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
3. A. Ben Chaim I. Paran R.C. Grube M. Jahn Rv. Wijk J. Peleman 2001 QTL mapping of fruit-related traits in pepper (Capsicum annuum) Theor. Appl. Genet. 102 1016 1028 10.1007/s001220000461 (Pubitemid 32532706)
4. J.E. Bowers C. Abbey S. Anderson C. Chang X. Draye A.H. Hoppe R. Jessup C. Lemke J. Lennington Z. Li, 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 1:CAS:528:DC%2BD3sXosFalur4%3D
5. J.M. Bradeen J.E. Staub C. Wye R. Antonise J. Peleman 2001 Towards an expanded and integrated linkage map of cucumber (Cucumis sativus L.) Genomes 44 111 119 1:CAS:528:DC%2BD3MXhslKhtb4%3D 10.1139/gen-44-1-111 (Pubitemid 32247834)
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. C. Chen Q. Yu S. Hou Y. Li M. Eustice R.L. Skelton O. Veatch R.E. Herdes L. Diebold J. Saw, 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 17947401 1:CAS:528:DC%2BD1cXhtlCjtrs%3D 10.1534/genetics.107.081463 (Pubitemid 350277020)
8. N. Chiba K. Suwabe R. Nunome M. Hirai 2003 Develoment of microsatellite markers in melon (Cucumis melo L.) and their application to major cucurbit crops Breed. Sci. 53 21 27 1:CAS:528:DC%2BD3sXjtlynt7g%3D 10.1270/jsbbs.53.21
9. A. Collins D. Milbourne L. Ramsay C. Meyer C. Chatot-Balandras P. Overhagemann W. De Jong C. Gebhardt E. Connel R. Waugh 1999 QTL for field resistance to late blight in potato are strongly correlated with maurity and vigour Mol. Breed. 5 387 398 1:CAS:528:DyaK1MXms1WgsLo%3D 10.1023/A: 1009601427062 (Pubitemid 29429129)
10. A. Doligez A.F. Adam-Blondon G. Cipriani G. Di Gaspero V. Laucou D. Merdinoglu C.P. Meredith S. Riaz C. Roux P. This 2006 An integrated SSR map of grapevine based on five mapping populations Theor. Appl. Genet. 113 369 382 16799809 1:CAS:528:DC%2BD28Xms1Oit7k%3D 10.1007/s00122-006-0295-1 (Pubitemid 44035027)
11. J.E. Frelichowski Jr M.B. Palmer D. Main J.P. Tomkins R.G. Cantrell D.M. Stelly J. Yu R.J. Kohel M. Ulloa 2006 Cotton genome mapping with new microsatellites from Acala' Maxxa' BAC-ends Mol. Gen. Genomics 275 479 491 1:CAS:528:DC%2BD28XksFShtLY%3D 10.1007/s00438-006-0106-z (Pubitemid 43725265)
12. Y. Guo S. Saha J.Z. Yu J.N. Jenkins R.J. Kohel B.E. Scheffler D.M. Stelly 2008 BAC-derived SSR markers chromosome locations in cotton Euphytica 161 361 370 1:CAS:528:DC%2BD1cXltFequrc%3D 10.1007/s10681-007-9585-1
13. Z. Han C. Wang X. Song W. Guo J. Guo C. Li X. Chen T. Zhang 2006 Characteristics, development and mapping of Gossypium hirsutum derived EST-SSRs in allotetraploid cotton Theor. Appl. Genet. 112 430 439 16341684 1:CAS:528:DC%2BD28Xnt1yjsLg%3D 10.1007/s00122-005-0142-9 (Pubitemid 43081586)
14. K. Hayashi N. Hashimoto M. Daigen I. Ashikawa 2004 Development of PCR-based SNP markers for rice blast resistance genes at the Piz locus Theor. Appl. Genet. 108 1212 1220 14740086 1:CAS:528:DC%2BD2cXjtlOqsrs%3D 10.1007/s00122-003-1553-0 (Pubitemid 38630162)
15. P.R. Hearnden P.J. Eckermann G.L. McMichael M.J. Hayden J.K. Eglinton K.J. Chalmers 2007 A genetic map of 1,000 SSR and DArT markers in a wide barley cross Theor. Appl. Genet. 115 383 391 17639300 1:CAS:528:DC%2BD2sXnvFKqtr0%3D 10.1007/s00122-007-0572-7 (Pubitemid 47087412)
16. V. Kanazin L.F. Marex R.C. Shoemaker 1996 Resistance gene analogs are conserved and clustered in soybean Proc. Natl. Acad. Sci. USA 93 11746 11750 8876208 1:CAS:528:DyaK28XmtlansLw%3D 10.1073/pnas.93.21.11746 (Pubitemid 26347194)
17. 2 linkage map in pepper using RFLP and AFLP markers Theor. Appl. Genet. 102 531 539 1:CAS:528:DC%2BD3MXjtlKgu7o%3D 10.1007/s001220051678 (Pubitemid 32235410)
