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Characterization and molecular genetic mapping of microsatellite loci in pepper

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Abstract

Microsatellites or simple sequence repeats are highly variable DNA sequences that can be used as informative markers for the genetic analysis of plants and animals. For the development of microsatellite markers in Capsicum, microsatellites were isolated from two small-insert genomic libraries and the GenBank database. Using five types of oligonucleotides, (AT)15, (GA)15, (GT)15, (ATT)10 and (TTG)10, as probes, positive clones were isolated from the genomic libraries, and sequenced. Out of 130 positive clones, 77 clones showed microsatellite motifs, out of which 40 reliable microsatellite markers were developed. (GA) n and (GT) n sequences were found to occur most frequently in the pepper genome, followed by (TTG) n and (AT) n . Additional 36 microsatellite primers were also developed from GenBank and other published data. To measure the information content of these markers, the polymorphism information contents (PICs) were calculated. Capsicum microsatellite markers from the genomic libraries have shown a high level of PIC value, 0.76, twice the value for markers from GenBank data. Forty six microsatellite loci were placed on the SNU-RFLP linkage map, which had been derived from the interspecific cross between Capsicum annuum “TF68” and Capsicum chinense “Habanero”. The current “SNU2” pepper map with 333 markers in 15 linkage groups contains 46 SSR and 287 RFLP markers covering 1,761.5 cM with an average distance of 5.3 cM between markers.

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References

  • Arumuganathan K, Earle ED (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9:208–218

    CAS  Google Scholar 

  • Bell CJ, Ecker JR (1994) Assignment of 30 microsatellite loci to the linkage map of Arabidopsis. Genomics 19:137–144

    Article  CAS  PubMed  Google Scholar 

  • Ben Chaim A, Paran I, Grube RC, Jahn M, van Wijk R, Peleman J (2001) QTL mapping of fruit-related traits in pepper (Capsicum annuum). Theor Appl Genet 102:1016–1028

    Article  Google Scholar 

  • Broun P, Tanksley SD (1996) Characterization and genetic mapping of simple repeat sequences in the tomato genome. Mol Gen Genet 250:39–49

    CAS  PubMed  Google Scholar 

  • Chin ECL, Senior ML, Shu H, Smith JSC (1996) Maize simple repetitive DNA sequences: abundance and allele variation. Genome 39:866–873

    CAS  PubMed  Google Scholar 

  • Cho YG, Ishii T, Temnykh S, Chen X, Lipovich L, McCouch SR, Park WD, Ayres N, Cartinhour (2000) Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.). Theor Appl Genet 100:713–722

    CAS  Google Scholar 

  • Depeiges A, Goubely C, Lenoir A, Cocherel S, Picard G, Raynal M, Grellet F, Delseny M (1995) Identification of the most represented repeated motifs in Arabidopsis thaliana microsatellite loci. Theor Appl Genet 91:160–168

    CAS  Google Scholar 

  • Edwards A, Civitello H, Hammond HA, Caskey CT (1991) DNA typing and genetic mapping with a trimeric tetrameric tandem repeat. Am J Hum Genet 49:746–756

    Google Scholar 

  • Huh JH, Kang BC, Nahm SH, Kim S, Ha KS, Lee MH, Kim BD (2001) A candidate gene approach identified phytoene synthase as the locus for mature fruit color in red pepper (Capsicum spp.). Theor Appl Genet 102:524–530

    Article  CAS  Google Scholar 

  • Huang S, Zhang B, Milbourne D, Cardle L, Yang G, Guo J (2000) Development of pepper SSR markers from sequence databases. Euphytica 117:163–167

    Google Scholar 

  • Innan H, Terauchi R, Miyashita NT (1997) Microsatellite polymorphism in natural populations of the wild plant Arabidopsis thaliana. Genetics 146:1441–52

    CAS  PubMed  Google Scholar 

  • Jacob HJ, Lindpaintner K, Lincodpaintner K, Lincoln SE, Kusumi K, Bunker RK, Mao YP, Ganten D, Dzau VJ, Lander ES (1991) Genetic mapping of a gene causing hypertension in the stroke-prone spontaneously hypertensile rat. Cell 67:213–224