18. H.J. Kim S.H. Nahm H.R. Lee G.B. Yoon K.T. Kim B.C. Kang D. Choi O.Y. Kweon M.C. Cho J.K. Kwon, et al. 2008 BAC-derived markers converted from RFLP related to Phytophthora capsici resistance in pepper (Capsicum annuum L.) Theor Appl. Genet. 118 15 27 1:CAS:528:DC%2BD1cXhtlGhtLnM 10.1007/s00122-008-0873-5
19. H.J. Kim H.R. Lee J.H. Han S.I. Yeom C.H. Harn B.D. Kim 2008 Marker production by PCR amplification with primer pairs from conserved sequences of WRKY genes in the chili pepper Mol. Cells 25 196 204 18414014 1:CAS:528:DC%2BD1cXlvFCjs7s%3D
20. D.D. Kosambi 1944 The estimation of map distance from recombination values Ann. Eugenics 12 172 175
21. J.M. Lee S.H. Nahm Y.M. Kim B.D. Kim 2004 Characterization and molecular genetic mapping of microsatellite loci in pepper Theor. Appl. Genet. 108 619 627 14647898 1:CAS:528:DC%2BD2cXhsFWqtb4%3D 10.1007/s00122-003-1467-x (Pubitemid 38319200)
22. V. Lefebvre A. Palloix C. Caranta E. Pochard 1995 Construction of an intra-specific integrated linkage map of pepper using molecular markers and doubled-haploid progenies Genome 38 112 121 18470157 1:CAS:528: DyaK2MXlt1emuro%3D
23. V. Lefebvre S. Pflieger A. Habuis C. Caranta C. Blattes J.C. Chauvet A.M. Caubeze A. Palloix 2002 Towards the saturation of the pepper linkage map by alignment of three intraspecific maps including known-function genes Genome 45 839 854 12416616 1:CAS:528:DC%2BD38XovFWqs78%3D 10.1139/g02-053 (Pubitemid 35371718)
24. K.D. Livingstone V.K. Lackney J.R. Blauth R. van Wijk M.K. Jahn 1999 Genome mapping in capsicum and the evolution of genome structure in the solanaceae Genetics 152 1183 1202 10388833 1:CAS:528:DyaK1MXltVWnsbs%3D
25. Y. Minamiyama M. Tsuro M. Hirai 2006 An SSR-based linkage map of Capsicum annuum Mol. Breed. 18 157 169 1:CAS:528:DC%2BD28XptVGqs78%3D 10.1007/s11032-006-9024-3 (Pubitemid 44351272)
26. Y. Minamiyama M. Tsuro T. Kubo M. Hirai 2007 QTL analysis for resistance to Phytophthora Capsici in pepper using high density SSR-based map Breed. Sci. 57 129 134 1:CAS:528:DC%2BD2sXptFKisrg%3D 10.1270/jsbbs.57.129 (Pubitemid 46890400)
27. W.K. Min J.H. Han W.H. Kang H.R. Lee B.D. Kim 2008 Reverse random amplified microsatellite polymorphism reveals enhanced polymorphisms in the 3′ end of simple sequence repeats on pepper genome Mol. Cells 26 250 257 18483466 1:CAS:528:DC%2BD1cXht1elsbbK
28. P. Oberhagemann C. Chatot-Balandras R. Schafer-Pregl D. Wegener C. Palomino F. Salamini E. Bonnel C. Gebhardt 1999 A genetic analysis of quantitative resistance to late blight in potato, towards marker-assisted selection Mol. Breed. 5 399 415 1:CAS:528:DyaK1MXms1WgsLs%3D 10.1023/A:1009623212180 (Pubitemid 29429130)
29. E.A. Ogundiwin T.F. Berke M. Massoudi L.L. Black G. Huestis D. Choi S. Lee J.P. Prince 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 16094437 1:CAS:528:DC%2BD2MXhtFegtL%2FL 10.1139/g05-028 (Pubitemid 41483427)
30. I. Paran J.R. van der Voort V. Lefebvre M. Jahn L. Landry M. van Schriek B. Tanyolac C. Caranta A. Ben Chaim K. Livingstone, et al. 2004 An integrated genetic linkage map of pepper (Capsicum spp.) Mol. Breed. 13 251 261 1:CAS:528:DC%2BD2cXisl2msLw%3D 10.1023/B:MOLB.0000022526.30914.31 (Pubitemid 39001301)
31. G.U. Rao A. Ben Chaim Y. Borovsky I. Paran 2003 Mapping of yield-related QTLs in pepper in an interspecific cross of Capsicum annuum and C. frutescens Theor Appl. Genet. 106 1457 1466 1:CAS:528:DC%2BD3sXjslamsrc%3D
32. Sambrook, J., Fritsch, E.F., and Maniatis, T. (1989). Molecular Cloning: A Laboratory Manual, (NY, USA; Cold Spring Harbor, Laboratory Press).