    CAS  PubMed  Google Scholar 

  • Kang, BC, Yu JW, Lee MH, Kim BD (1997) Applicability of AFLP on hot pepper genetic analysis. J Korean Soc Hort Sci 38:698–703

    CAS  Google Scholar 

  • Kang BC, Nahm SH, Huh JH, Yoo HS, Yu JW, Lee MH, Kim BD (2001) An interspecific (Capsicum annuum × C. chinese) F2 linkage map in pepper using RFLP and AFLP markers. Theor Appl Genet 102:531–539

    Article  CAS  Google Scholar 

  • Kosambi DD (1944) The estimation of map distance from recombination values. Ann Eugenics 12:172–175

    Google Scholar 

  • Lander ES, Green P, Abrahamson J, Barlow A, Daly MJ, Lincoln SE, Newberg L (1987) MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–181

    CAS  PubMed  Google Scholar 

  • Lagercrantz U, Ellegren H, Andersson L (1993) The abundance of various polymorphic microsatellite motifs differs between plants and vertebrates. Nucleic Acids Res 21:1111–1115

    CAS  PubMed  Google Scholar 

  • Lee SJ (2000) Isolation and molecular characterization of two SA-inducible genes from hot pepper plants (Capsicum annuum L.). PhD thesis, Seoul National University

  • Lefebvre V, Palloix A, Caranta C, Pochard E (1995) Construction of an intraspecific integrated linkage map of pepper using molecular markers and doubled-haploid progenies. Genome 38:112–121

    CAS  Google Scholar 

  • Litt M, Luty JA (1989) A hypervariable microsatellite revealed by in vitro amplication of a dinucleotide repeat within the cardiac muscle action gene. Am J Hum Genet 44:388–396

    CAS  PubMed  Google Scholar 

  • Livingstone KD, Lackney VK, Blauth JR, Van Wijk R, Jahn MK (1999) Genome mapping in Capsicum and evolution of genome structure in the Solanaceae. Genetics 152:1183–1202

    CAS  PubMed  Google Scholar 

  • Milbourne D, Meyer RC, Collins AJ, Ramsay LD, Gebhardt C, Waugh R (1998) Isolation, characterisation and mapping of simple sequence repeat loci in potato. Mol Gen Genet 259:233–45

    CAS  PubMed  Google Scholar 

  • Morgante M, Olivieri AM (1993) PCR-amplified microsatellites as markers in plant genetics. Plant J 3:175–182

    CAS  PubMed  Google Scholar 

  • Morgante M, Hanafey M, Powell W (2002) Microsatellites are preferentially associated with non-repetitive DNA in plant genomes. Nature Genet 30:194–200

    CAS  PubMed  Google Scholar 

  • Nagy I, Polley A, Ganal M (1998) Development and characterization of microsatellte markers in pepper. Xth Meeting on Genetics and Breeding of Capsicum and Eggplant, pp 235–237

  • Nahm SH, Yu JW, Kang BC, Kim BD (1997) Election of parental lines for the hot pepper mapping population using RFLP and AFLP analyses. J Korean Soc Hort Sci 38:693–697

    Google Scholar 

  • Paran I, Aftergoot E, Shifriss C (1998) Variation in Capsicum annuum revealed by RAPD and AFLP markers. Euphytica 99:167–173

    Article  Google Scholar 

  • Powell W, Morgante M. Andre C, Hanafey M, Vogel J, Tingey S, Rafalski A (1996) The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Mol Breed 2:225–238

    CAS  Google Scholar 

  • Prince JP, Lackney VK, Angeles C, Blauth JR, Kyle MM (1995) A survey of DNA polymorphism within the genus Capsicum and the fingerprinting of pepper cultivar. Genome 36:404–417

    Google Scholar 

  • Ramsay L, Macaulay M, Cardle L, Morgante M, Ivanissevich S, Maestri E, Powell W, Waugh R (1999) Intimate association of microsatellite repeats with retrotransposons and other dispersed repetitive elements in barley. Plant J 17:415–25