33. Z. Sun Z. Wang J. Tu J. Zhang F. Yu P.B.E. McVetty G. Li 2007 An ultradense genetic recombination map for Brassica napus, consistingof 13551 SRAP markers Theor. Appl. Genet. 114 1305 1317 17426959 1:CAS:528: DC%2BD2sXltVWgtb8%3D 10.1007/s00122-006-0483-z (Pubitemid 46733374)
34. S.D. Tanksley M.W. Ganal J.P. Prince M.C. de Vicente M.W. Bonierbale P. Broun T.M. Fulton J.J. Giovannoni S. Grandillo G.B. Martin, et al. 1992 High density molecular linkage maps of the tomato and potato genomes; biological inferences and practical applications Genetics 132 1141 1160 1360934 1:STN:280:ByyD1Mzktl0%3D
35. M. Troggio G. Malacarne C. Coppola C. Segala D.A. Gartwright M. Pindo M. Stefanini R. Mank M. Moroldo M. Morgante, 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 17603124 1:CAS:528:DC%2BD2sXhtFGmsr3M 10.1534/genetics.106.067462 (Pubitemid 47360689)
36. M.J. Truco R. Antonise D. Lavelle O. Ochoa A. Kozik H. Witsenboer S.B. Fort M.J.W. Jeuken R.V. Kesseli P. Lindhout, et al. 2007 A high-density, integrated genetic linkage map of lettuce (Lactuca spp.) Theor. Appl. Genet. 115 735 746 17828385 1:CAS:528:DC%2BD2sXhtVKru7zO 10.1007/s00122-007-0599-9 (Pubitemid 47460469)
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. R.E. Voorrips 2002 MapChart, Software for the graphical presentation of linkage maps and QTLs J. Hered. 93 77 78 12011185 1:CAS:528:DC%2BD38XktlOntrw%3D 10.1093/jhered/93.1.77
39. P. Vos R. Hogers M. Bleeker M. Reijans T. van de Lee M. Hornes A. Frijters J. Pot J. Peleman M. Kuiper, et al. 1995 AFLP, a new technique for DNA fingerprinting Nucleic Acids Res. 23 4407 4414 7501463 1:CAS:528: DyaK2MXpslensbo%3D 10.1093/nar/23.21.4407
40. X. Wenkai X. Mingliang Z. Jiuren W. Fengge L. Jiansheng D. Jingrui 2006 Genome-wide isolation of resistance gene analogs in maize (Zea mays L.) Theor. Appl. Genet. 113 63 72 16607513 10.1007/s00122-006-0272-8 (Pubitemid 43910101)
41. Z. Yan C. Denneboom A. Hattendorf O. Dolstra T. Debener P. Stam P.B. Visser 2005 Construction of an integrated map of rose with AFLP, SSR, PK, RGA, RFLP, SCAR and morphological markers Theor. Appl. Genet. 110 766 777 15672277 1:CAS:528:DC%2BD2MXhsFShtbY%3D 10.1007/s00122-004-1903-6 (Pubitemid 40383393)
42. G. Yi J.M. Lee S. Lee D. Choi B.D. Kim 2006 Exploitation of pepper EST-SSRs and an SSR-based linkage map Theor. Appl. Genet. 114 113 130 17047912 1:CAS:528:DC%2BD28Xht1WltrnJ 10.1007/s00122-006-0415-y (Pubitemid 44786540)
43. E.Y. Yoo S. Kim Y.H. Kim C.J. Lee B.D. Kim 2003 Construction of a deep coverage BAC library from Capsicum Annuum 'CM334' Theor. Appl. Genet. 107 540 543 12748763 1:CAS:528:DC%2BD3sXmslSisb8%3D 10.1007/s00122-003-1279-z (Pubitemid 37007841)