    CAS  PubMed  Google Scholar 

  • Roder MS, Korzun V, Wendehake K, Plaschke J, Tixier MH, Leroy P, Ganal MW (1998) A microsatellite map of wheat. Genetics 149:2007–23

    PubMed  Google Scholar 

  • Rodriguez JM, Berke T, Engle L, Nienhuis J (1999) Variation among and within Capsicum species revealed by RAPD markers. Theor Appl Genet 99:147–156

    CAS  Google Scholar 

  • Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York

    Google Scholar 

  • Schlotterer C, Tauz D (1992) Slippage synthesis of simple sequence DNA. Nucleic Acids Res 20:211–215

    PubMed  Google Scholar 

  • Schmidt T, Heslop-Harrison JS (1996) The physical and genomic organization of microsatellites in sugar beet. Proc Natl Acad Sci USA 93:8761–8765

    CAS  PubMed  Google Scholar 

  • Smulders MJM, Bredemeijer G, Rus Kortekaas W, Arens P, Vosman B (1997) Use of short microsatellites from database sequences to generate polymorphisms among Lycopersicon esculentum cultivars and accessions of other Lycopersicon species. Theor Appl Genet 94:264–272

    Article  CAS  Google Scholar 

  • Tai TH, Dahlbeck D, Clark ET, Gajiwala P, Pasion R, Whalen MC, Stall RE, Staskawicz BJ (1999) Expression of the Bs2 pepper gene confers resistance to bacterial spot disease in tomato. Proc Natl Acad Sci USA 23:14153–14158

    Article  Google Scholar 

  • Tanksley SD, Ganal MW, Prince JP, de Vicente MC, Bonierbale MW, Broun P, Fulton TM, Giovannoni JJ, Grandillo S, Martin GB, Messeguer R, Miller JC, Miller L, Paterson AH, Pineda O, Roder MS, Wing RA, Wu W, Young ND (1992) High density molecular linkage maps of the tomato and potato genomes; Biological inferences and practical applications. Genetics 132:1141–1160

    CAS  PubMed  Google Scholar 

  • Temnykh S, Park WD, Ayres N, Cartinhour S, Hauck N, Lipovich L, Cho YG, Ishii T, McCouch S (2000) Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.). Theor Appl Genet 100:697–712

    CAS  Google Scholar 

  • Yoshioka Y, Matsumoto S, Kojima S, Ohshima K, Okada N, Machida Y (1993) Molecular characterization of a short interspersed repetitive element from tobacco that exhibits sequence homology to specific transfer RNAs. Proc Natl Acad Sci USA 90:6562–6566

    PubMed  Google Scholar 

  • Yu JW (2001) Isolation and molecular characterization of three MADS genes from the hot pepper plant (Capsicum annuum L.). PhD thesis, Seoul National University

Download references

Acknowledgement

This work was supported by a grant from the R & D Promotion Center for Agriculture and Forestry, and from the KOSEF through the Center for Plant Molecular Genetics and Breeding Research.

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Author notes

  1. S. H. Nahm

    Present address: Biotechnology Center, Nong Woo Bio Co., Ltd, 537-17 Jeongdan, Kanam, Kyonggi 469-880, Yeoju, Korea

  2. Y. M. Kim

    Present address: Kumho Life and Environmental Science Laboratory, 1 Oryong-dong, Buk-gu, 500-712, Kwangju, Korea

Authors and Affiliations

  1. Department of Plant Science, College of Agriculture and Life Sciences and Center for Plant Molecular Genetics and Breeding Research, Seoul National University, Seoul 151-742, Korea

    J. M. Lee, S. H. Nahm, Y. M. Kim & B. D. Kim

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  1. J. M. Lee
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  2. S. H. Nahm
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  4. B. D. Kim
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Correspondence to B. D. Kim.

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Communicated by J. Dvorak

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Lee, J.M., Nahm, S.H., Kim, Y.M. et al. Characterization and molecular genetic mapping of microsatellite loci in pepper. Theor Appl Genet 108, 619–627 (2004). https://doi.org/10.1007/s00122-003-1467-x

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  • DOI: https://doi.org/10.1007/s00122-003-1467-x

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